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2.  Human Normal Bronchial Epithelial Cells: A Novel In Vitro Cell Model for Toxicity Evaluation 
PLoS ONE  2015;10(4):e0123520.
Human normal cell-based systems are needed for drug discovery and toxicity evaluation. hTERT or viral genes transduced human cells are currently widely used for these studies, while these cells exhibited abnormal differentiation potential or response to biological and chemical signals. In this study, we established human normal bronchial epithelial cells (HNBEC) using a defined primary epithelial cell culture medium without transduction of exogenous genes. This system may involve decreased IL-1 signaling and enhanced Wnt signaling in cells. Our data demonstrated that HNBEC exhibited a normal diploid karyotype. They formed well-defined spheres in matrigel 3D culture while cancer cells (HeLa) formed disorganized aggregates. HNBEC cells possessed a normal cellular response to DNA damage and did not induce tumor formation in vivo by xenograft assays. Importantly, we assessed the potential of these cells in toxicity evaluation of the common occupational toxicants that may affect human respiratory system. Our results demonstrated that HNBEC cells are more sensitive to exposure of 10~20 nm-sized SiO2, Cr(VI) and B(a)P compared to 16HBE cells (a SV40-immortalized human bronchial epithelial cells). This study provides a novel in vitro human cells-based model for toxicity evaluation, may also be facilitating studies in basic cell biology, cancer biology and drug discovery.
doi:10.1371/journal.pone.0123520
PMCID: PMC4393029  PMID: 25861018
3.  Olfactory ensheathing cell tumor: A case report and review of the literature 
Oncology Letters  2015;9(5):2078-2084.
Olfactory ensheathing cell tumors (OECTs) are rare malignancies that occur in the anterior fossa. Little is known with regard to their clinical, radiological and immunohistochemical characteristics. The current study reports the case of a 20-year-old male with an OECT, who presented with a severe headache and a generalized convulsion. Cranial magnetic resonance imaging revealed heterogeneous enhancement of the tumor in the left anterior fossa. Complete removal of the tumor via a left frontal craniotomy was conducted, which relieved the patient's headache; however, this resulted in left-sided anosmia that remained during the two-month follow-up. The tumor was immunopositive for vimentin and S-100, and immunonegative for epithelial membrane antigen and Leu-7. The clinical data, imaging features, intraoperative findings and immunohistochemical characteristics of an additional seven cases reported in the literature are also reviewed and analyzed, providing important clinical information for the pre-operative diagnosis and intraoperative removal of OECTs.
doi:10.3892/ol.2015.3042
PMCID: PMC4467262  PMID: 26137016
olfactory groove schwannoma; immunohistochemistry; diagnosis; olfactory ensheathing cell tumor
4.  Renal graft biopsy assists diagnosis and treatment of renal allograft dysfunction after kidney transplantation: a report of 106 cases 
Acute antibody mediated rejection (AMR) is one of the most important complications after kidney transplantation. Renal graft biopsy is safe and reliable without adverse effects on the patients and transplanted kidneys, which was of great instructive significance in diagnosis and treatment of renal allograft dysfunction after renal transplantation. This paper reported a case series of 106 patients underwent renal allograft biopsies. All biopsies were evaluated according to the Banff 2007 schema. 52 examples were obtained within 1 month after transplantation, and there were another 20 examples in one to two months and other 34 examples in two to three months. Appropriate therapy was applied and clinical outcomes were observed. All patients received renal biopsies and anti-inflammatory and hemostasis treatment without complications. There were 2 cases of hyperacute rejection, and 15 cases of acute AMR. All Paraffin-embedded samples were stained by HE, periodic acid-Schiff (PAS), Masson, and immunohistochemistry (C4d, cd20, cd45RO, SV40). All samples were found C4d immunohistochemical staining positive. Patients with acute AMR were managed by steroid intravenous pulse therapy, Rabbit anti-thymocyte globulin intravenous pulse therapy, anti CD20 monoclonal antibody intravenous therapy and so on. Two cases of hyperacute rejection had renal failure, and received kidney excision; 12 cases in 15 cases of AMR recovered, another 2 cases did not recover with high-level creatine, and other 2 cases of renal allograft received excision.
PMCID: PMC4443241  PMID: 26064407
Kidney transplantation; renal insufficiency; renal biopsy; perioperative period
5.  Spindle cell oncocytoma of the adenohypophysis: Two case reports and a review of the literature 
Molecular Medicine Reports  2015;12(1):871-876.
Spindle cell oncocytoma (SCO) of the adenohy-pophysis is a rare tumor in the sellar region. Due to its rarity, little information is available regarding SCO. It is often misdiagnosed as another type of sellar tumor. In the present study, two cases of SCO were reported. One patient was a 35-year-old female presenting with decreased visual acuity, amenorrhea and lactation. The other patient was a 62-year-old female with no clear symptoms or signs. Cranial magnetic resonance imaging (MRI) revealed a suprasellar mass with marked homogeneous enhancement in the two cases. A craniotomy was performed to completely resect the tumors. The tumors were immunopositive for vimentin, epithelial membrane antigen (EMA), S-100 and thyroid transcription factor-1 (TTF-1). The tumors were pathologically diagnosed as SCO. No recurrence occurred during the follow-up period of 15–21 months. In the present study, the literature was reviewed and the clinical data, imaging features, intraoperative findings and recurrence of 24 cases were analyzed in the literature as well as the present two cases. The average age of the SCO patients was 58.5 years and no gender preference was observed for the disease. The tumor exhibited homogeneous enhancement on the MRI. The intraoperative assessment revealed that the tumor had a rich blood supply and the SCO tumors were immunopositive for vimentin, S-100, EMA and TTF-1. These findings provided valuable clinical data for the preoperative diagnosis and surgical removal of SCO tumors.
doi:10.3892/mmr.2015.3476
PMCID: PMC4438875  PMID: 25777996
spindle cell oncocytoma; surgical resection; pathological diagnosis
6.  Evidence for a Hexaheteromeric Methylenetetrahydrofolate Reductase in Moorella thermoacetica 
Journal of Bacteriology  2014;196(18):3303-3314.
Moorella thermoacetica can grow with H2 and CO2, forming acetic acid from 2 CO2 via the Wood-Ljungdahl pathway. All enzymes involved in this pathway have been characterized to date, except for methylenetetrahydrofolate reductase (MetF). We report here that the M. thermoacetica gene that putatively encodes this enzyme, metF, is part of a transcription unit also containing the genes hdrCBA, mvhD, and metV. MetF copurified with the other five proteins encoded in the unit in a hexaheteromeric complex with an apparent molecular mass in the 320-kDa range. The 40-fold-enriched preparation contained per mg protein 3.1 nmol flavin adenine dinucleotide (FAD), 3.4 nmol flavin mononucleotide (FMN), and 110 nmol iron, almost as predicted from the primary structure of the six subunits. It catalyzed the reduction of methylenetetrahydrofolate with reduced benzyl viologen but not with NAD(P)H in either the absence or presence of oxidized ferredoxin. It also catalyzed the reversible reduction of benzyl viologen with NADH (diaphorase activity). Heterologous expression of the metF gene in Escherichia coli revealed that the subunit MetF contains one FMN rather than FAD. MetF exhibited 70-fold-higher methylenetetrahydrofolate reductase activity with benzyl viologen when produced together with MetV, which in part shows sequence similarity to MetF. Heterologously produced HdrA contained 2 FADs and had NAD-specific diaphorase activity. Our results suggested that the physiological electron donor for methylenetetrahydrofolate reduction in M. thermoacetica is NADH and that the exergonic reduction of methylenetetrahydrofolate with NADH is coupled via flavin-based electron bifurcation with the endergonic reduction of an electron acceptor, whose identity remains unknown.
doi:10.1128/JB.01839-14
PMCID: PMC4135698  PMID: 25002540
7.  Comparative Analysis of the Transcriptome across Distant Species 
Gerstein, Mark B. | Rozowsky, Joel | Yan, Koon-Kiu | Wang, Daifeng | Cheng, Chao | Brown, James B. | Davis, Carrie A | Hillier, LaDeana | Sisu, Cristina | Li, Jingyi Jessica | Pei, Baikang | Harmanci, Arif O. | Duff, Michael O. | Djebali, Sarah | Alexander, Roger P. | Alver, Burak H. | Auerbach, Raymond | Bell, Kimberly | Bickel, Peter J. | Boeck, Max E. | Boley, Nathan P. | Booth, Benjamin W. | Cherbas, Lucy | Cherbas, Peter | Di, Chao | Dobin, Alex | Drenkow, Jorg | Ewing, Brent | Fang, Gang | Fastuca, Megan | Feingold, Elise A. | Frankish, Adam | Gao, Guanjun | Good, Peter J. | Guigó, Roderic | Hammonds, Ann | Harrow, Jen | Hoskins, Roger A. | Howald, Cédric | Hu, Long | Huang, Haiyan | Hubbard, Tim J. P. | Huynh, Chau | Jha, Sonali | Kasper, Dionna | Kato, Masaomi | Kaufman, Thomas C. | Kitchen, Robert R. | Ladewig, Erik | Lagarde, Julien | Lai, Eric | Leng, Jing | Lu, Zhi | MacCoss, Michael | May, Gemma | McWhirter, Rebecca | Merrihew, Gennifer | Miller, David M. | Mortazavi, Ali | Murad, Rabi | Oliver, Brian | Olson, Sara | Park, Peter J. | Pazin, Michael J. | Perrimon, Norbert | Pervouchine, Dmitri | Reinke, Valerie | Reymond, Alexandre | Robinson, Garrett | Samsonova, Anastasia | Saunders, Gary I. | Schlesinger, Felix | Sethi, Anurag | Slack, Frank J. | Spencer, William C. | Stoiber, Marcus H. | Strasbourger, Pnina | Tanzer, Andrea | Thompson, Owen A. | Wan, Kenneth H. | Wang, Guilin | Wang, Huaien | Watkins, Kathie L. | Wen, Jiayu | Wen, Kejia | Xue, Chenghai | Yang, Li | Yip, Kevin | Zaleski, Chris | Zhang, Yan | Zheng, Henry | Brenner, Steven E. | Graveley, Brenton R. | Celniker, Susan E. | Gingeras, Thomas R | Waterston, Robert
Nature  2014;512(7515):445-448.
doi:10.1038/nature13424
PMCID: PMC4155737  PMID: 25164755
8.  Comparative analysis of regulatory information and circuits across distant species 
Nature  2014;512(7515):453-456.
Summary
Despite the large evolutionary distances, metazoan species show remarkable commonalities, which has helped establish fly and worm as model organisms for human biology1,2. Although studies of individual elements and factors have explored similarities in gene regulation, a large-scale comparative analysis of basic principles of transcriptional regulatory features is lacking. We mapped the genome-wide binding locations of 165 human, 93 worm, and 52 fly transcription-regulatory factors (RFs) generating a total of 1,019 data sets from diverse cell-types, developmental stages, or conditions in the three species, of which 498 (48.9%) are presented here for the first time. We find that structural properties of regulatory networks are remarkably conserved and that orthologous RF families recognize similar binding motifs in vivo and show some similar co-associations. Our results suggest that gene-regulatory properties previously observed for individual factors are general principles of metazoan regulation that are remarkably well-preserved despite extensive functional divergence of individual network connections. The comparative maps of regulatory circuitry provided here will drive an improved understanding in the regulatory underpinnings of model organism biology and how these relate to human biology, development, and disease.
doi:10.1038/nature13668
PMCID: PMC4336544  PMID: 25164757
Transcription Factor; Regulatory Information; Gene Regulation; Single Nucleotide Polymorphisms; ChIP-seq
9.  An intraventricular meningioma and recurrent astrocytoma collision tumor: a case report and literature review 
Background
Intracranial meningioma and glioma collision tumors are relatively uncommon and are even more rarely located within the ventricles.
Case presentation
Here, we report a case of a patient with an intraventricular meningioma and astrocytoma collision tumor. A 39-year-old man previously underwent excision of an astrocytoma in the triangle area of the lateral ventricle and exhibited good post-surgery recovery. The astrocytoma recurred in situ six years after the surgery, and the case was complicated by a malignant meningioma. The patient recovered well after surgery to treat the recurrence and was administered radiotherapy after discharge. In addition to reporting on this case, we conducted a literature review of collision tumors; based on this review, we propose several hypotheses regarding the formation of collision tumors.
Conclusions
We conclude that a possible cause of the collision tumor formation between the intracranial meningioma and the astrocytoma was the recurrence of an astrocytoma-induced malignancy of the arachnoid cells in the choroid plexus.
doi:10.1186/s12957-015-0436-6
PMCID: PMC4329203  PMID: 25889820
10.  Poly(ADP-ribose) glycohydrolase silencing down-regulates TCTP and Cofilin-1 associated with metastasis in benzo(a)pyrene carcinogenesis 
Benzo(a)pyrene (BaP) is a ubiquitously distributed environmental pollutant. BaP is a known carcinogen and can induce malignant transformation of rodent and human cells. Many evidences suggest that inhibitor of poly(ADP-ribose) glycohydrolase (PARG) is potent anticancer drug candidate. However, the effect of PARG on BaP carcinogenesis remains unclear. We explored this question in a PARG-deficient human bronchial epithelial cell line (shPARG cells) treated with various concentration of BaP for 15 weeks. Soft agar assay was used to examine BaP-induced cell malignancy of human bronchial epithelial cells and shPARG cells. Mechanistic investigations were used by 2D-DIGE and mass spectrometry. Western blot analysis and Double immunofluorescence detection were used to confirm some of the results obtained from DIGE experiments. We found that PARG silencing could dramatically inhibit BaP-induced cell malignancy of human bronchial epithelial cells in soft agar assay. Altered levels of expression induced by BaP were observed within shPARG cells for numerous proteins, including proteins required for cell mobility, stress response, DNA repair and cell proliferation pathways. Among these proteins, TCTP and Cofilin-1 involved in malignancy, were validated by western blot analysis and immunofluorescence assay. PARG inhibition contributed to down-regulation of TCTP and Cofilin-1. This is the first experimental demonstration of a link between PARG silencing and reduced cell migration after BaP exposure. We propose that PARG silencing might down-regulate TCTP and Cofilin-1 associated with metastasis in BaP carcinogenesis.
PMCID: PMC4300713  PMID: 25628927
poly(ADP-ribosyl)ation; poly(ADP-ribose) glycohydrolase; benzo(a)pyrene; DNA damage; human bronchial epithelial cells (16HBE cells)
11.  Serum Amyloid A and Clusterin as Potential Predictive Biomarkers for Severe Hand, Foot and Mouth Disease by 2D-DIGE Proteomics Analysis 
PLoS ONE  2014;9(9):e108816.
Hand, foot, and mouth disease (HFMD) affects more than one million children, is responsible for several hundred child deaths every year in China and is the cause of widespread concerns in society. Only a small fraction of HFMD cases will develop further into severe HFMD with neurologic complications. A timely and accurate diagnosis of severe HFMD is essential for assessing the risk of progression and planning the appropriate treatment. Human serum can reflect the physiological or pathological states, which is expected to be an excellent source of disease-specific biomarkers. In the present study, a comparative serological proteome analysis between severe HFMD patients and healthy controls was performed via a two-dimensional difference gel electrophoresis (2D-DIGE) and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) strategy. Fifteen proteins were identified as differentially expressed in the sera of the severe HFMD patients compared with the controls. The identified proteins were classified into different groups according to their molecular functions, biological processes, protein classes and physiological pathways by bioinformatics analysis. The up-regulations of two identified proteins, serum amyloid A (SAA) and clusterin (CLU), were confirmed in the sera of the HFMD patients by ELISA assay. This study not only increases our background knowledge about and scientific insight into the mechanisms of HFMD, but also reveals novel potential biomarkers for the clinical diagnosis of severe HFMD.
doi:10.1371/journal.pone.0108816
PMCID: PMC4182520  PMID: 25268271
12.  Prediction of LDL cholesterol response to statin using transcriptomic and genetic variation 
Genome Biology  2014;15(9):460.
Background
Statins are widely prescribed for lowering LDL-cholesterol (LDLC) levels and risk of cardiovascular disease. There is, however, substantial inter-individual variation in the magnitude of statin-induced LDLC reduction. To date, analysis of individual DNA sequence variants has explained only a small proportion of this variability. The present study was aimed at assessing whether transcriptomic analyses could be used to identify additional genetic contributions to inter-individual differences in statin efficacy.
Results
Using expression array data from immortalized lymphoblastoid cell lines derived from 372 participants of the Cholesterol and Pharmacogenetics clinical trial, we identify 100 signature genes differentiating high versus low statin responders. A radial-basis support vector machine prediction model of these signature genes explains 12.3% of the variance in statin-mediated LDLC change. Addition of SNPs either associated with expression levels of the signature genes (eQTLs) or previously reported to be associated with statin response in genome-wide association studies results in a combined model that predicts 15.0% of the variance. Notably, a model of the signature gene associated eQTLs alone explains up to 17.2% of the variance in the tails of a separate subset of the Cholesterol and Pharmacogenetics population. Furthermore, using a support vector machine classification model, we classify the most extreme 15% of high and low responders with high accuracy.
Conclusions
These results demonstrate that transcriptomic information can explain a substantial proportion of the variance in LDLC response to statin treatment, and suggest that this may provide a framework for identifying novel pathways that influence cholesterol metabolism.
Electronic supplementary material
The online version of this article (doi:10.1186/s13059-014-0460-9) contains supplementary material, which is available to authorized users.
doi:10.1186/s13059-014-0460-9
PMCID: PMC4180544  PMID: 25316374
13.  Neuroprotective effects of Buyang Huanwu decoction on cerebral ischemia-induced neuronal damage 
Neural Regeneration Research  2014;9(17):1621-1627.
Among the various treatment methods for stroke, increasing attention has been paid to traditional Chinese medicines. Buyang Huanwu decoction is a commonly used traditional Chinese medicine for the treatment of stroke. This paper summarizes the active components of the Chinese herb, which is composed of Huangqi (Radix Astragali seu Hedysari), Danggui (Radix Angelica sinensis), Chishao (Radix Paeoniae Rubra), Chuanxiong (Rhizoma Ligustici Chuanxiong), Honghua (Flos Carthami), Taoren (Semen Persicae) and Dilong (Pheretima), and identifies the therapeutic targets and underlying mechanisms that contribute to the neuroprotective properties of Buyang Huanwu decoction.
doi:10.4103/1673-5374.141791
PMCID: PMC4211205  PMID: 25368650
nerve regeneration; Buyang Huanwu decoction; traditional Chinese medicine; cerebral ischemia; clinical application; neuroprotection; review; neural regeneration
14.  6-Hydroxy-3-Succinoylpyridine Hydroxylase Catalyzes a Central Step of Nicotine Degradation in Agrobacterium tumefaciens S33 
PLoS ONE  2014;9(7):e103324.
Nicotine is a main alkaloid in tobacco and is also the primary toxic compound in tobacco wastes. It can be degraded by bacteria via either pyridine pathway or pyrrolidine pathway. Previously, a fused pathway of the pyridine pathway and the pyrrolidine pathway was proposed for nicotine degradation by Agrobacterium tumefaciens S33, in which 6-hydroxy-3-succinoylpyridine (HSP) is a key intermediate connecting the two pathways. We report here the purification and properties of an NADH-dependent HSP hydroxylase from A. tumefaciens S33. The 90-kDa homodimeric flavoprotein catalyzed the oxidative decarboxylation of HSP to 2,5-dihydroxypyridine (2,5-DHP) in the presence of NADH and FAD at pH 8.0 at a specific rate of about 18.8±1.85 µmol min−1 mg protein−1. Its gene was identified by searching the N-terminal amino acid residues of the purified protein against the genome draft of the bacterium. It encodes a protein composed of 391 amino acids with 62% identity to HSP hydroxylase (HspB) from Pseudomonas putida S16, which degrades nicotine via the pyrrolidine pathway. Considering the application potential of 2,5-DHP in agriculture and medicine, we developed a route to transform HSP into 2,5-DHP with recombinant HSP hydroxylase and an NADH-regenerating system (formate, NAD+ and formate dehydrogenase), via which around 0.53±0.03 mM 2,5-DHP was produced from 0.76±0.01 mM HSP with a molar conversion as 69.7%. This study presents the biochemical properties of the key enzyme HSP hydroxylase which is involved in the fused nicotine degradation pathway of the pyridine and pyrrolidine pathways and a new green route to biochemically synthesize functionalized 2,5-DHP.
doi:10.1371/journal.pone.0103324
PMCID: PMC4108407  PMID: 25054198
15.  Diet-induced obesity causes long QT and reduces transcription of voltage-gated potassium channels 
In humans, obesity is associated with long QT, increased frequency of premature ventricular complexes, and sudden cardiac death. The mechanisms of the pro-arrhythmic electrophysiologic remodeling of obesity are poorly understood. We tested the hypothesis that there is decreased expression of voltage-gated potassium channels in the obese heart, leading to long QT. Using implanted telemeters, we found that diet-induced obese (DIO) wild-type mice have impaired cardiac repolarization, demonstrated by long QT, as well as more frequent ventricular ectopy, similar to obese humans. DIO mice have reduced protein and mRNA levels of the potassium channel Kv1.5 caused by a reduction of the transcription factor cyclic AMP response element binding protein (CREB) in DIO hearts. We found that CREB knock-down by siRNA reduces Kv1.5, CREB binds to the Kv1.5 promoter in the heart, and CREB increases transcription of mouse and human Kv1.5 promoters. The reduction in CREB protein during lipotoxicity can be rescued by inhibiting protein kinase D (PKD). Our results identify a mechanism for obesity-induced electrophysiologic remodeling in the heart, namely PKD-induced reduction of CREB, which in turn decreases expression of the potassium channel Kv1.5.
doi:10.1016/j.yjmcc.2013.03.007
PMCID: PMC3647001  PMID: 23517696
obesity; arrhythmia; cyclic AMP response element binding protein; Kv1.5; protein kinase D
16.  NADP-Specific Electron-Bifurcating [FeFe]-Hydrogenase in a Functional Complex with Formate Dehydrogenase in Clostridium autoethanogenum Grown on CO 
Journal of Bacteriology  2013;195(19):4373-4386.
Flavin-based electron bifurcation is a recently discovered mechanism of coupling endergonic to exergonic redox reactions in the cytoplasm of anaerobic bacteria and archaea. Among the five electron-bifurcating enzyme complexes characterized to date, one is a heteromeric ferredoxin- and NAD-dependent [FeFe]-hydrogenase. We report here a novel electron-bifurcating [FeFe]-hydrogenase that is NADP rather than NAD specific and forms a complex with a formate dehydrogenase. The complex was found in high concentrations (6% of the cytoplasmic proteins) in the acetogenic Clostridium autoethanogenum autotrophically grown on CO, which was fermented to acetate, ethanol, and 2,3-butanediol. The purified complex was composed of seven different subunits. As predicted from the sequence of the encoding clustered genes (fdhA/hytA-E) and from chemical analyses, the 78.8-kDa subunit (FdhA) is a selenocysteine- and tungsten-containing formate dehydrogenase, the 65.5-kDa subunit (HytB) is an iron-sulfur flavin mononucleotide protein harboring the NADP binding site, the 51.4-kDa subunit (HytA) is the [FeFe]-hydrogenase proper, and the 18.1-kDa (HytC), 28.6-kDa (HytD), 19.9-kDa (HytE1), and 20.1-kDa (HytE2) subunits are iron-sulfur proteins. The complex catalyzed both the reversible coupled reduction of ferredoxin and NADP+ with H2 or formate and the reversible formation of H2 and CO2 from formate. We propose the complex to have two functions in vivo, namely, to normally catalyze CO2 reduction to formate with NADPH and reduced ferredoxin in the Wood-Ljungdahl pathway and to catalyze H2 formation from NADPH and reduced ferredoxin when these redox mediators get too reduced during unbalanced growth of C. autoethanogenum on CO (E0′ = −520 mV).
doi:10.1128/JB.00678-13
PMCID: PMC3807470  PMID: 23893107
17.  Clostridium acidurici Electron-Bifurcating Formate Dehydrogenase 
Applied and Environmental Microbiology  2013;79(19):6176-6179.
Cell extracts of uric acid-grown Clostridium acidurici catalyzed the coupled reduction of NAD+ and ferredoxin with formate at a specific activity of 1.3 U/mg. The enzyme complex catalyzing the electron-bifurcating reaction was purified 130-fold and found to be composed of four subunits encoded by the gene cluster hylCBA-fdhF2.
doi:10.1128/AEM.02015-13
PMCID: PMC3811350  PMID: 23872566
18.  Association between Obesity, Serum Lipids, and Colorectal Polyps in Old Chinese People 
Background. Colorectal cancer mostly arises from the polyps of colon. The aim of our study was to examine the association of body mass index (BMI) and serum lipids with the colorectal polyps in old Chinese people. Methods. The risk of developing colorectal polyps was studied in 244 subjects (212 men and 32 women, 74.63 ± 11.63 years old) who underwent colonoscopy for the first time from January 2008 to July 2012 at the Navy General Hospital, Beijing, China. According to the results of colonoscopy, all the subjects were divided into 112 normal control, 38 right colorectal polyps, 53 left colorectal polyps, and 41 both right and left colorectal polyps groups. The total plasma cholesterol, plasma triglyceride, plasma creatinine concentration, blood urinary nitrogen, and fasting glucose were determined using a multichannel analyzer. Results. There were significant differences among normal control, right colorectal polyps, left colorectal polyps, and both right and left polyps groups, which were the BMI, total cholesterol, triglycerides, creatinine, and urinary nitrogen. In binary logistic regression analysis, there were two risk factors associated with the occurrence of colorectal polyps, which included BMI and systolic blood pressure. Conclusions. Colorectal polyps were significantly associated with increased BMI, total cholesterol, and triglycerides levels.
doi:10.1155/2013/931084
PMCID: PMC3806499  PMID: 24198829
19.  Development of Recombinant Antigen Array for Simultaneous Detection of Viral Antibodies 
PLoS ONE  2013;8(9):e73842.
Protein microarrays have been developed to study antibody reactivity against a large number of antigens, demonstrating extensive perspective for clinical application. We developed a viral antigen array by spotting four recombinant antigens and synthetic peptide, including glycoprotein G of herpes simplex virus (HSV) type 1 and 2, phosphoprotein 150 of cytomegalovirus (CMV), Rubella virus (RV) core plus glycoprotein E1 and E2 as well as a E1 peptide with the optimal concentrations on activated glass slides to simultaneously detect IgG and IgM against HSV1, HSV2, CMV and RV in clinical specimens of sera and cerebrospinal fluids (CSFs). The positive reference sera were initially used to measure the sensitivity and specificity of the array with the optimal conditions. Then clinical specimens of 144 sera and 93 CSFs were tested for IgG and IgM antibodies directed against HSV1, HSV2, CMV and RV by the antigen array. Specificity of the antigen array for viral antibodies detection was satisfying compared to commercial ELISA kits but sensitivity of the array varied relying on quality and antigenic epitopes of the spotting antigens. In short, the recombinant antigen array has potential to simultaneous detect multiple viral antibodies using minute amount (3 µl) of samples, which holds the particularly advantage to detect viral antibodies in clinical CSFs being suspicious of neonatal meningitis and encephalitis.
doi:10.1371/journal.pone.0073842
PMCID: PMC3772810  PMID: 24058498
20.  A Reversible Electron-Bifurcating Ferredoxin- and NAD-Dependent [FeFe]-Hydrogenase (HydABC) in Moorella thermoacetica 
Journal of Bacteriology  2013;195(6):1267-1275.
Moorella thermoacetica was long the only model organism used to study the biochemistry of acetogenesis from CO2. Depending on the growth substrate, this Gram-positive bacterium can either form H2 or consume it. Despite the importance of H2 in its metabolism, a hydrogenase from the organism has not yet been characterized. We report here the purification and properties of an electron-bifurcating [FeFe]-hydrogenase from M. thermoacetica and show that the cytoplasmic enzyme efficiently catalyzes both H2 formation and H2 uptake. The purified heterotrimeric iron-sulfur flavoprotein (HydABC) catalyzed the coupled reduction of ferredoxin (Fd) and NAD+ with H2 at 55°C at pH 7.5 at a specific rate of about 100 μmol min−1 mg protein−1 and the reverse reaction, the coupled reduction of protons to H2 with reduced ferredoxin and NADH, at a specific rate of about 10 μmol min−1 mg protein−1 in the stoichiometry Fdox + NAD+ + 2H2 ⇋ Fdred2− + NADH + 3H+. When ferredoxin from Clostridium pasteurianum, NAD+, and the enzyme were incubated at pH 7.0 under 100% H2 in the gas phase (E0′ = −414 mV), more than 95% of the ferredoxin (E0′ = −400 mV) was reduced, which indicated that ferredoxin reduction with H2 is driven by the exergonic reduction of NAD+ (E0′ = −320 mV) with H2. In the absence of NAD+, ferredoxin was not reduced. We identified the genes encoding HydABC within the transcriptional unit hydCBAX and mapped the transcription start site.
doi:10.1128/JB.02158-12
PMCID: PMC3591994  PMID: 23316038
21.  Biclustering of Linear Patterns In Gene Expression Data 
Journal of Computational Biology  2012;19(6):619-631.
Abstract
Identifying a bicluster, or submatrix of a gene expression dataset wherein the genes express similar behavior over the columns, is useful for discovering novel functional gene interactions. In this article, we introduce a new algorithm for finding biClusters with Linear Patterns (CLiP). Instead of solely maximizing Pearson correlation, we introduce a fitness function that also considers the correlation of complementary genes and conditions. This eliminates the need for a priori determination of the bicluster size. We employ both greedy search and the genetic algorithm in optimization, incorporating resampling for more robust discovery. When applied to both real and simulation datasets, our results show that CLiP is superior to existing methods. In analyzing RNA-seq fly and worm time-course data from modENCODE, we uncover a set of similarly expressed genes suggesting maternal dependence. Supplementary Material is available online (at www.liebertonline.com/cmb).
doi:10.1089/cmb.2012.0032
PMCID: PMC3375643  PMID: 22697238
algorithms; gene clusters; probability
22.  Using biologically interrelated experiments to identify pathway genes in Arabidopsis 
Bioinformatics  2012;28(6):815-822.
Motivation: Pathway genes are considered as a group of genes that work cooperatively in the same pathway constituting a fundamental functional grouping in a biological process. Identifying pathway genes has been one of the major tasks in understanding biological processes. However, due to the difficulty in characterizing/inferring different types of biological gene relationships, as well as several computational issues arising from dealing with high-dimensional biological data, deducing genes in pathways remain challenging.
Results: In this work, we elucidate higher level gene–gene interactions by evaluating the conditional dependencies between genes, i.e. the relationships between genes after removing the influences of a set of previously known pathway genes. These previously known pathway genes serve as seed genes in our model and will guide the detection of other genes involved in the same pathway. The detailed statistical techniques involve the estimation of a precision matrix whose elements are known to be proportional to partial correlations (i.e. conditional dependencies) between genes under appropriate normality assumptions. Likelihood ratio tests on two forms of precision matrices are further performed to see if a candidate pathway gene is conditionally independent of all the previously known pathway genes. When used effectively, this is a promising approach to recover gene relationships that would have otherwise been missed by standard methods. The advantage of the proposed method is demonstrated using both simulation studies and real datasets. We also demonstrated the importance of taking into account experimental dependencies in the simulation and real data studies.
Contact: hhuang@stat.berkeley.edu; ljfeldman@berkeley.edu
Supplementary information:Supplementary data are available at Bioinformatics online.
doi:10.1093/bioinformatics/bts038
PMCID: PMC3307114  PMID: 22271267
23.  Electron Bifurcation Involved in the Energy Metabolism of the Acetogenic Bacterium Moorella thermoacetica Growing on Glucose or H2 plus CO2 
Journal of Bacteriology  2012;194(14):3689-3699.
Moorella thermoacetica ferments glucose to three acetic acids. In the oxidative part of the fermentation, the hexose is converted to 2 acetic acids and 2 CO2 molecules with the formation of 2 NADH and 2 reduced ferredoxin (Fdred2−) molecules. In the reductive part, 2 CO2 molecules are reduced to acetic acid, consuming the 8 reducing equivalents generated in the oxidative part. An open question is how the two parts are electronically connected, since two of the four oxidoreductases involved in acetogenesis from CO2 are NADP specific rather than NAD specific. We report here that the 2 NADPH molecules required for CO2 reduction to acetic acid are generated by the reduction of 2 NADP+ molecules with 1 NADH and 1 Fdred2− catalyzed by the electron-bifurcating NADH-dependent reduced ferredoxin:NADP+ oxidoreductase (NfnAB). The cytoplasmic iron-sulfur flavoprotein was heterologously produced in Escherichia coli, purified, and characterized. The purified enzyme was composed of 30-kDa (NfnA) and 50-kDa (NfnB) subunits in a 1-to-1 stoichiometry. NfnA harbors a [2Fe2S] cluster and flavin adenine dinucleotide (FAD), and NfnB harbors two [4Fe4S] clusters and FAD. M. thermoacetica contains a second electron-bifurcating enzyme. Cell extracts catalyzed the coupled reduction of NAD+ and Fd with 2 H2 molecules. The specific activity of this cytoplasmic enzyme was 3-fold higher in H2-CO2-grown cells than in glucose-grown cells. The function of this electron-bifurcating hydrogenase is not yet clear, since H2-CO2-grown cells additionally contain high specific activities of an NADP+-dependent hydrogenase that catalyzes the reduction of NADP+ with H2. This activity is hardly detectable in glucose-grown cells.
doi:10.1128/JB.00385-12
PMCID: PMC3393501  PMID: 22582275
24.  Mice with cardiac overexpression of PPARγ have impaired repolarization and spontaneous fatal ventricular arrhythmias (Morrow, PPARγ overexpression induces fatal arrhythmias) 
Circulation  2011;124(25):2812-2821.
Background
Diabetes and obesity, which confer an increased risk of sudden cardiac death, are associated with cardiomyocyte lipid accumulation and altered cardiac electrical properties, manifested by prolongation of the QRS duration and QT interval. It is difficult to distinguish the contribution of cardiomyocyte lipid accumulation versus the contribution of global metabolic defects to the increased incidence of sudden death and electrical abnormalities.
Methods and Results
In order to study the effects of metabolic abnormalities on arrhythmias without the complex systemic effects of diabetes and obesity, we studied cardiac-specific transgenic mice expressing PPARγ1 via the cardiac α-myosin heavy-chain promoter. The PPARγ-transgenic mice develop abnormal accumulation of intracellular lipids and die as young adults, prior to a significant reduction in systolic function. Using implantable ECG telemeters, we found that these mice have prolongation of the QRS and QT intervals, and spontaneous ventricular arrhythmias, including polymorphic ventricular tachycardia and ventricular fibrillation. Isolated cardiomyocytes demonstrated prolonged action potential duration caused by reduced expression and function of the potassium channels responsible for repolarization. Short-term exposure to pioglitazone, a PPARγ agonist, had no effect on mortality or rhythm in WT mice, but further exacerbated the arrhythmic phenotype and increased the mortality in the PPARγ TG mice.
Conclusions
Our findings support an important link between PPARγ activation, cardiomyocyte lipid accumulation, ion channel remodeling and increased cardiac mortality.
doi:10.1161/CIRCULATIONAHA.111.056309
PMCID: PMC3258098  PMID: 22124376
arrhythmia; metabolism; ion channels
25.  The gamma-aminobutyric acid type B (GABAB) receptor agonist baclofen inhibits morphine sensitization by decreasing the dopamine level in rat nucleus accumbens 
Background
Repeated morphine exposure can induce behavioral sensitization. There are evidences have shown that central gamma-aminobutyric acid (GABA) system is involved in morphine dependence. However, the effect of a GABAB receptor agonist baclofen on morphine-induced behavioral sensitization in rats is unclear.
Methods
We used morphine-induced behavioral sensitization model in rat to investigate the effects of baclofen on behavioral sensitization. Moreover, dopamine release in the shell of the nucleus accumbens was evaluated using microdialysis assay in vivo.
Results
The present study demonstrated that morphine challenge (3 mg/kg, s.c.) obviously enhanced the locomotor activity following 4-day consecutive morphine administration and 3-day withdrawal period, which indicated the expression of morphine sensitization. In addition, chronic treatment with baclofen (2.5, 5 mg/kg) significantly inhibited the development of morphine sensitization. It was also found that morphine challenge 3 days after repeated morphine administration produced a significant increase of extracellular dopamine release in nucleus accumbens. Furthermore, chronic treatment with baclofen decreased the dopamine release induced by morphine challenge.
Conclusions
Our results indicated that gamma-aminobutyric acid system plays an important role in the morphine sensitization in rat and suggested that behavioral sensitization is a promising model to study the mechanism underlying drug abuse.
doi:10.1186/1744-9081-8-20
PMCID: PMC3393629  PMID: 22559224
GABA receptor; Morphine; Sensitization; Dopamine; Nucleus accumbens; Baclofen

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