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1.  On the Modeling of Polar Component of Solvation Energy using Smooth Gaussian-Based Dielectric Function 
Journal of theoretical & computational chemistry  2014;13(3):10.1142/S0219633614400021.
Traditional implicit methods for modeling electrostatics in biomolecules use a two-dielectric approach: a biomolecule is assigned low dielectric constant while the water phase is considered as a high dielectric constant medium. However, such an approach treats the biomolecule-water interface as a sharp dielectric border between two homogeneous dielectric media and does not account for inhomogeneous dielectric properties of the macromolecule as well. Recently we reported a new development, a smooth Gaussian-based dielectric function which treats the entire system, the solute and the water phase, as inhomogeneous dielectric medium (J Chem Theory Comput. 2013 Apr 9; 9(4): 2126-2136.). Here we examine various aspects of the modeling of polar solvation energy in such inhomogeneous systems in terms of the solute-water boundary and the inhomogeneity of the solute in the absence of water surrounding. The smooth Gaussian-based dielectric function is implemented in the DelPhi finite-difference program, and therefore the sensitivity of the results with respect to the grid parameters is investigated, and it is shown that the calculated polar solvation energy is almost grid independent. Furthermore, the results are compared with the standard two-media model and it is demonstrated that on average, the standard method overestimates the magnitude of the polar solvation energy by a factor 2.5. Lastly, the possibility of the solute to have local dielectric constant larger than of a bulk water is investigated in a benchmarking test against experimentally determined set of pKa's and it is speculated that side chain rearrangements could result in local dielectric constant larger than 80.
doi:10.1142/S0219633614400021
PMCID: PMC4092036  PMID: 25018579
dielectric constant; Poisson-Boltzmann equation; electrostatics; finite-difference method; protein flexibility
2.  Decreased miR-204 in H. pylori-Associated Gastric Cancer Promotes Cancer Cell Proliferation and Invasion by Targeting SOX4 
PLoS ONE  2014;9(7):e101457.
Background
The molecular mechanism between Helicobacter pylori (H. pylori) infection and gastric cancer remained largely unknown. In this study, we determined the role of miRNA in H. pylori induced gastric cancer.
Methods and Results
We found that miR-204 was decreased in H. pylori positive tissues by qRT-PCR. Knockdown of miR-204 enhanced the invasion and proliferation ability of gastric cancer cells in vitro. Luciferase assay revealed that SOX4 was target gene of miR-204, which was found up-regulated in H. pylori positive tissues. Down-regulation of miR-204 and over-expression of SOX4 promoted epithelial-mesenchymal transition process.
Conclusion
Taken together, our findings demonstrated that miR-204 may act as a tumor suppressor in H. pylori induced gastric cancer by targeting SOX4.
doi:10.1371/journal.pone.0101457
PMCID: PMC4077842  PMID: 24984017
3.  Synergistic Apoptosis-Inducing Effects on A375 Human Melanoma Cells of Natural Borneol and Curcumin 
PLoS ONE  2014;9(6):e101277.
This study was to investigate the synergistic effect of NB/Cur on growth and apoptosis in A375 human melanoma cell line by MTT assay, flow cytometry and Western blotting. Our results demonstrated that NB effectively synergized with Cur to enhance its antiproliferative activity on A375 human melanoma cells by induction of apoptosis, as evidenced by an increase in sub-G1 cell population, DNA fragmentation, PARP cleavage and caspase activation. Further mechanistic studies by Western blotting showed that after treatment of the cells with NB/Cur, up-regulation of the expression level of phosphorylated JNK and down-regulation of the expression level of phosphorylated ERK and Akt contributed to A375 cells apoptosis. Moreover, NB also potentiated Cur to trigger intracellular ROS overproduction and the DNA damage with up-regulation of the expression level of phosphorylated ATM, phosphorylated Brca1 and phosphorylated p53. The results indicate the combinational application potential of NB and Cur in treatments of cancers.
doi:10.1371/journal.pone.0101277
PMCID: PMC4074168  PMID: 24971451
4.  Interventional therapy for human breast cancer in nude mice with 131I gelatin microspheres (131I-GMSs) following intratumoral injection 
Introduction
The aim of this study was to investigate the effects of 131I gelatin microspheres (131I-GMS) on human breast cancer cells (MCF-7) in nude mice and the biodistribution of 131I-GMSs following intratumoral injections.
Methods
A total of 20 tumor-bearing mice were divided into a treatment group and control group and received intratumoral injections of 2.5 mci 131I-GMSs and nonradioactive GMSs, respectively. Tumor size was measured once per week. Another 16 mice received intratumoral injections of 0.4 mci 131I-GMSs and were subjected to single photon emission computed tomography (SPECT) scans and tissue radioactivity concentration measurements on day 1, 4, 8 and 16 postinjection. The 20 tumor-bearing mice received intratumoral injections of 0.4 mci [131I] sodium iodide solution and were subjected to SPECT scans and intratumoral radioactivity measurements at 1, 6, 24, 48 and 72 h postinjection. The tumors were collected for histological examination.
Results
The average tumor volume in the 131I-GMSs group on post-treatment day 21 decreased to 86.82 ± 63.6%, while it increased to 893.37 ± 158.12% in the control group (P < 0.01 vs. the 131I-GMSs group). 131I-GMSs provided much higher intratumoral retention of radioactivity, resulting in 19.93 ± 5.24% of the injected radioactivity after 16 days, whereas the control group retained only 1.83 ± 0.46% of the injected radioactivity within the tumors at 1 h postinjection.
Conclusions
131I-GMSs suppressed the growth of MCF-7 in nude mice and provided sustained intratumoral radioactivity retention. The results suggest the potential of 131I-GMSs for clinical applications in radiotherapy for breast cancer.
doi:10.1186/1748-717X-9-144
PMCID: PMC4083354  PMID: 24958442
131I; Gelatin microspheres; Breast neoplasms; Intratumoral injection; Treatment outcome; Biodistribution
5.  Acute Aerobic Exercise Increases Cortical Activity during Working Memory: A Functional MRI Study in Female College Students 
PLoS ONE  2014;9(6):e99222.
There is increasing evidence that acute aerobic exercise is associated with improved cognitive function. However, neural correlates of its cognitive plasticity remain largely unknown. The present study examined the effect of a session of acute aerobic exercise on working memory task-evoked brain activity as well as task performance. A within-subjects design with a counterbalanced order was employed. Fifteen young female participants (M = 19.56, SD = 0.81) were scanned using functional magnetic resonance imaging while performing a working memory task, the N-back task, both following an acute exercise session with 20 minutes of moderate intensity and a control rest session. Although an acute session of exercise did not improve behavioral performance, we observed that it had a significant impact on brain activity during the 2-back condition of the N-back task. Specifically, acute exercise induced increased brain activation in the right middle prefrontal gyrus, the right lingual gyrus, and the left fusiform gyrus as well as deactivations in the anterior cingulate cortexes, the left inferior frontal gyrus, and the right paracentral lobule. Despite the lack of an effect on behavioral measures, significant changes after acute exercise with activation of the prefrontal and occipital cortexes and deactivation of the anterior cingulate cortexes and left frontal hemisphere reflect the improvement of executive control processes, indicating that acute exercise could benefit working memory at a macro-neural level. In addition to its effects on reversing recent obesity and disease trends, our results provide substantial evidence highlighting the importance of promoting physical activity across the lifespan to prevent or reverse cognitive and neural decline.
doi:10.1371/journal.pone.0099222
PMCID: PMC4050105  PMID: 24911975
6.  3D IMAGING OF THE MITOCHONDRIAL REDOX STATE OF RAT HEARTS UNDER NORMAL AND FASTING CONDITIONS 
The heart requires continuous ATP availability that is generated in the mitochondria. Although studies using the cell culture and perfused organ models have been carried out to investigate the biochemistry in the mitochondria in response to a change in substrate supply, mitochondrial bioenergetics of heart under normal feed or fasting conditions has not been studied at the tissue level with a sub-millimeter spatial resolution either in vivo or ex vivo. Oxidation of many food-derived metabolites to generate ATP in the mitochondria is realized through the NADH/NAD+ couple acting as a central electron carrier. We employed the Chance redox scanner — the low-temperature fluorescence scanner to image the three-dimensional (3D) spatial distribution of the mitochondrial redox states in heart tissues of rats under normal feeding or an overnight starvation for 14.5 h. Multiple consecutive sections of each heart were imaged to map three redox indices, i.e., NADH, oxidized flavoproteins (Fp, including flavin adenine dinucleotide (FAD)) and the redox ratio NADH/Fp. The imaging results revealed the micro-heterogeneity and the spatial distribution of these redox indices. The quantitative analysis showed that in the fasted hearts the standard deviation of both NADH and Fp, i.e., SD_NADH and SD_Fp, significantly decreased with a p value of 0.032 and 0.045, respectively, indicating that the hearts become relatively more homogeneous after fasting. The fasted hearts contained 28.6% less NADH (p = 0.038). No significant change in Fp was found (p = 0.4). The NADH/Fp ratio decreased with a marginal p value (0.076). The decreased NADH in the fasted hearts is consistent with the cardiac cells’ reliance of fatty acids consumption for energy metabolism when glucose becomes scarce. The experimental observation of NADH decrease induced by dietary restriction in the heart at tissue level has not been reported to our best knowledge. The Chance redox scanner demonstrated the feasibility of 3D imaging of the mitochondrial redox state in the heart and provides a useful tool to study heart metabolism and function under normal, dietary-change and pathological conditions at tissue level.
doi:10.1142/S1793545813500454
PMCID: PMC4048726  PMID: 24917891
Mitochondrion; metabolism; bioenergetics; cardiomyocyte; NADH; flavoproteins; Fp; FAD; caloric restriction; food deprivation
7.  Urban Chinese Smokers From Lower Socioeconomic Backgrounds Face More Barriers to Quitting: Results From the International Tobacco Control-China Survey 
Nicotine & Tobacco Research  2012;15(6):1044-1051.
Introduction:
Research findings on social disparities in barriers to quitting faced by smokers from mainly Western English-language countries may or may not generalize to smokers in China. This paper sought to determine whether nicotine dependence, quitting self-efficacy, quitting interest differ by socio-economic status (SES), and whether they mediate the relationship between SES and quitting behavior of urban Chinese smokers.
Methods:
Data come from 7,309 adult smokers who participated in the first 3 waves of the International Tobacco Control-China survey conducted in 7 cities across China. The association of socio-economic indicators with nicotine dependence, quitting self-efficacy, quitting interest, and behavior was evaluated using generalized estimating equations models along with a formal test of mediational effects.
Results:
The SES index indicated that those from lower SES were significantly more addicted (p < .001), less confident (p < .001), and less interested in quitting (p < .05). This finding was replicated by education and employment status, but it was not clearly related to income. Mediational analyses revealed that the effects of SES on making quit attempts and quit success among those who tried were indirect. For quit attempts, self-efficacy, interest to quit, and heaviness of smoking index (HSI) were all significant mediators of the SES effect (p < .001), but for maintenance, only HSI was a significant mediator (p < .001).
Conclusions:
Urban Chinese smokers from lower socio- economic backgrounds experience greater levels of psychological and behavioral barriers to quitting than their counterparts from higher socio-economic backgrounds and as such, they need more help to quit and do so successfully.
doi:10.1093/ntr/nts234
PMCID: PMC3646648  PMID: 23125438
8.  Redox Imaging of Human Breast Cancer Core Biopsies 
Academic radiology  2013;20(6):764-768.
Rationale and Objectives
The clinical gold standard for breast cancer diagnosis relies on invasive biopsies followed by tissue fixation for subsequent histopathological examination. This process renders the specimens to be much less suitable for biochemical or metabolic analysis. Our previous metabolic imaging data in tumor xenograft models showed that the mitochondrial redox state is a sensitive indicator that can distinguish between normal and tumor tissue. In this study, we investigated whether the same redox imaging technique can be applied to core biopsy samples of human breast cancer and whether the mitochondrial redox state may serve as a novel metabolic biomarker that may be used to distinguish between normal and malignant breast tissue in the clinic. Our long-term objective was to identify novel metabolic imaging biomarkers for breast cancer diagnosis.
Materials and Methods
Both normal and cancerous tissue specimens were collected from the cancer-bearing breasts of three patients shortly after surgical resection. Core biopsies and tissue blocks were obtained from tumor and normal adjacent breast tissue, respectively. All specimens were snap-frozen with liquid nitrogen, embedded in chilled mounting medium with flavin adenine dinucleotide and reduced nicotinamide adenine dinucleotide reference standards adjacently placed, and scanned using the Chance redox scanner (ie, cryogenic nicotinamide adenine dinucleotide/oxidized flavoprotein fluorescence imager).
Results
Our preliminary data showed cancerous tissues had up to 10-fold higher oxidized flavoprotein signals and had elevated oxidized redox state compared to the normal tissues from the same patient. A high degree of tumor tissue heterogeneity in the redox indices was observed.
Conclusions
Our finding suggests that the identified redox imaging indices could differentiate between cancer and noncancer breast tissues without subjecting tissues to fixatives. We propose that this novel redox scanning procedure may assist in tissue diagnosis in freshly procured biopsy samples before tissue fixation.
doi:10.1016/j.acra.2013.02.006
PMCID: PMC3791620  PMID: 23664401
Mitochondria; oxidized flavoprotein (Fp); NADH; redox state; metabolic biomarker; the Chance redox scanner
9.  Mass Spectrometry Methodology in Lipid Analysis 
Lipidomics is an emerging field, where the structures, functions and dynamic changes of lipids in cells, tissues or body fluids are investigated. Due to the vital roles of lipids in human physiological and pathological processes, lipidomics is attracting more and more attentions. However, because of the diversity and complexity of lipids, lipid analysis is still full of challenges. The recent development of methods for lipid extraction and analysis and the combination with bioinformatics technology greatly push forward the study of lipidomics. Among them, mass spectrometry (MS) is the most important technology for lipid analysis. In this review, the methodology based on MS for lipid analysis was introduced. It is believed that along with the rapid development of MS and its further applications to lipid analysis, more functional lipids will be identified as biomarkers and therapeutic targets and for the study of the mechanisms of disease.
doi:10.3390/ijms150610492
PMCID: PMC4100164  PMID: 24921707
lipidomics; mass spectrometry; lipids extraction; bioinformatics technology
10.  Expression and clinical significance of FXYD3 in endometrial cancer 
Oncology Letters  2014;8(2):517-522.
FXYD3 expression is upregulated in numerous cancer cell types. The present study compared the FXDY3 expression in normal endometrium, premalignant lesion and endometrial cancer tissue samples, and investigated the correlation between FXDY3 expression and clinicopathological features. FXYD3 expression was analyzed by streptavidin-peroxidase immunohistochemistry in 21 normal endometrial tissue samples, 18 atypical endometrial hyperplasia samples and 50 tissues obtained from patients diagnosed with endometrial cancer. The percentage of FXYD3-positive cell expression in the normal endometrium, atypical hyperplasia and endometrial cancer tissues samples was 0, 22, and 26%, respectively. The differences between the atypical hyperplasia and endometrial cancer groups were statistically significant when compared with the normal group (P=0.007 and P=0.037, respectively). There was no significant difference between the atypical hyperplasia and endometrial cancer groups. The percentage of FXYD3-positive cells correlated with the fertility frequency (P<0.05). In conclusion, FXYD3 is a potential biomarker for endometrial cancer, and its upregulation may be an early event in endometrial carcinoma progression. In addition, FXYD3 expression in endometrial carcinoma correlates with fertility frequency.
doi:10.3892/ol.2014.2170
PMCID: PMC4081380  PMID: 25013464
FXYD3; endometrial hyperplasia; endometrial neoplasm; immunohistochemistry
11.  Time-Intensity Curve Parameters in Rectal Cancer Measured Using Endorectal Ultrasonography with Sterile Coupling Gels Filling the Rectum: Correlations with Tumor Angiogenesis and Clinicopathological Features 
BioMed Research International  2014;2014:587806.
The primary aim of this study was to investigate the relationship between contrast-enhanced ultrasonography (CEUS) imaging parameters and clinicopathological features of rectal carcinoma and assess their potential as new radiological prognostic predictors. A total of 66 rectal carcinoma patients were analyzed with the time-intensity curve of CEUS. The parameter arrival time (AT), time to peak enhancement (TTP), wash-in time (WIT), enhanced intensity (EI), and ascending slope (AS) were measured. Microvessel density (MVD) was evaluated by immunohistochemical staining of surgical specimens. All findings were analysed prospectively and correlated with tumor staging, histological grading, and MVD. The mean values of AT, TTP, WIT, EI, and AS value of the rectal carcinoma were 10.84 ± 3.28 s, 20.61 ± 5.52 s, 9.78 ± 2.83 s, 28.68 ± 4.67 dB, and 3.20 ± 1.10, respectively. A positive linear correlation was found between the EI and MVD in rectal carcinoma (r = 0.295, P = 0.016), and there was a significant difference for EI among histological grading (r = −0.264, P = 0.007). EI decreased as T stage increased with a trend of association noted (P = 0.096). EI of contrast enhanced endorectal ultrasonography provides noninvasive biomarker of tumor angiogenesis in rectal cancer. CEUS data have the potential to predict patient prognosis.
doi:10.1155/2014/587806
PMCID: PMC4036556  PMID: 24900973
12.  miR-639 promotes the proliferation and invasion of breast cancer cell in vitro 
Breast cancer is characterised by an elevated capacity for tumour invasion and lymph node metastasis, but the cause remains to be determined. Recent studies suggest that microRNAs can regulate the evolution of malignant behaviours by regulating multiple target genes. In this study, we have first confirmed that miR-639 is up-regulated in metastatic breast cancer tissues and cell line with highly invasive capacity. Furthermore, we provided evidence to demonstrate that up-regulation of miR-639 contributes breast cancer invasion and metastasis. These data reveal a key role of miR-639 in breast cancer metastasis and support biological and clinical links between miR-639 and breast cancer.
doi:10.1186/1475-2867-14-39
PMCID: PMC4050991  PMID: 24917697
miR-639; Breast cancer; Invasion; Metastases
13.  Identification of optimum scopes of environmental factors for snails using spatial analysis techniques in Dongting Lake Region, China 
Parasites & Vectors  2014;7:216.
Background
Owing to the harmfulness and seriousness of Schistosomiasis japonica in China, the control and prevention of S. japonica transmission are imperative. As the unique intermediate host of this disease, Oncomelania hupensis plays an important role in the transmission. It has been reported that the snail population in Qiangliang Lake district, Dongting Lake Region has been naturally declining and is slowly becoming extinct. Considering the changes of environmental factors that may cause this phenomenon, we try to explore the relationship between circumstance elements and snails, and then search for the possible optimum scopes of environmental factors for snails.
Methods
Moisture content of soil, pH, temperature of soil and elevation were collected by corresponding apparatus in the study sites. The LISA statistic and GWR model were used to analyze the association between factors and mean snail density, and the values in high-high clustered areas and low-low clustered areas were extracted to find out the possible optimum ranges of these elements for snails.
Results
A total of 8,589 snail specimens were collected from 397 sampling sites in the study field. Besides the mean snail density, three environmental factors including water content, pH and temperature had high spatial autocorrelation. The spatial clustering suggested that the possible optimum scopes of moisture content, pH, temperature of the soil and elevation were 58.70 to 68.93%, 6.80 to 7.80, 22.73 to 24.23°C and 23.50 to 25.97 m, respectively. Moreover, the GWR model showed that the possible optimum ranges of these four factors were 36.58 to 61.08%, 6.541 to 6.89, 24.30 to 25.70°C and 23.50 to 29.44 m, respectively.
Conclusion
The results indicated the association between snails and environmental factors was not linear but U-shaped. Considering the results of two analysis methods, the possible optimum scopes of moisture content, pH, temperature of the soil and elevation were 58.70% to 68.93%, 6.6 to 7.0, 22.73°C to 24.23°C, and 23.5 m to 26.0 m, respectively. The findings in this research will help in making an effective strategy to control snails and provide a method to analyze other factors.
doi:10.1186/1756-3305-7-216
PMCID: PMC4025561  PMID: 24886456
Schistosomiasis japonica; Oncomelania hupensis; Environmental factors; Spatial clustering; GWR
14.  Mdb1, a Fission Yeast Homolog of Human MDC1, Modulates DNA Damage Response and Mitotic Spindle Function 
PLoS ONE  2014;9(5):e97028.
During eukaryotic DNA damage response (DDR), one of the earliest events is the phosphorylation of the C-terminal SQ motif of histone H2AX (H2A in yeasts). In human cells, phosphorylated H2AX (γH2AX) is recognized by MDC1, which serves as a binding platform for the accumulation of a myriad of DDR factors on chromatin regions surrounding DNA lesions. Despite its important role in DDR, no homolog of MDC1 outside of metazoans has been described. Here, we report the characterization of Mdb1, a protein from the fission yeast Schizosaccharomyces pombe, which shares significant sequence homology with human MDC1 in their C-terminal tandem BRCT (tBRCT) domains. We show that in vitro, recombinant Mdb1 protein binds a phosphorylated H2A (γH2A) peptide, and the phospho-specific binding requires two conserved phospho-binding residues in the tBRCT domain of Mdb1. In vivo, Mdb1 forms nuclear foci at DNA double strand breaks (DSBs) induced by the HO endonuclease and ionizing radiation (IR). IR-induced Mdb1 focus formation depends on γH2A and the phospho-binding residues of Mdb1. Deleting the mdb1 gene does not overtly affect DNA damage sensitivity in a wild type background, but alters the DNA damage sensitivity of cells lacking another γH2A binder Crb2. Overexpression of Mdb1 causes severe DNA damage sensitivity in a manner that requires the interaction between Mdb1 and γH2A. During mitosis, Mdb1 localizes to spindles and concentrates at spindle midzones at late mitosis. The spindle midzone localization of Mdb1 requires its phospho-binding residues, but is independent of γH2A. Loss of Mdb1 or mutating its phospho-binding residues makes cells more resistant to the microtubule depolymerizing drug thiabendazole. We propose that Mdb1 performs dual roles in DDR and mitotic spindle regulation.
doi:10.1371/journal.pone.0097028
PMCID: PMC4013092  PMID: 24806815
15.  Impact of Y181C and/or H221Y mutation patterns of HIV-1 reverse transcriptase on phenotypic resistance to available non-nucleoside and nucleoside inhibitors in China 
BMC Infectious Diseases  2014;14:237.
Background
The aim of this study was to investigate the role of K101Q, Y181C and H221Y emerging in HIV-1 reverse transcriptase with different mutations patterns in phenotypic susceptibility to currently available NNRTIs (nevirapine NVP, efavirenz EFV) and NRTIs (zidovudine AZT, lamivudine 3TC, stavudine d4T) in China.
Methods
Phenotype testing of currently available NNRTIs (NVP, EFV) and NRTIs (AZT, 3TC, d4T) was performed on TZM-b1 cells using recombined virus strains. P ≤ 0.05 was defined significant considering the change of 50% inhibitory drug concentration (IC50) compared with the reference, while P ≤ 0.01 was considered to be statistically significant considering multiple comparisons.
Results
Triple-mutation K101Q/Y181C/H221Y and double-mutation K101Q/Y181C resulted in significant increase in NVP resistance (1253.9-fold and 986.4-fold), while only K101Q/Y181C/H221Y brought a 5.00-fold significant increase in EFV resistance. Remarkably, K101Q/H221Y was hypersusceptible to EFV (FC = 0.04), but was significantly resistant to the three NRTIs. Then, the interaction analysis suggested the interaction was not significant to NVP (F = 0.77, P = 0.4061) but significant to EFV and other three NRTIs.
Conclusion
Copresence of mutations reported to be associated with NNRTIs confers significant increase to NVP resistance. Interestingly, some may increase the susceptibility to EFV. Certainly, the double mutation (K101Q/H221Y) also changes the susceptibility of viruses to NRTIs. Interaction between two different sites makes resistance more complex.
doi:10.1186/1471-2334-14-237
PMCID: PMC4024112  PMID: 24885612
Nucleoside reverse transcriptase inhibitors (NRTIs); Non-nucleoside reverse transcriptase inhibitors (NNRTIs); HIV-1 resistance mutation; 50% inhibitory drug concentration
16.  Proteomic analysis of liver mitochondria from rats with nonalcoholic steatohepatitis 
AIM: To explore mitochondrial dysfunction in nonalcoholic steatohepatitis (NASH) by analyzing the proteome of liver mitochondria from a NASH model.
METHODS: The NASH rat model was established by feeding rats a fat-rich diet for 24 wk and was confirmed using hematoxylin and eosin staining of liver tissue and by changes in the levels of serum alanine transaminase, aspartate aminotransferase, triglyceride, total cholesterol and other markers. Liver mitochondria from each group were isolated using differential centrifugation. The mitochondrial samples were lyzed, purified and further analyzed using two-dimensional electrophoresis combined with matrix-assisted laser desorption/ionization tandem time-of-flight mass spectrometry. Bioinformatic analyses of assigned gene ontology and biological pathway was used to study functional enrichments in the abundant proteomic data.
RESULTS: Eight up-regulated and sixteen down-regulated proteins were identified that showed greater than 1.5-fold differences between the controls and the NASH group. These dysregulated proteins were predicted to be involved in different metabolic processes including fatty acid β-oxidation processes, lipid metabolic processes, cell-cycle arrest, cell polarity maintenance, and adenosine triphosphate/sex hormone metabolic processes. Novel proteins that may be involved in NASH pathogenesis including the trifunctional enzyme Hadha, thyroxine, prohibitin, aldehyde dehydrogenase ALDH1L2, UDP-glucuronosyltransferase 2B31, and carbamoyl-phosphate synthase were identified using bioinformatics tools. The decreased expression of Hadha in NASH liver was verified by Western blotting, which was used as a complementary technique to confirm the proteomic results.
CONCLUSION: This novel report on the liver mitochondrial proteome of a NASH model may provide a reservoir of information on the pathogenesis and treatment of NASH.
doi:10.3748/wjg.v20.i16.4778
PMCID: PMC4000516  PMID: 24782632
Nonalcoholic steatohepatitis; Hadha; Proteomics; Rat model
17.  Biological Evaluation of 131I- and CF750-Labeled Dmab(scFv)-Fc Antibodies for Xenograft Imaging of CD25-Positive Tumors 
BioMed Research International  2014;2014:459676.
A Dmab(scFv)-Fc antibody containing the single chain variable fragment of a humanized daclizumab antibody and the Fc fragment of a human IgG1 antibody was produced via recombinant expression in Pichia pastoris. The Dmab(scFv)-Fc antibody forms a dimer in solution, and it specifically binds CD25-positive tumor cells and tumor tissues. For tumor imaging, the Dmab(scFv)-Fc antibody was labeled with the 131I isotope and CF750 fluorescent dye, respectively. After intravenous injection of mice bearing CD25-positive tumor xenografts, tumor uptake of the 131I-Dmab(scFv)-Fc antibody was visible at 1 h, and clear images were obtained at 5 h using SPECT/CT. After systemic administration of the CF750-Dmab(scFv)-Fc antibody, tumor uptake was present as early as 1 h, and tumor xenografts could be kinetically imaged within 9 h after injection. These results indicate that the Dmab(scFv)-Fc antibody rapidly and specifically targets CD25-positive tumor cells, suggesting the potential of this antibody as an imaging agent for the diagnosis of lymphomatous-type ATLL.
doi:10.1155/2014/459676
PMCID: PMC4017786  PMID: 24864244
18.  Genome-wide profiling of 5-formylcytosine reveals its roles in epigenetic priming 
Cell  2013;153(3):678-691.
SUMMARY
TET proteins oxidize 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC). 5fC and 5caC are excised by mammalian DNA glycosylase TDG, implicating 5mC oxidation in DNA demethylation. Here we show that the genomic locations of 5fC can be determined by coupling chemical reduction with biotin tagging. Genome-wide mapping of 5fC in mouse embryonic stem cells (mESCs) reveals that 5fC preferentially occurs at poised enhancers among other gene regulatory elements. Application to Tdg null mESCs further suggests that 5fC production coordinates with p300 in remodeling epigenetic states of enhancers. This process, which is not influenced by 5hmC, appears to be associated with further oxidation of 5hmC and commitment to demethylation through 5fC. Finally, we resolved 5fC at base-resolution by hydroxylamine-based protection from bisulfite-mediated deamination, thereby confirming sites of 5fC accumulation. Our results reveal roles of active 5mC/5hmC oxidation and TDG-mediated demethylation in epigenetic tuning at regulatory elements.
doi:10.1016/j.cell.2013.04.001
PMCID: PMC3657391  PMID: 23602153
19.  Which Models Are Appropriate for Six Subtropical Forests: Species-Area and Species-Abundance Models 
PLoS ONE  2014;9(4):e95890.
The species-area relationship is one of the most important topic in the study of species diversity, conservation biology and landscape ecology. The species-area relationship curves describe the increase of species number with increasing area, and have been modeled by various equations. In this paper, we used detailed data from six 1-ha subtropical forest communities to fit three species-area relationship models. The coefficient of determination and F ratio of ANOVA showed all the three models fitted well to the species-area relationship data in the subtropical communities, with the logarithm model performing better than the other two models. We also used the three species-abundance distributions, namely the lognormal, logcauchy and logseries model, to fit them to the species-abundance data of six communities. In this case, the logcauchy model had the better fit based on the coefficient of determination. Our research reveals that the rare species always exist in the six communities, corroborating the neutral theory of Hubbell. Furthermore, we explained why all species-abundance figures appeared to be left-side truncated. This was due to subtropical forests have high diversity, and their large species number includes many rare species.
doi:10.1371/journal.pone.0095890
PMCID: PMC3995945  PMID: 24755956
20.  A Platform for Screening Potential Anticholinesterase Fractions and Components Obtained from Anemarrhena asphodeloides Bge for Treating Alzheimer's Disease 
Alzheimer's disease (AD) is a neurodegenerative disease characterized by progressive memory loss and cognitive impairment. Cholinesterase inhibitors are widely used for the symptomatic treatment of Alzheimer's disease to enhance central cholinergic transmission. In this study, a bioactivity-oriented screening platform based on a modified Ellman's method and HPLC-QTOF MS technique was developed to rapidly screen active agents of Anemarrhena asphodeloides Bge. The 60% ethanol fraction from an ethyl acetate extract exhibited the most potential anticholinesterase activity. Fifteen steroid saponins were identified by the mass spectrum, standards and literature reports. Twenty-five compounds were isolated from the active fraction. The results showed that compounds with the C6–C3–C6 skeleton probably had both AChE and BuChE inhibitory activities. Xanthone and benzene derivatives exhibited no or little activity. Lignans showed weak BuChE inhibitory activity. The steroidal saponins demonstrated moderate or weak AChE inhibitory activity.
doi:10.1155/2014/524650
PMCID: PMC4016847  PMID: 24864153
21.  A Tensor-Product-Kernel Framework for Multiscale Neural Activity Decoding and Control 
Brain machine interfaces (BMIs) have attracted intense attention as a promising technology for directly interfacing computers or prostheses with the brain's motor and sensory areas, thereby bypassing the body. The availability of multiscale neural recordings including spike trains and local field potentials (LFPs) brings potential opportunities to enhance computational modeling by enriching the characterization of the neural system state. However, heterogeneity on data type (spike timing versus continuous amplitude signals) and spatiotemporal scale complicates the model integration of multiscale neural activity. In this paper, we propose a tensor-product-kernel-based framework to integrate the multiscale activity and exploit the complementary information available in multiscale neural activity. This provides a common mathematical framework for incorporating signals from different domains. The approach is applied to the problem of neural decoding and control. For neural decoding, the framework is able to identify the nonlinear functional relationship between the multiscale neural responses and the stimuli using general purpose kernel adaptive filtering. In a sensory stimulation experiment, the tensor-product-kernel decoder outperforms decoders that use only a single neural data type. In addition, an adaptive inverse controller for delivering electrical microstimulation patterns that utilizes the tensor-product kernel achieves promising results in emulating the responses to natural stimulation.
doi:10.1155/2014/870160
PMCID: PMC4009155  PMID: 24829569
22.  An Improved Clustering Algorithm of Tunnel Monitoring Data for Cloud Computing 
The Scientific World Journal  2014;2014:630986.
With the rapid development of urban construction, the number of urban tunnels is increasing and the data they produce become more and more complex. It results in the fact that the traditional clustering algorithm cannot handle the mass data of the tunnel. To solve this problem, an improved parallel clustering algorithm based on k-means has been proposed. It is a clustering algorithm using the MapReduce within cloud computing that deals with data. It not only has the advantage of being used to deal with mass data but also is more efficient. Moreover, it is able to compute the average dissimilarity degree of each cluster in order to clean the abnormal data.
doi:10.1155/2014/630986
PMCID: PMC3996860  PMID: 24982971
23.  Smurf1-Mediated Lys29-Linked Nonproteolytic Polyubiquitination of Axin Negatively Regulates Wnt/β-Catenin Signaling 
Molecular and Cellular Biology  2013;33(20):4095-4105.
Ubiquitination plays important and diverse roles in modulating protein functions. As a C2-WW-HECT-type ubiquitin ligase, Smad ubiquitination regulatory factor 1 (Smurf1) commonly serves to regulate ubiquitin-dependent protein degradation in a number of signaling pathways. Here, we report a novel function of Smurf1 in regulating Wnt/β-catenin signaling through targeting axin for nonproteolytic ubiquitination. Our data unambiguously demonstrate that Smurf1 ubiquitinates axin through Lys 29 (K29)-linked polyubiquitin chains. Unexpectedly, Smurf1-mediated axin ubiquitination does not lead to its degradation but instead disrupts its interaction with the Wnt coreceptors LRP5/6, which subsequently attenuates Wnt-stimulated LRP6 phosphorylation and represses Wnt/β-catenin signaling. The inhibitory function of Smurf1 on Wnt/β-catenin signaling is further evidenced by analysis with Smurf1 knockout murine embryonic fibroblasts. We next identified K789 and K821 in axin as the ubiquitination sites by Smurf1. Consistently, Smurf1 could neither disrupt the interaction of an axinK789/821R double mutant with LRP5/6 nor attenuate the phosphorylation of LRP6 in axinK789/821R-expressing cells. Collectively, our studies uncover Smurf1 as a new regulator for the Wnt/β-catenin signaling pathway via modulating the activity of axin.
doi:10.1128/MCB.00418-13
PMCID: PMC3811687  PMID: 23959799
24.  Network of brain protein level changes in glutaminase deficient fetal mice 
Journal of proteomics  2013;80:10.1016/j.jprot.2013.01.013.
Glutaminase is a multifunctional enzyme encoded by gene Gls involved in energy metabolism, ammonia trafficking and regeneration of neurotransmitter glutamate. To address the proteomic basis for the neurophenotypes of glutaminase-deficient mice, brain proteins from late gestation wild type, Gls+/- and Gls-/- male mice were subjected to two-dimensional gel electrophoresis, with subsequent identification by mass spectrometry using nano-LC-ESI-MS/MS. Protein spots that showed differential genotypic variation were quantified by immunoblotting. Differentially expressed proteins unambiguously identified by MS/MS included neurocalcin delta, retinol binding protein-1, reticulocalbin-3, cytoskeleton proteins fascin and tropomyosin alpha-4-chain, dihydropyrimidinase-related protein-5, apolipoprotein IV and proteins from protein metabolism proteasome subunits alpha type 2, type 7, heterogeneous nuclear ribonucleoprotein C1/C2 and H, voltage-gated anion-selective channel protein 1 and 2, ATP synthase subunit ß and transitional endoplasmic reticulum ATPase. An interaction network determined by Ingenuity Pathway Analysis revealed a link between glutaminase and calcium, Akt and retinol signaling, cytoskeletal elements, ATPases, ion channels, protein synthesis and the proteasome system, intermediary, nucleic acid and lipid metabolism, huntingtin, guidance cues, transforming growth factor beta-1 and hepatocyte nuclear factor 4-alpha. The network identified involves (a) cellular assembly and organization and (b) cell signaling and cell cycle, suggesting that Gls is crucial for neuronal maturation.
doi:10.1016/j.jprot.2013.01.013
PMCID: PMC3874211  PMID: 23376484
Glutaminase; Gls; Schizophrenia; Protein network; LC-MS/MS
25.  In silico investigation of pH-dependence of prolactin and human growth hormone binding to human prolactin receptor 
Experimental data shows that the binding of human prolactin (hPRL) to human prolactin receptor (hPRLr-ECD) is strongly pH-dependent, while the binding of the same receptor to human growth hormone (hGH) is pH-independent. Here we carry in silico analysis of the molecular effects causing such a difference and reveal the role of individual amino acids. It is shown that the computational modeling correctly predicts experimentally determined pKa’s of histidine residues in an unbound state in the majority of the cases and the pH-dependence of the binding free energy. Structural analysis carried in conjunction with calculated pH-dependence of the binding revealed that the main reason for pH-dependence of the binding of hPRL-hPRLr-ECD is a number of salt- bridges across the interface of the complex, while no salt-bridges are formed in the hGH-hPRlr-ECD. Specifically, most of the salt-bridges involve histidine residues and this is the reason for the pH-dependence across a physiological range of pH. The analysis not only revealed the molecular mechanism of the pH-dependence of the hPRL-hPRLr-ECD, but also provided critical insight into the underlying physic-chemical mechanism.
PMCID: PMC3966486  PMID: 24683423
human prolactin; human prolactin receptor; human growth hormone; pKa calculations; pH-dependence; electrostatics

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