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Articles by H Chen
Total Records ( 21 ) for H Chen
  H Chen , W Wang , C Song , S Yu and C. Ding
 

Currently available vaccines against Mycobacterium bovis, the causative agent of tuberculosis, do not provide reliable efficacy and there is therefore a need for a novel vaccine with improved efficacy. Here, we use protein transduction technology to deliver DNA vaccines expressing mycobacterial antigens directly to target cells. We used various protein transduction domain (PTD) proteins including the VP22 conjugate from Marek's disease virus serotype 1 (MDV-1), as delivery systems for DNA constructs encoding the antigens early secretory antigenic target-6 kDa (ESAT-6) protein and culture filtrate protein 10 (CFP-10) of M. bovis. The eukaryotic expression plasmid pZ106, encoding antigens ESAT-6 and CFP-10, conjugated to various PTDs, was used to construct experimental preparations. Our findings demonstrated that VP22 alone or in combination with CFP-10:ESAT-6 fusion protein could spread into all the nuclei of the cell monolayer surrounding the transfected cells. Whereas trans-activating transcriptional PTD showed limited delivery of the fusion protein and 8R peptide was unable to deliver the fusion protein into any untransfected cells. We have demonstrated that immunization with a preparation fused to VP22 leads to a higher antibody and interferon- titer (P < 0.05). Taken together, our results demonstrated that MDV-1 VP22 serves as a potential immune enhancer in gene therapy and immunization using DNA vaccines, offering a novel approach for the prevention of M. bovis infection.

  R Muniyappa , H Chen , R. H Muzumdar , F. H Einstein , X Yan , L. Q Yue , N Barzilai and M. J. Quon
 

Assessing insulin resistance in rodent models gives insight into mechanisms that cause type 2 diabetes and the metabolic syndrome. The hyperinsulinemic euglycemic glucose clamp, the reference standard for measuring insulin sensitivity in humans and animals, is labor intensive and technically demanding. A number of simple surrogate indexes of insulin sensitivity/resistance have been developed and validated primarily for use in large human studies. These same surrogates are also frequently used in rodent studies. However, in general, these indexes have not been rigorously evaluated in animals. In a recent validation study in mice, we demonstrated that surrogates have a weaker correlation with glucose clamp estimates of insulin sensitivity/resistance than in humans. This may be due to increased technical difficulties in mice and/or intrinsic differences between human and rodent physiology. To help distinguish among these possibilities, in the present study, using data from rats substantially larger than mice, we compared the clamp glucose infusion rate (GIR) with surrogate indexes, including QUICKI, HOMA, 1/HOMA, log (HOMA), and 1/fasting insulin. All surrogates were modestly correlated with GIR (r = 0.34–0.40). Calibration analyses of surrogates adjusted for body weight demonstrated similar predictive accuracy for GIR among all surrogates. We conclude that linear correlations of surrogate indexes with clamp estimates and predictive accuracy of surrogate indexes in rats are similar to those in mice (but not as substantial as in humans). This additional rat study (taken with the previous mouse study) suggests that application of surrogate insulin sensitivity indexes developed for humans may not be appropriate for determining primary outcomes in rodent studies due to intrinsic differences in metabolic physiology. However, use of surrogates may be appropriate in rodents, where feasibility of clamps is an obstacle and measurement of insulin sensitivity is a secondary outcome.

  P Singal , R Muniyappa , R Chisholm , G Hall , H Chen , M. J Quon and K. J. Mather
 

After a constant insulin infusion is initiated, determination of steady-state conditions for glucose infusion rates (GIR) typically requires ≥3 h. The glucose infusion follows a simple time-dependent rise, reaching a plateau at steady state. We hypothesized that nonlinear fitting of abbreviated data sets consisting of only the early portion of the clamp study can provide accurate estimates of steady-state GIR. Data sets from two independent laboratories were used to develop and validate this approach. Accuracy of the predicted steady-state GDR was assessed using regression analysis and Altman-Bland plots, and precision was compared by applying a calibration model. In the development data set (n = 88 glucose clamp studies), fitting the full data set with a simple monoexponential model predicted reference GDR values with good accuracy (difference between the 2 methods –0.37 mg·kg–1·min–1) and precision [root mean square error (RMSE) = 1.11], validating the modeling procedure. Fitting data from the first 180 or 120 min predicted final GDRs with comparable accuracy but with progressively reduced precision [fitGDR-180 RMSE = 1.27 (P = NS vs. fitGDR-full); fitGDR-120 RMSE = 1.56 (P < 0.001)]. Similar results were obtained with the validation data set (n = 183 glucose clamp studies), confirming the generalizability of this approach. The modeling approach also derives kinetic parameters that are not available from standard approaches to clamp data analysis. We conclude that fitting a monoexponential curve to abbreviated clamp data produces steady-state GDR values that accurately predict the GDR values obtained from the full data sets, albeit with reduced precision. This approach may help reduce the resources required for undertaking clamp studies.

  C Blanco , R. G Heimberg , F. R Schneier , D. M Fresco , H Chen , C. L Turk , D Vermes , B. A Erwin , A. B Schmidt , H. R Juster , R Campeas and M. R. Liebowitz
 

Context  Medication and cognitive behavioral treatment are the best-established treatments for social anxiety disorder, yet many individuals remain symptomatic after treatment.

Objective  To determine whether combined medication and cognitive behavioral treatment is superior to either monotherapy or pill placebo.

Design  Randomized, double-blind, placebo-controlled trial.

Setting  Research clinics at Columbia University and Temple University.

Participants  One hundred twenty-eight individuals with a primary DSM-IV diagnosis of social anxiety disorder.

Interventions  Cognitive behavioral group therapy (CBGT), phenelzine sulfate, pill placebo, and combined CBGT plus phenelzine.

Main Outcome Measures  Liebowitz Social Anxiety Scale and Clinical Global Impression (CGI) scale scores at weeks 12 and 24.

Results  Linear mixed-effects models showed a specific order of effects, with steepest reductions in Liebowitz Social Anxiety Scale scores for the combined group, followed by the monotherapies, and the least reduction in the placebo group (Williams test = 4.97, P < .01). The CGI response rates in the intention-to-treat sample at week 12 were 9 of 27 (33.3%) (placebo), 16 of 34 (47.1%) (CBGT), 19 of 35 (54.3%) (phenelzine), and 23 of 32 (71.9%) (combined treatment) (21 = 8.76, P < .01). Corresponding remission rates (CGI = 1) were 2 of 27 (7.4%), 3 of 34 (8.8%), 8 of 35 (22.9%), and 15 of 32 (46.9%) (21 = 15.92, P < .01). At week 24, response rates were 9 of 27 (33.3%), 18 of 34 (52.9%), 17 of 35 (48.6%), and 25 of 32 (78.1%) (21 = 12.02, P = .001). Remission rates were 4 of 27 (14.8%), 8 of 34 (23.5%), 9 of 35 (25.7%), and 17 of 32 (53.1%) (21 = 10.72, P = .001).

Conclusion  Combined phenelzine and CBGT treatment is superior to either treatment alone and to placebo on dimensional measures and on rates of response and remission.

  H Chen , R. S Sippel and S. Schaefer
 

Background  Many surgeons have shown that radio-guided resection of parathyroid glands can facilitate intraoperative localization in selected patients with primary hyperparathyroidism, especially in the reoperative setting. However, in patients with negative technetium Tc 99m–sestamibi (hereafter referred to as "sestamibi") scans, the usefulness of the gamma probe is unclear. Thus, we were interested in determining the role of radio-guided techniques in patients with primary hyperparathyroidism and negative or nonlocalizing sestamibi scans.

Design  Retrospective analysis of a prospective parathyroid database.

Setting  Academic medical center.

Patients  Seven hundred sixty-nine patients with primary hyperparathyroidism who had a sestamibi scan and underwent surgical invention by a single surgeon. All patients had radioguided parathyroidectomy using a handheld gamma probe.

Main Outcome Measures  Radioactive counts, eucalcemia rate, and complications were compared between patients with positive and patients with negative sestamibi scans.

Results  All enlarged parathyroid glands were localized with the gamma probe in patients with a negative or with a positive sestamibi scan with similar sensitivities. This occurred despite the fact that smaller parathryoid glands were present, on average, in patients with negative sestamibi scans (428 mg vs 828 mg, P = .001). Equivalent high postoperative eucalcemia rates (>98%) and low complication rates (0.5%) were achieved with radioguided techniques in both patient populations.

Conclusions  Radioguided techniques are equally effective in patients with negative (nonlocalizing) sestamibi scans undergoing parathyroidectomy for primary hyperparathyroidism. Moreover, use of the gamma probe led to the detection of all parathyroid glands, including ectopically located ones. These data suggest that the gamma probe has an important role for localization of parathyroid glands in patients with negative preoperative sestamibi scans.

  L Wang , C Yu , H Chen , W Qin , Y He , F Fan , Y Zhang , M Wang , K Li , Y Zang , T. S Woodward and C. Zhu
 

Numerous studies argue that cortical reorganization may contribute to the restoration of motor function following stroke. However, the evolution of changes during the post-stroke reorganization has been little studied. This study sought to identify dynamic changes in the functional organization, particularly topological characteristics, of the motor execution network during the stroke recovery process. Ten patients (nine male and one female) with subcortical infarctions were assessed by neurological examination and scanned with resting-state functional magnetic resonance imaging across five consecutive time points in a single year. The motor execution network of each subject was constructed using a functional connectivity matrix between 21 brain regions and subsequently analysed using graph theoretical approaches. Dynamic changes in topological configuration of the network during the process of recovery were evaluated by a mixed model. We found that the motor execution network gradually shifted towards a random mode during the recovery process, which suggests that a less optimized reorganization is involved in regaining function in the affected limbs. Significantly increased regional centralities within the network were observed in the ipsilesional primary motor area and contralesional cerebellum, whereas the ipsilesional cerebellum showed decreased regional centrality. Functional connectivity to these brain regions demonstrated consistent alterations over time. Notably, these measures correlated with different clinical variables, which provided support that the findings may reflect the adaptive reorganization of the motor execution network in stroke patients. In conclusion, the study expands our understanding of the spectrum of changes occurring in the brain after stroke and provides a new avenue for investigating lesion-induced network plasticity.

  P Wang , Z Chen , Z. Q Meng , J Fan , J. M Luo , W Liang , J. H Lin , Z. H Zhou , H Chen , K Wang , Y. H Shen , Z. D Xu and L. M. Liu
 

Ski used to be defined as an oncogene that contributes to the resistance of tumor cells to transforming growth factor-β (TGF-β)-induced growth arrest. As TGF-β has a dual effect on tumor growth with both tumor-suppressing and -promoting activity depending on the stage of carcinogenesis and the cell type, the precise role of Ski in carcinogenesis remains unclear. In this study, we show that downregulation of Ski through lentivirus-mediated RNA interference decreases tumor growth both in vitro and in vivo, yet promotes cell invasiveness in vitro, and lung metastasis in vivo in the pancreatic cancer cell line SW1990, which contain wild-type Smad4 expression, and the BxPC3 cell line, which is Smad4 deficient. We also show that the downregulation of Ski increases TGF-β-induced transcriptional activity, which is associated with increased TGF-β-dependent Smad2/3 phosphorylation, and results in an altered expression profile of TGF-β-inducible genes involved in metastasis, angiogenesis and cell proliferation and epithelial–mesenchymal transition. Immunohistochemical analysis of specimens from 71 patients with pancreatic adenocarcinoma showed a significant association between overexpression of Ski and decreased patient survival time (P = 0.0024). Our results suggest that Ski may act as a tumor proliferation-promoting factor or as a metastatic suppressor in human pancreatic cancer.

  S Zhang , J Lu , X Zhao , W Wu , H Wang , Q Wu , X Chen , W Fan , H Chen , F Wang , Z Hu , L Jin , Q Wei , H Shen , W Huang and D. Lu
 

Checkpoint kinase (CHEK) 2, a tumor suppressor gene, plays an essential role in the DNA damage checkpoint response cascade. We first investigated two polymorphisms in the proximal promoter of the CHEK2 gene and evaluated their associations with the risk of lung cancer in a case–control study using 500 incident lung cancer cases and 517 cancer-free controls. We found that CHEK2 rs2236141 –48 G > A was significantly associated with lung cancer risk (P = 0.0018). Similar results were obtained in a follow-up replication study in 575 lung cancer patients and 589 controls (P = 0.042). Quantitative polymerase chain reaction showed that individuals with the G allele had lower levels of CHEK2 transcripts in peripheral blood mononuclear cells and normal lung tissues. The –48 G->A variant eliminated a methylation site and thereby relieve the transcriptional repression of CHEK2. Therefore, this polymorphism affected downstream transcription through genetic and epigenetic modifications. Luciferase reporter assays demonstrated that the major G allele significantly attenuated reporter gene expression when methylated. Electrophoretic Mobility shift assays and surface plasmon resonance revealed that the methylated G allele increased transcription factor accessibility. We used in vivo chromatin immunoprecipitation to confirm that the relevant transcription factor was Sp1. Using lung tissue heterozygous for the G/A single-nucleotide polymorphism, we found that Sp1 acted as a repressor and had a stronger binding affinity for the G allele. These results support our hypothesis that the CHEK2 rs2236141 variant modifies lung cancer susceptibility in the Chinese population by affecting CHEK2 expression.

  H Chen , T Kluz , R Zhang and M. Costa
 

Epigenetic silencing of tumor suppressor genes commonly occurs in human cancers via increasing DNA methylation and repressive histone modifications at gene promoters. However, little is known about how pathogenic environmental factors contribute to cancer development by affecting epigenetic regulatory mechanisms. Previously, we reported that both hypoxia and nickel (an environmental carcinogen) increased global histone H3 lysine 9 methylation in cells through inhibiting a novel class of iron- and -ketoglutarate-dependent histone demethylases. Here, we investigated whether inhibition of histone demethylase JMJD1A by hypoxia and nickel could lead to repression/silencing of JMJD1A-targeted gene(s). By using Affymetrix GeneChip and ChIP-on-chip technologies, we identified Spry2 gene, a key regulator of receptor tyrosine kinase/extracellular signal-regulated kinase (ERK) signaling, as one of the JMJD1A-targeted genes in human bronchial epithelial BEAS-2B cells. Both hypoxia and nickel exposure increased the level of H3K9me2 at the Spry2 promoter by inhibiting JMJD1A, which probably led to a decreased expression of Spry2 in BEAS-2B cells. Repression of Spry2 potentiated the nickel-induced ERK phosphorylation, and forced expression of Spry2 in BEAS-2B cells decreased the nickel-induced ERK phosphorylation and significantly suppressed nickel-induced anchorage-independent growth. Taken together, our results suggest that histone demethylases could be targets of environmental carcinogens and their inhibition may lead to altered gene expression and eventually carcinogenesis.

  M Guo , H Feng , J Zhang , W Wang , Y Wang , Y Li , C Gao , H Chen , Y Feng and Z. G. He
 

Sequence-specific DNA-binding transcription factors have widespread biological significance in the regulation of gene expression. However, in lower prokaryotes and eukaryotic metazoans, it is usually difficult to find transcription regulatory factors that recognize specific target promoters. To address this, we have developed in this study a new bacterial one-hybrid reporter vector system that provides a convenient and rapid strategy to determine the specific interaction between target DNA sequences and their transcription factors. Using this system, we have successfully determined the DNA-binding specificity of the transcription regulator Rv3133c to a previously reported promoter region of the gene Rv2031 in Mycobacterium tuberculosis. In addition, we have tested more than 20 promoter regions of M. tuberculosis genes using this approach to determine if they interact with ~150 putative regulatory proteins. A variety of transcription factors are found to participate in the regulation of stress response and fatty acid metabolism, both of which comprise the core of in vivo-induced genes when M. tuberculosis invades macrophages. Interestingly, among the many new discovered potential transcription factors, the WhiB-like transcriptional factor WhiB3 was identified for the first time to bind with the promoter sequences of most in vivo-induced genes. Therefore, this study offers important data in the dissection of the transcription regulations in M. tuberculosis, and the strategy should be applicable in the study of DNA-binding factors in a wide range of biological organisms.

  T Fei , K Xia , Z Li , B Zhou , S Zhu , H Chen , J Zhang , Z Chen , H Xiao , J. D. J Han and Y. G. Chen
 

Embryonic stem (ES) cells are under precise control of both intrinsic self-renewal gene regulatory network and extrinsic growth factor-triggered signaling cascades. How external signaling pathways connect to core self-renewal transcriptional circuits is largely unknown. To probe this, we chose BMP signaling, which is previously recognized as a master control for both self-renewal and lineage commitment of murine ES cells. Here, we mapped target gene promoter occupancy of SMAD1/5 and SMAD4 on a genome-wide scale and found that they associate with a large group of developmental regulators that are enriched for H3K27 trimethylation and H3K4 trimethylation bivalent marks and are repressed in the self-renewing state, whereas they are rapidly induced upon differentiation. Smad knockdown experiments further indicate that SMAD-mediated BMP signaling is largely required for differentiation-related processes rather than directly influencing self-renewal. Among the SMAD-associated genes, we further identified Dpysl2 (previously known as Crmp2) and the H3K27 demethylase Kdm6b (previously known as Jmjd3) as BMP4-modulated early neural differentiation regulators. Combined with computational analysis, our results suggest that SMAD-mediated BMP signaling balances self-renewal versus differentiation by modulating a set of developmental regulators.

  H Chen , N Patterson and D. Reich
 

Selective sweeps can increase genetic differentiation among populations and cause allele frequency spectra to depart from the expectation under neutrality. We present a likelihood method for detecting selective sweeps that involves jointly modeling the multilocus allele frequency differentiation between two populations. We use Brownian motion to model genetic drift under neutrality, and a deterministic model to approximate the effect of a selective sweep on single nucleotide polymorphisms (SNPs) in the vicinity. We test the method with extensive simulated data, and demonstrate that in some scenarios the method provides higher power than previously reported approaches to detect selective sweeps, and can provide surprisingly good localization of the position of a selected allele. A strength of our technique is that it uses allele frequency differentiation between populations, which is much more robust to ascertainment bias in SNP discovery than methods based on the allele frequency spectrum. We apply this method to compare continentally diverse populations, as well as Northern and Southern Europeans. Our analysis identifies a list of loci as candidate targets of selection, including well-known selected loci and new regions that have not been highlighted by previous scans for selection.

  X Wang , Q Li , X Niu , H Chen , L Xu and C. Qi
 

Sspg1d, one of endopolygalacturonases, is an important fungal effector secreted by the necrotrophic fungus Sclerotinia sclerotiorum during early infection. Using sspg1d as bait, a small C2 domain protein (designated as IPG-1) was identified by yeast two-hybrid screening of a canola cDNA library. Deletion analysis confirmed that the C-terminus of IPG-1 is responsible for its interaction with sspg1d in the yeast two-hybrid assay. The sspg1d/IPG-1 interaction was further confirmed in plant cells by a biomolecular fluorescence complementation (BiFC) assay. A transient expression assay showed that the IPG-1–GFP fusion protein was targeted to the plasma membrane and nucleus in onion epidermal cells. Following treatment with a Ca2+ ionophore, it was distributed throughout the cytosol. Real-time PCR assay demonstrated that IPG-1 was highly induced by Sclerotinia sclerotiorum in canola leaves and stems. Southern blot analysis indicated the presence of about five homologues of IPG-1 in the canola genome. Two additional members of the IPG-1gene family were isolated by RT-PCR. Their sequence similarity with IPG-1 is as high as 95%. However, they did not interact with sspg1d in the yeast two-hybrid assay. Possible roles of IPG-1 and its association with sspg1d in the defence signalling pathway were discussed.

  H Chen , J. M Burke , T Mosindy , P. M Fedorak and E. E. Prepas
 

Euphotic water samples were collected monthly from 16 sites in Lake of the Woods, Ontario, Canada from July to September, 2006 and 2007. Sites represented a range of inorganic nitrogen and phosphorus concentrations and mixing regimes, which was reflected in the spatial variability in phytoplankton biomass and community composition, and cyanobacterial toxin [microcystin-LR (MC-LR)] concentrations. Nutrient concentrations decreased along a south to north transect, concomitant with distance from the main river inlet at the south end of the lake. Filamentous, nitrogen-fixing Aphanizomenon spp. and Anabaena spp. were dominant at most sites: Aphanizomenon was more abundant at southern sites and Anabaena was more abundant at northern sites. MC-LR was detected at all sites at least once (maximum concentration 0.69 µg L–1). However, there was no correlation between MC-LR concentration and the biomass of Anabaena, a documented MC-LR producer. For the pooled data set, total phosphorus and ammonium concentrations were the two parameters most strongly related with MC-LR concentration. Principal components analysis was used to analyze the data set; it indicated that two factors accounted for 81% of the variability among the 12 environmental parameters tested. Factor 1 represented physicochemical characteristics and phytoplankton biomass and Factor 2 represented Anabaena and Woronichinia biomass.

  G. S Song , H. L Zhai , Y. G Peng , L Zhang , G Wei , X. Y Chen , Y. G Xiao , L Wang , Y. J Chen , B Wu , B Chen , Y Zhang , H Chen , X. J Feng , W. K Gong , Y Liu , Z. J Yin , F Wang , G. Z Liu , H. L Xu , X. L Wei , X. L Zhao , P. B. F Ouwerkerk , T Hankemeier , T Reijmers , R. v. d Heijden , C. M Lu , M Wang , J. v. d Greef and Z. Zhu
 

Heterosis is a biological phenomenon whereby the offspring from two parents show improved and superior performance than either inbred parental lines. Hybrid rice is one of the most successful apotheoses in crops utilizing heterosis. Transcriptional profiling of F1 super-hybrid rice Liangyou-2186 and its parents by serial analysis of gene expression (SAGE) revealed 1183 differentially expressed genes (DGs), among which DGs were found significantly enriched in pathways such as photosynthesis and carbon-fixation, and most of the key genes involved in the carbon-fixation pathway exhibited up-regulated expression in F1 hybrid rice. Moreover, increased catabolic activity of corresponding enzymes and photosynthetic efficiency were also detected, which combined to indicate that carbon fixation is enhanced in F1 hybrid, and might probably be associated with the yield vigor and heterosis in super-hybrid rice. By correlating DGs with yield-related quantitative trait loci (QTL), a potential relationship between differential gene expression and phenotypic changes was also found. In addition, a regulatory network involving circadian-rhythms and light signaling pathways was also found, as previously reported in Arabidopsis, which suggest that such a network might also be related with heterosis in hybrid rice. Altogether, the present study provides another view for understanding the molecular mechanism underlying heterosis in rice.

  Y Zhong , Y Huang , T Zhang , C Ma , S Zhang , W Fan , H Chen , J Qian and D. Lu
 

O6-methylguanine-DNA methyltransferase is one of the rare proteins to directly remove alkylating agents in the human DNA direct reversal repair pathway. Its two common single-nucleotide polymorphisms, Leu84Phe and Ile143Val, had previously been identified to contribute to susceptibility of cancer. However, there are conflicting results in studies on the association of the two polymorphisms with cancer. Therefore, we conducted a meta-analysis to clarify the paradox with a large collected sample (13 069 cancer patients and 20 290 controls). We found significant association between the T allele (84Phe) and cancer risk, under the recessive genetic model [P = 0.023, odds ratio (OR) = 1.251, 95% confidence interval (CI) 1.031–1.517, Pheterogeneity = 0.270], TT versus CC comparison (P = 0.035, OR = 1.239, 95% CI 1.015–1.511, Pheterogeneity = 0.225) and TT versus CT comparison (P = 0.007, OR = 1.292, 95% CI 1.071–1.559, Pheterogeneity = 0.374), using the random-effect model. In the ethnicity subgroup analysis, a significant association with cancer among Caucasians was found under the recessive genetic model, homozygote comparison and TT versus TC comparison. In the tumour sites subgroup analysis, only the protective effects of Leu84Phe polymorphism were found in colorectal cancer, under CT versus CC comparison. No significant association between the G allele of Ile143Val and cancer risk was found. The G allele showed an increased lung cancer risk under the dominant genetic model and AG versus AA comparison in all Hardy–Weinberg equilibrium subjects, only when the fixed-effect model was used. However, it was insignificant in the random-effect model.

  Y. D Yang , P Spratt , H Chen , C Park and D. Kihara
 

Computational protein tertiary structure prediction has made significant progress over the past years. However, most of the existing structure prediction methods are not equipped with functionality to predict accuracy of constructed models. Knowing the accuracy of a structure model is crucial for its practical use since the accuracy determines potential applications of the model. Here we have developed quality assessment methods, which predict real value of the global and local quality of protein structure models. The global quality of a model is defined as the root mean square deviation (RMSD) and the LGA score to its native structure. The local quality is defined as the distance between the corresponding C positions of a model and its native structure when they are superimposed. Three regression methods are employed to combine different types of quality assessment measures of models, including alignment-level scores, residue-position level scores, atomic-detailed structure level scores and composite scores. The regression models were tested on a large benchmark data set of template-based protein structure models of various qualities. In predicting RMSD and the LGA score, a combination of two terms, length-normalized SPAD, a score that assesses alignment stability by considering suboptimal alignments, and Verify3D normalized by the square of the model length shows a significant performance, achieving 97.1 and 83.6% accuracy in identifying models with an RMSD of <2 and 6 Å, respectively. For predicting the local quality of models, we find that a two-step approach, in which the global RMSD predicted in the first step is further combined with the other terms, can dramatically increase the accuracy. Finally, the developed regression equations are applied to assess the quality of structure models of whole E. coli proteome.

  H Chen , J Miao and N. Wang
 

We develop a dynamic incomplete-markets model of entrepreneurial firms, and demonstrate the implications of nondiversifiable risks for entrepreneurs' interdependent consumption, portfolio allocation, financing, investment, and business exit decisions. We characterize the optimal capital structure via a generalized tradeoff model where risky debt provides significant diversification benefits. Nondiversifiable risks have several important implications: More risk-averse entrepreneurs default earlier, but choose higher leverage; lack of diversification causes entrepreneurial firms to underinvest relative to public firms, and risky debt partially alleviates this problem; and entrepreneurial risk aversion can overturn the risk-shifting incentives induced by risky debt. We also analytically characterize the idiosyncratic risk premium.

  H Xu , B Zhang , J Li , H Chen , J Tooley and F. K. Ghishan
 

Sodium/hydrogen exchangers (NHEs) play a major role in Na+ absorption, cell volume regulation, and intracellular pH regulation. Of the nine identified mammalian NHEs, three (NHE2, NHE3, and NHE8) are localized on the apical membrane of epithelial cells in the small intestine and the kidney. Although the regulation of NHE2 and NHE3 expression has been extensively studied in the past decade, little is known about the regulation of NHE8 gene expression under physiological conditions. The current studies were performed to explore the role of epidermal growth factor (EGF) on NHE8 expression during intestinal maturation. Brush-border membrane vesicles (BBMV) were isolated from intestinal epithelia, and Western blot analysis was performed to determine NHE8 protein expression of sucking male rats treated with EGF. Real-time PCR was used to quantitate NHE8 mRNA expression in rats and Caco-2 cells. Human NHE8 promoter activity was characterized through transfection of Caco-2 cells. Gel mobility shift assays (GMSAs) were used to identify the promoter sequences and the transcriptional factors involved in EGF-mediated regulation. Our results showed that intestinal NHE8 mRNA expression was decreased in EGF-treated rats and Caco-2 cells, and NHE8 protein abundance was also decreased in EGF-treated rats. The activity of the human NHE8 gene promoter transfected in Caco-2 cells was also reduced by EGF treatment. This could be explained by reduced binding of transcription factor Sp3 on the NHE8 basal promoter region in the presence of EGF. Pretreatment with MEK1/2 inhibitor UO-126 could prevent EGF-mediated inhibition of NHE8 gene expression. In conclusion, this study showed that EGF inhibits NHE8 gene expression through reducing its basal transcription, suggesting an important role of EGF in regulating NHE expression during intestinal maturation.

  V Pastukh , H Chen , S Wu , C. J Jong , M Alexeyev and S. W. Schaffer
 

Hypernatremia exerts multiple cellular effects, many of which could influence the outcome of an ischemic event. To further evaluate these effects of hypernatremia, isolated neonatal cardiomyocytes were chronically incubated with medium containing either normal (142 mM) or elevated sodium (167 mM) and then transferred to medium containing deoxyglucose and the electron transport chain inhibitor amobarbital. Chronic hypernatremia diminished the degree of calcium accumulation and reactive oxygen species generation during the period of metabolic inhibition. The improvement in calcium homeostasis was traced in part to the downregulation of the CaV3.1 T-type calcium channel, as deficiency in the CaV3.1 subtype using short hairpin RNA or treatment with an inhibitor of the CaV3.1 variant of the T-type calcium channel (i.e., diphenylhydantoin) attenuated energy deficiency-mediated calcium accumulation and cell death. Although hyperosmotically stressed cells (exposed to 50 mM mannitol) had no effect on T-type calcium channel activity, they were also resistant to death during metabolic inhibition. Both hyperosmotic stress and hypernatremia activated Akt, suggesting that they initiate the phosphatidylinositol 3-kinase/Akt cytoprotective pathway, which protects the cell against calcium overload and oxidative stress. Thus hypernatremia appears to protect the cell against metabolic inhibition by promoting the downregulation of the T-type calcium channel and stimulating cytoprotective protein kinase pathways.

  Y Wei , Y Ge , F Zhou , H Chen , C Cui , D Liu , Z Yang , G Wu , J Gu and J. Jiang
 

ATF5, a member of ATF/CREB family of b-ZIP transcription factors, is highly expressed in a wide variety of neoplasms and regulates cell differentiation, cell survival and apoptosis. However, the mechanism of human ATF5 transcriptional regulation has not been clarified. Here, we identified the transcription start site of the ATF5 gene, cloned its 5'-flanking region and identified the region –105 to +3 relative to the transcription start site as that having promoter activity. This region contained potential binding sites for several transcription factors, including EBF1, Sp1 and E2F1. EBF1 transcription factor binds to the ATF5 promoter and regulates the ATF5 transcription in an EBF-binding site independent manner. Thus, our studies not only provided molecular basis of ATF5 transcriptional regulation, but also identified ATF5 as a target gene of EBF1 transcription factor.

 
 
 
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