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1.  A systematic confirmation study of reported prostate cancer risk-associated SNPs in Chinese men 
Cancer science  2011;102(10):1916-1920.
More than 30 prostate cancer (PCa) risk-associated loci have been identified in populations of European descent by genome-wide association studies (GWAS). We hypothesized that a subset of these loci may be associated with PCa risk in Chinese men. To test this hypothesis, 33 single nucleotide polymorphisms (SNPs), one each from the 33 independent PCa risk-associated loci reported in populations of European descent, were investigated for their associations with PCa risk in a case-control study of Chinese men (1,108 cases and 1,525 controls). We found that 11 of the 33 SNPs were significantly associated with PCa risk in Chinese men (P < 0.05). The reported risk alleles were associated with increased risk for PCa, with allelic odds ratios ranging from 1.12 to 1.44. The most significant locus was located on 8q24 Region 2 (rs16901979, P = 5.14×10−9) with a genome-wide significance (P < 10−8), and three loci reached the Bonferroni correction significance level (P < 1.52×10−3), including 8q24 Region 1 (rs1447295, P = 7.04×10−6), 8q24 Region 5 (rs10086908, P = 9.24×10−4), and 8p21 (rs1512268, P = 9.39×10−4). Our results suggest that a subset of the PCa risk-associated SNPs discovered by GWAS among men of European descent is also associated with PCa risk in Chinese men. This finding provides evidence of ethnic differences and similarity in genetic susceptibility to PCa. GWAS in Chinese men are needed to identify Chinese-specific PCa risk-associated SNPs.
doi:10.1111/j.1349-7006.2011.02036.x
PMCID: PMC3581323  PMID: 21756274
2.  Full Genome Sequence of Giant Panda Rotavirus Strain CH-1 
Genome Announcements  2013;1(1):e00241-12.
We report here the complete genomic sequence of the giant panda rotavirus strain CH-1. This work is the first to document the complete genomic sequence (segments 1 to 11) of the CH-1 strain, which offers an effective platform for providing authentic research experiences to novice scientists.
doi:10.1128/genomeA.00241-12
PMCID: PMC3587948  PMID: 23469354
3.  Replication and cumulative effects of GWAS-identified genetic variations for prostate cancer in Asians: a case–control study in the ChinaPCa consortium 
Carcinogenesis  2011;33(2):356-360.
A recent genome-wide association study has identified five new genetic variants for prostate cancer susceptibility in a Japanese population, but it is unknown whether these newly identified variants are associated with prostate cancer risk in other populations, including Chinese men. We genotyped these five variants in a case–control study of 1524 patients diagnosed with prostate cancer and 2169 control subjects from the Chinese Consortium for Prostate Cancer Genetics (ChinaPCa). We found that three of the five genetic variants were associated with prostate cancer risk (P = 4.33 × 10−8 for rs12653946 at 5p15, 4.43 × 10−5 for rs339331 at 6q22 and 8.42 × 10−4 for rs9600079 at 13q22, respectively). A cumulative effect was observed in a dose-dependent manner with increasing numbers of risk variant alleles (Ptrend = 2.58 × 10−13), and men with 5–6 risk alleles had a 2-fold higher risk of prostate cancer than men with 0–2 risk alleles (odds ratio = 2.26, 95% confidence interval = 1.78–2.87). Furthermore, rs339331 T allele was significantly associated with RFX6 and GPRC6A higher messenger RNA expression, compared with the C allele. However, none of the variants was associated with clinical stage, Gleason score or family history. These results provide further evidence that the risk loci identified in Japanese men also contribute to prostate cancer susceptibility in Chinese men.
doi:10.1093/carcin/bgr279
PMCID: PMC3271266  PMID: 22114074
4.  PEP-1-CAT-Transduced Mesenchymal Stem Cells Acquire an Enhanced Viability and Promote Ischemia-Induced Angiogenesis 
PLoS ONE  2012;7(12):e52537.
Objective
Poor survival of mesenchymal stem cells (MSC) compromised the efficacy of stem cell therapy for ischemic diseases. The aim of this study is to investigate the role of PEP-1-CAT transduction in MSC survival and its effect on ischemia-induced angiogenesis.
Methods
MSC apoptosis was evaluated by DAPI staining and quantified by Annexin V and PI double staining and Flow Cytometry. Malondialdehyde (MDA) content, lactate dehydrogenase (LDH) release, and Superoxide Dismutase (SOD) activities were simultaneously measured. MSC mitochondrial membrane potential was analyzed with JC-1 staining. MSC survival in rat muscles with gender-mismatched transplantation of the MSC after lower limb ischemia was assessed by detecting SRY expression. MSC apoptosis in ischemic area was determined by TUNEL assay. The effect of PEP-1-CAT-transduced MSC on angiogenesis in vivo was determined in the lower limb ischemia model.
Results
PEP-1-CAT transduction decreased MSC apoptosis rate while down-regulating MDA content and blocking LDH release as compared to the treatment with H2O2 or CAT. However, SOD activity was up-regulated in PEP-1-CAT-transduced cells. Consistent with its effect on MSC apoptosis, PEP-1-CAT restored H2O2-attenuated mitochondrial membrane potential. Mechanistically, PEP-1-CAT blocked H2O2-induced down-regulation of PI3K/Akt activity, an essential signaling pathway regulating MSC apoptosis. In vivo, the viability of MSC implanted into ischemic area in lower limb ischemia rat model was increased by four-fold when transduced with PEP-1-CAT. Importantly, PEP-1-CAT-transduced MSC significantly enhanced ischemia-induced angiogenesis by up-regulating VEGF expression.
Conclusions
PEP-1-CAT-transduction was able to increase MSC viability by regulating PI3K/Akt activity, which stimulated ischemia-induced angiogenesis.
doi:10.1371/journal.pone.0052537
PMCID: PMC3532064  PMID: 23285080
5.  Notch2 regulates matrix metallopeptidase 9 via PI3K/AKT signaling in human gastric carcinoma cell MKN-45 
AIM: To clarify the role of activated Notch2 in the invasiveness of gastric cancer.
METHODS: To investigate the invasiveness of silencing Notch2 gene expression, we established a Notch2 small interfering RNA (siRNA) transfected cell line using the MKN-45 gastric cancer cell line. After the successful transfection confirmed by real-time reverse transcription-polymerase chain reaction (RT-PCR) and Western blotting, migration and invasion assays were employed to evaluate the aggressiveness of the gastric cancer. RT-PCR and Western blottings were employed to confirm the down-regulation of Notch2 and to evaluate the expression of epithelial mesenchymal transition-related gene matrix metallopeptidase 9 (MMP9), Akt, p-Akt. To confirm the relationship between PI3K-Akt and MMP9, the PI3K inhibitor LY294002 was used to treat MKN-45 cells.
RESULTS: Notch2 expression was dramatically decreased after Notch2 siRNA transfection (100.00% ± 9.74% vs 11.61% ± 3.85%, P < 0.01 by qRT-PCR). There was also a marked reduction of Notch target gene Hes1 (100.00% ± 4.74% vs 61.61% ± 3.58%, P < 0.05) at the mRNA, indicating an inhibition of Notch signaling. Inhibition of Notch signaling was also confirmed by the marked reduction of Notch2 intracellular domain at the protein levels (100.00% ± 9.74% vs 65.61% ± 7.58%, P < 0.05). Down-regulation of Notch2 by siRNA enhanced tumor cell invasion (100.00% ± 21.64% vs 162.22% ± 16.84%, P < 0.05) and expression of MMP9 (1.56 fold, P < 0.05), and activated the pro-MMP9 protein to its active form (1.48 fold, P < 0.05). There was no significant difference in the protein levels of Akt between the two groups (100.00% ± 10.87% vs 96.61% ± 7.33%, P > 0.05), while down-regulation of Notch2 elevated p-Akt expression (100.00% ± 9.87% vs 154.61% ± 13.10%, P < 0.05). Furthermore, p-Akt and MMP9 was down-regulated in response to the inhibitor LY294002 (p-Akt 100.00% ± 8.87% vs 58.27% ± 5.01%, P < 0.05; MMP9 100.00% ± 9.17% vs 50.03% ± 4.88%, P < 0.05).
CONCLUSION: Notch2 may negatively regulate cell invasion by inhibiting the PI3K-Akt signaling pathway in gastric cancer.
doi:10.3748/wjg.v18.i48.7262
PMCID: PMC3544028  PMID: 23326131
Notch2; Stomach; Cancer; Invasion; Epithelial mesenchymal transition; Matrix metallopeptidase 9; RNA interference
6.  Chronic Exposure to Nicotine Enhances Insulin Sensitivity through α7 Nicotinic Acetylcholine Receptor-STAT3 Pathway 
PLoS ONE  2012;7(12):e51217.
This study was to investigate the effect of nicotine on insulin sensitivity and explore the underlying mechanisms. Treatment of Sprague-Dawley rats with nicotine (3 mg/kg/day) for 6 weeks reduced 43% body weight gain and 65% blood insulin level, but had no effect on blood glucose level. Both insulin tolerance test and glucose tolerance test demonstrated that nicotine treatment enhanced insulin sensitivity. Pretreatment of rats with hexamethonium (20 mg/kg/day) to antagonize peripheral nicotinic receptors except for α7 nicotinic acetylcholine receptor (α7-nAChR) had no effect on the insulin sensitizing effect of nicotine. However, the insulin sensitizing effect but not the bodyweight reducing effect of nicotine was abrogated in α7-nAChR knockout mice. Further, chronic treatment with PNU-282987 (0.53 mg/kg/day), a selective α7-nAChR agonist, significantly enhanced insulin sensitivity without apparently modifying bodyweight not only in normal mice but also in AMP-activated kinase-α2 knockout mice, an animal model of insulin resistance with no sign of inflammation. Moreover, PNU-282987 treatment enhanced phosphorylation of signal transducer and activator of transcription 3 (STAT3) in skeletal muscle, adipose tissue and liver in normal mice. PNU-282987 treatment also increased glucose uptake by 25% in C2C12 myotubes and this effect was total abrogated by STAT3 inhibitor, S3I-201. All together, these findings demonstrated that nicotine enhanced insulin sensitivity in animals with or without insulin resistance, at least in part via stimulating α7-nAChR-STAT3 pathway independent of inflammation. Our results contribute not only to the understanding of the pharmacological effects of nicotine, but also to the identifying of new therapeutic targets against insulin resistance.
doi:10.1371/journal.pone.0051217
PMCID: PMC3520975  PMID: 23251458
7.  Deficiency of SR-BI Leads to Impaired Lymphocyte Homeostasis and Autoimmune Disorders in Mice 
Objective
Scavenger receptor BI (SR-BI) is an HDL receptor. Recent studies revealed that SR-BI protects against sepsis via modulating innate immunity. However, its role in adaptive immunity is unclear.
Methods and Results
SR-BI null mice exhibited impaired lymphocyte homeostasis as shown by splenomegaly and imbalanced expansion of T and B lymphocytes in the spleens. Importantly, the activated T and B lymphocytes were increased 3–4-fold, indicating a heightened active status of T and B lymphocytes. More importantly, in line with the accumulation of the activated T and B lymphocytes, SR-BI null mice developed systemic autoimmune disorders characterized by the presence of autoantibodies in circulation, the deposition of immune complexes in glomeruli, and the leukocyte infiltration in kidney. Further analyses revealed that SR-BI deficiency enhances lymphocyte proliferation, causes imbalanced IFN-g and IL-4 production in lymphocytes and elevated inflammatory cytokine production in macrophages. Furthermore, HDL from SR-BI null mice exhibited less capability of suppressing lymphocyte proliferation.
Conclusions
SR-BI regulates lymphocyte homeostasis likely through its roles in modulating the proliferation of lymphocytes, the cytokine production by lymphocytes and macrophages, and the function of HDL. Its deficiency leads to impaired lymphocyte homeostasis and autoimmune disorders. Our findings reveal a previously unrecognized role of SR-BI in adaptive immunity.
doi:10.1161/ATVBAHA.111.234716
PMCID: PMC3202973  PMID: 21836069
lymphocytes; adaptive immunity; scavenger receptor BI; Scarb1; HDL
8.  GOLPH3 overexpression correlates with tumor progression and poor prognosis in patients with clinically N0 oral tongue cancer 
Background
Overexpression of GOLPH3 (Golgi phosphoprotein 3, 34 kDa) is associated with the progression of many solid tumor types leading to an unfavorable clinical outcome. We aimed to investigate the clinical significance of GOLPH3 expression in the development and progression of clinically N0 (cN0) oral tongue cancer.
Methods
Real-time PCR and Western blotting analyses were employed to examine GOLPH3 expression in four oral tongue cancer cell lines, primary cultured normal tongue epithelial cells (TEC), eight matched pairs of oral tongue cancer samples and adjacent noncancerous tissue samples from the same patient. Immunohistochemistry (IHC) was performed to examine GOLPH3 protein expression in paraffin-embedded tissues from 179 cN0 oral tongue cancer patients. Statistical analyses were applied to evaluate the diagnostic value and the associations of GOLPH3 expression with clinical parameters.
Results
GOLPH3 mRNA and protein was up-regulated in oral tongue cancer cell lines and cancerous tissues compared with that in primary cultured normal tongue epithelial cells (TEC) and adjacent noncancerous tissue samples. GOLPH3 protein level was positively correlated with clinical stage (P = 0.001), T classification (P = 0.001), N classification (P = 0.043) and recurrence (P = 0.009). Patients with higher GOLPH3 expression had shorter overall survival time, whereas those with lower GOLPH3 expression had longer survival time.
Conclusion
Our results suggest GOLPH3 overexpression is associated with poor prognosis for cN0 oral tongue cancer patients and may represent a novel and useful prognostic indicator for cN0 oral tongue cancer.
doi:10.1186/1479-5876-10-168
PMCID: PMC3480894  PMID: 22905766
GOLPH3; Prognosis; cN0 oral tongue cancer
9.  Microarray Я US: a user-friendly graphical interface to Bioconductor tools that enables accurate microarray data analysis and expedites comprehensive functional analysis of microarray results 
BMC Research Notes  2012;5:282.
Background
Microarray data analysis presents a significant challenge to researchers who are unable to use the powerful Bioconductor and its numerous tools due to their lack of knowledge of R language. Among the few existing software programs that offer a graphic user interface to Bioconductor packages, none have implemented a comprehensive strategy to address the accuracy and reliability issue of microarray data analysis due to the well known probe design problems associated with many widely used microarray chips. There is also a lack of tools that would expedite the functional analysis of microarray results.
Findings
We present Microarray Я US, an R-based graphical user interface that implements over a dozen popular Bioconductor packages to offer researchers a streamlined workflow for routine differential microarray expression data analysis without the need to learn R language. In order to enable a more accurate analysis and interpretation of microarray data, we incorporated the latest custom probe re-definition and re-annotation for Affymetrix and Illumina chips. A versatile microarray results output utility tool was also implemented for easy and fast generation of input files for over 20 of the most widely used functional analysis software programs.
Conclusion
Coupled with a well-designed user interface, Microarray Я US leverages cutting edge Bioconductor packages for researchers with no knowledge in R language. It also enables a more reliable and accurate microarray data analysis and expedites downstream functional analysis of microarray results.
doi:10.1186/1756-0500-5-282
PMCID: PMC3459790  PMID: 22681702
Microarray data analysis; Gene expression; Probe reannotation
10.  What compound words mean to children with specific language impairment 
Applied psycholinguistics  2010;31(03):463-487.
Sixteen children (17 age mates, 17 vocabulary mates) with specific language impairment (SLI) participated in two studies. In the first, they named fantasy objects. All groups coined novel noun–noun compounds on a majority of trials but only the SLI group had difficulty ordering the nouns as dictated by semantic context. In the second study, the children described the meaning of conventional noun–noun compounds. The SLI and AM groups did not differ in parsing the nouns, but the SLI group was poorer at explaining the semantic relationships between them. Compared to vocabulary mates, a larger proportion of the SLI group successfully parsed the compounds but a smaller proportion could explain them. These difficulties may reflect problems in the development of links within the semantic lexicon.
doi:10.1017/S014271641000007X
PMCID: PMC3354768  PMID: 22611295
11.  Deficiency of calcium and magnesium induces apoptosis via scavenger receptor BI 
Life sciences  2011;88(13-14):606-612.
Aims
Cell undergoes apoptosis in stressed status such as intracellular calcium overload or extracellular calcium/magnesium deficiency. The mechanisms of how deficiency of the divalent metal ions induces apoptosis remain to be defined. Scavenger receptor BI (SRBI) is a high density lipoprotein (HDL) receptor. Recent studies demonstrated that SR-BI is a stress response molecule which induces apoptosis upon serum deprivation. In this study, we assessed our hypothesis that the deficiency of calcium/magnesium induces apoptosis via SR-BI apoptotic pathway.
Main methods
We employed CHO cell lines expressing vector and SR-BI to test the effect of SR-BI on apoptosis induced by deficiency of calcium, magnesium and zinc in culture medium. The regain of different metal ions in deficient medium was also performed, respectively. Cell death was detected by morphological changes and quantified by LDH cytotoxicity assay. Apoptosis was also assessed by DNA ladder assay and DNA condensation assay. The SR-BIC323G mutant cells which lack the apoptotic activity of SR-BI were employed to verify the SR-BI-dependent effect on calcium/magnesium induced apoptosis.
Key findings
The deficiency of calcium/magnesium induced cell apoptosis CHO-SR-BI cells, but not in CHO-vector cells. Moreover, no apoptotic cell death was observed in SR-BIC323G mutant cells, indicating that the deficiency of divalent metal ions induces apoptosis in a SR-BI-dependent manner. Furthermore, the restoration of calcium or magnesium, but not zinc, protected CHO-SR-BI cells from apoptotic cell death, in a dose-dependent fashion.
Significance
These findings extend our understanding about how calcium and magnesium deficiency induces apoptosis.
doi:10.1016/j.lfs.2011.01.020
PMCID: PMC3061308  PMID: 21291896
calcium; magnesium; apoptosis; scavenger receptor BI
12.  Microglia activation mediates fibrillar amyloid-β toxicity in the aged primate cortex 
Neurobiology of aging  2009;32(3):387-397.
The amyloid-β peptide (Aβ) plays a central role in the pathogenesis of Alzheimer's disease (AD). The fibrillar form of Aβ (fAβ) exerts toxic effects on neurons through mechanisms not well understood. We have shown that the aged primate cortex is selectively vulnerable to fAβ toxicity at low concentrations. In addition to neuronal loss, fAβ induced massive activation of microglia in the aged rhesus cortex. We now demonstrate that inhibition of microglia activation abolishes fAβ toxicity. Injection or pump delivery of macrophage/microglia inhibitory factor (MIF) significantly reduced activation of microglia and the volume of damage caused by fAβ. Microglia isolated from aged rhesus cortex produced substantial reactive oxygen species when stimulated by fAβ, which was inhibited by MIF in a dose-dependent manner. This is the first definitive in vivo demonstration that the fAβ-induced microglia activation and inflammation mediate, at least in part, its toxic effects on neurons. Combined with our earlier observations, these findings suggest that aged primate microglia may display an exaggerated inflammatory response to fAβ when compared with young microglia.
doi:10.1016/j.neurobiolaging.2009.02.025
PMCID: PMC2888944  PMID: 19349094
Amyloid toxicity; Microglia; Fibrillar; Neuronal loss; Non-human primate
13.  HGF stimulates proliferation through the HGF/c-Met pathway in nasopharyngeal carcinoma cells 
Oncology Letters  2012;3(5):1124-1128.
Hepatocyte growth factor (HGF) and its receptor c-Met are important in the development and homeostasis of a variety of human malignancies. However, the role of the HGF/c-Met signaling pathway in nasopharyngeal carcinoma (NPC) has not been clearly elucidated. This study examined the effect of HGF/c-Met on proliferation and migration in several NPC cell lines. RT-PCR was used to detect the HGF gene in CNE-1, CNE-2, HK-1, HONE-1 and SUNE-1 NPC cells. However, HGF gene expression was not detected in any of these cells. Using immunoblotting analysis, the Met25 protein was identified in HONE-1, HK-1 and CNE-1 cells. Results from fluorescence-activated cell sorting (FACS) analysis revealed that anti-Met25 mAb specifically bound Met-expressing HONE-1, HK-1 and CNE-1 cells. It was further demonstrated that exogenous HGF was able to stimulate the proliferation of HONE-1 and HK-1 cells and the healing of scrape wounds in HONE-1 NPC cells. Our results reveal the potential therapeutic applications of combination therapy with antibodies targeting HGF in NPC patients.
doi:10.3892/ol.2012.613
PMCID: PMC3389637  PMID: 22783404
nasopharyngeal carcinoma, HGF; c-Met, proliferation, migration
14.  Optimization of the Extraction of Anthocyanins from the Fruit Skin of Rhodomyrtus tomentosa (Ait.) Hassk and Identification of Anthocyanins in the Extract Using High-Performance Liquid Chromatography-Electrospray Ionization-Mass Spectrometry (HPLC-ESI-MS) 
Anthocyanins are naturally occurring polyphenols that impart bright color to fruits, vegetables and plants. In this study, the extraction of anthocyanins from freeze-dried fruit skin of downy rose-myrtle (Rhodomyrtus tomentosa (Ait.) Hassk var. Gangren) was optimized using response surface methodology (RSM). Using 60% ethanol containing 0.1% (v/v) hydrochloric acid as extraction solvent, the optimal conditions for maximum yields of anthocyanin (4.358 ± 0.045 mg/g) were 15.7:1 (v/w) liquid to solid ratio, 64.38 °C with a 116.88 min extraction time. The results showed good fits with the proposed model for the anthocyanin extraction (R2 = 0.9944). Furthermore, the results of high-performance liquid chromatography-electrospray ionization-mass spectrometry (HPLC-ESI-MS) analysis of the anthocyanins extracted from the fruit skin of downy rose-myrtle revealed the presence of five anthocyanin components, which were tentatively identified as delphinidin-3-glucoside, cyanidin-3-glucoside, peonidin-3-glucoside, petunidin-3-glucoside and malvidin-3-glucoside.
doi:10.3390/ijms13056292
PMCID: PMC3382815  PMID: 22754365
anthocyanins; Rhodomyrtus tomentosa (Ait.) Hassk; response surface methodology; HPLC-ESI-MS
15.  Astrocyte elevated gene-1 (AEG-1) is a marker for aggressive salivary gland carcinoma 
Background
Astrocyte elevated gene-1 (AEG-1) is associated with tumorigenesis and progression in diverse human cancers. The present study was aimed to investigate the clinical and prognostic significance of AEG-1 in salivary gland carcinomas (SGC).
Methods
Real-time PCR and western blot analyses were employed to examine AEG-1 expression in two normal salivary gland tissues, eight SGC tissues of various clinical stages, and five pairs of primary SGC and adjacent salivary gland tissues from the same patient. Immunohistochemistry (IHC) was performed to examine AEG-1 protein expression in paraffin-embedded tissues from 141 SGC patients. Statistical analyses was applies to evaluate the diagnostic value and associations of AEG-1 expression with clinical parameters.
Results
AEG-1 expression was evidently up-regulated in SGC tissues compared with that in the normal salivary gland tissues and in matched adjacent salivary gland tissues. AEG-1 protein level was positively correlated with clinical stage (P < 0.001), T classification (P = 0.008), N classification (P = 0.008) and M classifications (P = 0.006). Patients with higher AEG-1 expression had shorter overall survival time, whereas those with lower tumor AEG-1 expression had longer survival time.
Conclusions
Our results suggest that AEG-1 expression is associated with SGC progression and may represent a novel and valuable predictor for prognostic evaluation of SGC patients.
doi:10.1186/1479-5876-9-205
PMCID: PMC3286424  PMID: 22133054
AEG-1; Biomarker; Prognosis; Salivary gland carcinomas
16.  Improved power by collapsing rare and common variants based on a data-adaptive forward selection strategy 
BMC Proceedings  2011;5(Suppl 9):S114.
Genome-wide association studies have been used successfully to detect associations between common genetic variants and complex diseases, but common single-nucleotide polymorphisms (SNPs) detected by these studies explain only 5–10% of disease heritability. Alternatively, the common disease/rare variants hypothesis suggests that complex diseases are often caused by multiple rare variants with moderate to high effects. Under this hypothesis, the analysis of the cumulative effect of rare variants may thus help us discover the missing genetic variations. Collapsing all rare variants across a functional region is currently a popular method to find rare variants that may have a causal effect on certain diseases. However, the power of tests based on collapsing methods is often impaired by misclassification of functional variants. We develop a data-adaptive forward selection procedure that selectively chooses only variants that improve the association signal between functional regions and the disease risk. We apply our strategy to the Genetic Analysis Workshop 17 unrelated individuals data with quantitative traits. The type I error rate and the power of different collapsing functions are evaluated. The substantially higher power of the proposed strategy was demonstrated. The new method provides a useful strategy for the association study of sequencing data by taking advantage of the selection of rare variants.
doi:10.1186/1753-6561-5-S9-S114
PMCID: PMC3287838  PMID: 22373230
17.  Global transcriptome analysis of two ameiotic1 alleles in maize anthers: defining steps in meiotic entry and progression through prophase I 
BMC Plant Biology  2011;11:120.
Background
Developmental cues to start meiosis occur late in plants. Ameiotic1 (Am1) encodes a plant-specific nuclear protein (AM1) required for meiotic entry and progression through early prophase I. Pollen mother cells (PMCs) remain mitotic in most am1 mutants including am1-489, while am1-praI permits meiotic entry but PMCs arrest at the leptotene/zygotene (L/Z) transition, defining the roles of AM1 protein in two distinct steps of meiosis. To gain more insights into the roles of AM1 in the transcriptional pre-meiotic and meiotic programs, we report here an in depth analysis of gene expression alterations in carefully staged anthers at 1 mm (meiotic entry) and 1.5 mm (L/Z) caused by each of these am1 alleles.
Results
1.0 mm and 1.5 mm anthers of am1-489 and am1-praI were profiled in comparison to fertile siblings on Agilent® 4 × 44 K microarrays. Both am1-489 and am1-praI anthers are cytologically normal at 1.0 mm and show moderate transcriptome alterations. At the 1.5-mm stage both mutants are aberrant cytologically, and show more drastic transcriptome changes. There are substantially more absolute On/Off and twice as many differentially expressed genes (sterile versus fertile) in am1-489 than in am1-praI. At 1.5 mm a total of 4,418 genes are up- or down-regulated in either am1-489 or am1-praI anthers. These are predominantly stage-specific transcripts. Many putative meiosis-related genes were found among them including a small subset of allele-specific, mis-regulated genes specific to the PMCs. Nearly 60% of transcriptome changes in the set of transcripts mis-regulated in both mutants (N = 530) are enriched in PMCs, and only 1% are enriched in the tapetal cell transcriptome. All array data reported herein will be deposited and accessible at MaizeGDB http://www.maizegdb.org/.
Conclusions
Our analysis of anther transcriptome modulations by two distinct am1 alleles, am1-489 and am1-praI, redefines the role of AM1 as a modulator of expression of a subset of meiotic genes, important for meiotic progression and provided stage-specific insights into the genetic networks associated with meiotic entry and early prophase I progression.
doi:10.1186/1471-2229-11-120
PMCID: PMC3180651  PMID: 21867558
meiosis; meiocytes; transcriptomes; leptotene/zygotene transition; pollen mother cells
18.  A tetra­gonal polymorph of bis­[hydro­tris­(pyrazol-1-yl)borato]iron(II) 
The title compound, [Fe(C9H10BN6)2], is a polymorph of a compound reported previously [Oliver et al. (1980 ▶). Inorg. Chem. 19, 165–168]. In the previous report, the compound crystallized in the monoclinic space group P21/c (Z = 4), whereas the crystal symmetry of the compound reported here is tetra­gonal (P42/ncm, Z = 4). The mol­ecular structure is comprised of two hydro­tris­(1-pyrazol­yl)borate ligands (Tp−) and a central FeII ion, which is coordinated by six pyrazole N atoms from two two Tp− ligands, yielding a distorted bipyramidal FeN6 geometry. The complete molecule exhibits symmetry 2/m.
doi:10.1107/S1600536811025839
PMCID: PMC3212124  PMID: 22090826
19.  Accumulation and expression of serum amyloid P component in human atherosclerotic lesions 
Atherosclerosis  2010;211(1):90-95.
Serum amyloid P component (SAP) is a member of pentraxins. Previous studies indicate that SAP exists in human atherosclerotic aortic intima and the plasma SAP levels are associated with cardiovascular disease. In this study, we characterized SAP in normal and atherosclerotic intima, investigated the source of SAP in atherosclerotic lesions, and assessed the effect of SAP on HDL function. Immunohistochemical staining and electroimmunoassay indicated that SAP is not present in normal aortic intima which excludes the possibility that SAP nonspecifically deposits in aortic intima via its binding to microfibrils. Notably, SAP levels are correlated with the severity of atherosclerotic lesions. Fast protein liquid chromatography (FPLC) and western blot analysis revealed that SAP exists in atherosclerotic lesions in multiple forms. Soluble SAP accumulates in the lesions as decamer in free or bound forms via ligand-binding to its ligand(s). Insoluble SAP accumulates in the lesions in covalent-bound forms conjugated to collagen/collagen-like substances via disulfide (-S-S-) bonds. In situ hybridization and RT-PCR analysis revealed that SAP is generated in atherosclerotic lesions, at least partly, by macrophages and smooth muscle cells in neointima. Functional analysis demonstrated that SAP associated with HDL promotes SR-BI-dependent cholesterol efflux and lipid-free SAP enhances ABCA1-dependent cholesterol efflux. In conclusion, our findings demonstrate that SAP is specifically accumulated and expressed in atherosclerotic lesions. SAP may be involved in cholesterol clearance through its role in promoting cholesterol efflux.
doi:10.1016/j.atherosclerosis.2010.01.046
PMCID: PMC2888759  PMID: 20189569
amyloid P component; pentraxin; HDL; cardiovascular disease; cholesterol efflux; scavenger receptor BI; ABCA1
20.  Comparison of disposable sutureless silicone ring and traditional metal ring in 23-gauge vitrectomy combined with cataract surgery 
Background:
The purpose of this prospective, interventional, comparative case series was to evaluate the efficiency and feasibility of a disposable sutureless silicone lens ring for corneal contact lens stabilization during combined 23-gauge vitrectomy and cataract surgery.
Methods:
We developed a ring consisting of a single silicone component with three footplates along the ring margin to fit cannulae for holding conventional contact lenses. Thirty eyes from 30 patients with cataract and vitreoretinal disease were included, and divided into two matched groups according to disease type and ring used. In Group A, we used a 23-gauge transconjunctival vitrectomy system and a disposable sutureless silicone lens ring (n = 15). In Group B, we used a 23-gauge transconjunctival vitrectomy system and a conventional metal lens ring (n = 15). The main outcome measures were: time required for vitrectomy preparation, rate of intraoperative corneal limbus bleeding, and limbus scar rate at the final follow-up visit.
Results:
Thirty cases were successfully completed. The average vitrectomy preparation time was less in Group A than in Group B (P < 0.01), and the average preparation time saved was 3.94 minutes. None of the Group A patients had intraoperative bleeding or postoperative scarring, whereas all 15 Group B cases had bleeding and five had scarring. There was a statistically significant difference between Group A and Group B for these complications (P ≤ 0.05).
Conclusion:
This report demonstrates the advantages of using a sutureless silicone ring during combined 23-gauge vitrectomy and cataract surgery. Using this method could allow extra time for the surgeon to pay more attention to complex vitreoretinal procedures.
doi:10.2147/OPTH.S18963
PMCID: PMC3133009  PMID: 21760720
pars plana vitrectomy; contact lens; silicone ring; cataract surgery
21.  Epigenetic Dysregulation in Mesenchymal Stem Cell Aging and Spontaneous Differentiation 
PLoS ONE  2011;6(6):e20526.
Background
Mesenchymal stem cells (MSCs) hold great promise for the treatment of difficult diseases. As MSCs represent a rare cell population, ex vivo expansion of MSCs is indispensable to obtain sufficient amounts of cells for therapies and tissue engineering. However, spontaneous differentiation and aging of MSCs occur during expansion and the molecular mechanisms involved have been poorly understood.
Methodology/Principal Findings
Human MSCs in early and late passages were examined for their expression of genes involved in osteogenesis to determine their spontaneous differentiation towards osteoblasts in vitro, and of genes involved in self-renewal and proliferation for multipotent differentiation potential. In parallel, promoter DNA methylation and hostone H3 acetylation levels were determined. We found that MSCs underwent aging and spontaneous osteogenic differentiation upon regular culture expansion, with progressive downregulation of TERT and upregulation of osteogenic genes such as Runx2 and ALP. Meanwhile, the expression of genes associated with stem cell self-renewal such as Oct4 and Sox2 declined markedly. Notably, the altered expression of these genes were closely associated with epigenetic dysregulation of histone H3 acetylation in K9 and K14, but not with methylation of CpG islands in the promoter regions of most of these genes. bFGF promoted MSC proliferation and suppressed its spontaneous osteogenic differentiation, with corresponding changes in histone H3 acetylation in TERT, Oct4, Sox2, Runx2 and ALP genes.
Conclusions/Significance
Our results indicate that histone H3 acetylation, which can be modulated by extrinsic signals, plays a key role in regulating MSC aging and differentiation.
doi:10.1371/journal.pone.0020526
PMCID: PMC3111432  PMID: 21694780
22.  The combined transduction of copper, zinc-superoxide dismutase and catalase mediated by cell-penetrating peptide, PEP-1, to protect myocardium from ischemia-reperfusion injury 
Background
Our previous studies indicate that either PEP-1-superoxide dismutase 1 (SOD1) or PEP-1-catalase (CAT) fusion proteins protects myocardium from ischemia-reperfusion-induced injury in rats. The aim of this study is to explore whether combined use of PEP-1-SOD1 and PEP-1-CAT enhances their protective effects.
Methods
SOD1, PEP-1-SOD1, CAT or PEP-1-CAT fusion proteins were prepared and purified by genetic engineering. In vitro and in vivo effects of these proteins on cell apoptosis and the protection of myocardium after ischemia-reperfusion injury were measured. Embryo cardiac myocyte H9c2 cells were used for the in vitro studies. In vitro cellular injury was determined by the expression of lactate dehydrogenase (LDH). Cell apoptosis was quantitatively assessed with Annexin V and PI double staining by Flow cytometry. In vivo, rat left anterior descending coronary artery (LAD) was ligated for one hour followed by two hours of reperfusion. Hemodynamics was then measured. Myocardial infarct size was evaluated by TTC staining. Serum levels of myocardial markers, creatine kinase-MB (CK-MB) and cTnT were quantified by ELISA. Bcl-2 and Bax expression in left ventricle myocardium were analyzed by western blot.
Results
In vitro, PEP-1-SOD1 or PEP-1-CAT inhibited LDH release and apoptosis rate of H9c2 cells. Combined transduction of PEP-1-SOD1 and PEP-1-CAT, however, further reduced the LDH level and apoptosis rate. In vivo, combined usage of PEP-1-SOD1 and PEP-1-CAT produced a greater effect than individual proteins on the reduction of CK-MB, cTnT, apoptosis rate, lipoxidation end product malondialdehyde, and the infarct size of myocardium. Functionally, the combination of these two proteins further increased left ventricle systolic pressure, but decreased left ventricle end-diastolic pressure.
Conclusion
This study provided a basis for the treatment or prevention of myocardial ischemia-reperfusion injury with the combined usage of PEP-1-SOD1 and PEP-1-CAT fusion proteins.
doi:10.1186/1479-5876-9-73
PMCID: PMC3120689  PMID: 21600015
23.  A functional polymorphism of TGFBR2 is associated with risk of breast cancer with ER+, PR+, ER+PR+ and HER2− expression in women 
Oncology Letters  2011;2(4):653-658.
Little is known about the correlation between TGFBR2 G-875A and breast cancer risk. Moreover, the associations of the expression of estrogen receptor (ER), progesterone receptor (PR) and human epidermal growth factor receptor-2 (HER2) in breast cancer tissues with the TGFB1 C-509T, T+29C and TGFBR2 G-875A polymorphisms remain to be determined. In this study, we genotyped for TGFB1 C-509T, T+29C and TGFBR2 G-875A in fresh surgically resected tissues (n=82) and archived paraffin-embedded specimens (n=88) from 170 patients with breast cancer, as well as peripheral blood samples from 178 cancer-free female individuals. Evaluation of ER, PR and HER2 expression was performed using immunohistochemical staining. Logistic regression analysis was carried out to determine the risk of breast cancer by calculating the odds ratios (ORs) and their 95% confidence intervals (CIs). As a result, no difference was observed in the TGFB1 C-509T, T+29C genotype and allele frequencies between patients and controls. However, the frequency of the TGFBR2 −875A allele was marginally higher in cancer-free female individuals than that of women with breast cancer (24.2 vs. 17.9%, P=0.05). Notably, when stratification was performed by ER, PR and HER2 expression, the TGFBR2 −875A allele was found to correlate significantly to a decreased risk of breast cancer with ER+ (OR=0.57, 95% CI 0.35–0.92), PR+ (OR=0.54, 95% CI 0.34–0.88), ER+PR+ (OR=0.55, 95% CI 0.33–0.92) and HER2− (OR=0.55, 95% CI 0.34–0.88) under a dominant genetic model. In conclusion, this is the first study to suggest that the TGFBR2 −875A allele modifies predisposition to breast cancer with an expression of ER+, PR+, ER+PR+ and HER2−.
doi:10.3892/ol.2011.312
PMCID: PMC3406483  PMID: 22848244
TGFBR2; TGFB1; polymorphism; breast cancer; risk
24.  Nesprin 1 is critical for nuclear positioning and anchorage 
Human Molecular Genetics  2009;19(2):329-341.
Nesprin 1 is an outer nuclear membrane protein that is thought to link the nucleus to the actin cytoskeleton. Recent data suggest that mutations in Nesprin 1 may also be involved in the pathogenesis of Emery-Dreifuss muscular dystrophy. To investigate the function of Nesprin 1 in vivo, we generated a mouse model in which all isoforms of Nesprin 1 containing the C-terminal spectrin-repeat region with or without KASH domain were ablated. Nesprin 1 knockout mice are marked by decreased survival rates, growth retardation and increased variability in body weight. Additionally, nuclear positioning and anchorage are dysfunctional in skeletal muscle from knockout mice. Physiological testing demonstrated no significant reduction in stress production in Nesprin 1-deficient skeletal muscle in either neonatal or adult mice, but a significantly lower exercise capacity in knockout mice. Nuclear deformation testing revealed ineffective strain transmission to nuclei in muscle fibers lacking Nesprin 1. Overall, our data show that Nesprin 1 is essential for normal positioning and anchorage of nuclei in skeletal muscle.
doi:10.1093/hmg/ddp499
PMCID: PMC2796894  PMID: 19864491
25.  Prognostic significance of Oct4 and Sox2 expression in hypopharyngeal squamous cell carcinoma 
Background
Oct4 and Sox2 are two major transcription factors related to the stem cell self-renewal and differentiation. The aim of this study was to examine the association between Oct4 and Sox2 expression levels with both the clinicopathological characteristics and prognoses of patients with hypopharyngeal squamous cell carcinoma.
Method
Tumor tissue samples from 85 patients with hypopharyngeal squamous cell carcinoma were collected, and the clinical follow-up data of these patients were recorded, and expression status of Oct4 and Sox2 were examined in these tissue samples by immunohistochemistry (IHC).
Results
Oct4 expression was found to be an independent predictive factor for overall survival (p = 0.004) in patients with hypopharyngeal squamous cell carcinoma and was independently related to loco-regional control (p = 0.001). Although Sox2 expression status showed no significant association with overall survival (p = 0.166), disease-free survival (p = 0.680) or loco-regional control (p = 0.383), when using a subgroup analysis, the subgroup with both high Oct4 and Sox2 expression had the best prognosis (p = 0.000). Sox2 expression could be a potential prognostic predictor for patients with hypopharyngeal squamous cell carcinoma. Simultaneous analyses of Oct4 and Sox2 expression could be more effective in evaluating the prognoses of patients with hypopharyngeal squamous cell carcinoma.
Conclusion
Oct4 expression is an independent predictive factor for patients with hypopharyngeal squamous cell carcinoma, suggesting that Oct4 expression may be a useful indicator for predicting the prognosis of hypopharyngeal squamous cell carcinoma.
doi:10.1186/1479-5876-8-94
PMCID: PMC2958910  PMID: 20937145

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