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Find video protocols related to scientific articles indexed in Pubmed.
EPGA: de novo assembly using the distributions of reads and insert size.
Bioinformatics
PUBLISHED: 11-20-2014
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In genome assembly, the primary issue is how to determine upstream and downstream sequence regions of sequence seeds for constructing long contigs or scaffolds. When extending one sequence seed, repetitive regions in the genome always cause multiple feasible extension candidates which increase the difficulty of genome assembly. The universally accepted solution is choosing one based on read overlaps and paired-end (mate-pair) reads. However, this solution faces difficulties with regard to some complex repetitive regions. In addition, sequencing errors may produce false repetitive regions and uneven sequencing depth leads some sequence regions to have too few or too many reads. All the aforementioned problems prohibit existing assemblers from getting satisfactory assembly results.
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[Cognitive dysfuctions associated with essential tremor and Parkinson's disease].
Zhonghua Yi Xue Za Zhi
PUBLISHED: 11-18-2014
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To explore the incidence of cognitive dysfunction and associated factors in 62 essential tremor (ET) cases, 60 normal controls and 61 Parkinson's disease (PD) cases.
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[Clinical application of totally implantable central venous port].
Zhonghua Wai Ke Za Zhi
PUBLISHED: 11-06-2014
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To summarize the disposal methods and the reasons of complications in operation of totally implantable central venous port (TICVP).
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Prediction of disease genes using tissue-specified gene-gene network.
BMC Syst Biol
PUBLISHED: 10-22-2014
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Tissue specificity is an important aspect of many genetic diseases in the context of genetic disorders as the disorder affects only few tissues. Therefore tissue specificity is important in identifying disease-gene associations. Hence this paper seeks to discuss the impact of using tissue specificity in predicting new disease-gene associations and how to use tissue specificity along with phenotype information for a particular disease.
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Prediction of disease-related genes based on weighted tissue-specific networks by using DNA methylation.
BMC Med Genomics
PUBLISHED: 10-22-2014
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Predicting disease-related genes is one of the most important tasks in bioinformatics and systems biology. With the advances in high-throughput techniques, a large number of protein-protein interactions are available, which make it possible to identify disease-related genes at the network level. However, network-based identification of disease-related genes is still a challenge as the considerable false-positives are still existed in the current available protein interaction networks (PIN).
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Identifying disease genes by integrating multiple data sources.
BMC Med Genomics
PUBLISHED: 10-22-2014
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Now multiple types of data are available for identifying disease genes. Those data include gene-disease associations, disease phenotype similarities, protein-protein interactions, pathways, gene expression profiles, etc.. It is believed that integrating different kinds of biological data is an effective method to identify disease genes.
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Synthesis and characterisation of multifunctional alginate microspheres via the in situ formation of ZnO quantum dots and the graft of 4-(1-pyrenyl) butyric acid to sodium alginate.
J Microencapsul
PUBLISHED: 09-30-2014
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Abstract Growth factor-loaded fluorescent alginate microspheres, which can realise sustained growth factor release and fluorescence imaging, were synthesised by in situ formation of ZnO quantum dots (QDs) and covalent graft of 4-(1-pyrenyl) butyric acid (PBA). BSA was chosen as a growth factor model protein to study the release kinetic of growth factors from alginate microspheres. The microsphere size and fluorescent properties were also investigated. Investigations of cell culture were used for evaluating biocompatibility of BSA-loaded fluorescent microspheres and fluorescence imaging property of ZnO QDs and PBA-grafted sodium alginate from the microspheres. The results show that they have good fluorescent property either to microspheres or to cells and fluorescent microspheres have good biocompatibility and property in sustained release of growth factors. The obtained microspheres will be expected to realise the imaging of cells and materials and also the release of growth factor in tissue engineering or in cell culture.
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Development and application of loop-mediated isothermal amplification for detection of the F167Y mutation of carbendazim-resistant isolates in Fusarium graminearum.
Sci Rep
PUBLISHED: 09-29-2014
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Resistance of Fusarium graminearum to carbendazim is caused by point mutations in the ?2-tubulin gene. The point mutation at codon 167 (TTT ? TAT, F167Y) occurs in more than 90% of field resistant isolates in China. To establish a suitable method for rapid detection of the F167Y mutation in F. graminearum, an efficient and simple method with high specificity was developed based on loop-mediated isothermal amplification (LAMP). A set of four primers was designed and optimized to specially distinguish the F167Y mutation genotype. The LAMP reaction was optimal at 63°C for 60?min. When hydroxynaphthol blue dye (HNB) was added prior to amplification, samples with DNA of the F167Y mutation developed a characteristic sky blue color after the reaction but those without DNA or with different DNA did not. Results of HNB staining method were reconfirmed by gel electrophoresis. The developed LAMP had good specificity, stability and repeatability and was suitable for monitoring carbendazim-resistance populations of F. graminearum in agricultural production.
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Plant genetics. Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome.
Science
PUBLISHED: 08-21-2014
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Oilseed rape (Brassica napus L.) was formed ~7500 years ago by hybridization between B. rapa and B. oleracea, followed by chromosome doubling, a process known as allopolyploidy. Together with more ancient polyploidizations, this conferred an aggregate 72× genome multiplication since the origin of angiosperms and high gene content. We examined the B. napus genome and the consequences of its recent duplication. The constituent An and Cn subgenomes are engaged in subtle structural, functional, and epigenetic cross-talk, with abundant homeologous exchanges. Incipient gene loss and expression divergence have begun. Selection in B. napus oilseed types has accelerated the loss of glucosinolate genes, while preserving expansion of oil biosynthesis genes. These processes provide insights into allopolyploid evolution and its relationship with crop domestication and improvement.
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Schistosoma japonicum soluble egg antigens facilitate hepatic stellate cell apoptosis by downregulating Akt expression and upregulating p53 and DR5 expression.
PLoS Negl Trop Dis
PUBLISHED: 08-21-2014
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The induction of hepatic stellate cell (HSC) apoptosis has potential as a potent strategy to diminish the progression of liver fibrosis. Previous studies have demonstrated the ability of soluble egg antigens (SEA) from schistosomes to inhibit HSC activation and to induce apoptosis in vitro. In this study, we aimed to explore the mechanism of SEA-induced apoptosis in HSCs.
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Small-molecule survivin inhibitor YM155 enhances radiosensitization in esophageal squamous cell carcinoma by the abrogation of G2 checkpoint and suppression of homologous recombination repair.
J Hematol Oncol
PUBLISHED: 08-20-2014
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Survivin is overexpressed in cancer cells and plays a crucial role in apoptosis evasion. YM155, a small-molecule inhibitor of survivin, could enhance the cytotoxicity of various DNA-damaging agents. Here, we evaluated the radiosensitizaion potential of YM155 in human esophageal squamous cell carcinoma (ESCC).
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A method to evaluate genome-wide methylation in archival formalin-fixed, paraffin-embedded ovarian epithelial cells.
PLoS ONE
PUBLISHED: 08-18-2014
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The use of DNA from archival formalin and paraffin embedded (FFPE) tissue for genetic and epigenetic analyses may be problematic, since the DNA is often degraded and only limited amounts may be available. Thus, it is currently not known whether genome-wide methylation can be reliably assessed in DNA from archival FFPE tissue.
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Prediction of Essential Proteins Based on Overlapping Essential Modules.
IEEE Trans Nanobioscience
PUBLISHED: 08-07-2014
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Many computational methods have been proposed to identify essential proteins by using the topological features of interactome networks. However, the precision of essential protein discovery still needs to be improved. Researches show that majority of hubs (essential proteins) in the yeast interactome network are essential due to their involvement in essential complex biological modules and hubs can be classified into two categories: date hubs and party hubs. In this study, combining with gene expression profiles, we propose a new method to predict essential proteins based on overlapping essential modules, named POEM. In POEM, the original protein interactome network is partitioned into many overlapping essential modules. The frequencies and weighted degrees of proteins in these modules are employed to decide which categories does a protein belong to? The comparative results show that POEM outperforms the classical centrality measures: Degree Centrality (DC), Information Centrality (IC), Eigenvector Centrality (EC), Subgraph Centrality (SC), Betweenness Centrality (BC), Closeness Centrality (CC), Edge Clustering Coefficient Centrality (NC) and two newly proposed essential proteins prediction methods: PeC and CoEWC. Experimental results indicate that the precision of predicting essential proteins can be improved by considering the modularity of proteins and integrating gene expression profiles with network topological features.
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Exploring conformational search protocols for ligand-based virtual screening and 3-D QSAR modeling.
J. Comput. Aided Mol. Des.
PUBLISHED: 08-03-2014
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3-D ligand conformations are required for most ligand-based drug design methods, such as pharmacophore modeling, shape-based screening, and 3-D QSAR model building. Many studies of conformational search methods have focused on the reproduction of crystal structures (i.e. bioactive conformations); however, for ligand-based modeling the key question is how to generate a ligand alignment that produces the best results for a given query molecule. In this work, we study different conformation generation modes of ConfGen and the impact on virtual screening (Shape Screening and e-Pharmacophore) and QSAR predictions (atom-based and field-based). In addition, we develop a new search method, called common scaffold alignment, that automatically detects the maximum common scaffold between each screening molecule and the query to ensure identical coordinates of the common core, thereby minimizing the noise introduced by analogous parts of the molecules. In general, we find that virtual screening results are relatively insensitive to the conformational search protocol; hence, a conformational search method that generates fewer conformations could be considered "better" because it is more computationally efficient for screening. However, for 3-D QSAR modeling we find that more thorough conformational sampling tends to produce better QSAR predictions. In addition, significant improvements in QSAR predictions are obtained with the common scaffold alignment protocol developed in this work, which focuses conformational sampling on parts of the molecules that are not part of the common scaffold.
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Induction of Nur77 by Hyperoside Inhibits Vascular Smooth Muscle Cell Proliferation and Neointimal Formation.
Biochem. Pharmacol.
PUBLISHED: 08-01-2014
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Nur77 is an orphan nuclear receptor that belongs to the nuclear receptor 4A (NR4A) subfamily, which has been implicated in a variety of biological events, such as cell apoptosis, proliferation, inflammation, and metabolism. Activation of Nur77 has recently been shown to be beneficial for the treatment of cardiovascular and metabolic diseases. The purpose of this study is to identify novel natural Nur77 activators and investigate their roles in preventing vascular diseases. By measuring Nur77 expression using quantitative RT-PCR, we screened active ingredients extracted from Chinese herb medicines with beneficial cardiovascular effects. Hyperoside (quercetin 3-D-galactoside) was identified as one of the potent activators for inducing Nur77 expression and activating its transcriptional activity in vascular smooth muscle cells (VSMCs). We demonstrated that hyperoside, in a time and dose dependent manner, markedly increased the expression of Nur77 in rat VSMCs, with an EC50 of ?0.83?M. Mechanistically, we found that hyperoside significantly increased the phosphorylation of ERK1/2 MAP kinase and its downstream target cAMP response element-binding protein (CREB), both of which contributed to the hyperoside-induced Nur77 expression in rat VSMCs. Moreover, through activation of Nur77 receptor, hyperoside markedly inhibited both vascular smooth muscle cell proliferation in vitro and the carotid artery ligation-induced neointimal formation in vivo. These findings demonstrate that hyperoside is a potent natural activator of Nur77 receptor, which can be potentially used for prevention and treatment of occlusive vascular diseases.
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Synthesis of core-shell graphitic carbon@silica nanospheres with dual-ordered mesopores for cancer-targeted photothermochemotherapy.
ACS Nano
PUBLISHED: 07-22-2014
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Tumor site-directed multifunctional therapeutic platforms such as photothermochemotherapy that respond to tumor-focused physical and biological stimuli are highly demanded for effective cancer therapy. Herein, targeting peptide-conjugated core–shell graphitic carbon@silica nanospheres with dual-ordered mesopores (MMPS) were successfully fabricated and developed as antitumoral doxorubicin (DOX) delivery system (MMPSD) for synergistic targeted photothermal chemotherapy of breast cancer. The hydrophilic mesoporous silica shell guarantees good water dispersity of MMPSD. The hydrophobic graphitic mesoporous carbon core provides excellent hydrophobic drug loading, immediate contact between the drug and photothermal hotspots, and high NIR photothermal conversion efficiency. SP13 peptide facilitates MMPSD for targeted and enhanced delivery of DOX within HER2-positive SK-BR-3 breast cancer cells, while PEGylation ensures biocompatibility. Thus, the MMPSD system exhibited efficient drug loading capacity, high targeting ability, sensitive NIR/pH-responsive DOX release, sustained release, and excellent combined antitumor activity.
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Vehicle density based forwarding protocol for safety message broadcast in VANET.
ScientificWorldJournal
PUBLISHED: 07-10-2014
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In vehicular ad hoc networks (VANETs), the medium access control (MAC) protocol is of great importance to provide time-critical safety applications. Contemporary multihop broadcast protocols in VANETs usually choose the farthest node in broadcast range as the forwarder to reduce the number of forwarding hops. However, in this paper, we demonstrate that the farthest forwarder may experience large contention delay in case of high vehicle density. We propose an IEEE 802.11-based multihop broadcast protocol VDF to address the issue of emergency message dissemination. To achieve the tradeoff between contention delay and forwarding hops, VDF adaptably chooses the forwarder according to the vehicle density. Simulation results show that, due to its ability to decrease the transmission collisions, the proposed protocol can provide significantly lower broadcast delay.
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Inhibition of cardiomyocyte hypertrophy by protein arginine methyltransferase 5.
J. Biol. Chem.
PUBLISHED: 07-10-2014
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Protein arginine methyltransferase 5 (PRMT5), a protein arginine methyltransferase that catalyzes the symmetrical dimethylation of arginine residues within target proteins, has been implicated in many essential cellular processes ranging from the regulation of gene expression to cell proliferation and differentiation. PRMT5 is highly expressed in the heart; the functional role of PRMT5 in the heart, however, remains largely elusive. In the present study, we show that PRMT5 specifically interacts with GATA4 in both co-transfected HEK293T cells and neonatal rat cardiomyocytes by co-immunoprecipitation. Importantly, this interaction leads to the arginine methylation of GATA4 at positions of 229, 265, and 317, which leads to an inhibition of the GATA4 transcriptional activity, predominantly through blocking the p300-mediated acetylation of GATA4 in cardiomyocytes. Moreover, overexpression of PRMT5 substantially inhibited the acetylation of GATA4 and cardiac hypertrophic responses in phenylephrine-stimulated cardiomyocytes, whereas knockdown of PRMT5 induced GATA4 activation and cardiomyocyte hypertrophy. Furthermore, in response to phenylephrine stimulation, PRMT5 translocates into the cytoplasm, thus relieving its repression on GATA4 activity in the nucleus and leading to hypertrophic gene expression in cardiomyocytes. These findings indicate that PRMT5 is an essential regulator of myocardial hypertrophic signaling and suggest that strategies aimed at activating PRMT5 in the heart may represent a potential therapeutic approach for the prevention of cardiac hypertrophy and heart failure.
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Biological characteristics and resistance analysis of the novel fungicide SYP-1620 against Botrytis cinerea.
Pestic Biochem Physiol
PUBLISHED: 07-08-2014
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SYP-1620, a quinone-outside-inhibitor (QoI), is a novel broad-spectrum fungicide. In this study, 108 isolates of Botrytis cinerea from different geographical regions in Jiangsu Province of China were characterized for baseline sensitivity to SYP-1620. The curves of baseline sensitivity were unimodal with a mean EC50 value of 0.0130±0.0109 ?g/mL for mycelial growth, 0.01147±0.0062 ?g/mL for spore germination, respectively. The biological characterization of SYP-1620 against B. cinerea was determined in vitro. The results indicated that SYP-1620 has a strong inhibiting effect on spore germination, mycelial growth, and respiration. The protective and curative test of SYP-1620 suggested that protective effect was better than curative either on strawberry leaves or on cucumber leaves in vivo. In addition, the biological characterization of SYP-1620-resistant mutants of B. cinerea was investigated. SYP-1620 has no cross-resistance with other types of fungicide. Compared to the sensitive isolates, the resistant mutants had lower mycelial growth and virulence but not differ in mycelial dry weight. Sequencing indicated that SYP-1620 resistance was associated with a single point mutation (G143A) in the cytochrome b gene.
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Dt2 is a gain-of-function MADS-domain factor gene that specifies semideterminacy in soybean.
Plant Cell
PUBLISHED: 07-08-2014
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Similar to Arabidopsis thaliana, the wild soybeans (Glycine soja) and many cultivars exhibit indeterminate stem growth specified by the shoot identity gene Dt1, the functional counterpart of Arabidopsis TERMINAL FLOWER1 (TFL1). Mutations in TFL1 and Dt1 both result in the shoot apical meristem (SAM) switching from vegetative to reproductive state to initiate terminal flowering and thus produce determinate stems. A second soybean gene (Dt2) regulating stem growth was identified, which, in the presence of Dt1, produces semideterminate plants with terminal racemes similar to those observed in determinate plants. Here, we report positional cloning and characterization of Dt2, a dominant MADS domain factor gene classified into the APETALA1/SQUAMOSA (AP1/SQUA) subfamily that includes floral meristem (FM) identity genes AP1, FUL, and CAL in Arabidopsis. Unlike AP1, whose expression is limited to FMs in which the expression of TFL1 is repressed, Dt2 appears to repress the expression of Dt1 in the SAMs to promote early conversion of the SAMs into reproductive inflorescences. Given that Dt2 is not the gene most closely related to AP1 and that semideterminacy is rarely seen in wild soybeans, Dt2 appears to be a recent gain-of-function mutation, which has modified the genetic pathways determining the stem growth habit in soybean.
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MicroRNA-7 directly targets insulin-like growth factor 1 receptor to inhibit cellular growth and glucose metabolism in gliomas.
Diagn Pathol
PUBLISHED: 07-07-2014
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BackgroundRecent studies observed that altered energy metabolism has become widespread in cancer cells along with other cancer-associated traits that have been accepted as hallmarks of cancer. Akt signaling pathway is involved in the aerobic glycolysis program. However, mechanisms underlying the regulation of aerobic glycolysis and Akt activity in gliomas remain unclear. MicroRNAs are a group of small non-coding RNAs that can function as endogenous RNA interference to regulate expression of targeted genes. This study was conducted to detect the function of miR-7 targeting insulin-like growth factor 1 receptor (IGF-1R), which is an upstream regulator of Akt.MethodsMicroRNA expression data for gliomas and normal controls were downloaded from The Cancer Genome Atlas (TCGA) database. Quantitative real-time PCR was used to measure the microRNA-7 (miR-7) expression level, and Western blot was performed to detect protein expression in U87 and U251 cells. Colony formation assay and glycolysis stress test were also conducted. Luciferase reporter assay was used to identify the mechanism of IGF-1R and miR-7 regulation.ResultsmiR-7 was downregulated in human glioma tissues based on TCGA database. Forced expression of miR-7 or IGF-1R knockdown inhibited colony formation and glucose metabolic capabilities of glioma cells in vitro and decreased the p-Akt expression level. Bioinformatics analysis results indicated that IGF-1R could be a target of miR-7. Western blot and luciferase reporter assays showed that miR-7 modulated IGF-1R expression by directly targeting the binding site within the 3¿-untranslated region.ConclusionsThis study provides the first evidence that miR-7 inhibits cellular growth and glucose metabolism in gliomas, at least partially, by regulating the IGF-1R/Akt signaling pathway. Therefore, miR-7 is a promising molecular drug for glioma treatment.Virtual SlidesThe virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/13000_2014_211.
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Activity of a novel strobilurin fungicide benzothiostrobin against Sclerotinia sclerotiorum.
Pestic Biochem Physiol
PUBLISHED: 07-04-2014
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Benzothiostrobin is a novel strobilurin fungicide. In this study, baseline sensitivity of Sclerotinia sclerotiorum (Lib.) de Bary to benzothiostrobin was determined using 100 strains collected during 2012 and 2013 from different geographical regions in Jiangsu Province of China, and the average EC50 value was 0.0218 (±0.0111)?g/mL for mycelial growth. After benzothiostrobin treatment, hyphae were contorted with offshoot of top increasing and cell membrane permeability increased markedly, while sclerotial production and oxalic acid content significantly decreased. Benzothiostrobin strongly inhibited mycelial respiration within 12h and the oxygen consumption of the mycelia could not be inhibited after 24h. On detached rapeseed leaves, the protective and curative activity test of benzothiostrobin suggested that benzothiostrobin had good control efficiency against S. sclerotiorum, and protective activity was better than curative activity. These results will contribute to us evaluating the potential of the new strobilurin fungicide benzothiostrobin for management of diseases caused by S. sclerotiorum and understanding the mode of action of benzothiostrobin against S. sclerotiorum.
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Orphan nuclear receptor Nur77 is a novel negative regulator of endothelin-1 expression in vascular endothelial cells.
J. Mol. Cell. Cardiol.
PUBLISHED: 07-02-2014
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Endothelin-1 (ET-1) produced by vascular endothelial cells plays essential roles in the regulation of vascular tone and development of cardiovascular diseases. The objective of this study is to identify novel regulators implicated in the regulation of ET-1 expression in vascular endothelial cells (ECs). By using quantitative real-time PCR (qRT-PCR) and enzyme-linked immunosorbent assay (ELISA), we show that either ectopic expression of orphan nuclear receptor Nur77 or pharmacological activation of Nur77 by 6-mercaptopurine (6-MP) substantially inhibits ET-1 expression in human umbilical vein endothelial cells (HUVECs), under both basal and thrombin-stimulated conditions. Furthermore, thrombin-stimulated ET expression is significantly augmented in both Nur77 knockdown ECs and aort from Nur77 knockout mice, suggesting that Nur77 is a negative regulator of ET-1 expression. Inhibition of ET-1 expression by Nur77 occurs at gene transcriptional levels, since Nur77 potently inhibits ET-1 promoter activity, without affecting ET-1 mRNA stability. As shown in electrophoretic mobility shift assay (EMSA), Nur77 overexpression markedly inhibits both basal and thrombin-stimulated transcriptional activity of AP-1. Mechanistically, we demonstrate that Nur77 specially interacts with c-Jun and inhibits AP-1 dependent c-Jun promoter activity, which leads to a decreased expression of c-Jun, a critical component involved in both AP-1 transcriptional activity and ET-1 expression in ECs. These findings demonstrate that Nur77 is a novel negative regulator of ET-1 expression in vascular ECs through an inhibitory interaction with the c-Jun/AP-1 pathway. Activation of Nur77 may represent a useful therapeutic strategy for preventing certain cardiovascular diseases, such as atherosclerosis and pulmonary artery hypertension.
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De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits.
Nat. Biotechnol.
PUBLISHED: 07-02-2014
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Wild relatives of crops are an important source of genetic diversity for agriculture, but their gene repertoire remains largely unexplored. We report the establishment and analysis of a pan-genome of Glycine soja, the wild relative of cultivated soybean Glycine max, by sequencing and de novo assembly of seven phylogenetically and geographically representative accessions. Intergenomic comparisons identified lineage-specific genes and genes with copy number variation or large-effect mutations, some of which show evidence of positive selection and may contribute to variation of agronomic traits such as biotic resistance, seed composition, flowering and maturity time, organ size and final biomass. Approximately 80% of the pan-genome was present in all seven accessions (core), whereas the rest was dispensable and exhibited greater variation than the core genome, perhaps reflecting a role in adaptation to diverse environments. This work will facilitate the harnessing of untapped genetic diversity from wild soybean for enhancement of elite cultivars.
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Identifying hierarchical and overlapping protein complexes based on essential protein-protein interactions and "seed-expanding" method.
Biomed Res Int
PUBLISHED: 06-30-2014
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Many evidences have demonstrated that protein complexes are overlapping and hierarchically organized in PPI networks. Meanwhile, the large size of PPI network wants complex detection methods have low time complexity. Up to now, few methods can identify overlapping and hierarchical protein complexes in a PPI network quickly. In this paper, a novel method, called MCSE, is proposed based on ?-module and "seed-expanding." First, it chooses seeds as essential PPIs or edges with high edge clustering values. Then, it identifies protein complexes by expanding each seed to a ?-module. MCSE is suitable for large PPI networks because of its low time complexity. MCSE can identify overlapping protein complexes naturally because a protein can be visited by different seeds. MCSE uses the parameter ?_th to control the range of seed expanding and can detect a hierarchical organization of protein complexes by tuning the value of ?_th. Experimental results of S. cerevisiae show that this hierarchical organization is similar to that of known complexes in MIPS database. The experimental results also show that MCSE outperforms other previous competing algorithms, such as CPM, CMC, Core-Attachment, Dpclus, HC-PIN, MCL, and NFC, in terms of the functional enrichment and matching with known protein complexes.
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Targets and molecular mechanisms of triptolide in cancer therapy.
Chin. J. Cancer Res.
PUBLISHED: 05-29-2014
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Triptolide (TPL/TL) is a natural drug with novel anticancer effects. Preclinical studies indicated that TPL inhibits cell proliferation, induces cell apoptosis, inhibits tumor metastasis and enhances the effect of other therapeutic methods in various cancer cell lines. Multiple molecules and signaling pathways, such as caspases, heat-shock proteins, NF-?B, and deoxyribonucleic acid (DNA) repair-associated factors, are associated with the anti-cancer effect. TPL also improves chemoradiosensitivity in cancer therapy. Phase I trials indicate the potential clinical value of TPL use. However, further trials with larger sample sizes are needed to confirm these results.
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Prioritization of orphan disease-causing genes using topological feature and GO similarity between proteins in interaction networks.
Sci China Life Sci
PUBLISHED: 05-23-2014
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Identification of disease-causing genes among a large number of candidates is a fundamental challenge in human disease studies. However, it is still time-consuming and laborious to determine the real disease-causing genes by biological experiments. With the advances of the high-throughput techniques, a large number of protein-protein interactions have been produced. Therefore, to address this issue, several methods based on protein interaction network have been proposed. In this paper, we propose a shortest path-based algorithm, named SPranker, to prioritize disease-causing genes in protein interaction networks. Considering the fact that diseases with similar phenotypes are generally caused by functionally related genes, we further propose an improved algorithm SPGOranker by integrating the semantic similarity of GO annotations. SPGOranker not only considers the topological similarity between protein pairs in a protein interaction network but also takes their functional similarity into account. The proposed algorithms SPranker and SPGOranker were applied to 1598 known orphan disease-causing genes from 172 orphan diseases and compared with three state-of-the-art approaches, ICN, VS and RWR. The experimental results show that SPranker and SPGOranker outperform ICN, VS, and RWR for the prioritization of orphan disease-causing genes. Importantly, for the case study of severe combined immunodeficiency, SPranker and SPGOranker predict several novel causal genes.
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Melittin enhances radiosensitivity of hypoxic head and neck squamous cell carcinoma by suppressing HIF-1?.
Tumour Biol.
PUBLISHED: 05-22-2014
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Hypoxia is a widespread phenomenon present in many human solid tumors and is associated with a poor prognosis and therapy resistance. Here, we tested the feasibility of melittin, a major component of bee venom, on radiosensitization of hypoxic head and neck squamous cell carcinoma (HNSCC). CNE-2 and KB cells were treated with melittin and radiation response was determined. Cell viability, cytotoxicity and apoptosis induction were examined by CCK-8 assay, colony formation assay, and flow cytometry. Expression of hypoxia-inducible factor 1-alpha (HIF-1?) and vascular endothelial growth factor (VEGF) proteins were assessed using western blotting. Additionally, we also examined the effect of melittin on tumor growth and radiosensitivity in vivo using a xenograft model of HNSCC. Treatment with melittin resulted in cell growth inhibition, induction of cell apoptosis, and reduction of HIF-1? and VEGF expression, which has been linked to hypoxia cell radioresistance. In addition, intraperitoneal injection of melittin significantly reduced the growth of HNSCC tumors in CNE-2 tumor-bearing mice. These data suggest that melittin enhances radiosensitivity of HNSCC under hypoxia condition, and this is associated with the suppression of HIF-1? expression. Melittin appears to be a potential radiotherapy sensitization agent due to its significant antihypoxia activity.
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Disease gene identification by using graph kernels and Markov random fields.
Sci China Life Sci
PUBLISHED: 05-21-2014
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Genes associated with similar diseases are often functionally related. This principle is largely supported by many biological data sources, such as disease phenotype similarities, protein complexes, protein-protein interactions, pathways and gene expression profiles. Integrating multiple types of biological data is an effective method to identify disease genes for many genetic diseases. To capture the gene-disease associations based on biological networks, a kernel-based MRF method is proposed by combining graph kernels and the Markov random field (MRF) method. In the proposed method, three kinds of kernels are employed to describe the overall relationships of vertices in five biological networks, respectively, and a novel weighted MRF method is developed to integrate those data. In addition, an improved Gibbs sampling procedure and a novel parameter estimation method are proposed to generate predictions from the kernel-based MRF method. Numerical experiments are carried out by integrating known gene-disease associations, protein complexes, protein-protein interactions, pathways and gene expression profiles. The proposed kernel-based MRF method is evaluated by the leave-one-out cross validation paradigm, achieving an AUC score of 0.771 when integrating all those biological data in our experiments, which indicates that our proposed method is very promising compared with many existing methods.
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Predicting protein functions by using unbalanced bi-random walk algorithm on protein-protein interaction network and functional interrelationship network.
Curr. Protein Pept. Sci.
PUBLISHED: 05-07-2014
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Accurate annotation of protein functions is still a big challenge for understanding life in the post-genomic era. Recently, some methods have been developed to solve the problem by incorporating functional similarity of GO terms into protein-protein interaction (PPI) network, which are based on the observation that a protein tends to share some common functions with proteins that interact with it in PPI network, and two similar GO terms in functional interrelationship network usually co-annotate some common proteins. However, these methods annotate functions of proteins by considering at the same level neighbors of proteins and GO terms respectively, and few attempts have been made to investigate their difference. Given the topological and structural difference between PPI network and functional interrelationship network, we firstly investigate at which level neighbors of proteins tend to have functional associations and at which level neighbors of GO terms usually co-annotate some common proteins. Then, an unbalanced Bi-random walk (UBiRW) algorithm which iteratively walks different number of steps in the two networks is adopted to find protein-GO term associations according to some known associations. Experiments are carried out on S. cerevisiae data. The results show that our method achieves better prediction performance not only than methods that only use PPI network data, but also than methods that consider at the same level neighbors of proteins and of GO terms.
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Rheological characterization of cataplasm bases composed of cross-linked partially neutralized polyacrylate hydrogel.
AAPS PharmSciTech
PUBLISHED: 05-07-2014
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Viscoelasticity is a useful parameter for characterizing the intrinsic properties of the cross-linked polyacrylate hydrogel used in cataplasm bases. The aim of this study was to investigate the effects of various formulation parameters on the rheological characteristics of polyacrylate hydrogel. The hydrogel layers were formed using a partially neutralized polyacrylate (Viscomate(™)), which contained acrylic acid and sodium acrylate in different copolymerization ratios, as the cross-linked gel framework. Dihydroxyaluminum aminoacetate (DAAA), which produces aluminum ions, was used as the cross-linking agent. Rheological analyses were performed using a "stress amplitude sweep" and a "frequency sweep". The results showed that greater amounts of acrylic acid in the structure of Viscomate as well as higher concentrations of DAAA and Viscomate led to an increase in the elastic modulus (G'). However, greater amounts of acrylic acid in the structure of Viscomate and higher concentrations of DAAA had an opposite on the viscous modulus (G?); this might be owing to higher steric hindrance. The results of this study can serve as guidelines for the optimization of formulations for cataplasms.
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STAT3 inhibitor NSC74859 radiosensitizes esophageal cancer via the downregulation of HIF-1?.
Tumour Biol.
PUBLISHED: 04-27-2014
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Radiotherapy is the main therapy for inoperable and locally advanced esophageal squamous cell carcinoma (ESCC). However, radioresistance in ESCC remains a challenge. The aim of this study is to investigate the radiosensitizing effects of STAT3 inhibitor NSC74859 on ESCC and explore the underlying mechanisms. ECA109 and TE13 cells were exposed to hypoxia, and treated with NSC74859 or radiation, alone or in combination. Cell proliferation, survival, apoptosis, and double-stranded DNA breaks (DSBs) were examined. Nude mice model of ECA109 xenograft was treated with radiation and/or NSC74859. The levels of STAT3, p-STAT3, HIF-1?, and VEGF were detected by Western blot analysis. NSC74859 efficiently radiosensitized ESCC cells and xenografts in nude mice, and inhibited hypoxia-/radiation-induced activation of STAT3 and upregulation of HIF-1? and VEGF expression. NSC74859 confers radiosensitivity in ESCC via the inhibition of STAT3 activation and the downregulation of HIF-1? and VEGF expression. NSC74859 may become a promising radiosensitizer for ESCC radiotherapy.
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The Brassica oleracea genome reveals the asymmetrical evolution of polyploid genomes.
Nat Commun
PUBLISHED: 04-22-2014
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Polyploidization has provided much genetic variation for plant adaptive evolution, but the mechanisms by which the molecular evolution of polyploid genomes establishes genetic architecture underlying species differentiation are unclear. Brassica is an ideal model to increase knowledge of polyploid evolution. Here we describe a draft genome sequence of Brassica oleracea, comparing it with that of its sister species B. rapa to reveal numerous chromosome rearrangements and asymmetrical gene loss in duplicated genomic blocks, asymmetrical amplification of transposable elements, differential gene co-retention for specific pathways and variation in gene expression, including alternative splicing, among a large number of paralogous and orthologous genes. Genes related to the production of anticancer phytochemicals and morphological variations illustrate consequences of genome duplication and gene divergence, imparting biochemical and morphological variation to B. oleracea. This study provides insights into Brassica genome evolution and will underpin research into the many important crops in this genus.
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CPP Mediated Insulin Delivery: Current Status and Promising Future.
Curr Pharm Biotechnol
PUBLISHED: 04-19-2014
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A variety of methods including penetrating enhancers, enzyme inhibitors, as well as cargo mediated drug delivery have been explored to improve the intolerance of parenteral administrated insulin, but little success has been achieved so far. Under this background, cell penetrating peptides (CPPs), with their ability to enhance transport efficiency of macromolecular drugs have been demonstrated to be able to increase insulin bioavailability (BA) in a number of studies, of which a BA up to 50.7% relative to subcutaneously administered insulin could be achieved by nasal route under optimal conditions. Furthermore, CPPs could be conveniently formulated with insulin, or be grafted onto drug-loaded cargoes to facilitate the cargo mediated insulin delivery. Here we reviewed the recent achievements on CPP-mediated insulin transport, and outlined various CPP-based delivery strategies which are expected to show potential in clinical translation in the future.
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Haploinsufficiency of an RB-E2F1-Condensin II complex leads to aberrant replication and aneuploidy.
Cancer Discov
PUBLISHED: 04-16-2014
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Genome instability is a characteristic of malignant cells; however, evidence for its contribution to tumorigenesis has been enigmatic. In this study, we demonstrate that the retinoblastoma protein, E2F1, and Condensin II localize to discrete genomic locations including major satellite repeats at pericentromeres. In the absence of this complex, aberrant replication ensues followed by defective chromosome segregation in mitosis. Surprisingly, loss of even one copy of the retinoblastoma gene reduced recruitment of Condensin II to pericentromeres and caused this phenotype. Using cancer genome data and gene-targeted mice, we demonstrate that mutation of one copy of RB1 is associated with chromosome copy-number variation in cancer. Our study connects DNA replication and chromosome structure defects with aneuploidy through a dosage-sensitive complex at pericentromeric repeats.
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Transittability of complex networks and its applications to regulatory biomolecular networks.
Sci Rep
PUBLISHED: 04-09-2014
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We have often observed unexpected state transitions of complex systems. We are thus interested in how to steer a complex system from an unexpected state to a desired state. Here we introduce the concept of transittability of complex networks, and derive a new sufficient and necessary condition for state transittability which can be efficiently verified. We define the steering kernel as a minimal set of steering nodes to which control signals must directly be applied for transition between two specific states of a network, and propose a graph-theoretic algorithm to identify the steering kernel of a network for transition between two specific states. We applied our algorithm to 27 real complex networks, finding that sizes of steering kernels required for transittability are much less than those for complete controllability. Furthermore, applications to regulatory biomolecular networks not only validated our method but also identified the steering kernel for their phenotype transitions.
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Ginsenoside Rg3 enhances radiosensitization of hypoxic oesophageal cancer cell lines through vascular endothelial growth factor and hypoxia inducible factor 1?
J. Int. Med. Res.
PUBLISHED: 04-01-2014
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To determine if the pretreatment of hypoxic human oesophageal carcinoma cell lines (EC109, TE1 and KYSE170) with ginsenoside Rg3 (Rg3) increases their radiosensitivity to X-rays.
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Berberine inhibits the expression of hypoxia induction factor-1alpha and increases the radiosensitivity of prostate cancer.
Diagn Pathol
PUBLISHED: 03-24-2014
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The radiation resistance of prostate cancer remains the primary obstacle to improve patient survival. This study aimed to investigate the effects of berberine, a commonly used natural product, on the radiosensitivity of prostate cancer.
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Expression of microRNA-454 in TGF-?1-stimulated hepatic stellate cells and in mouse livers infected with Schistosoma japonicum.
Parasit Vectors
PUBLISHED: 03-17-2014
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In the process of hepatic fibrosis, hepatic stellate cells (HSCs) can be activated by many inflammatory cytokines. The transforming growth factor-?1 (TGF-?1) is one of the main profibrogenic mediators. Recently, some studies have also shown that microRNAs (miRNAs) play essential roles in the progress of liver fibrosis by being involved in the differentiation, fat metabolism and ECM production of HSCs.
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Improving protein function prediction using domain and protein complexes in PPI networks.
BMC Syst Biol
PUBLISHED: 03-14-2014
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Characterization of unknown proteins through computational approaches is one of the most challenging problems in silico biology, which has attracted world-wide interests and great efforts. There have been some computational methods proposed to address this problem, which are either based on homology mapping or in the context of protein interaction networks.
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SchA-p85-FAK complex dictates isoform-specific activation of Akt2 and subsequent PCBP1-mediated post-transcriptional regulation of TGF?-mediated epithelial to mesenchymal transition in human lung cancer cell line A549.
Tumour Biol.
PUBLISHED: 03-11-2014
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A post-transcriptional pathway by which TGF-? modulates expression of specific proteins, Disabled-2 (Dab2) and Interleukin-like EMT Inducer (ILEI), inherent to epithelial to mesenchymal transition (EMT) in murine epithelial cells through Akt2-mediated phosphorylation of poly r(C) binding protein (PCBP1), has been previously elucidated. The aims of the current study were to determine if the same mechanism is operative in the non-small cell lung cancer (NSCLC) cell line, A549, and to delineate the underlying mechanism. Steady-state transcript and protein expression levels of Dab2 and ILEI were examined in A549 cells treated with TGF-? for up to 48 h. Induction of translational de-repression in this model was quantified by polysomal fractionation followed by qRT-PCR. The underlying mechanism of isoform-specific activation of Akt2 was elucidated through a combination of co-immunoprecipitation studies. TGF-? induced EMT in A549 cells concomitant with translational upregulation of Dab2 and ILEI proteins through isoform-specific activation of Akt2 followed by phosphorylation of PCBP1 at serine-43. Our experiments further elucidated that the adaptor protein SchA is phosphorylated at tyrosine residues following TGF-? treatment, which initiated a signaling cascade resulting in the sequential recruitment of p85 subunit of PI3K and focal adhesion kinase (FAK). The SchA-FAK-p85 complex subsequently selectively recruited and activated Akt2, not Akt1. Inhibition of the p85 subunit through phosphorylated 1257 peptide completely attenuated EMT in these cells. We have defined the underlying mechanism responsible for isoform-specific recruitment and activation of Akt2, not Akt1, during TGF-?-mediated EMT in A549 cells. Inhibition of the formation of this complex thus represents an important and novel therapeutic target in metastatic lung carcinoma.
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Structural and biochemical insights into the V/I505T mutation found in the EIAV gp45 vaccine strain.
Retrovirology
PUBLISHED: 03-10-2014
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The equine infectious anemia virus (EIAV) is a lentivirus of the Retrovirus family, which causes persistent infection in horses often characterized by recurrent episodes of high fever. It has a similar morphology and life cycle to the human immunodeficiency virus (HIV). Its transmembrane glycoprotein, gp45 (analogous to gp41 in HIV), mediates membrane fusion during the infection. However, the post-fusion conformation of EIAV gp45 has not yet been determined. EIAV is the first member of the lentiviruses for which an effective vaccine has been successfully developed. The attenuated vaccine strain, FDDV, has been produced from a pathogenic strain by a series of passages in donkey dermal cells. We have previously reported that a V/I505T mutation in gp45, in combination with other mutations in gp90, may potentially contribute to the success of the vaccine strain. To this end, we now report on our structural and biochemical studies of the gp45 protein from both wide type and vaccine strain, providing a valuable structural model for the advancement of the EIAV vaccine.
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Porous nanoapatite scaffolds synthesized using an approach of interfacial mineralization reaction and their bioactivity.
J. Biomed. Mater. Res. Part B Appl. Biomater.
PUBLISHED: 03-06-2014
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There is a growing interest in the use of calcium phosphate, used to fabricate porous scaffolds for bone tissue regeneration and repair. However, it is difficult to obtain interconnected pores with very high porosity and to engineer the topography of the pore walls for calcium phosphate ceramic scaffolds. In this study, a novelty method interfacial mineralization reaction was used to fabricate porous nano-calcium phosphate ceramic scaffolds with three-dimensional surface topography of walls, which was tuned using different surfactants; using this method, porous scaffolds with different shapes were obtained, which demonstrates that interfacial mineralization reaction is not only a good method to prepare porous ceramic scaffolds of calcium phosphate but also an efficient approach to engineer the topography of the pore walls. The as-prepared porous ceramic scaffolds have also been proved to have good biocompatibility, bioactivity, and biodegradability, which are necessary for the clinical application. In vivo experimental results revealed that not only osteoconduction but also osteoinduction was responsible for the bone formation in our scaffolds, which accelerated the formation of new bone, and that the degradation process of our porous scaffolds could match osteoinduction, mineralization of matrix and bone, and reconstruction of new bone very well, and porous scaffolds could be completely substituted by the new bone.
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A novel algorithm for detecting protein complexes with the breadth first search.
Biomed Res Int
PUBLISHED: 01-27-2014
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Most biological processes are carried out by protein complexes. A substantial number of false positives of the protein-protein interaction (PPI) data can compromise the utility of the datasets for complexes reconstruction. In order to reduce the impact of such discrepancies, a number of data integration and affinity scoring schemes have been devised. The methods encode the reliabilities (confidence) of physical interactions between pairs of proteins. The challenge now is to identify novel and meaningful protein complexes from the weighted PPI network. To address this problem, a novel protein complex mining algorithm ClusterBFS (Cluster with Breadth-First Search) is proposed. Based on the weighted density, ClusterBFS detects protein complexes of the weighted network by the breadth first search algorithm, which originates from a given seed protein used as starting-point. The experimental results show that ClusterBFS performs significantly better than the other computational approaches in terms of the identification of protein complexes.
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Identifying dynamic protein complexes based on gene expression profiles and PPI networks.
Biomed Res Int
PUBLISHED: 01-25-2014
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Identification of protein complexes from protein-protein interaction networks has become a key problem for understanding cellular life in postgenomic era. Many computational methods have been proposed for identifying protein complexes. Up to now, the existing computational methods are mostly applied on static PPI networks. However, proteins and their interactions are dynamic in reality. Identifying dynamic protein complexes is more meaningful and challenging. In this paper, a novel algorithm, named DPC, is proposed to identify dynamic protein complexes by integrating PPI data and gene expression profiles. According to Core-Attachment assumption, these proteins which are always active in the molecular cycle are regarded as core proteins. The protein-complex cores are identified from these always active proteins by detecting dense subgraphs. Final protein complexes are extended from the protein-complex cores by adding attachments based on a topological character of "closeness" and dynamic meaning. The protein complexes produced by our algorithm DPC contain two parts: static core expressed in all the molecular cycle and dynamic attachments short-lived. The proposed algorithm DPC was applied on the data of Saccharomyces cerevisiae and the experimental results show that DPC outperforms CMC, MCL, SPICi, HC-PIN, COACH, and Core-Attachment based on the validation of matching with known complexes and hF-measures.
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Effective identification of essential proteins based on priori knowledge, network topology and gene expressions.
Methods
PUBLISHED: 01-16-2014
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Identification of essential proteins is very important for understanding the minimal requirements for cellular life and also necessary for a series of practical applications, such as drug design. With the advances in high throughput technologies, a large number of protein-protein interactions are available, which makes it possible to detect proteins' essentialities from the network level. Considering that most species already have a number of known essential proteins, we proposed a new priori knowledge-based scheme to discover new essential proteins from protein interaction networks. Based on the new scheme, two essential protein discovery algorithms, CPPK and CEPPK, were developed. CPPK predicts new essential proteins based on network topology and CEPPK detects new essential proteins by integrating network topology and gene expressions. The performances of CPPK and CEPPK were validated based on the protein interaction network of Saccharomyces cerevisiae. The experimental results showed that the priori knowledge of known essential proteins was effective for improving the predicted precision. The predicted precisions of CPPK and CEPPK clearly exceeded that of the other 10 previously proposed essential protein discovery methods: Degree Centrality (DC), Betweenness Centrality (BC), Closeness Centrality (CC), Subgraph Centrality (SC), Eigenvector Centrality (EC), Information Centrality (IC), Bottle Neck (BN), Density of Maximum Neighborhood Component (DMNC), Local Average Connectivity-based method (LAC), and Network Centrality (NC). Especially, CPPK achieved 40% improvement in precision over BC, CC, SC, EC, and BN, and CEPPK performed even better. CEPPK was also compared to four other methods (EPC, ORFL, PeC, and CoEWC) which were not node centralities and CEPPK was showed to achieve the best results.
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Expression and prognostic significance of p21-activated kinase 6 in hepatocellular carcinoma.
J. Surg. Res.
PUBLISHED: 01-15-2014
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p21-activated protein kinase (PAK) 6 is a serine-threonine kinase belonging to the PAK family. Previous studies have indicated that abnormal expressions of PAK1, PAK2, and PAK5 played critical roles in hepatocellular carcinoma (HCC). Recent studies suggested that deregulation of PAK6 expression played an important role in oncogenesis. To explore the potential roles of PAK6 in HCC, expression of PAK6 was detected in human HCC specimens.
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Molecular response to the pathogen Phytophthora sojae among ten soybean near isogenic lines revealed by comparative transcriptomics.
BMC Genomics
PUBLISHED: 01-07-2014
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Phytophthora root and stem rot (PRR) of soybean, caused by Phytophthora sojae, is controlled by Rps genes. However, little is known regarding the Rps-induced molecular responses to P. sojae and how they actually overlap. We thus sequenced, analyzed, and compared the transcriptomes of 10 near isogenic lines (NILs), each with a unique Rps gene/allele, and the susceptible parent Williams, pre- and post-inoculation with the pathogen.
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Enhanced absorption and bioavailability of hydrochlorothiazide by Chinese medicines in the Zhenju antihypertensive compound.
J. Pharm. Pharmacol.
PUBLISHED: 01-07-2014
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This study was performed to investigate the influence of traditional Chinese medicines in the Zhenju antihypertensive compound (ZJAHC) on the oral absorption of hydrochlorothiazide (HCT) both in vitro and in vivo.
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Study of bilineage differentiation of human-bone-marrow-derived mesenchymal stem cells in oxidized sodium alginate/N-succinyl chitosan hydrogels and synergistic effects of RGD modification and low-intensity pulsed ultrasound.
Acta Biomater
PUBLISHED: 01-03-2014
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The level of formation of new bone and vascularization in bone tissue engineering scaffold implants is considered as a critical factor for clinical application. In this study, an approach using an RGD-grafted oxidized sodium alginate/N-succinyl chitosan (RGD-OSA/NSC) hydrogel as a scaffold and low-intensity pulsed ultrasound (LIPUS) as mechanical stimulation was proposed to achieve a high level of formation of new bone and vascularization. An in vitro study of endothelial and osteogenic differentiations of human-bone-marrow-derived mesenchymal stem cells (hMSCs) was conducted to evaluate it. The results showed that RGD-OSA/NSC composite hydrogels presented good biological properties in attachment, proliferation and differentiation of cells. The MTT cell viability assay showed that the total number of cells increased more significantly in the LIPUS-stimulated groups with RGD than that in the control ones; similar results were obtained for alkaline phosphatase activity/staining and mineralized nodule formation assay of osteogenic induction and immunohistochemical test of endothelial induction. The positive synergistic effect of LIPUS and RGD on the enhancement of proliferation and differentiation of hMSCs was observed. These findings suggest that the hybrid use of RGD modification and LIPUS might provide one approach to achieve a high level of formation of new bone and vascularization in bone tissue engineering scaffold implants.
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Anatomical analysis on the lateral bone window of the sella turcica: a study on 530 adult dry skull base specimens.
Int J Med Sci
PUBLISHED: 01-01-2014
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To investigate the morphometric characteristics of the lateral bone window (LBW) of the sella turica.
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Computational approaches to predicting essential proteins: a survey.
Proteomics Clin Appl
PUBLISHED: 12-16-2013
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Essential proteins are indispensable to support cellular life. Identifying essential proteins can help us understand the minimal requirements for cell survival, which plays a significant role in the emerging field of synthetic biology. Moreover, essential proteins also serve as candidates of drug targets for developing novel therapy of diseases, such as cancer or infectious disease caused by emerging pathogens. However, it is expensive and time consuming to experimentally identify essential proteins. With accumulation of sequenced genomes, the gap between genome-wide essential protein data and sequence data become increasingly wide. Thus, computational approaches for detecting essential proteins are useful complements to limited experimental methods. There are many features related to protein essentiality. By taking advantage of these features, many computational approaches have been proposed to identify essential proteins. In this paper, we review the state-of-the-art techniques for computational detection of essential proteins, and discuss some challenges for future research in this field.
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Berberine radiosensitizes human nasopharyngeal carcinoma by suppressing hypoxia-inducible factor-1? expression.
Acta Otolaryngol.
PUBLISHED: 12-10-2013
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Abstract Conclusion: Berberine confers radiosensitivity on nasopharyngeal carcinoma (NPC) and this is associated with the down-regulation of hypoxia-inducible factor-1? (HIF-1?) and vascular endothelial growth factor (VEGF) expression. Berberine could be a promising radiosensitizer for NPC radiotherapy. Objectives: NPC has a poor prognosis. Radiotherapy as first-line therapy significantly increases patient survival but radioresistance is a problem. This study aimed to investigate the radiosensitizing effects of berberine on NPC and explore the underlying mechanisms. Methods: CNE-1 and CNE-2 cells were exposed to hypoxia and treated with berberine at different concentrations. The MTT assay, clonogenic assay, and flow cytometry were performed to analyze cell proliferation, colony formation, and apoptosis. The expression of HIF-1? and VEGF was assessed by Western blot and immunofluorescence analysis. Male nude mice inoculated subcutaneously with CNE-2 cells were used to examine the sensitizing effects of berberine in vivo. Results: Berberine efficiently radiosensitized NPC cells and xenografts in mice, and inhibited hypoxia/radiation-induced up-regulation of HIF-1? and VEGF expression.
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Diagnosis of multiple primary lung cancer: A systematic review.
J. Int. Med. Res.
PUBLISHED: 11-23-2013
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A substantial percentage (8%) of all newly diagnosed cancer cases are in patients with previous tumours, with a similar trend in lung cancer. Cases of multiple primary lung cancer (MPLC) are increasing worldwide, due to improved diagnostic and surveillance mechanisms and the ageing population. Diagnosis of MPLC is complicated by difficulties in distinguishing it from lung cancer metastasis. Clinicopathological assessment, diagnosis and management have evolved, but remain severely limited by the lack of robust and dependable molecular markers for the differential diagnosis of metastasis and MPLC. This systematic review evaluates diagnostic criteria for MPLC, and the subsequent management and success rates. The incorporation of molecular biology techniques into the diagnostic process for MPLC is also discussed.
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Simple signal-to-signal beat interference cancellation receiver based on balanced detection for a single-sideband optical OFDM signal with a reduced guard band.
Opt Lett
PUBLISHED: 11-02-2013
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A simple signal-to-signal beat interference cancellation receiver based on balanced detection (ICRBD) with an interleaver, a 2×2 three-decibel optical coupler, and a balanced photodiode pair is proposed for a single-sideband optical orthogonal frequency division multiplexing (SSB-OOFDM) signal with a reduced guard band (GB). Simulation demonstration of the ICRBD for a 40 Gbit/s 16-QAM SSB-OOFDM signal with a reduced GB was achieved successfully.
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Prediction of essential proteins based on gene expression programming.
BMC Genomics
PUBLISHED: 10-01-2013
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Essential proteins are indispensable for cell survive. Identifying essential proteins is very important for improving our understanding the way of a cell working. There are various types of features related to the essentiality of proteins. Many methods have been proposed to combine some of them to predict essential proteins. However, it is still a big challenge for designing an effective method to predict them by integrating different features, and explaining how these selected features decide the essentiality of protein. Gene expression programming (GEP) is a learning algorithm and what it learns specifically is about relationships between variables in sets of data and then builds models to explain these relationships.
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Clustering based on multiple biological information: approach for predicting protein complexes.
IET Syst Biol
PUBLISHED: 09-27-2013
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Protein complexes are a cornerstone of many biological processes. Protein-protein interaction (PPI) data enable a number of computational methods for predicting protein complexes. However, the insufficiency of the PPI data significantly lowers the accuracy of computational methods. In the current work, the authors develop a novel method named clustering based on multiple biological information (CMBI) to discover protein complexes via the integration of multiple biological resources including gene expression profiles, essential protein information and PPI data. First, CMBI defines the functional similarity of each pair of interacting proteins based on the edge-clustering coefficient and the Pearson correlation coefficient. Second, CMBI selects essential proteins as seeds to build the protein complexes. A redundancy-filtering procedure is performed to eliminate redundant complexes. In addition to the essential proteins, CMBI also uses other proteins as seeds to expand protein complexes. To check the performance of CMBI, the authors compare the complexes discovered by CMBI with the ones found by other techniques by matching the predicted complexes against the reference complexes. The authors use subsequently GO::TermFinder to analyse the complexes predicted by various methods. Finally, the effect of parameters T and R is investigated. The results from GO functional enrichment and matching analyses show that CMBI performs significantly better than the state-of-the-art methods.
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Berberine enhances radiosensitivity of esophageal squamous cancer by targeting HIF-1? in vitro and in vivo.
Cancer Biol. Ther.
PUBLISHED: 09-12-2013
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Radiation therapy is an important treatment approach for esophageal squamous cell carcinoma (ESCC). However, how to promote radiation sensitivity in ESCC remains a challenge. This study aimed to evaluate the effects of berberine, a common used Chinese medicine, on the radiosensitivity of ESCC. ECSS cell line ECA109 and TE13 were subjected to hypoxia and/or ionizing radiation (IR), in the presence or absence of berberine treatment. Cell growth and survival, and apoptosis were evaluated. In addition, ECA109 cells were xenografted into nude mice and subjected to IR and/or berberine treatment. The expression of HIF-1? and VEGF was detected by western blot and immunohistochemical analysis. Our results showed that berberine increased radiosensitivity of ESCC cells and xenografts, and this was associated with the inhibition of HIF-1? and VEGF expression. These data suggest that berberine may be a potential radiotherapy sensitization drugs due to its significant anti-hypoxia activity.
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MicroRNA-663 regulates human vascular smooth muscle cell phenotypic switch and vascular neointimal formation.
Circ. Res.
PUBLISHED: 09-06-2013
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Abnormal phenotypic switch of vascular smooth muscle cell (VSMC) is a hallmark of vascular disorders such as atherosclerosis and restenosis after angioplasty. MicroRNAs (miRNAs) have emerged as important regulators for VSMC function, and we recently identified miR-663 as critical for controlling human aortic smooth muscle cell proliferation.
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Identification of genes expressed by immune cells of the colon that are regulated by colorectal cancer-associated variants.
Int. J. Cancer
PUBLISHED: 09-05-2013
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A locus on human chromosome 11q23 tagged by marker rs3802842 was associated with colorectal cancer (CRC) in a genome-wide association study; this finding has been replicated in case-control studies worldwide. In order to identify biologic factors at this locus that are related to the etiopathology of CRC, we used microarray-based target selection methods, coupled to next-generation sequencing, to study 103 kb at the 11q23 locus. We genotyped 369 putative variants from 1,030 patients with CRC (cases) and 1,061 individuals without CRC (controls) from the Ontario Familial Colorectal Cancer Registry. Two previously uncharacterized genes, COLCA1 and COLCA2, were found to be co-regulated genes that are transcribed from opposite strands. Expression levels of COLCA1 and COLCA2 transcripts correlate with rs3802842 genotypes. In colon tissues, COLCA1 co-localizes with crystalloid granules of eosinophils and granular organelles of mast cells, neutrophils, macrophages, dendritic cells and differentiated myeloid-derived cell lines. COLCA2 is present in the cytoplasm of normal epithelial, immune and other cell lineages, as well as tumor cells. Tissue microarray analysis demonstrates the association of rs3802842 with lymphocyte density in the lamina propria (p = 0.014) and levels of COLCA1 in the lamina propria (p = 0.00016) and COLCA2 (tumor cells, p = 0.0041 and lamina propria, p = 6 × 10(-5) ). In conclusion, genetic, expression and immunohistochemical data implicate COLCA1 and COLCA2 in the pathogenesis of colon cancer. Histologic analyses indicate the involvement of immune pathways.
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Smac mimetic compound LCL161 sensitizes esophageal carcinoma cells to radiotherapy by inhibiting the expression of inhibitor of apoptosis protein.
Tumour Biol.
PUBLISHED: 08-29-2013
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Currently, unresectable esophageal squamous cell carcinoma (ESCC) is primarily treated by chemoradiotherapy. However, the outcome has not improved significantly due to radioresistance of cancer cells. This study aimed to determine the radiosensitizing effect of LCL161, a novel second mitochondrial-derived activator of caspase (Smac) mimetic, in ESCC cells. ESCC cell lines were treated with LCL161 or radiation, alone or in combination. Cell proliferation was detected by MTT assay. Radiosensitization was evaluated by clonogenic survival assay. Cell apoptosis was detected by flow cytometry. The results showed that LCL161 potently sensitized ESCC cells to radiation with a sensitization enhancement ratio of 1.4-2.0. LCL161 increased radiation-induced DNA double-stranded breaks and promoted the apoptosis of ESCC cells, which could be abrogated by a pan-caspase inhibitor z-VAD-FMK. Furthermore, LCL161 decreased the level of cIAP1 in ESCC cells in a dose-dependent manner and synthesized with irradiation to promote the activation of caspase 8 and the upregulation of TNF? expression in ESCC cells. In conclusion, LCL161 acts as a strong radiosensitizer in human esophageal cancer cells by inhibiting the expression of cIAP1 and promoting the activation of caspase 8, leading to enhanced apoptosis.
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Mining featured patterns of MiRNA interaction based on sequence and structure similarity.
IEEE/ACM Trans Comput Biol Bioinform
PUBLISHED: 08-10-2013
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MicroRNA (miRNA) is an endogenous small noncoding RNA that plays an important role in gene expression through the post-transcriptional gene regulation pathways. There are many literature works focusing on predicting miRNA targets and exploring gene regulatory networks of miRNA families. We suggest, however, the study to identify the interaction between miRNAs is insufficient. This paper presents a framework to identify relationships between miRNAs using joint entropy, to investigate the regulatory features of miRNAs. Both the sequence and secondary structure are taken into consideration to make our method more relevant from the biological viewpoint. Further, joint entropy is applied to identify correlated miRNAs, which are more desirable from the perspective of the gene regulatory network. A data set including Drosophila melanogaster and Anopheles gambiae is used in the experiment. The results demonstrate that our approach is able to identify known miRNA interaction and uncover novel patterns of miRNA regulatory network.
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A model for family-based case-control studies of genetic imprinting and epistasis.
Brief. Bioinformatics
PUBLISHED: 07-24-2013
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Genetic imprinting, or called the parent-of-origin effect, has been recognized to play an important role in the formation and pathogenesis of human diseases. Although the epigenetic mechanisms that establish genetic imprinting have been a focus of many genetic studies, our knowledge about the number of imprinting genes and their chromosomal locations and interactions with other genes is still scarce, limiting precise inference of the genetic architecture of complex diseases. In this article, we present a statistical model for testing and estimating the effects of genetic imprinting on complex diseases using a commonly used case-control design with family structure. For each subject sampled from a case and control population, we not only genotype its own single nucleotide polymorphisms (SNPs) but also collect its parents genotypes. By tracing the transmission pattern of SNP alleles from parental to offspring generation, the model allows the characterization of genetic imprinting effects based on Pearson tests of a 2 × 2 contingency table. The model is expanded to test the interactions between imprinting effects and additive, dominant and epistatic effects in a complex web of genetic interactions. Statistical properties of the model are investigated, and its practical usefulness is validated by a real data analysis. The model will provide a useful tool for genome-wide association studies aimed to elucidate the picture of genetic control over complex human diseases.
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Construction and application of dynamic protein interaction network based on time course gene expression data.
Proteomics
PUBLISHED: 06-26-2013
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In recent years, researchers have tried to inject dynamic information into static protein interaction networks (PINs). The paper first proposes a three-sigma method to identify active time points of each protein in a cellular cycle, where three-sigma principle is used to compute an active threshold for each gene according to the characteristics of its expression curve. Then a dynamic protein interaction network (DPIN) is constructed, which includes the dynamic changes of protein interactions. To validate the efficiency of DPIN, MCL, CPM, and core attachment algorithms are applied on two different DPINs, the static PIN and the time course PIN (TC-PIN) to detect protein complexes. The performance of each algorithm on DPINs outperforms those on other networks in terms of matching with known complexes, sensitivity, specificity, f-measure, and accuracy. Furthermore, the statistics of three-sigma principle show that 23-45% proteins are active at a time point and most proteins are active in about half of cellular cycle. In addition, we find 94% essential proteins are in the group of proteins that are active at equal or great than 12 timepoints of GSE4987, which indicates the potential existence of feedback mechanisms that can stabilize the expression level of essential proteins and might provide a new insight for predicting essential proteins from dynamic protein networks.
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A novel porous bioceramics scaffold by accumulating hydroxyapatite spherulites for large bone tissue engineering in vivo. II. Construct large volume of bone grafts.
J Biomed Mater Res A
PUBLISHED: 06-05-2013
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In vivo engineering of bone autografts using bioceramic scaffolds with appropriate porous structures is a potential approach to prepare autologous bone grafts for the repair of critical-sized bone defects. This study investigated the evolutionary process of osteogenesis, angiogenesis, and compressive strength of bioceramic scaffolds implanted in two non-osseous sites of dogs: the abdominal cavity and the dorsal muscle. Hydroxyapatite (HA) sphere-accumulated scaffolds with controlled porous structures were prepared and placed in the two sites for up to 6 months. Analyses of retrieved scaffolds found that osteogenesis and angiogenesis were faster in scaffolds implanted in dorsal muscles compared with those placed in abdominal cavities. The abdominal cavity, however, can accommodate larger bone grafts with designed shape. Analyses of scaffolds implanted in abdominal cavities [an environment of a low mesenchymal stem cell (MSC) density] further demonstrated that angiogenesis play critical roles during osteogenesis in the scaffolds, presumably by supplying progenitor cells and/or MSCs as seed cells. This study also examined the relationship between the volume of bone grafts and the physiological environment of in vivo bioreactor. These results provide basic information for the selection of appropriate implanting sites and culture time required to engineer autologous bone grafts for the clinical bone defect repair. Based on these positive results, a pilot study has applied the grafts constructed in canine abdominal cavity to repair segmental bone defect in load-bearing sites (limbs). © 2013 Wiley Periodicals, Inc. J Biomed Mater Res Part A, 2013.
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Resveratrol attenuates radiation-induced salivary gland dysfunction in mice.
Laryngoscope
PUBLISHED: 06-04-2013
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In our study we investigated the radioprotective effect of resveratrol (RES) in a murine model of radiation-induced salivary gland dysfunction.
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A two-component histidine kinase Shk1 controls stress response, sclerotial formation and fungicide resistance in Sclerotinia sclerotiorum.
Mol. Plant Pathol.
PUBLISHED: 06-03-2013
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Fungal histidine kinases (HKs) are involved in osmotic and oxidative stress responses, hyphal development, fungicide sensitivity and virulence. Members of HK class III are known to signal through the high-osmolarity glycerol mitogen-activated protein kinase (HOG MAPK). In this study, we characterized the Shk1 gene (SS1G_12694.3), which encodes a putative class III HK, from the plant pathogen Sclerotinia sclerotiorum. Disruption of Shk1 resulted in resistance to phenylpyrrole and dicarboximide fungicides and increased sensitivity to hyperosmotic stress and H2 O2 -induced oxidative stress. The Shk1 mutant showed a significant reduction in vegetative hyphal growth and was unable to produce sclerotia. Quantitative real-time polymerase chain reaction (qRT-PCR and glycerol determination assays showed that the expression of SsHOG1 (the last kinase of the Hog pathway) and glycerol accumulation were regulated by the Shk1 gene, but PAK (p21-activated kinase) was not. In addition, the Shk1 mutant showed no change in virulence. All the defects were restored by genetic complementation of the Shk1 deletion mutant with the wild-type Shk1 gene. These findings indicate that Shk1 is involved in vegetative differentiation, sclerotial formation, glycerol accumulation and adaption to hyperosmotic and oxidative stresses, and to fungicides, in S.?sclerotiorum. Taken together, our results demonstrate, for the first time, the role of two-component HKs in Sclerotinia.
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What is Visualize?

JoVE Visualize is a tool created to match the last 5 years of PubMed publications to methods in JoVE's video library.

How does it work?

We use abstracts found on PubMed and match them to JoVE videos to create a list of 10 to 30 related methods videos.

Video X seems to be unrelated to Abstract Y...

In developing our video relationships, we compare around 5 million PubMed articles to our library of over 4,500 methods videos. In some cases the language used in the PubMed abstracts makes matching that content to a JoVE video difficult. In other cases, there happens not to be any content in our video library that is relevant to the topic of a given abstract. In these cases, our algorithms are trying their best to display videos with relevant content, which can sometimes result in matched videos with only a slight relation.