PMCC PMCC

Search tips
Search criteria

Advanced
Results 1-25 (198)
 

Clipboard (0)
None

Select a Filter Below

Journals
more »
Year of Publication
more »
1.  Alternative polyadenylation of MeCP2 
RNA biology  2010;7(3):361-372.
The human MeCP 2 gene encodes a ubiquitously expressed methyl CpG binding protein. Mutations in this gene cause a neurodevelopmental disorder called Rett Syndrome (RS). Mutations identified in the coding region of MeCP 2 account for approximately 65% of all RS cases. However, 35% of all patients do not show mutations in the coding region of MeCP 2, suggesting that mutations in non-coding regions likely exist that affect MeCP 2 expression rather than protein function. The gene is unusual in that is has a >8.5 kb 3′ untranslated region (3′ UTR), and the size of the 3′UTR is differentially regulated in various tissues because of distinct polyadenylation signals. We have identified putative cis-acting auxiliary regulatory elements that play a role in alternative polyadenylation of MeCP 2 using an in vivo polyadenylation reporter assay and in a luciferase assay. These cis-acting auxiliary elements are found both upstream and downstream of the core CPS F binding sites. Mutation of one of these cis-acting auxiliary elements, a G-rich element (GRS) significantly reduced MeCP 2 polyadenylation efficiency in vivo. We further investigated what trans-acting factor(s) might be binding to this cis-acting element and found that hnRNP F protein binds specifically to the element. We next investigated the MeCP 2 3′ UTRs by performing quantitative real-time PC R; the data suggest that altered RNA stability is not a major factor in differential MeCP 2 3′ UTR usage. In sum, the mechanism(s) of regulated alternative 3′UTR usage of MeCP 2 are complex, and insight into these mechanisms will aid our understanding of the factors that influence MeCP 2 expression.
PMCID: PMC4096559  PMID: 20400852
polyadenylation; 3′ untranslated region (3′ UTR); MeCP2; cis-acting elements; trans-acting factors
2.  Fibulin-2 deficiency attenuates angiotensin II-induced cardiac hypertrophy by reducing transforming growth factor-β signalling 
AngII (angiotensin II) is a potent neurohormone responsible for cardiac hypertrophy, in which TGF (transforming growth factor)-β serves as a principal downstream mediator. We recently found that ablation of fibulin-2 in mice attenuated TGF-β signalling, protected mice against progressive ventricular dysfunction, and significantly reduced the mortality after experimental MI (myocardial infarction). In the present study, we investigated the role of fibulin-2 in AngII-induced TGF-β signalling and subsequent cardiac hypertrophy. We performed chronic subcutaneous infusion of AngII in fibulin-2 null (Fbln2−/− ), heterozygous (Fbln2+/− ) and WT (wild-type) mice by a mini-osmotic pump. After 4 weeks of subpressor dosage of AngII infusion (0.2 μg/kg of body weight per min), WT mice developed significant hypertrophy, whereas the Fbln2−/− showed no response. In WT, AngII treatment significantly up-regulated mRNAs for fibulin-2, ANP (atrial natriuretic peptide), TGF-β1, Col I (collagen type I), Col III (collagen type III), MMP (matrix metalloproteinase)-2 and MMP-9, and increased the phosphorylation of TGF-β-downstream signalling markers, Smad2, TAK1 (TGF-β-activated kinase 1) and p38 MAPK (mitogen-activated protein kinase), which were all unchanged in AngII-treated Fbln2−/− mice. The Fbln2+/− mice consistently displayed AngII-induced effects intermediate between WT and Fbln2−/− . Pressor dosage of AngII (2 mg/kg of body weight per min) induced significant fibrosis in WT but not in Fbln2−/− mice with comparable hypertension and hypertrophy in both groups. Isolated CFs (cardiac fibroblasts) were treated with AngII, in which direct AngII effects and TGF-β-mediated autocrine effects was observed in WT. The latter effects were totally abolished in Fbln2−/− cells, suggesting that fibulin-2 is essential for AngII-induced TGF-β activation. In conclusion our data indicate that fibulin-2 is essential for AngII-induced TGF-β-mediated cardiac hypertrophy via enhanced TGF-β activation and suggest that fibulin-2 is a potential therapeutic target to inhibit AngII-induced cardiac remodelling.
doi:10.1042/CS20120636
PMCID: PMC4075193  PMID: 23841699
angiotensin II (AngII); autoinduction; cardiac hypertrophy; extracellular matrix; signalling; transforming growth factor-β (TGF-β)
3.  AGROBEST: an efficient Agrobacterium-mediated transient expression method for versatile gene function analyses in Arabidopsis seedlings 
Plant Methods  2014;10:19.
Background
Transient gene expression via Agrobacterium-mediated DNA transfer offers a simple and fast method to analyze transgene functions. Although Arabidopsis is the most-studied model plant with powerful genetic and genomic resources, achieving highly efficient and consistent transient expression for gene function analysis in Arabidopsis remains challenging.
Results
We developed a highly efficient and robust Agrobacterium-mediated transient expression system, named AGROBEST (Agrobacterium-mediated enhanced seedling transformation), which achieves versatile analysis of diverse gene functions in intact Arabidopsis seedlings. Using β-glucuronidase (GUS) as a reporter for Agrobacterium-mediated transformation assay, we show that the use of a specific disarmed Agrobacterium strain with vir gene pre-induction resulted in homogenous GUS staining in cotyledons of young Arabidopsis seedlings. Optimization with AB salts in plant culture medium buffered with acidic pH 5.5 during Agrobacterium infection greatly enhanced the transient expression levels, which were significantly higher than with two existing methods. Importantly, the optimized method conferred 100% infected seedlings with highly increased transient expression in shoots and also transformation events in roots of ~70% infected seedlings in both the immune receptor mutant efr-1 and wild-type Col-0 seedlings. Finally, we demonstrated the versatile applicability of the method for examining transcription factor action and circadian reporter-gene regulation as well as protein subcellular localization and protein–protein interactions in physiological contexts.
Conclusions
AGROBEST is a simple, fast, reliable, and robust transient expression system enabling high transient expression and transformation efficiency in Arabidopsis seedlings. Demonstration of the proof-of-concept experiments elevates the transient expression technology to the level of functional studies in Arabidopsis seedlings in addition to previous applications in fluorescent protein localization and protein–protein interaction studies. In addition, AGROBEST offers a new way to dissect the molecular mechanisms involved in Agrobacterium-mediated DNA transfer.
doi:10.1186/1746-4811-10-19
PMCID: PMC4076510  PMID: 24987449
Agrobacterium; Arabidopsis; Transient transformation; Gene expression; Innate immunity; Gain-of-function
4.  Target Proteomic Profiling of Frozen Pancreatic CD24+ Adenocarcinoma Tissues by Immuno-Laser Capture Microdissection and Nano-LC-MS/MS 
Journal of proteome research  2013;12(6):2791-2804.
Cellular heterogeneity of solid tumors represents a common problem in mass spectrometry (MS)-based analysis of tissue specimens. Combining immuno-laser capture microdissection (iLCM) and mass spectrometry (MS) provides a means to study proteins that are specific for pure cell subpopulations in complex tissues. CD24, as a cell surface marker for detecting pancreatic cancer stem cells (CSCs), is directly correlated with the development and metastasis of pancreatic cancer. Herein, we describe an in-depth proteomic profiling of frozen pancreatic CD24+ adenocarcinoma cells from early stage tumors using iLCM and LC-MS/MS, and a comparison with CD24− cells dissected from patient-matched adjacent normal tissues. Approximately 40 nL tissue was procured from each specimen and subjected to tandem MS analysis in triplicate. A total of 2665 proteins were identified, with 375 proteins in common that were significantly differentially expressed in CD24+ versus CD24− cells by at least a 2-fold change. The major groups of the differentially overexpressed proteins are involved in promoting tumor cell migration and invasion, immune escape and tumor progression. Three selected candidates relevant to mediating immune escape, CD59, CD70 and CD74, and a tumor promoter, TGFBI, were further validated by immunohistochemistry analysis on tissue microarrays. These proteins showed significantly increased expression in a large group of clinical pancreatic adenocarcinomas but were negative in all normal pancreas samples. The significant coexpression of these proteins with CD24 suggests that they may play important roles in the progression of pancreatic cancer and could serve as promising prognosis markers and novel therapeutic targets for this deadly disease.
doi:10.1021/pr400139c
PMCID: PMC3726273  PMID: 23679566
pancreatic cancer; CD24; frozen tissue; laser capture microdissection; LC-MS/MS; proteome profiling; spectral count
5.  An Isobaric Protein-Level Labeling Strategy for Serum Glycoprotein Quantification Analysis by LC-MS/MS 
Analytical chemistry  2013;85(11):5353-5357.
While peptide-level labeling using isobaric tag reagents has been widely applied for quantitative proteomics experiments, there are comparatively few reports of protein-level labeling. Intact protein labeling could be broadly applied to quantification experiments utilizing protein-level separations or enrichment schemes. Here, protein-level isobaric labeling was explored as an alternative strategy to peptide-level labeling for serum glycoprotein quantification. Labeling and digestion conditions were optimized by comparing different organic solvents and enzymes. Digestions with Asp-N and trypsin were found highly complementary; combining the results enabled quantification of 30% more proteins than either enzyme alone. Three commercial reagents were compared for protein-level labeling. Protein identification rates were highest with iTRAQ 4-plex when compared to TMT 6-plex and iTRAQ 8-plex using higher-energy collisional dissociation on an Orbitrap Elite mass spectrometer. The compatibility of isobaric protein-level labeling with lectin-based glycoprotein enrichment was also investigated. More than 74% of lectin-bound labeled proteins were known glycoproteins, which was similar to results from unlabeled and peptide-level labeled serum samples. Finally, protein-level and peptide-level labeling strategies were compared for serum glycoprotein quantification. Isobaric protein-level labeling gave comparable identification levels and quantitative precision to peptide-level labeling.
doi:10.1021/ac400838s
PMCID: PMC3690282  PMID: 23638883
Isobaric labeling; Protein level; Glycoprotein; Serum; Quantitative proteomics
6.  Increasing incidence of hemorrhagic fever with renal syndrome could be associated with livestock husbandry in Changchun, Northeastern China 
BMC Infectious Diseases  2014;14:301.
Background
Since the end of the 1990s, the incidence of hemorrhagic fever with renal syndrome (HFRS) has been increasing dramatically in Changchun, northeastern China. However, it is unknown which, and how, underlying risk factors have been involved in the reemergence of the disease.
Methods
Data on HFRS cases at the county scale were collected from 1998 to 2012. Data on livestock husbandry including the numbers of large animals (cattle, horses, donkeys and mules), sheep, and deer, and on climatic and land cover variables were also collected. Epidemiological features, including the spatial, temporal and human patterns of disease were characterized. The potential factors related to spatial heterogeneity and temporal trends were analyzed using standard and time-series Poisson regression analysis, respectively.
Results
Annual incidence varied among the 10 counties. Shuangyang County in southeastern Changchun had the highest number of cases (1,525 cases; 35.9% of all cases), but its population only accounted for 5.6% of the total population. Based on seasonal pattern in HFRS incidence, two epidemic phases were identified. One was a single epidemic peak at the end of each year from 1988 to 1997 and the other consisted of dual epidemic peaks at both the end and the beginning of each year from 1998 to the end of the study period. HFRS incidence was higher in males compared to females, and most of the HFRS cases occurred in peasant populations. The results of the Poisson regression analysis indicated that the spatial distribution and the increasing incidence of HFRS were significantly associated with livestock husbandry and climate factors, particularly with deer cultivation.
Conclusions
Our results indicate that the re-emergence of HFRS in Changchun has been accompanied by changing seasonal patterns over the past 25 years. Integrated measures focusing on areas related to local livestock husbandry could be helpful for the prevention and control of HFRS.
doi:10.1186/1471-2334-14-301
PMCID: PMC4050097  PMID: 24894341
7.  Immunohistochemical Staining, Laser Capture Microdissection and FASP Assisted Proteomic Analysis of Target Cell Populations within Tissue Samples 
Electrophoresis  2013;34(11):1627-1636.
An important problem involves isolating sub-populations of cells defined by protein markers in clinical tissue samples for proteomic studies. We describe a method termed Immunohistochemical staining, Laser capture microdissection and FASP Assisted Proteomic analysis of Target cell populations within tissue samples (ILFAPT). The principle of ILFAPT is that a target cell population expressing a protein of interest can be lit up by immunohistochemical staining and isolated from tissue sections using laser capture microdissection (LCM) for filter-aided sample preparation (FASP) and proteomic analysis. Using this method, we isolated a small population of CD90+ stem-like cells from glioblastoma multiforme tissue sections and identified 674 high-confidence (FDR < 0.01) proteins from 32 nL of CD90+ cells by LC-MS/MS using an Orbitrap Elite mass spectrometer. We further quantified the relative abundance of proteins identified from equal volumes of LCM-captured CD90+ and CD90- cells, where 109 differentially expressed proteins were identified. The major group of these differentially expressed proteins was relevant to cell adhesion and cellular movement. This ILFAPT method has demonstrated the ability to provide in-depth proteome analysis of a very small specific cell population within tissues. It can be broadly applied to the study of target cell populations within clinical specimens.
doi:10.1002/elps.201200566
PMCID: PMC3766629  PMID: 23436586
Immunohistochemical staining; Laser capture microdissection; Proteomics; Target cell population; Tissue sample
8.  Cracking the O-GlcNAc Code in Metabolism 
Nuclear, cytoplasmic and mitochondrial proteins are extensively modified by an O-linked β-N-acetylglucosamine (O-GlcNAc) moiety. This sugar modification regulates fundamental cellular processes in response to diverse nutritional and hormonal cues. The enzymes O-GlcNAc transferase (OGT) and O-linked β-N-acetylglucosaminase (O-GlcNAcase) mediate the addition and removal of O-GlcNAc, respectively. Aberrant O-GlcNAcylation has been implicated in a plethora of human diseases, including diabetes, cancer, aging, cardiovascular disease and neurodegenerative disease. As metabolic dysregulation is a vital component of these diseases, unraveling the roles of O-GlcNAc in metabolism is of emerging importance. Here, we review the current understanding of the functions of O-GlcNAc in cell signaling and gene transcription involved in metabolism, and focus on its relevance to diabetes, cancer, circadian rhythm, and mitochondrial function.
doi:10.1016/j.tem.2013.02.002
PMCID: PMC3783028  PMID: 23647930
O-GlcNAc; hexosamine biosynthesis; insulin resistance; cancer metabolism; circadian rhythm; mitochondria
9.  Mineralocorticoid-receptor signalling in vascular smooth muscle 
Nephrology Dialysis Transplantation  2013;28(6):1360-1362.
Human data suggest that eplerenone and spironolactone lowers blood pressure by mechanisms independent of the distal tubule. Now, a novel inducible conditional knockout model of the mineralocorticoid receptor (MR) in vascular smooth muscle cells (VSMCs) brings out understanding further.
doi:10.1093/ndt/gfs562
PMCID: PMC4007112  PMID: 23439586
aldosterone; cre recombinase; hypertension; LoxP; mineralocorticoid receptor
10.  Prevalence of Unprotected Anal Intercourse among Men Who Have Sex with Men in China: An Updated Meta-Analysis 
PLoS ONE  2014;9(5):e98366.
Objective
The purpose of this review was to assess the prevalence of unprotected anal intercourse (UAI) among men who have sex with men (MSM) in China.
Methods
A comprehensive search was conducted including online databases like “Wanfang”, Chinese National Knowledge Infrastructure, PubMed and manual searches. Analyses using random-effects models were performed to estimate the prevalence of UAI among MSM in China.
Results
Sixty-two articles reporting eighty-two studies were selected. The pooled prevalence rates of UAI with any male partner, with regular male partners, with non-regular male partners, with casual male partners, and with commercial male partners among MSM were 53%(95%CI: 51–56%), 45%(95%CI: 39–51%), 34%(95%CI: 24–45%), 33%(95%CI: 30–36%), 12% (95%CI: 5–26%), respectively. A cumulative meta-analysis found that the pooled UAI prevalence decreased over time.
Conclusions
Although the prevalence of UAI with male partners among MSM in China presents a decreasing trend over the past decade, the concomitant rise in HIV prevalence and incidence indicates that current prevention intervention efforts are insufficient to effectively contain the spread of HIV. Therefore, the persistently high prevalence of risky sexual behaviors underscores the need for innovative and effective prevention strategies among MSM.
doi:10.1371/journal.pone.0098366
PMCID: PMC4038612  PMID: 24874882
11.  Regulatory T Cells Protect Fine Particulate Matter-Induced Inflammatory Responses in Human Umbilical Vein Endothelial Cells 
Mediators of Inflammation  2014;2014:869148.
Objective. To investigate the role of CD4+CD25+ T cells (Tregs) in protecting fine particulate matter (PM-) induced inflammatory responses, and its potential mechanisms. Methods. Human umbilical vein endothelial cells (HUVECs) were treated with graded concentrations (2, 5, 10, 20, and 40 µg/cm2) of suspension of fine particles for 24h. For coculture experiment, HUVECs were incubated alone, with CD4+CD25− T cells (Teff), or with Tregs in the presence of anti-CD3 monoclonal antibodies for 48 hours, and then were stimulated with or without suspension of fine particles for 24 hours. The expression of adhesion molecules and inflammatory cytokines was examined. Results. Adhesion molecules, including vascular cell adhesion molecule-1 (VCAM-1) and intercellular adhesion molecule-1 (ICAM-1), and inflammatory cytokines, such as interleukin (IL-) 6 and IL-8, were increased in a concentration-dependent manner. Moreover, the adhesion of human acute monocytic leukemia cells (THP-1) to endothelial cells was increased and NF-κB activity was upregulated in HUVECs after treatment with fine particles. However, after Tregs treatment, fine particles-induced inflammatory responses and NF-κB activation were significantly alleviated. Transwell experiments showed that Treg-mediated suppression of HUVECs inflammatory responses impaired by fine particles required cell contact and soluble factors. Conclusions. Tregs could attenuate fine particles-induced inflammatory responses and NF-κB activation in HUVECs.
doi:10.1155/2014/869148
PMCID: PMC4060066  PMID: 24987196
12.  Screening to Identify Commonly Used Chinese Herbs That Affect ERBB2 and ESR1 Gene Expression Using the Human Breast Cancer MCF-7 Cell Line 
Aim. Our aim the was to screen the commonly used Chinese herbs in order to detect changes in ERBB2 and ESR1 gene expression using MCF-7 cells. Methods. Using the MCF-7 human breast cancer cell line, cell cytotoxicity and proliferation were evaluated by MTT and trypan blue exclusion assays, respectively. A luciferase reporter assay was established by transient transfecting MCF-7 cells with plasmids containing either the ERBB2 or the ESR1 promoter region linked to the luciferase gene. Chinese herbal extracts were used to treat the cells at 24 h after transfection, followed by measurement of their luciferase activity. The screening results were verified by Western blotting to measure HER2 and ERα protein expression. Results. At concentrations that induced little cytotoxicity, thirteen single herbal extracts and five compound recipes were found to increase either ERBB2 or ESR1 luciferase activity. By Western blotting, Si-Wu-Tang, Kuan-Shin-Yin, and Suan-Tsao-Ren-Tang were found to increase either HER2 or ERα protein expression. In addition, Ligusticum chuanxiong was shown to have a great effect on ERBB2 gene expression and synergistically with estrogen to stimulate MCF-7 cell growth. Conclusion. Our results provide important information that should affect clinical treatment strategies among breast cancer patients who are receiving hormonal or targeted therapies.
doi:10.1155/2014/965486
PMCID: PMC4058453  PMID: 24987437
13.  Chronic Stable Angina Is Associated with Lower Health-Related Quality of Life: Evidence from Chinese Patients 
PLoS ONE  2014;9(5):e97294.
Objectives
To compare health-related quality of life (HRQoL) between patients with stable angina and the general population in China and to examine factors associated with HRQoL among patients with stable angina.
Methods
A cross-sectional HRQoL survey of stable angina patients recruited from 4 hospitals (n = 411) and the general population recruited from 3 Physical Examination Centers (n = 549) was conducted from July to December, 2011 in two large cities, Tianjin and Chengdu. HRQoL was assessed using the EQ-5D, EQ-VAS, and SF-6D instruments. The health status specific to patients with stable angina was assessed using the Seattle Angina Questionnaire (SAQ). Information on socio-demographic, clinical, and lifestyle factors were also collected. Nested regressions were performed to explore how these factors were associated with HRQoL in patients with stable angina.
Results
Compared with the general population (44.2±10 years, 49.9% females), stable angina patients (68.1±12 years, 50.4% females) had significantly lower HRQoL scores in EQ-5D utility index (0.75±0.19 vs. 0.90±0.20, p<0.05), SF-6D utility index (0.68±0.12 vs. 0.85±0.11, p<0.05), and EQ-VAS (71.2±12.3 vs. 83.9±10.9, p<0.05). The differences remained (−0.05 for EQ-5D, −9.27 for EQ-VAS and −0.13 for SF-6D) after controlling for socio-economic characteristics. SAQ scores showed that stable angina patients experienced impaired disease-specific health status, especially in angina stability (40.5±34.6). Nested regressions indicated stable angina-specific health status explained most of the variation in HRQoL, among which disease perception, physical limitation, and angina stability were the strongest predictors. More physical exercise and better sleep were positively related with HRQoL.
Conclusions
Compared to the general population, stable angina patients were associated with lower HRQoL and lower health utility scores, which were largely impacted by clinical symptoms. Further studies are needed to characterize the influence of geographic and cultural factors on the variations of health-related utility in stable angina patients.
doi:10.1371/journal.pone.0097294
PMCID: PMC4026133  PMID: 24842793
14.  Maternal Serum Disintegrin and Metalloprotease Protein-12 in Early Pregnancy as a Potential Marker of Adverse Pregnancy Outcomes 
PLoS ONE  2014;9(5):e97284.
Objectives
The aim of this study was to determine whether the concentration of disintegrin and metalloprotease protein12 (ADAM12) in first trimester maternal serum can be used as a marker for first-trimester complete spontaneous abortions, missed abortions, ectopic pregnancies and hydatidiform moles.
Methods
The maternal serum concentrations of ADAM12 were measured in the range of 5–9+6 weeks of gestation using an automated AutoDelfia immunoassay platform in 9 cases of complete spontaneous abortion, 27 cases of missed abortions, 56 cases of ectopic pregnancies, 12 cases of hydatidiform moles, and 100 controls. Logistic regression analysis was used to determine significant factors for predicting adverse pregnancy outcomes in early pregnancy. Screening performance was assessed using receiver operating characteristic curves.
Results
Two hundred and four women were enrolled in the study. In the control group, the level of ADAM12 increased with gestational age. The median ADAM12 levels in the spontaneous abortion (0.430 MoM), ectopic pregnancy (0.460 MoM) and hydatidiform mole (0.037 MoM) groups were lower than that in the control group, while the median ADAM12 level in the missed abortion group (1.062 MoM) was not significant from the controls (1.002 MoM). Logistic regression analysis demonstrated that the level of ADAM12 in maternal serum facilitated the detection of ectopic pregnancies (OR = 0.909; 95% CI = 0.841∼0.982) and complete spontaneous abortion (OR = 0.863; 95% CI = 0.787∼0.946).
Conclusions
In complete spontaneous abortion and ectopic pregnancy, ADAM12 maintained at low levels in early pregnancies, and there were significant differences compared to normal pregnancies. ADAM12 is a promising marker for the diagnosis of complete spontaneous abortion and ectopic pregnancy in symptomatic women, and under certain conditions, ADAM12 can diagnose ectopic pregnancy and spontaneous abortion before an ultrasonographic detection of the conditions.
doi:10.1371/journal.pone.0097284
PMCID: PMC4022643  PMID: 24830297
15.  Analysis of horse genomes provides insight into the diversification and adaptive evolution of karyotype 
Scientific Reports  2014;4:4958.
Karyotypic diversification is more prominent in Equus species than in other mammals. Here, using next generation sequencing technology, we generated and de novo assembled quality genomes sequences for a male wild horse (Przewalski's horse) and a male domestic horse (Mongolian horse), with about 93-fold and 91-fold coverage, respectively. Portion of Y chromosome from wild horse assemblies (3 M bp) and Mongolian horse (2 M bp) were also sequenced and de novo assembled. We confirmed a Robertsonian translocation event through the wild horse's chromosomes 23 and 24, which contained sequences that were highly homologous with those on the domestic horse's chromosome 5. The four main types of rearrangement, insertion of unknown origin, inserted duplication, inversion, and relocation, are not evenly distributed on all the chromosomes, and some chromosomes, such as the X chromosome, contain more rearrangements than others, and the number of inversions is far less than the number of insertions and relocations in the horse genome. Furthermore, we discovered the percentages of LINE_L1 and LTR_ERV1 are significantly increased in rearrangement regions. The analysis results of the two representative Equus species genomes improved our knowledge of Equus chromosome rearrangement and karyotype evolution.
doi:10.1038/srep04958
PMCID: PMC4021364  PMID: 24828444
16.  Radiosensitization Effect of Nedaplatin on Nasopharyngeal Carcinoma Cells in Different Status of Epstein-Barr Virus Infection 
BioMed Research International  2014;2014:713674.
This study aims to evaluate the radiosensitization effect of nedaplatin on nasopharyngeal carcinoma (NPC) cell lines with different Epstein-Barr virus (EBV) status. Human NPC cell lines CNE-2 (EBV-negative) and C666 (EBV-positive) were treated with 0–100 μg/mL nedaplatin, and inhibitory effects on cell viability and IC50 were calculated by MTS assay. We assessed changes in radiosensitivity of cells by MTS and colony formation assays, and detected the apoptosis index and changes in cell cycle by flow cytometry. MTS assay showed that nedaplatin caused significant cytotoxicity in CNE-2 and C666 cells in a time- and dose-dependent manner. After 24 h, nedaplatin inhibited growth of CNE-2 and C666 cells with IC50 values of 34.32 and 63.69 μg/mL, respectively. Compared with radiation alone, nedaplatin enhanced the radiation effect on both cell lines. Nedaplatin markedly increased apoptosis and cell cycle arrest in G2/M phase. Nedaplatin radiosensitized human NPC cells CNE-2 and C666, with a significantly greater effect on the former. The mechanisms of radiosensitization include induction of apoptosis and enhancement of cell cycle arrest in G2/M phase.
doi:10.1155/2014/713674
PMCID: PMC4036599  PMID: 24900979
17.  The effect of transcutaneous electrical acupoint stimulation on pregnancy rates in women undergoing in vitro fertilization: a study protocol for a randomized controlled trial 
Trials  2014;15:162.
Background
The latest meta-analysis demonstrated that acupuncture improves pregnancy rates among women undergoing in vitro fertilization-embryo transfer (IVF-ET), and surface acupoint stimulation, such as transcutaneous electrical acupoint stimulation (TEAS), may have the same or better potential.
Methods/Design
To explore the effect of TEAS on the clinical pregnancy rate (CPR) and live birth rate (LBR) compared with real acupuncture and controls in women undergoing IVF, a multicenter, randomized controlled trial will be conducted. The inclusion criteria are the following: infertile women <40 years of age undergoing a fresh IVF or intracytoplasmic sperm injection cycle, and the study will be restricted to women with the potential for a lower success rate as defined by two or more previous unsuccessful ETs (fresh or frozen). Those who have severe illnesses possibly precluding IVF or pregnancy, have FSH levels greater than 20 IU/L, received donor eggs, had been previously randomized for this study or had undergone acupuncture (in any modality) as infertility treatment will be excluded. The subjects will be randomly assigned to the TEAS group (IVF + TEAS), the electro-acupuncture (EA) group (IVF + EA), or the control group (only IVF). A total sample size of 2,220 women is required to detect differences in CPR among the three groups. TEAS or EA treatments will start once every two or three days from day 3 of menstruation in the ovarian stimulation cycle until the day of ET. The parameters of TEAS or EA will be the following: a frequency of 2/100 Hz, a moderate electrical current of 3 to 5 mA for TEAS and 0.8 to 1.0 mA for EA. The primary outcome is CPR. Secondary outcomes are LBR, the number of oocytes aspirated and the total gonadotropin dose used in the stimulation cycle.
Discussion
This study will provide significant evidence for using a new method (TEAS) in IVF.
Trial registration
ClinicalTrials.govID: NCT01608048 (05/24/2012).
doi:10.1186/1745-6215-15-162
PMCID: PMC4020380  PMID: 24886647
acupuncture; transcutaneous electrical acupoint stimulation; TEAS
18.  In Silico Prediction of T and B Cell Epitopes of Der f 25 in Dermatophagoides farinae 
The house dust mites are major sources of indoor allergens for humans, which induce asthma, rhinitis, dermatitis, and other allergic diseases. Der f 25 is a triosephosphate isomerase, representing the major allergen identified in Dermatophagoides farinae. The objective of this study was to predict the B and T cell epitopes of Der f 25. In the present study, we analyzed the physiochemical properties, function motifs and domains, and structural-based detailed features of Der f 25 and predicted the B cell linear epitopes of Der f 25 by DNAStar protean system, BPAP, and BepiPred 1.0 server and the T cell epitopes by NetMHCIIpan-3.0 and NetMHCII-2.2. As a result, the sequence and structure analysis identified that Der f 25 belongs to the triosephosphate isomerase family and exhibited a triosephosphate isomerase pattern (PS001371). Eight B cell epitopes (11–18, 30–35, 71–77, 99–107, 132–138, 173–187, 193–197, and 211–224) and five T cell epitopes including 26–34, 38–54, 66–74, 142–151, and 239–247 were predicted in this study. These results can be used to benefit allergen immunotherapies and reduce the frequency of mite allergic reactions.
doi:10.1155/2014/483905
PMCID: PMC4033504  PMID: 24895543
19.  Coprescription of Chinese herbal medicine and Western medication among female patients with breast cancer in Taiwan: analysis of national insurance claims 
Background
Many female breast cancer (FBC) patients take Chinese herbal medicine (CHM) and Western medication (WM) concurrently in Taiwan. Despite the possibility of interactions between the CHM and WM mentioned in previous studies, the pattern of these coprescriptions in FBC patients remains unclear. Hence, the aim of the present study is to investigate the utilization of coprescriptions of CHM and WM among the FBC patients in Taiwan.
Methods
The study was a cross-sectional survey using the sampled cohort in 2009 obtained from the National Health Insurance Research Database in Taiwan. There were 3,507 FBC patients identified from the registry for catastrophic illness patients. Ambulatory visit records, corresponding prescriptions, and the data of beneficiaries belonging to the FBC patients were further extracted. A total of 1,086 FBC patients used CHM at least once. CHM and WM prescribed within any overlapping duration were defined as coprescriptions.
Results
There were 868 (80.0%) patients simultaneously receiving CHM and WM. A total of 4,927 CHM prescriptions and 6,358 WM prescriptions were prescribed concurrently. Among these coprescriptions, the most frequently used CHM was jia-wei-xiao-yao-san (21.2%), and the most frequently coprescribed WM was acetaminophen (38.9%), followed by tamoxifen (25.5%). There were 346 patients using systemic adjuvant therapy and CHM concurrently. The most commonly coprescribed CHM with chemotherapy, endocrine therapy, and trastuzumab was xiang-sha-liu-jun-zi-tang, jia-wei-xiao-yao-san, and zhi-gan-cao-tang, respectively.
Conclusion
The combined use of CHM with WM is prevalent. The main purpose of combining CHM with systemic cancer treatment is to alleviate the treatment-related adverse effects. However, the combination may result in the potential risk of drug–herb interactions. Further clinical studies are needed to evaluate the efficacy and safety of the CHM and WM coprescriptions for FBC patients.
doi:10.2147/PPA.S61280
PMCID: PMC4019611  PMID: 24855343
drug utilization patterns; complementary and alternative medicine; pharmacoepidemiology
20.  Naturally Occurring Lactic Acid Bacteria Isolated from Tomato Pomace Silage 
Silage making has become a significant method of forage conservation worldwide. To determine how tomato pomace (TP) may be used effectively as animal feed, it was ensilaged for 90 days and microbiology counts, fermentation characteristics and chemical composition of tomato pomace silage (TPS) were evaluated at the 30th, 60th, and 90th days, respectively. In addition, 103 lactic acid bacteria were isolated from TPS. Based on the phenotypic and chemotaxonomic characteristics, 16S rDNA sequence and carbohydrate fermentation tests, the isolates were identified as 17 species namely: Lactobacillus coryniformis subsp. torquens (0.97%), Lactobacillus pontis (0.97%), Lactobacillus hilgardii (0.97%), Lactobacillus pantheris (0.97%), Lactobacillus amylovorus (1.9%), Lactobacillus panis (1.9%), Lactobacillus vaginalis (1.9%), Lactobacillus rapi (1.9%), Lactobacillus buchneri (2.9%), Lactobacillus parafarraginis (2.9%), Lactobacillus helveticus (3.9%), Lactobacillus camelliae (3.9%), Lactobacillus fermentum (5.8%), Lactobacillus manihotivorans (6.8%), Lactobacillus plantarum (10.7%), Lactobacillus harbinensis (16.5%) and Lactobacillus paracasei subsp. paracasei (35.0%). This study has shown that TP can be well preserved for 90 days by ensilaging and that TPS is not only rich in essential nutrients, but that physiological and biochemical properties of the isolates could provide a platform for future design of lactic acid bacteria (LAB) inoculants aimed at improving the fermentation quality of silage.
doi:10.5713/ajas.2013.13670
PMCID: PMC4093187  PMID: 25049999
Lactic Acid Bacteria; Silage; Tomato Pomace; 16S rRNA Gene
21.  Host-derived nitrate boosts growth of E. coli in the inflamed gut 
Science (New York, N.Y.)  2013;339(6120):708-711.
Changes in the microbial community structure are observed in individuals with intestinal inflammatory disorders. These changes are often characterized by a depletion of obligate anaerobic bacteria, whereas the relative abundance of facultative anaerobic Enterobacteriaceae increases. The mechanisms by which the host response shapes the microbial community structure, however, remain unknown. We show that nitrate generated as a by-product of the inflammatory response conferred a growth advantage to the commensal bacterium Escherichia coli in the large intestine of mice. Mice deficient for inducible nitric oxide synthase (iNOS) did not support growth of E. coli by nitrate respiration, suggesting that nitrate generated during inflammation was host-derived. Thus the inflammatory host response selectively enhances growth of commensal Enterobacteriaceae by generating electron acceptors for anaerobic respiration.
doi:10.1126/science.1232467
PMCID: PMC4004111  PMID: 23393266
22.  MAPT rs242562 and GSK3B rs334558 are associated with Parkinson’s Disease in central China 
BMC Neuroscience  2014;15:54.
Background
Microtubule-associated protein tau (MAPT) is a neuronal protein involved in the pathogenesis of several neurodegenerative diseases including Parkinson’s Disease (PD). Glycogen synthase kinase 3 beta (GSK3B) catalyzes phosphorylation in multiple sites of tau protein. However, whether or not there is any association between the GSK3B gene alteration, MAPT haplotype and PD remains unexplored in Chinese population, especially in central Chinese population.
Results
Here, we aimed at studying the effect of MAPT rs242562 and GSK3B rs334558 on the risk of PD by performing a case-control association study in central China. Our data showed that all PD patients and controls were of MAPT H1/H1 diplotype in our study, thus confirming that the distribution of the MAPT H1 haplotype is common in China. GG genotype of MAPT rs242562 serves protection effect on PD risk in central Chinese population, while genotype of GSK3B rs334558 showed no difference between PD patients and controls.
Conclusions
We conclude that the MAPT rs242562 is associated with PD in central China in the background of MAPT H1/H1 diplotype. The GG genotype of rs242562 displays protection against PD in subgroup with GSK3B rs334558 T carrier.
doi:10.1186/1471-2202-15-54
PMCID: PMC4021090  PMID: 24779391
MAPT H1 haplotype; GSK3β; Parkinson’s disease; Genetic risk factor
24.  Apparent diffusion coefficient histogram analysis stratifies progression-free and overall survival in patients with recurrent GBM treated with bevacizumab: a multi-center study 
Journal of neuro-oncology  2012;108(3):491-498.
We have tested the predictive value of apparent diffusion coefficient (ADC) histogram analysis in stratifying progression-free survival (PFS) and overall survival (OS) in bevacizumab-treated patients with recurrent glioblastoma multiforme (GBM) from the multi-center BRAIN study. Available MRI’s from patients enrolled in the BRAIN study (n = 97) were examined by generating ADC histograms from areas of enhancing tumor on T1 weighted post-contrast images fitted to a two normal distribution mixture curve. ADC classifiers including the mean ADC from the lower curve (ADC-L) and the mean lower curve proportion (LCP) were tested for their ability to stratify PFS and OS by using Cox proportional hazard ratios and the Kaplan–Meier method with log-rank test. Mean ADC-L was 1,209 × 10−6mm2/s ± 224 (SD), and mean LCP was 0.71 ± 0.23 (SD). Low ADC-L was associated with worse outcome. The hazard ratios for 6-month PFS, overall PFS, and OS in patients with less versus greater than mean ADC-L were 3.1 (95 % confidence interval: 1.6, 6.1; P = 0.001), 2.3 (95 % CI: 1.3, 4.0; P = 0.002), and 2.4 (95 % CI: 1.4, 4.2; P = 0.002), respectively. In patients with ADC-L<1,209 and LCP>0.71 versus ADC-L>1,209 and LCP <0.71, there was a 2.28-fold reduction in the median time to progression, and a 1.42-fold decrease in the median OS. The predictive value of ADC histogram analysis, in which low ADC-L was associated with poor outcome, was confirmed in bevacizumab-treated patients with recurrent GBM in a post hoc analysis from the multi-center (BRAIN) study.
doi:10.1007/s11060-012-0847-y
PMCID: PMC3997502  PMID: 22426926
Apparent diffusion coefficient; Glioblastoma multiforme; Progression-free survival
25.  Comparison of methods for fecal microbiome biospecimen collection 
BMC Microbiology  2014;14:103.
Background
Effective means are needed to efficiently collect fecal samples for microbiome analysis in large-scale epidemiological studies. Using twenty-four fecal aliquots prepared from three healthy individuals, we compared the following four fecal sample collection methods for assessment of human gut microbiome: 1) fecal occult blood test cards, held at room temperature for three days, 2) Eppendorf tubes, at room temperature for three days, 3) Eppendorf tubes with RNAlater, at room temperature, and 4) as controls, samples immediately frozen at −80°C. The 24 samples were assayed by 16S rRNA gene sequencing to compare overall microbiome structure and taxon distributions according to collection method.
Results
Storing fecal occult blood test card samples at room temperature for three days did not affect total DNA purity and relative 16S rRNA bacterial gene contents, compared with fresh frozen collection. Overall microbiome structure, based on phylogenetic UniFrac index, differed significantly by subject (p = 0.001), but microbiome structure (p = 0.497) and relative abundance of major microbial taxa (phyla) (p > 0.05) did not differ significantly by collection method.
Conclusions
Our findings suggest that low-cost fecal occult blood test card collection may be a feasible means of sample collection for fecal microbiome assessment in large-scale population-based studies.
doi:10.1186/1471-2180-14-103
PMCID: PMC4005852  PMID: 24758293
Comparison; Methods; Fecal; Microbiome; Collection

Results 1-25 (198)