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Find video protocols related to scientific articles indexed in Pubmed.
Pseudomonas aeruginosa LysR PA4203 regulator NmoR acts as a repressor of the PA4202 nmoA gene encoding a nitronate monooxygenase.
J. Bacteriol.
PUBLISHED: 11-12-2014
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The PA4203 gene encodes a LysR regulator and lies between the ppgL gene (PA4204), which encodes a periplasmic gluconolactonase, and in the opposite orientation the PA4202 nmoA gene coding for a nitronate monooxygenase and ddlA (PA4201) encoding a D-alanine alanine ligase. The intergenic regions between PA4203 and ppgL, and nmoA are very short (79 and 107 nucleotides, respectively). Here we show that PA4203 (nmoR) represses its own transcription and the expression of nmoA. A chromatin immunoprecipation analysis showed the presence of a single NmoR binding site between nmoA and nmoR, which was confirmed by Electrophoretic mobility shift assays (EMSAs) with the purified NmoR protein. Despite this, a transcriptome analysis revealed more genes to be affected in an nmoR mutant, including genes known to be part of the MexT LysR activator regulon. The PA1225 gene encoding a quinone oxidoreductase is the most highly up-regulated in the nmoR deletion mutant, independently of MexT. Finally, deletion of the nmoA gene resulted in an increased sensitivity of the cells to 3-nitropropionic acid (3-NPA), confirming the role of nitronate monooxygenase protein in the detoxification of nitronate.
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Two new triterpenoids from Callicarpa kwangtungensis.
J Asian Nat Prod Res
PUBLISHED: 11-01-2014
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Two new triterpenoids, 2?,3?,16?,19?,23-pentahydroxyolean-12-en-28-oic acid (1) and 2?,3?,11?,21?,23-pentahydroxyurs-12-en-28-oic acid (2), were isolated from the aerial parts of Callicarpa kwangtungensis. Their structures were elucidated by 1D and 2D analyses, as well as MS and IR spectra.
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MOLECULAR CHARACTERIZATION OF AN APOLIPOPHORIN-III GENE FROM THE CHINESE OAK SILKWORM, Antheraea pernyi (LEPIDOPTERA: SATURNIIDAE).
Arch. Insect Biochem. Physiol.
PUBLISHED: 10-29-2014
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Apolipophorin-III (ApoLp-III) acts in lipid transport, lipoprotein metabolism, and innate immunity in insects. In this study, an ApoLp-III gene of Antheraea pernyi pupae (Ap-ApoLp-III) was isolated and characterized. The full-length cDNA of Ap-ApoLp-III is 687 bp, including a 5'-untranslated region (UTR) of 40 bp, 3'-UTR of 86 bp and an open reading frame of 561 bp encoding a polypeptide of 186 amino acids that contains an Apolipophorin-III precursor domain (PF07464). The deduced Ap-apoLp-III protein sequence has 68, 59, and 23% identity with its orthologs of Manduca sexta, Bombyx mori, and Aedes aegypti, respectively. Phylogenetic analysis showed that the Ap-apoLp-III was close to that of Bombycoidea. qPCR analysis revealed that Ap-ApoLp-III expressed during the four developmental stages and in integument, fat body, and ovaries. After six types of microorganism infections, expression levels of the Ap-ApoLp-III gene were upregulated significantly at different time points compared with control. RNA interference (RNAi) of Ap-ApoLp-III showed that the expression of Ap-ApoLp-III was significantly downregulated using qPCR after injection of E. coli. We infer that the Ap-ApoLp-III gene acts in the innate immunity of A. pernyi.
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X-ray Structure of a Hg(2+) Complex of Mercuric Reductase (MerA) and Quantum Mechanical/Molecular Mechanical Study of Hg(2+) Transfer between the C-Terminal and Buried Catalytic Site Cysteine Pairs.
Biochemistry
PUBLISHED: 10-25-2014
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Mercuric reductase, MerA, is a key enzyme in bacterial mercury resistance. This homodimeric enzyme captures and reduces toxic Hg(2+) to Hg(0), which is relatively unreactive and can exit the cell passively. Prior to reduction, the Hg(2+) is transferred from a pair of cysteines (C558' and C559' using Tn501 numbering) at the C-terminus of one monomer to another pair of cysteines (C136 and C141) in the catalytic site of the other monomer. Here, we present the X-ray structure of the C-terminal Hg(2+) complex of the C136A/C141A double mutant of the Tn501 MerA catalytic core and explore the molecular mechanism of this Hg transfer with quantum mechanical/molecular mechanical (QM/MM) calculations. The transfer is found to be nearly thermoneutral and to pass through a stable tricoordinated intermediate that is marginally less stable than the two end states. For the overall process, Hg(2+) is always paired with at least two thiolates and thus is present at both the C-terminal and catalytic binding sites as a neutral complex. Prior to Hg(2+) transfer, C141 is negatively charged. As Hg(2+) is transferred into the catalytic site, a proton is transferred from C136 to C559' while C558' becomes negatively charged, resulting in the net transfer of a negative charge over a distance of ?7.5 Å. Thus, the transport of this soft divalent cation is made energetically feasible by pairing a competition between multiple Cys thiols and/or thiolates for Hg(2+) with a competition between the Hg(2+) and protons for the thiolates.
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Positive association between serum levels of bone resorption marker CTX and HbA1c in women with normal glucose tolerance.
J. Clin. Endocrinol. Metab.
PUBLISHED: 10-25-2014
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Context: The bone formation marker, osteocalcin (OCN), has beneficial impacts on glucose metabolism. In mice, the OCN bioactivity is induced by bone resorption. But in humans, the role of bone resorption in modulating glucose homeostasis is not clear. Objective: Our study aimed to examine the relationship between bone resorption and glucose homeostasis in humans. Design and Setting: This was a cross-sectional study conducted in a university teaching hospital. Subjects: A total of 195 women with normal glucose tolerance (NGT) were analyzed. Main Outcome Measures: Serum OCN, C-terminal telopeptide of type I collagen (CTX), fasting plasma glucose and 2h post-challenge glucose levels during oral glucose tolerance test, fasting insulin, glycated hemoglobin A1c (HbA1c), hepatic and renal functions, electrolytes, and bone mineral densities (BMDs) at lumbar-spine and proximal femur, and anthropometric parameters were measured. Results: CTX was positively associated with HbA1c after adjustments for multiple confounding factors (r=0.269, p=0.006). OCN (?=0.015, p=0.000), L2-4 BMD (?=-0.218, p=0.003) and HbA1c (?=0.051, p=0.01) were the major determinants of the variations of CTX (adjusted R(2) for the model=0.608, p=0.01) based on multivariate regression analysis. Compared with those in the lowest HbA1c tertile, individuals in the highest tertile (0.37±0.15 ng/ml vs 0.26±0.11 ng/ml, p=0.000) had significantly higher CTX concentrations, even when multiple confounders were adjusted (p for trend=0.015). Conclusions: Bone resorption marker serum CTX was independently associated HbA1c in NGT women. Whether the increased CTX level in NGT subjects is an early marker predicting the subtle impairment of glucose homeostasis and the risk of occurrence of diabetes requires further studies.
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Sleep characteristics and psychological symptoms in patients with locally advanced nasopharyngeal carcinoma before and after intensity-modulated radiotherapy and concurrent chemotherapy.
Psychol Health Med
PUBLISHED: 10-10-2014
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Sleep disturbances and psychological distress are the most common adverse effects associated with cancer diagnosis and treatment. The aim of this study was to examine sleep and psychological characteristics in patients with local-advanced nasopharyngeal carcinoma (NPC) following completion of intensity-modulated radiotherapy (IMRT) and concurrent chemotherapy, and to describe the predictors of post-test psychological symptoms after treatment. Sleep quality and psychological symptoms were measured using Pittsburgh sleep-quality index (PSQI) and symptom checklist-90 in 60 local-advanced NPC patients treated with IMRT and concurrent chemotherapy, respectively. After treatment, the subscores of subjective sleep quality, sleep latency, sleep duration, habitual sleep efficiency, sleep disturbances, use of sleeping medication, and daytime dysfunction increased significantly compared with their pre-test scores. Similar results were observed for the mean PSQI global score. However, for psychological symptoms, only subscores of somatization and depression were higher than their baseline level. Multivariate analysis revealed that concurrent chemotherapy cycle was the only predictor of depression after treatment among all of the psychological symptoms assessed. These findings indicate that sleep disturbance and psychological distress are significant problems in NPC patients treated with IMRT and concurrent chemotherapy. Patients who receive many cycles of concurrent chemotherapy may be at an increased risk of depression after completion of IMRT.
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Five New Taraxerene-Type Triterpenes from the Branch Barks of Davidia involucrata.
Molecules
PUBLISHED: 10-08-2014
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Five new taraxerene-type triterpenes, 2-nor-D-friedoolean-14-en-28-ol (1), 2-nor-d-friedoolean-14-en-3?,28-diol (2), 6?-hydroxy-2-nor-D-friedoolean-14-en-3,21-dione (3), 6?,11?,29-trihydroxy-D-friedoolean-14-en-3,16,21-trione (4), and 6?,23,29-trihydroxy-D-friedoolean-14-en-3,16,21-trione (5), were isolated from the MeOH extract of the branch barks of Davidia involucrata, together with five known compounds. Their structures were elucidated by means of various spectroscopic analyses. Five of the identified compounds showed moderate cytotoxicities against the cell proliferation of SGC-7901, MCF-7, and BEL-7404.
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Eu-MOFs with 2-(4-Carboxyphenyl)imidazo[4,5-f]-1,10-phenanthroline and Ditopic Carboxylates as Coligands: Synthesis, Structure, High Thermostability, and Luminescence Properties.
Inorg Chem
PUBLISHED: 10-06-2014
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Hydrothermal reactions of europium(III) salt with 2-(4-carboxyphenyl)imidazo[4,5-f]-1,10-phenanthroline and dicarboxylic acid as coligands-benzene-1,4-dicarboxylic acid, 4,4'-biphenyldicarboxylic acid, 2,5-dibromoterephthalic acid, and naphthalene-1,4-dicarboxylic acid-lead to four europium fluorescent materials (1-4). Structural analyses reveal that 1-4 have binuclear 3D metal-organic frameworks with different channels, void volumes, and conjugated structures tuned by ditopic carboxylates. There are no latticed and coordinated water molecules occurring in 1-3, while the free water molecules fill in 1D channels of 4. 4' was readily obtained via water removal of 4. Thermal analyses of all compounds show the high thermal stability of the main framework up to 450 °C. Optical studies indicate that 1-4 and 4' show the characteristic red luminescence emission of the Eu(III) ion in the visible regions at room temperature. On the basis of emission spectra, their luminescence lifetimes were determined. In particular, compound 4' shows a longer lifetime (? = 0.942 ms) and significantly enhanced quantum yield (39%) compared with those of 1 (11%, 0.770 ms), 2 (4%, 0.414 ms), 3 (18%, 0.807 ms), and 4 (26%, 0.858 ms).
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PFP/ESG: automated protein function prediction servers enhanced with Gene Ontology visualization tool.
Bioinformatics
PUBLISHED: 10-01-2014
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Protein function prediction (PFP) is an automated function prediction method that predicts Gene Ontology (GO) annotations for a protein sequence using distantly related sequences and contextual associations of GO terms. Extended similarity group (ESG) is another GO prediction algorithm that makes predictions based on iterative sequence database searches. Here, we provide interactive web servers for the PFP and ESG algorithms that are equipped with an effective visualization of the GO predictions in a hierarchical topology. Availability: PFP/ESG servers are freely available at http://kiharalab.org/web/pfp.php and http://kiharalab.org/web/esg.php, or access both at http://kiharalab.org/pfp_esg.php CONTACT: : dkihara@purdue.edu Supplementary information: Supplementary data are available at Bioinformatics online.
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A triple-bridged azido-Cu(II) chain compound fine-tuned by mixed carboxylate/ethanol linkers displays slow-relaxation and ferromagnetic order: synthesis, crystal structure, magnetic properties and DFT calculations.
Dalton Trans
PUBLISHED: 09-05-2014
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A new azido-Cu(II) compound, [Cu(4-fba)(N3)(C2H5OH)] (4-fba = 4-fluorobenzoic acid) (1), has been synthesized and characterized. The X-ray crystal structure analysis demonstrates that only one crystallographically independent Cu(II) ion in the asymmetric unit of 1 exhibits a stretched octahedral geometry in which two azido N atoms and two carboxylic O atoms locate in the equatorial square, while two ethanol O atoms occupy the apical positions, forming a 1D Cu(II) chain with an alternating triple-bridge of EO-azido, syn,syn-carboxylate, and ?2-ethanol. The title compound consists of ferromagnetically interacting ferromagnetic chains, which exhibit ferromagnetic order (T(c) = 7.0 K). The strong ferromagnetic coupling between adjacent Cu(II) ions within each chain is due to the countercomplementarity of the super-exchange pathways, whereas the ferromagnetic interchain interactions--responsible for the long-range magnetic ordering--are most likely due to the presence of coordinated ethanol molecules establishing hydrogen bonds with neighboring chains. DFT calculations have been performed on compound 1 to offer a qualitative theoretical explanation of the magnetic behavior.
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The complete mitochondrial genome of the diamondback moth, Plutella xylostella (Lepidoptera: Plutellidae).
Mitochondrial DNA
PUBLISHED: 09-04-2014
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Abstract The complete mitochondrial genome (mitogenome) of Plutella xylostella (Lepidoptera: Plutellidae) was determined (GenBank accession No. KM023645). The length of this mitogenome is 16,014?bp with 13 protein-coding genes (PCGs), 2 rRNA genes, 22 tRNA genes and an A?+?T-rich region. It presents the typical gene organization and order for completely sequenced lepidopteran mitogenomes. The nucleotide composition of the genome is highly A?+?T biased, accounting for 81.48%, with a slightly positive AT skewness (0.005). All PCGs are initiated by typical ATN codons, except for the gene cox1, which uses CGA as its start codon. Some PCGs harbor TA (nad5) or incomplete termination codon T (cox1, cox2, nad2 and nad4), while others use TAA as their termination codons. The A?+?T-rich region is located between rrnS and trnM with a length of 888?bp.
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MiR-424-5p reversed epithelial-mesenchymal transition of anchorage-independent HCC cells by directly targeting ICAT and suppressed HCC progression.
Sci Rep
PUBLISHED: 09-01-2014
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Resistance to anoikis and Epithelial-mesenchymal transition (EMT) are two processes critically involved in cancer metastasis. In this study, we demonstrated that after anchorage deprival, hepatocellular carcinoma (HCC) cells not only resisted anoikis, but also exhibited EMT process. Microarray expression profiling revealed that expression of miR-424-5p was significantly decreased in anoikis-resistant HCC cells. Ectopic overexpression of miR-424-5p was sufficient to reverse resistance to anoikis, block EMT process and inhibit malignant behaviors of HCC cells. Target analysis showed that a potent ?-catenin inhibitor, ICAT/CTNNBIP1 was a direct target of miR-424-5p. Further study demonstrated that miR-424-5p reversed resistance to anoikis and EMT of HCCs by directly targeting ICAT and further maintaining the E-cadherin/?-catanin complex on the cellular membrance. In vivo study further demonstrated that miR-424-5p significantly inhibited the tumorigenicity of HCC cells in nude mice. Clinical investigation demonstrated that miR-424-5p was significantly downregulated in HCC tissues compared with that of the non-cancerous liver tissues, and this decreased expression of miR-424-5p was significantly correlated with higher pathological grades and more advanced TNM stages. Therefore, aberrant expression of miR-424-5p is critically involved in resistance to anoikis and EMT during the metastatic process of HCC, and its downregulation significantly contributes to liver cancer progression.
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Coordination of Swarming Motility, Biosurfactant Synthesis, and Biofilm Matrix Exopolysaccharide Production in Pseudomonas aeruginosa.
Appl. Environ. Microbiol.
PUBLISHED: 08-29-2014
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Biofilm formation is a complex process in which many factors are involved. Bacterial swarming motility and exopolysaccharides both contribute to biofilm formation, yet it is unclear how bacteria coordinate swarming motility and exopolysaccharide production. Psl and Pel are two key biofilm matrix exopolysaccharides in Pseudomonas aeruginosa. This opportunistic pathogen has three types of motility, swimming, twitching, and swarming. In this study, we found that elevated Psl and/or Pel production reduced the swarming motility of P. aeruginosa but had little effect on swimming and twitching. The reduction was due to decreased rhamnolipid production with no relation to the transcription of rhlAB, two key genes involved in the biosynthesis of rhamnolipids. Rhamnolipid-negative rhlR and rhlAB mutants synthesized more Psl, whereas exopolysaccharide-deficient strains exhibited a hyperswarming phenotype. These results suggest that competition for common sugar precursors catalyzed by AlgC could be a tactic for P. aeruginosa to balance the synthesis of exopolysaccharides and rhamnolipids and to control bacterial motility and biofilm formation inversely because the biosynthesis of rhamnolipids, Psl, and Pel requires AlgC to provide the sugar precursors and an additional algC gene enhances the biosynthesis of Psl and rhamnolipids. In addition, our data indicate that the increase in RhlI/RhlR expression attenuated Psl production. This implied that the quorum-sensing signals could regulate exopolysaccharide biosynthesis indirectly in bacterial communities. In summary, this study represents a mechanism that bacteria utilize to coordinate swarming motility, biosurfactant synthesis, and biofilm matrix exopolysaccharide production, which is critical for biofilm formation and bacterial survival in the environment.
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Upregulation of BNIP3 mediated by ERK/HIF-1? pathway induces autophagy and contributes to anoikis resistance of hepatocellular carcinoma cells.
Future Oncol
PUBLISHED: 07-24-2014
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Acquisition of anoikis resistance is the hallmark of cancer and has been shown to be involved in metastasis of melignant cells. Our previous work showed that anoikis resistance is associated with the metastasis of hepatocellular carcinoma (HCC) cells. The aim of this study is to elucidate the mechanisms of this course.
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Serum Sema3A is in a weak positive association with bone formation marker osteocalcin but not related to bone mineral densities in postmenopausal women.
J. Clin. Endocrinol. Metab.
PUBLISHED: 07-23-2014
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Context: The chemorepellent semaphorin3A (Sema3A) was shown to favor bone metabolism in mice, but its bone effects in humans are not described. Objective: The aim of the study was to investigate the associations between serum Sema3A, bone biochemical markers and bone mineral densities (BMDs) in women. Design, Setting, and Participants: This was a cross-sectional study involving 1012 pre- and postmenopausal women. Main Outcome Measures: Fasting serum Sema3A, osteocalcin (Ocn), and cross-linked C-telopeptide of type-1 collagen (CTX) were measured. Dual-energy X-ray absorptiometry (DXA) was performed to determine the BMDs at lumbar spine and femoral neck. History of osteoporotic fractures was reported by the participants. Results: In postmenopausal women (n=860), a significant positive association between Sema3A and Ocn levels was demonstrated (r=0.077, P=0.025) when age was adjusted. Serum Ocn level was significantly higher in the fourth quartile of serum Sema3A as compared with the first quartile (21.09±0.56ng/ml vs. 19.45±0.44ng/ml, P=0.018). Serum Sema3A concentrations were similar in subjects with normal BMD, osteopenia or osteoporosis, and those with and without osteoporotic fractures. Multiple stepwise regression analysis revealed that CTX, body mass index, creatinine, Sema3A, L1-4 BMDs and age were determinants of Ocn (adjusted R(2) for the model =0.532, p<0.001) . Conclusions: The positive correlation between Sema3A and bone formation marker Ocn revealed in this human study partly supports the recently findings in mice studies. However, the general effects of Sema3A on bone metabolism are weak and not clear as evidenced by lack of association between this parameter and BMDs and osteoporotic fractures.
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Solvent-induced syntheses, crystal structures, magnetic properties, and single-crystal-to-single-crystal transformation of azido-Cu(II) coordination polymers with 2-naphthoic acid as co-ligand.
Inorg Chem
PUBLISHED: 07-11-2014
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Based on the solvent-induced effect, three new azido-copper coordination polymers--[Cu(2-na)(N3)] (1), [Cu(2-na)(N3)] (2), and [Cu(2-na)(N3)(C2H5OH)] (3) (where 2-na = 2-naphthoic acid)--have been successfully prepared. Structure analysis shows that the Cu(II) cations in compounds 1-3 present tetra-, penta-, and hexa-coordination geometries, respectively. Compound 1 is a well-isolated one-dimensional (1D) chain with the EO-azido group, while 2 is an isomer of 1 and exhibits a two-dimensional (2D) layer involving the EE-azido group. Thermodynamically, density functional theory (DFT) calculation reveals that 2 occupies the stable state and 1 locates in the metastable state. Compound 3 consists of a 1D chain with triple bridging mode, which is derived from 1, and undergoes a single-crystal-to-single-crystal transformation by soaking in ethanol solvent; the powdery product of 1, namely 1b, could be yielded after the dealcoholization of compound 3. Magnetic measurements indicate that compounds 1-3 perform strong intrachain ferromagnetic interactions, experiencing long-range magnetic ordering and slow magnetic relaxation. Compound 1 features the metamagnetic behavior with a transition temperature of 15 K, while 2 and 3 display spin glass behavior with the phase transition temperatures of 15 and 12 K, respectively. Magneto-structure relationships are investigated as well.
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Thermal decomposition of solid phase nitromethane under various heating rates and target temperatures based on ab initio molecular dynamics simulations.
J Mol Model
PUBLISHED: 07-03-2014
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The Car-Parrinello molecular dynamics simulation was applied to study the thermal decomposition of solid phase nitromethane under gradual heating and fast annealing conditions. In gradual heating simulations, we found that, rather than C-N bond cleavage, intermolecular proton transfer is more likely to be the first reaction in the decomposition process. At high temperature, the first reaction in fast annealing simulation is intermolecular proton transfer leading to CH3NOOH and CH2NO2, whereas the initial chemical event at low temperature tends to be a unimolecular C-N bond cleavage, producing CH3 and NO2 fragments. It is the first time to date that the direct rupture of a C-N bond has been reported as the first reaction in solid phase nitromethane. In addition, the fast annealing simulations on a supercell at different temperatures are conducted to validate the effect of simulation cell size on initial reaction mechanisms. The results are in qualitative agreement with the simulations on a unit cell. By analyzing the time evolution of some molecules, we also found that the time of first water molecule formation is clearly sensitive to heating rates and target temperatures when the first reaction is an intermolecular proton transfer.
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Anisotropic responses and initial decomposition of condensed-phase ?-HMX under shock loadings via molecular dynamics simulations in conjunction with multiscale shock technique.
J Phys Chem B
PUBLISHED: 07-01-2014
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Molecular dynamics simulations in conjunction with multiscale shock technique (MSST) are performed to study the initial chemical processes and the anisotropy of shock sensitivity of the condensed-phase HMX under shock loadings applied along the a, b, and c lattice vectors. A self-consistent charge density-functional tight-binding (SCC-DFTB) method was employed. Our results show that there is a difference between lattice vector a (or c) and lattice vector b in the response to a shock wave velocity of 11 km/s, which is investigated through reaction temperature and relative sliding rate between adjacent slipping planes. The response along lattice vectors a and c are similar to each other, whose reaction temperature is up to 7000 K, but quite different along lattice vector b, whose reaction temperature is only up to 4000 K. When compared with shock wave propagation along the lattice vectors a (18 Å/ps) and c (21 Å/ps), the relative sliding rate between adjacent slipping planes along lattice vector b is only 0.2 Å/ps. Thus, the small relative sliding rate between adjacent slipping planes results in the temperature and energy under shock loading increasing at a slower rate, which is the main reason leading to less sensitivity under shock wave compression along lattice vector b. In addition, the C-H bond dissociation is the primary pathway for HMX decomposition in early stages under high shock loading from various directions. Compared with the observation for shock velocities V(imp) = 10 and 11 km/s, the homolytic cleavage of N-NO2 bond was obviously suppressed with increasing pressure.
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Heavy metal-induced metallothionein expression is regulated by specific protein phosphatase 2A complexes.
J. Biol. Chem.
PUBLISHED: 06-24-2014
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Induction of metallothionein (MT) expression is involved in metal homeostasis and detoxification. To identify the key pathways that regulate metal-induced cytotoxicity, we investigate how phosphorylated metal-responsive transcription factor-1 (MTF-1) contributed to induction of MT expression. Immortal human embryonic kidney cells (HEK cells) were treated with seven kinds of metals including cadmium chloride (CdCl2), zinc sulfate (ZnSO4), copper sulfate(CuSO4), lead acetate (PbAc), nickel sulfate (NiSO4), sodium arsenite (NaAsO2), and potassium bichromate (K2Cr2O7). The MT expression was induced in a dose-response and time-dependent manner upon various metal treatments. A cycle of phosphorylation and dephosphorylation was required for translocation of MTF-1 from cytoplasm to nucleus, leading to the up-regulation of MTs expression. Protein phosphatase 2A (PP2A) participated in regulating MT expression through dephosphorylation of MTF-1. A loss-of-function screen revealed that the specific PP2A complexes containing PR110 were involved in metal-induced MT expression. Suppression of PP2A PR110 in HEK cells resulted in the persistent MTF-1 phosphorylation and the disturbance of MTF-1 nuclear translocation, which was concomitant with a significant decrease of MT expression and enhanced cytotoxicity in HEK cells. Notably, MTF-1 was found in complex with specific PP2A complexes containing the PR110 subunit upon metal exposure. Furthermore, we identify that the dephosphorylation of MTF-1 at residue Thr-254 is directly regulated by PP2A PR110 complexes and responsible for MTF-1 activation. Taken together, these findings delineate a novel pathway that determines cytotoxicity in response to metal treatments and provide new insight into the role of PP2A in cellular stress response.
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Endoscopic variceal ligation caused massive bleeding due to laceration of an esophageal varicose vein with tissue glue emboli.
World J. Gastroenterol.
PUBLISHED: 06-18-2014
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Endoscopic variceal obturation of gastric varices with tissue glue is considered the first choice for management of gastric varices, and is usually safe and effective. However, there is still a low incidence of complications and some are even fatal. Here, we present a case in which endoscopic variceal ligation caused laceration of the esophageal varicose vein with tissue glue emboli and massive bleeding after 3 mo. Cessation of bleeding was achieved via variceal sclerotherapy using a cap-fitted gastroscope. Methods of recognizing an esophageal varicose vein with tissue glue plug are discussed.
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Hypoxia inducible factor-1? suppresses Peroxiredoxin 3 expression to promote proliferation of CCRCC cells.
FEBS Lett.
PUBLISHED: 06-06-2014
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Peroxiredoxin 3 (Prx3) is a mitochondrial member of the antioxidant family of thioredoxin peroxidases that uses mitochondrial thioredoxin 2 as a source of reducing equivalents to scavenge hydrogen peroxide (H2O2). Here, we report that the protein levels of Prx3 are significantly reduced in VHL-deficient clear cell renal cell carcinoma (CCRCC). Furthermore, stabilization of HIF-1? protein, caused either by VHL deficiency under normoxia, or by hypoxia, significantly reduced Prx3 expression. Luciferase-reporter and chromatin-immunoprecipitation assays indicated that HIF-1? binds to the hypoxia-responsive elements of PRDX3 promoter and represses its transcription. Finally, shRNA-based assays suggested that Prx3 downregulation is required for the HIF-1?-dependent proliferation of CCRCC cells. Taken together, our results shed new light onto the mechanism of HIF-1?-dependent proliferation in CCRCC cells.
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A proteomic analysis of rice seed germination as affected by high temperature and ABA treatment.
Physiol Plant
PUBLISHED: 05-04-2014
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Seed germination is a critical phase in the plant life cycle, but the specific events associated with seed germination are still not fully understood. In this study, we used two-dimensional gel electrophoresis followed by mass spectrometry to investigate the changes in the proteome during imbibition of Oryza sativa seeds at optimal temperature with or without abscisic acid (ABA) and high temperature (germination thermoinhibition) to further identify and quantify key proteins required for seed germination. A total of 121 protein spots showed a significant change in abundance (1.5-fold increase/decrease) during germination under all conditions. Among these proteins, we found seven proteins specifically associated with seed germination including glycosyl hydrolases family 38 protein, granule-bound starch synthase 1, Os03g0842900 (putative steroleosin-B), N-carbamoylputrescine amidase, spermidine synthase 1, tubulin ?-1 chain and glutelin type-A; and a total of 20 imbibition response proteins involved in energy metabolism, cell growth, cell defense and storage proteins. High temperature inhibited seed germination by decreasing the abundance of proteins involved in methionine metabolism, amino acid biosynthesis, energy metabolism, reserve degradation, protein folding and stress responses. ABA treatment inhibited germination and decreased the abundance of proteins associated with methionine metabolism, energy production and cell division. Our results show that changes in many biological processes including energy metabolism, protein synthesis and cell defense and rescue occurred as a result of all treatments, while enzymes involved in methionine metabolism and weakening of cell wall specifically accumulated when the seeds germinated at the optimal temperature.
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Antitumor constituents from Anthriscus sylvestris (L.) Hoffm.
Asian Pac. J. Cancer Prev.
PUBLISHED: 04-26-2014
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Bioassay-guided chemical investigation of the roots of Anthriscus sylvestris (L.) Hoffm. resulted in the isolation of nine compounds, whose structures were determined by spectroscopic methods. Compound 1 was isolated from this plant for the first time and compounds 3 and 9 were first found from this genus. Different polar fractions of A. sylvestris extract and compounds 1, 6-8 and 9 were evaluated for antitumor activities against HepG2 (human hepatocellular carcinoma), MG-63 (human osteosarcoma cells), B16 (melanoma cells) and HeLa (human cervical carcinoma cells) lines by the MTT method. The petroleum ether fraction of A. sylvestris extract exhibited excellent inhibitory activity with an IC50 value of 18.3 ?g/ml. Among the isolates from the petroleum ether fraction, compound 7 showed significant inhibition against the growth of the four tumor cells with IC50 values ranging from 12.2-43.3 ?g/ml.
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Valsalva leak point pressure-associated Q-tip angle and simple female stress urinary incontinence symptoms.
Int Urol Nephrol
PUBLISHED: 04-15-2014
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To clarify the association between clinically defined simple stress urinary incontinence (SUI) symptoms and urodynamic SUI, we examined the relationship between Valsalva leak point pressure (VLPP) as measured by the Q-tip test and Stamey grade in simple female SUI.
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Study of liver cirrhosis over ten consecutive years in Southern China.
World J. Gastroenterol.
PUBLISHED: 04-07-2014
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To investigate the etiology and complications of liver cirrhosis (LC) in Southern China.
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Acute diarrhea and metabolic acidosis caused by tuberculous vesico-rectal fistula.
World J. Gastroenterol.
PUBLISHED: 04-06-2014
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Acquired vesico-rectal fistula is an uncommon complication of pelvic malignant tumors, surgical injury, inflammatory disorders such as tuberculosis infection, radiotherapy and less commonly diverticulum of the urinary tract. The fistula is often identified by urinary tract abnormalities such as dysuria, recurrent urinary tract infection, pneumaturia, and fecaluria. Here, we report an unusual case of a patient with a vesico-rectal fistula of tuberculous origin, presenting with severe acute diarrhea, metabolic acidosis, hyperchloremia and hypokalemia while with only mild urinary tract symptoms. The patient was cured by tuberculostatic therapy.
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Activating hotspot L205R mutation in PRKACA and adrenal Cushing's syndrome.
Science
PUBLISHED: 04-03-2014
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Adrenal Cushing's syndrome is caused by excess production of glucocorticoid from adrenocortical tumors and hyperplasias, which leads to metabolic disorders. We performed whole-exome sequencing of 49 blood-tumor pairs and RNA sequencing of 44 tumors from cortisol-producing adrenocortical adenomas (ACAs), adrenocorticotropic hormone-independent macronodular adrenocortical hyperplasias (AIMAHs), and adrenocortical oncocytomas (ADOs). We identified a hotspot in the PRKACA gene with a L205R mutation in 69.2% (27 out of 39) of ACAs and validated in 65.5% of a total of 87 ACAs. Our data revealed that the activating L205R mutation, which locates in the P+1 loop of the protein kinase A (PKA) catalytic subunit, promoted PKA substrate phosphorylation and target gene expression. Moreover, we discovered the recurrently mutated gene DOT1L in AIMAHs and CLASP2 in ADOs. Collectively, these data highlight potentially functional mutated genes in adrenal Cushing's syndrome.
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A new strategy for storage and transportation of sensitive high-energy materials: guest-dependent energy and sensitivity of 3D metal-organic-framework-based energetic compounds.
Chemistry
PUBLISHED: 03-26-2014
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Reaction of Co(II) with the nitrogen-rich ligand N,N-bis(1H-tetrazole-5-yl)-amine (H2bta) leads to a mixed-valence, 3D, porous, metal-organic framework (MOF)-based, energetic material with the nitrogen content of 51.78%, [Co9(bta)10(Hbta)2(H2O)10]n?(22?H2O)n (1). Compound 1 was thermohydrated to produce a new, stable, energetic material with the nitrogen content of 59.85% and heat of denotation of 4.537?kcal?cm(-3), [Co9(bta)10(Hbta)2(H2O)10]n (2). Sensitivity tests show that 2 is more sensitivity to external stimuli than 1, reflecting guest-dependent energy and sensitivity of 3D, MOF-based, energetic materials. Less-sensitive 1 can be regarded as a more safe form for storage and transformation to sensitive 2.
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Three new ring-A modified ursane triterpenes from Davidia involucrata.
Molecules
PUBLISHED: 03-26-2014
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Three new ursane triterpenes, 3?,19?-dihydroxy-2-nor-urs-12-en-23,28-dioic acid-23-methyl ester (1), 19?,23-dihydroxy-3-oxo-2-nor-urs-12-en-28-oic acid (2), and 2,3-seco-3-methoxy-3,19?,23-trihydroxy-urs-12-en-2-al-28-oic acid (3), were isolated from the MeOH extract of the branch barks of Davidia involucrata, together with six known compounds. Their structures were elucidated by means of various spectroscopic analyses. The isolated triterpenes provide important evolutionary and chemotaxonomic knowledge about the monotypic genus Davidia. Five of the identified compounds showed moderate cytotoxicities against the cell proliferation of SGC-7901, MCF-7, and BEL-7404 with IC50 range from 7.26 to 47.41 ?M.
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Hippo-YAP signaling pathway: A new paradigm for cancer therapy.
Int. J. Cancer
PUBLISHED: 03-20-2014
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In the past decades, the Hippo signaling pathway has been delineated and shown to play multiple roles in the control of organ size in both Drosophila and mammals. In mammals, the Hippo pathway is a kinase cascade leading from Mst1/2 to YAP and its paralog TAZ. Several studies have demonstrated that YAP/TAZ is a candidate oncogene and that other members of the Hippo pathway are tumor suppressive genes. The dysregulation of the Hippo pathway has been observed in a variety of cancers. This review chronicles the recent progress in elucidating the function of Hippo signaling in tumorigenesis and provide a rich source of potential targets for cancer therapy.
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A combined method to quantify the retinal metabolic rate of oxygen using photoacoustic ophthalmoscopy and optical coherence tomography.
Sci Rep
PUBLISHED: 03-17-2014
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Quantitatively determining physiological parameters at a microscopic level in the retina furthers the understanding of the molecular pathways of blinding diseases, such as diabetic retinopathy and glaucoma. An essential parameter, which has yet to be quantified noninvasively, is the retinal oxygen metabolic rate (rMRO2). Quantifying rMRO2 is challenging because two parameters, the blood flow rate and hemoglobin oxygen saturation (sO2), must be measured together. We combined photoacoustic ophthalmoscopy (PAOM) with spectral domain-optical coherence tomography (SD-OCT) to tackle this challenge, in which PAOM measured the sO2 and SD-OCT mapped the blood flow rate. We tested the integrated system on normal wild-type rats, in which the measured rMRO2 was 297.86 ± 70.23 nl/minute. This quantitative method may shed new light on both fundamental research and clinical care in ophthalmology in the future.
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Tumor-associated macrophages promote the metastatic potential of thyroid papillary cancer by releasing CXCL8.
Carcinogenesis
PUBLISHED: 03-06-2014
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Tumor-associated macrophages (TAMs) can promote cancer initiation and progression by releasing cytokines. Previously, we have found the density of TAMs correlated with lymph node metastasis in papillary thyroid carcinoma (PTC). However, the mechanisms of how TAMs promote PTC progression remain unclear. In this study, we first showed that the TAMs density in the tumor core was associated with progressive PTC features and TAMs conditioned medium enhanced PTC cells invasion. Cytokine profiling identified a mixed M1/M2 phenotype and CXCL8 was the most consistently abundant cytokine in PTC-derived TAMs. CXCL8 receptors, CXCR1 and CXCR2, were positively stained in PTC cell lines and tissues, though no association with lymph node metastasis or extrathyroid extension. PTC cell invasion was abrogated by anti-CXCL8-neutralizing antibody, whereas addition of exogenous recombinant human CXCL8 enhanced the invasiveness. More importantly, CXCL8 promoted PTC metastasis in vivo. No difference was found for TAMs-derived CXCL8 expression in patients with and without lymph node metastasis or extrathyroid extension. These findings indicated that TAMs may facilitate PTC cell metastasis through CXCL8 and its paracrine interaction with CXCR1/2.
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Humoral immune responses to HIV in the mucosal secretions and sera of HIV-infected women.
Am. J. Reprod. Immunol.
PUBLISHED: 02-05-2014
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Although sera and all external secretions contain antibodies to human immunodeficiency virus (HIV), their levels, specificity, isotypes, and relevant effector functions display a great degree of variability. Antibodies that bind HIV antigens and neutralize the virus are predominantly associated with the IgG isotype in sera and in all external secretions, even where total levels of IgG are much lower than those of IgA. Rectal fluid that contains high IgA, but low IgG levels, displayed low neutralizing activity independent of antibodies. Therefore, external secretions should be evaluated before and after selective depletion of Ig. At the systemic level, HIV-specific IgA may interfere with the effector functions of IgG, as suggested by recent studies of individuals systemically immunized with an experimental HIV vaccine. Although HIV-specific IgG and IgA antibodies may exhibit their protective activities at mucosal surfaces through interference with viral entry and local neutralization at the systemic level, such antibodies may display discordant effector functions.
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The complete mitochondrial genome of the common cutworm, Spodoptera litura (Lepidoptera: Noctuidade).
Mitochondrial DNA
PUBLISHED: 02-05-2014
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Abstract The complete mitochondrial genome (mitogenome) of Spodoptera litura (Lepidoptera: Noctuidae) was determined to be 15,374?bp (GenBank accession No. KF543065), including 13 protein-coding genes (PCGs), two rRNA genes, 22 tRNA genes and an A?+?T-rich region. It has the typical gene organization and order of mitogenomes from lepidopteran insects. The AT skew of this mitogenome was slightly positive and the nucleotide composition was also biased toward A?+?T nucleotides (81.03%). All PCGs were initiated by ATN codons, except for cytochrome c oxidase subunit 1 (cox1) gene which was initiated by CGA. Four of the 13 PCGs harbor the incomplete termination codon by T. All the tRNA genes displayed a typical clover-leaf structure of mitochondrial tRNA, with the exception of trnS1 (AGN). The A?+?T-rich region of the mitogenome was 326?bp in length.
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A case of lepromatous leprosy complicated by hemophagocytosis misdiagnosed as hemophagocytic lymphohistiocytosis.
Int. J. Infect. Dis.
PUBLISHED: 02-01-2014
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Leprosy is an infectious chronic granulomatous disease caused by Mycobacterium leprae. The disease mainly affects the skin, peripheral nerves, mucosa, and viscera. The World Health Organization has reported that most countries with high endemicity have reached the goal of eliminating leprosy (defined as reaching a prevalence of <1 leprosy case per 10 000 population) at the national level, after years of proactive control campaigns. The incidence of leprosy has been decreasing across the globe year by year. However, misdiagnosis happens occasionally due to the complexity of clinical manifestations and lack of physician awareness of this disease. We report a case of lepromatous leprosy complicated by hemophagocytosis misdiagnosed as hemophagocytic lymphohistiocytosis.
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A theoretical study on the mechanism of a superficial mutation inhibiting the enzymatic activity of CYP1A2.
Interdiscip Sci
PUBLISHED: 01-28-2014
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CYP1A2, one of the major members of cytochrome P450 in human liver, participates in the metabolism of various drugs. While most harmful mutations are located near the catalytic core of CYP1A2, a recently found loss-of-function mutation, F186L, is on the surface. By far, function of this superficial residue remains unclear. In this paper, 7-ethoxyresorufin, a widely used agent in benchmarking the O-deethylation activities of CYP1A subfamily enzymes, was employed as a substrate to investigate the impact of the F186L mutation through ensemble docking and molecular dynamics simulations. It was found that the F186L mutation altered the binding inclination of the substrate through a series of changes on the catalytic pocket, which are, actually, long-range effects. The activities of access channels in the enzyme are also affected by the F186L mutation and the substrate binding. Based on these findings, a detailed mechanism of how F186 regulates the functions of CYP1A2 was proposed, and it may shed light on the diverse effects of SNPs and the personalized drug design.
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Gastrointestinal stromal tumor: 15-years' experience in a single center.
BMC Surg
PUBLISHED: 01-20-2014
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Gastrointestinal stromal tumor (GIST) is known for its wide variability in biological behaviors and it is difficult to predict its malignant potential. The aim of this study is to explore the characteristics and prognostic factors of GIST.
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Intestinal obstruction caused by extramedullary hematopoiesis and ascites in primary myelofibrosis.
World J. Gastroenterol.
PUBLISHED: 01-14-2014
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Primary myelofibrosis (PMF) is a clonal hematopoietic stem cell disorder. It is characterized by bone marrow fibrosis, extramedullary hematopoiesis with hepatosplenomegaly and leukoerythroblastosis in the peripheral blood. The main clinical manifestations of PMF are anemia, bleeding, hepatosplenomegaly, fatigue, and fever. Here we report a rare case of PMF with anemia, small bowel obstruction and ascites due to extramedullary hematopoiesis and portal hypertension. The diagnosis was difficult to establish before surgery and the differential diagnosis is discussed.
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Predicting protein-ligand interactions based on chemical preference features with its application to new D-amino acid oxidase inhibitor discovery.
Curr. Pharm. Des.
PUBLISHED: 01-09-2014
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In silico prediction of the new drug-target interactions from existing databases is of important value for the drug discovery process. Currently, the amount of protein targets that have been identified experimentally is still very small compared with the entire human proteins. In order to predict protein-ligand interactions in an accurate manner, we have developed a support vector machine (SVM) model based on the chemical-protein interactions from STITCH. New features from ligand chemical space and interaction networks have been selected and encoded as the feature vectors for SVM analysis. Both the 5-fold cross validation and independent test show high predictive accuracy that outperforms the state-of-the-art method based on ligand similarity. Moreover, 91 distinct pairs of features have been selected to rebuild a simplifier model, which still maintains the same performance as that based on all 332 features. Then, this refined model is used to search for the potential D-amino acid oxidase inhibitors from STITCH database and the predicted results are finally validated by our wet experiments. Out of 10 candidates obtained, seven D-amino acid oxidase inhibitors have been verified, in which four are newly found in the present study, and one may have a new application in therapy of psychiatric disorders other than being an antineoplastic agent. Clearly, our model is capable of predicting potential new drugs or targets on a large scale with high efficiency.
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Implementation of pharmacists' interventions and assessment of medication errors in an intensive care unit of a Chinese tertiary hospital.
Ther Clin Risk Manag
PUBLISHED: 01-01-2014
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Pharmacist interventions and medication errors potentially differ between the People's Republic of China and other countries. This study aimed to report interventions administered by clinical pharmacists and analyze medication errors in an intensive care unit (ICU) in a tertiary hospital in People's Republic of China.
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Genetic features of late onset primary hemophagocytic lymphohistiocytosis in adolescence or adulthood.
PLoS ONE
PUBLISHED: 01-01-2014
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Hemophagocytic lymphohistiocytosis (HLH) is a life-threatening condition of uncontrolled immune activation leading to extreme inflammation. Primary HLH was once believed to be a disease that occurred only in infancy or young children, and was rarely diagnosed in adults. It is now understood that patients can develop primary HLH in their adolescence or adulthood. This study included 252 adolescent and adult patients with a clinical diagnosis of HLH from 35 general medical institutions across mainland China. All exons and 50 bp of flanking intronic sequence of six HLH-related genes (PRF1, UNC13D, STX11, STXBP2, SH2D1A, and BIRC4) were sequenced in these patients. We identified mutations in 18/252 (7.1%) of the patients, with changes in PRF1 being most common. Late-onset HLH often features viral infection and other predisposing factors. We conclude that late-onset primary HLH is not as rare as previously thought. Older patients should not be delayed to receive HLH-related genes testing when they are suspected with HLH.
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Identification of human disease genes from interactome network using graphlet interaction.
PLoS ONE
PUBLISHED: 01-01-2014
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Identifying genes related to human diseases, such as cancer and cardiovascular disease, etc., is an important task in biomedical research because of its applications in disease diagnosis and treatment. Interactome networks, especially protein-protein interaction networks, had been used to disease genes identification based on the hypothesis that strong candidate genes tend to closely relate to each other in some kinds of measure on the network. We proposed a new measure to analyze the relationship between network nodes which was called graphlet interaction. The graphlet interaction contained 28 different isomers. The results showed that the numbers of the graphlet interaction isomers between disease genes in interactome networks were significantly larger than random picked genes, while graphlet signatures were not. Then, we designed a new type of score, based on the network properties, to identify disease genes using graphlet interaction. The genes with higher scores were more likely to be disease genes, and all candidate genes were ranked according to their scores. Then the approach was evaluated by leave-one-out cross-validation. The precision of the current approach achieved 90% at about 10% recall, which was apparently higher than the previous three predominant algorithms, random walk, Endeavour and neighborhood based method. Finally, the approach was applied to predict new disease genes related to 4 common diseases, most of which were identified by other independent experimental researches. In conclusion, we demonstrate that the graphlet interaction is an effective tool to analyze the network properties of disease genes, and the scores calculated by graphlet interaction is more precise in identifying disease genes.
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Proteomic Comparison between Maturation Drying and Prematurely Imposed Drying of Zea mays Seeds Reveals a Potential Role of Maturation Drying in Preparing Proteins for Seed Germination, Seedling Vigor, and Pathogen Resistance.
J. Proteome Res.
PUBLISHED: 12-27-2013
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We have studied the role(s) of maturation drying in the acquisition of germinability, seedling vigor and pathogen resistance by comparing the proteome changes in maize embryo and endosperm during mature and prematurely imposed drying. Prematurely imposed dried seeds at 40 days after pollination (DAP) germinated almost as well as mature seeds (at 65 DAP), but their seedling growth was slower and they were seriously infected by fungi. A total of 80 and 114 proteins were identified to change at least two-fold (p < 0.05) in abundance during maturation drying in embryo and endosperm, respectively. Fewer proteins (48 and 59 in embryo and endosperm, respectively) changed in abundance during prematurely imposed drying. A number of proteins, 33 and 38 in embryo and endosperm, respectively, changed similarly in abundance during both maturation and prematurely imposed drying. Storage proteins were abundant in this group and may contribute to the acquisition of seed germinability. However, a relatively large number of proteins changed in the embryo (47 spots) and endosperm (76 spots) specifically during maturation drying. Among these proteins, storage proteins in the embryo and defense proteins in the endosperm may be particularly important for seedling vigor and resistance to fungal infection, respectively.
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Effects of organic selenium on lead-induced impairments of spatial learning and memory as well as synaptic structural plasticity in rats.
Biol. Pharm. Bull.
PUBLISHED: 12-19-2013
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To study the effect of organic Se on spatial learning and memory deficits induced by Pb exposure at different developmental stages, and its relationship with alterations of synaptic structural plasticity, postnatal rat pups were randomly divided into five groups: Control; Pb (Weaned pups were exposed to Pb at postnatal day(PND) 21-42); Pb-Se (Weaned pups were exposed to Se at PND 43-63 after Pb exposure ); mPb (Parents were exposed to Pb from 3 weeks before mating to the weaning of pups); mPb-Se (Parents were exposed to Pb and weaned pups were exposed to Se at PND 43-63).The spatial learning and memory of rat pups was measured by Morris water maze (MWM) on PND 63. We found that rat pups in Pb-Se group performed significantly better than those in Pb group (p < 0.05). However, there was no significant difference in the ability of spatial learning and memory between the groups of mPb and mPb-Se (p > 0.05). We also found that, before MWM, the numbers of neurons and synapses significantly decreased in mPb group, but not in Pb group. After MWM, the number of synapses, the thickness of postsynaptic density (PSD), the length of synaptic active zone and the synaptic curvature increased significantly in Pb-Se and mPb-Se group; while the width of synaptic cleft decreased significantly (p < 0.05), compared to Pb group and mPb group, respectively. However, the number of synapses in mPb-Se group was still significantly lower than that in the control group (p < 0.05). Our data demonstrated that organic Se had protective effects on the impairments of spatial learning and memory as well as synaptic structural plasticity induced by Pb exposure in rats after weaning, but not by the maternal Pb exposure which reduced the numbers of neurons and synapses in the early neural development.
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Deregulated NLRP3 and NLRP1 Inflammasomes and Their Correlations with Disease Activity in Systemic Lupus Erythematosus.
J. Rheumatol.
PUBLISHED: 12-15-2013
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NOD-like receptor family, pyrin domain containing 3 and 1 (NLRP3 and NLRP1) inflammasomes are molecular platforms that sense the damage or danger signals of cells. We investigated whether NLRP3/NLRP1 inflammasomes are involved in the pathogenesis and progression of systemic lupus erythematosus (SLE).
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Rapid Creation of Forward-Genetics Tools for C. briggsae Using TALENs: Lessons for Nonmodel Organisms.
Mol. Biol. Evol.
PUBLISHED: 11-05-2013
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Although evolutionary studies of gene function often rely on RNA interference, the ideal approach would use reverse genetics to create null mutations for cross-species comparisons and forward genetics to identify novel genes in each species. We have used transcription activator-like effector nucleases (TALENs) to facilitate both approaches in Caenorhabditis nematodes. First, by combining golden gate cloning and TALEN technology, we can induce frameshifting mutations in any gene. Second, by combining this approach with bioinformatics we can predict and create the resources needed for forward genetic analysis in species like Caenorhabditis briggsae. Although developing genetic model organisms used to require years to isolate marker mutations, balancers, and tools, with TALENs, these reagents can now be produced in months. Furthermore, the analysis of nonsense mutants in related model organisms allows a directed approach for making these markers and tools. When used together, these methods could simplify the adaptation of other organisms for forward and reverse genetics.
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Transition fibre protein FBF1 is required for the ciliary entry of assembled intraflagellar transport complexes.
Nat Commun
PUBLISHED: 09-04-2013
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Sensory organelle cilia have critical roles in mammalian embryonic development and tissue homeostasis. Intraflagellar transport (IFT) machinery is required for the assembly and maintenance of cilia. Yet, how this large complex passes through the size-dependent barrier at the ciliary base remains enigmatic. Here we report that FBF1, a highly conserved transition fibre protein, is required for the ciliary import of assembled IFT particles at the ciliary base. We cloned dyf-19, the Caenorhabditis elegans homologue of human FBF1, in a whole-genome screen for ciliogenesis mutants. DYF-19 localizes specifically to transition fibres and interacts directly with the IFT-B component DYF-11/IFT54. Although not a structural component of transition fibres, DYF-19 is required for the transit of assembled IFT particles through the ciliary base. Furthermore, we found that human FBF1 shares conserved localization and function with its worm counterpart. We conclude that FBF1 is a key functional transition fibre component that actively facilitates the ciliary entry of assembled IFT machinery.
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Biofilm matrix and its regulation in Pseudomonas aeruginosa.
Int J Mol Sci
PUBLISHED: 08-21-2013
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Biofilms are communities of microorganisms embedded in extracellular polymeric substances (EPS) matrix. Bacteria in biofilms demonstrate distinct features from their free-living planktonic counterparts, such as different physiology and high resistance to immune system and antibiotics that render biofilm a source of chronic and persistent infections. A deeper understanding of biofilms will ultimately provide insights into the development of alternative treatment for biofilm infections. The opportunistic pathogen Pseudomonas aeruginosa, a model bacterium for biofilm research, is notorious for its ability to cause chronic infections by its high level of drug resistance involving the formation of biofilms. In this review, we summarize recent advances in biofilm formation, focusing on the biofilm matrix and its regulation in P. aeruginosa, aiming to provide resources for the understanding and control of bacterial biofilms.
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Deregulation of the NLRP3 inflammasome in hepatic parenchymal cells during liver cancer progression.
Lab. Invest.
PUBLISHED: 07-07-2013
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Hepatocellular carcinoma (HCC) is one of the most prevalent malignant tumors worldwide, and it is always the consequence of chronic hepatitis and liver cirrhosis. The nucleotide-binding domain, leucine-rich family (NLR), pyrin-containing 3 (NLRP3) inflammasome has been shown to orchestrate multiple innate and adaptive immune responses. However, little is known about its role in cancer. This study was performed to investigate the role of the NLRP3 inflammasome in the development and progression of HCC. The expression of NLRP3 inflammasome components was analyzed in HCC tissues and corresponding non-cancerous liver tissues at both the mRNA and protein levels. Our data demonstrate that the expression of all of the NLRP3 inflammasome components was either completely lost or significantly downregulated in human HCC, and that the deficiency correlated significantly with advanced stages and poor pathological differentiation. In addition, our data provide an overview of the expression of NLRP3 inflammasome components in the multi-stage development of HCC and indicate a surprising link between deregulation of the NLRP3 inflammasome molecular platform and HCC progression. In conclusion, this study presents a dynamic expression pattern of NLRP3 inflammasome components in multi-stage hepatocarcinogenesis and demonstrates that deregulated expression of the inflammasome is involved in HCC progression.
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Structural and energetic analysis of drug inhibition of the influenza A M2 proton channel.
Trends Pharmacol. Sci.
PUBLISHED: 06-25-2013
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The type A influenza virus matrix protein 2 (M2) is a highly selective proton channel in the viral envelope. Because of its crucial role in viral infection and replication, the M2 channel has been a target of anti-influenza drugs. Due to the occurrence of drug-resistant mutations in the M2 channel, existing anti-influenza drugs that block the M2 channel, such as amantadine and rimantadine, have lost their efficacy against these mutant channels. Recent experimental and computational efforts have made great progress in understanding the drug resistance mechanisms of these mutations as well as designing novel drug candidates to block the mutant M2 channels. In this review, we briefly summarize the structural characteristics of the M2 channel, and then we discuss these recent studies on drug resistance and drug design of the mutant channels, focusing on the structures and energetics. We show that structural biology experiments and molecular modeling have led to the successful design of novel drugs targeting mutant M2 channels.
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Car-Parrinello molecular dynamics/molecular mechanics (CPMD/MM) simulation study of coupling and uncoupling mechanisms of Cytochrome P450cam.
J Phys Chem B
PUBLISHED: 06-20-2013
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The relevance of the pathway through which the second proton is delivered to the active site of P450cam and the subsequent coupling/uncoupling reactions has been investigated using Car-Parrinello molecular dynamics/molecular mechanics (CPMD/MM) dynamics simulations. Five models have been prepared, representing delivery pathways in the wild-type enzyme and its mutants in which Thr252 mutated into other residues with different side-chain length and hydrophobicity. In the simulations, coupling reaction is observed in the wild-type enzyme (Model A) and its T252S mutant (Model B), while the uncoupling products are obtained in the other three models (C, D, and E). Different from previous studies, a dynamic process of the last stage of coupling/uncoupling was observed. We found that the peroxide bond cleavage in coupling, the Fe-O bond stretching in uncoupling, proton transfer, and electron delivery take place spontaneously. Moreover, besides the intrinsic chemical differences between the two peroxide oxygen atoms, water molecules in the active site and the proton transfer pathway may play an important role in the determination of coupling/uncoupling. We conclude that by maintaining a specific proton transfer channel, Asp251-Thr252 channel, the wild-type enzyme could efficiently deliver the second proton to the ideal position for coupling reaction.
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Whole exome sequencing of insulinoma reveals recurrent T372R mutations in YY1.
Nat Commun
PUBLISHED: 06-04-2013
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Functional pancreatic neuroendocrine tumours (PNETs) are mainly represented by insulinoma, which secrete insulin independent of glucose and cause hypoglycaemia. The major genetic alterations in sporadic insulinomas are still unknown. Here we identify recurrent somatic T372R mutations in YY1 by whole exome sequencing of 10 sporadic insulinomas. Further screening in 103 additional insulinomas reveals this hotspot mutation in 30% (34/113) of all tumours. T372R mutation alters the expression of YY1 target genes in insulinomas. Clinically, the T372R mutation is associated with the later onset of tumours. Genotyping of YY1, a target of mTOR inhibitors, may contribute to medical treatment of insulinomas. Our findings highlight the importance of YY1 in pancreatic ?-cells and may provide therapeutic targets for PNETs.
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Visible-light optical coherence tomography for retinal oximetry.
Opt Lett
PUBLISHED: 06-01-2013
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We applied a visible-light spectroscopic optical coherence tomography (vis-OCT) for in vivo retinal oximetry. To extract hemoglobin oxygen saturation (sO(2)) in individual retinal vessels, we established a comprehensive analytical model to describe optical absorption, optical scattering, and blood cell packing factor in the whole blood and fit the acquired vis-OCT signals from the bottom of each imaged vessel. We found that averaged sO(2) values in arterial and venous bloods were 95% and 72%, respectively.
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High dose of extracellular ATP switched autophagy to apoptosis in anchorage-dependent and anchorage-independent hepatoma cells.
Purinergic Signal.
PUBLISHED: 05-15-2013
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Extracellular adenosine triphosphate (eATP) transduces purinergic signal and plays an important regulatory role in many biological processes, including tumor cell growth and cell death. A large amount of eATP exists in the fast-growing tumor center and inflammatory tumor microenvironment. Tumor cells could acquire anoikis resistance and anchorage independence in tumor microenvironment and further cause metastatic lesion. Whether such a high amount of eATP has any effect on the anchored and non-anchored tumor cells in tumor microenvironment has not been elucidated and is investigated in this study. Our data showed that autophagy helped hepatoma cells to maintain survival under the treatment of no more than 1 mM of eATP. Only when eATP concentration reached a relatively high level (2.5 mM), cell organelle could not be further maintained by autophagy, and apoptosis and cell death occurred. In hepatoma cells under treatment of 2.5 mM of eATP, an AMP-activated protein kinase (AMPK) pathway was dramatically activated while mTOR signaling pathway was suppressed in coordination with apoptosis. Further investigation showed that the AMPK/mTOR axis played a key role in tipping the balance between autophagy-mediated cell survival and apoptosis-induced cell death under the treatment of eATP. This work provides evidence to explain how hepatoma cells escape from eATP-induced cytotoxicity as well as offers an important clue to consider effective manipulation of cancer.
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Effects of low-level organic selenium on lead-induced alterations in neural cell adhesion molecules.
Brain Res.
PUBLISHED: 05-11-2013
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Low-level lead (Pb) exposure has been reported to impair the formation and consolidation of learning and memory by inhibiting the expression of neural cell adhesion molecules (NCAMs) and altering the temporal profile of its polysialylation state. In this study, we investigated whether administration of low-level organic selenium (selenomethionine, Se) at different time points could affect Pb-induced changes of NCAMs in female Wistar rats. Here we reported that the exposure of Se (60?g/kg body weight/day) at different time points significantly alleviated Pb-induced reductions in the mRNA and protein levels of NCAMs, and increases in the mRNA levels of two polysialyltransferases (St8sia II, Stx; St8sia IV, Pst) as well as the sialyltransferase activity (p<0.05). The concentrations of Pb in blood and hippocampi of Wistar rats treated with the combination of Se and Pb were significantly lower than those treated with Pb alone (p<0.05). Our results suggest that low-level organic Se can not only prevent but also reverse Pb-induced alterations in the expression and polysialylated state of NCAMs as well as the concentration of Pb in rat blood and hippocampus.
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Structural comparison of the wild-type and drug-resistant mutants of the influenza A M2 proton channel by molecular dynamics simulations.
J Phys Chem B
PUBLISHED: 05-09-2013
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The influenza A M2 channel in the viral envelope is a pH-regulated proton channel that is crucial for viral infection and replication. Amantadine and rimantadine are two M2 inhibitors that have been widely used as anti-influenza drugs. However, due to naturally occurring drug-resistant mutations, their inhibition ability has gradually decreased. These drug-resistant mutations are found at various positions on the transmembrane domain of the M2 protein and could be categorized to three types: mutations close to the drug-binding site located at the pore-facing positions (V27A, A30T, S31N, and G34E); mutations at the interhelical interfaces at the N-terminal half of the channel (L26F); and mutations outside the drug-binding site lying at the interhelical interfaces (L38F, D44A). Investigating the structures and the M2-inhibitor interactions of these mutants would illuminate drug inhibition and drug resistance mechanisms and guide the design of novel anti-influenza drugs targeting these drug-resistant mutants. In this study, we chose four mutations at different positions (V27A, S31N, L26F, L38F) and conducted molecular dynamics simulations on both the apo-form and the drug-bound forms. The protein structures as well as the water structure in the channel pore were analyzed. Stable water clusters facilitating drug binding were found. Both the protein pore radius profiles and the structure of the water clusters were sensitive to the mutations. Based on our simulations, we compared the structures of the mutated proteins and proposed possible mechanisms for drug resistance of these mutations.
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Prognostic values of various clinical factors and genetic subtypes for diffuse large B-cell lymphoma patients: a retrospective analysis of 227 cases.
Asian Pac. J. Cancer Prev.
PUBLISHED: 04-30-2013
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To analyze the significance of different clinical factors for prognostic prediction in diffuse large B-cell lymphoma (DLBCL) patients.
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Characterization of the complete mitochondrial genome of Diaphania pyloalis (Lepidoptera: Pyralididae).
Gene
PUBLISHED: 04-26-2013
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The complete mitochondrial genome (mitogenome) of Diaphania pyloalis (Lepidoptera: Pyralididae) was determined to be 15,298 bp and has the typical gene organization of mitogenomes from lepidopteran insects. It consists of 13 protein-coding genes (PCGs), two rRNA genes, 22 tRNA genes and an A+T-rich region. The A+T content of this mitogenome is 80.83% and the AT skew is slightly positive. All PCGs are initiated by ATN codons, except for cytochrome c oxidase subunit 1 (cox1) gene which is initiated by CGA. Only the cox2 gene has an incomplete stop codon consisting of just a T. All the tRNA genes display a typical clover-leaf structure of mitochondrial tRNA. The A+T-rich region of the mitogenome is 332 bp in length, including several common features found in lepidopteran mitogenomes. Phylogenetic analysis showed that the D. pyloalis is close to Pyralididae.
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Identification of immune response-related genes in the Chinese oak silkworm, Antheraea pernyi by suppression subtractive hybridization.
J. Invertebr. Pathol.
PUBLISHED: 04-23-2013
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Insects possess an innate immune system that responds to invading microorganisms. In this study, a subtractive cDNA library was constructed to screen for immune response-related genes in the fat bodies of Antheraea pernyi (Lepidoptera: Saturniidae) pupa challenged with Escherichia coli. Four hundred putative EST clones were identified by suppression subtractive hybridization (SSH), including 50 immune response-related genes, three cytoskeleton genes, eight cell cycle and apoptosis genes, five respiration and energy metabolism genes, five transport genes, 40 metabolism genes, ten stress response genes, four transcription and translation regulation genes and 77 unknown genes. To verify the reliability of the SSH data, the transcription of a set of randomly selected immune response-related genes were confirmed by semi-quantitative reverse transcription-PCR (RT-PCR) and real-time quantitative reverse transcription-PCR (qRT-PCR). These identified immune response-related genes provide insight into understanding the innate immunity in A. pernyi.
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An independent positive relationship between the serum total osteocalcin level and fat-free mass in healthy premenopausal women.
J. Clin. Endocrinol. Metab.
PUBLISHED: 04-03-2013
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It is widely reported that osteocalcin is negatively associated with fat mass. However, there are few reports describing its correlation with fat-free mass, particularly in women.
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A lower value for quantitative ultrasound at radius is an additional indicator of metabolic syndrome and cardiovascular disease risk.
Clin. Endocrinol. (Oxf)
PUBLISHED: 04-01-2013
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The relationships between quantitative ultrasound (QUS) values, metabolic syndrome (MetS) and cardiovascular disease (CVD) risk are unclear. Objective The objective was to determine the relationships between QUS and MetS as well as CVD risk.
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[Clinicopathological features and management of gastrointestinal stromal tumors complicated with synchronous other alimentary malignant tumor].
Zhonghua Wei Chang Wai Ke Za Zhi
PUBLISHED: 03-29-2013
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To explore the clinicopathologic features, treatment and prognosis of gastrointestinal stromal tumor(GIST) complicated with synchronous other alimentary malignant tumors.
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Hypoxia-inducible factor 1? mediates the down-regulation of superoxide dismutase 2 in von Hippel-Lindau deficient renal clear cell carcinoma.
Biochem. Biophys. Res. Commun.
PUBLISHED: 03-26-2013
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Hypoxia-inducible factor 1? (HIF-1?) is an oxygen-sensitive subunit of HIF-1, the master transcription factor for cellular response to hypoxia. Down-regulation of the mitochondrial enzyme superoxide dismutase 2 (SOD2) contributes to the stabilization of HIF-1? under hypoxia due to the decreased dismutation of superoxide radical. Here we report that HIF-1? could also regulate the expression of SOD2. We found that both stabilization of HIF-1? expression under nomoxia caused by pVHL deficiency and hypoxia treatment significantly reduced SOD2 expression, and shRNAs specifically against HIF-1? restored SOD2 expression in both circumstances. Further analyses with luciferase reporter assay and chromatin immunoprecipitation assay revealed that HIF-1? inhibited and directly bound to the hypoxia-responsive element in SOD2 promoter. These findings indicated the existence of a positive feedback between HIF-1? and SOD2 and provided new clues for understanding the molecular mechanisms of hypoxia adaptation.
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Cobalt(II), copper(II), zinc(II) and cadmium(II) complexes based on dibenzimidazolyl bidentate ligands with alkanyl linkers: crystal structure, weak interactions and conformations.
Dalton Trans
PUBLISHED: 03-06-2013
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Eight metal complexes, {[Co(bibim-4)2(H2O)2](NO3)2}n (1), {[Cu(bibim-4)2(NO3)](NO3)}n (2), [Co(bibim-3)(TP)]n (3), [Zn2(bibim-3)]2(OAc)4] (4), [Co(bibim-2)(NO3)2]n (5), [Zn(bibim-4)(NO3)2]n (6), [Zn(bibim-4)(OAc)2]n (7) and [Cd(bibim-4)(NO3)2(DMF)]n (8) (bibim-2 = 1,2-bis(benzimidazol-l-yl)ethane, bibim-3 = 1,3-bis(benzimidazol-l-yl)propane, bibim-4 = 1,4-bis(benzimidazol-l-yl)butane and TP = terephthalate) have been prepared by means of the self-assembly of Co(II), Cu(II), Zn(II) or Cd(II) salts, dibenzimidazolyl bidentate ligands bearing alkanyl linkers and terephthalic acid. These complexes are structurally characterized by X-ray diffraction analyses. In complexes 1 and 2, 2D network layers with macrometallocycles are formed via metal centers and the ligand bibim-4. A 2D network layer with macrometallocycles in 3 is formed via Co(II) centers, the ligand bibim-3 and terephthalate molecules. In complex 4, a 20-membered macrometallocycle is formed by two bibim-3 ligands and two Zn(II) atoms. In complexes 5–8, 1D polymeric chains are formed via metal centers and the bibim-2 or bibim-4 ligands. In the crystal packings of complexes 1–8, 2D supramolecular layers and 3D supramolecular frameworks are formed via intermolecular weak interactions, including ?–? interactions and hydrogen bonds. The different types of ?–? interactions from the benzimidazole ring as well as the conformations of the ligands and metal complexes are described. Additionally, the fluorescence emission spectra of the ligands and metal complexes are reported.
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Exploring the ligand-protein networks in traditional chinese medicine: current databases, methods, and applications.
Evid Based Complement Alternat Med
PUBLISHED: 02-24-2013
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The traditional Chinese medicine (TCM), which has thousands of years of clinical application among China and other Asian countries, is the pioneer of the "multicomponent-multitarget" and network pharmacology. Although there is no doubt of the efficacy, it is difficult to elucidate convincing underlying mechanism of TCM due to its complex composition and unclear pharmacology. The use of ligand-protein networks has been gaining significant value in the history of drug discovery while its application in TCM is still in its early stage. This paper firstly surveys TCM databases for virtual screening that have been greatly expanded in size and data diversity in recent years. On that basis, different screening methods and strategies for identifying active ingredients and targets of TCM are outlined based on the amount of network information available, both on sides of ligand bioactivity and the protein structures. Furthermore, applications of successful in silico target identification attempts are discussed in detail along with experiments in exploring the ligand-protein networks of TCM. Finally, it will be concluded that the prospective application of ligand-protein networks can be used not only to predict protein targets of a small molecule, but also to explore the mode of action of TCM.
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Characterization of the complete mitochondrial genome of Bombyx mori strain H9 (Lepidoptera: Bombycidae).
Gene
PUBLISHED: 02-05-2013
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The complete mitochondrial genome (mitogenome) of Bombyx mori strain H9 (Lepidoptera: Bombycidae) is 15,670base pairs (bp) in length, encoding 13 protein-coding genes (PCGs), two rRNA genes, 22 tRNA genes and a control region. The nucleotide composition of the genome is highly A+T biased, accounting for 81.31%, with a slightly positive AT skewness (0.059). The arrangement of 13 PCGs is similar to that of other sequenced lepidopterans. All the PCGs are initiated by ATN codons, except for the cytochrome c oxidase subunit 1 (cox1) gene, which is proposed by the TTAG sequence as observed in other lepidopterans. Unlike the other PCGs, the cox1 and cytochrome c oxidase subunit 2 (cox2) genes have incomplete stop codons consisting of just a T. All tRNAs have typical structures of insect mitochondrial tRNAs, which is different from other sequenced lepidopterans. The structure of A+T-rich region is similar to that of other sequenced lepidopterans, including non-repetitive sequences, the ATAGA binding domain, a 18bp poly-T stretch and a poly-A element upstream of transfer RNA M (trnM) gene. Phylogenetic analysis shows that the domesticated silkmoth B. mori originated from the Chinese Bombyx mandarina.
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The changing clinical patterns of primary hyperparathyroidism in Chinese patients: data from 2000 to 2010 in a single clinical center.
J. Clin. Endocrinol. Metab.
PUBLISHED: 01-30-2013
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In Western countries, most patients with primary hyperparathyroidism (PHPT) are asymptomatic. The incidence of parathyroid cancer is as low as 1% but is trending upward. The clinical outlook for Chinese patients with PHPT is unclear.
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Integrated photoacoustic ophthalmoscopy and spectral-domain optical coherence tomography.
J Vis Exp
PUBLISHED: 01-29-2013
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Both the clinical diagnosis and fundamental investigation of major ocular diseases greatly benefit from various non-invasive ophthalmic imaging technologies. Existing retinal imaging modalities, such as fundus photography, confocal scanning laser ophthalmoscopy (cSLO), and optical coherence tomography (OCT), have significant contributions in monitoring disease onsets and progressions, and developing new therapeutic strategies. However, they predominantly rely on the back-reflected photons from the retina. As a consequence, the optical absorption properties of the retina, which are usually strongly associated with retinal pathophysiology status, are inaccessible by the traditional imaging technologies. Photoacoustic ophthalmoscopy (PAOM) is an emerging retinal imaging modality that permits the detection of the optical absorption contrasts in the eye with a high sensitivity. In PAOM nanosecond laser pulses are delivered through the pupil and scanned across the posterior eye to induce photoacoustic (PA) signals, which are detected by an unfocused ultrasonic transducer attached to the eyelid. Because of the strong optical absorption of hemoglobin and melanin, PAOM is capable of non-invasively imaging the retinal and choroidal vasculatures, and the retinal pigment epithelium (RPE) melanin at high contrasts. More importantly, based on the well-developed spectroscopic photoacoustic imaging, PAOM has the potential to map the hemoglobin oxygen saturation in retinal vessels, which can be critical in studying the physiology and pathology of several blinding diseases such as diabetic retinopathy and neovascular age-related macular degeneration. Moreover, being the only existing optical-absorption-based ophthalmic imaging modality, PAOM can be integrated with well-established clinical ophthalmic imaging techniques to achieve more comprehensive anatomic and functional evaluations of the eye based on multiple optical contrasts. In this work, we integrate PAOM and spectral-domain OCT (SD-OCT) for simultaneously in vivo retinal imaging of rat, where both optical absorption and scattering properties of the retina are revealed. The system configuration, system alignment and imaging acquisition are presented.
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Expression and diagnostic relevance of heat shock protein 90 and signal transducer and activator of transcription 3 in malignant pheochromocytoma.
J. Clin. Pathol.
PUBLISHED: 01-15-2013
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Malignant pheochromocytoma (PCC) is a rare catecholamine producing tumour with a poor prognosis. For many years predicting PCC behaviour has remained a highly difficult task. The aim of this study was to evaluate heat shock protein 90 (HSP90) and signal transducer and activator of transcription 3 (STAT3) as tissue-based markers to predict malignant PCC.
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JoVE Visualize is a tool created to match the last 5 years of PubMed publications to methods in JoVE's video library.

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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.