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Find video protocols related to scientific articles indexed in Pubmed.
Heparin makes differences: a molecular dynamics simulation study on the human ?II-tryptase monomer.
Mol Biosyst
PUBLISHED: 11-05-2014
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Human ?-tryptase, an enzyme with trypsin-like activity in mast cells, is an important target for the treatment of inflammatory and allergy related diseases. Heparin has been inferred to play a vital role in the stabilization of the tryptase structure and the maintenance of its active form. Up to now, the structure-function relationship between heparin and the ?II-tryptase monomer has not been studied with atomic resolution due to the lack of a complex structure of tryptase and heparin. To this end, the exact effect of heparin bonding to the ?II-tryptase monomer structure has been investigated using molecular docking and molecular dynamics (MD) simulation. The MD simulation results combined with MM-GB/SA calculations showed that heparin stabilized the ?-tryptase structure mainly through salt bridge interaction. The averaged noncovalent interaction (aNCI) method was employed for the visualization of nonbonding interactions. A crucial loop, which is located in the core region of ?II-tryptase monomer structure, has been found. Arg188 and Asp189 from this loop act as a salt bridge intermediary between 4-mer heparin and 0GX. The observation of a salt bridge between Asp189 and P1 groups of 0GX confirms the supposed interaction between these two groups. These two residues have been proved to be responsible for the direction of the P1 group of 0GX. Our study revealed that how heparin affected the activity of the human ?II-tryptase monomer (hBTM) through salt bridge interactions. The knowledge of heparin binding characteristics and the key residue contributions in this study may enlighten further the inhibitor design of this enzyme and may also improve our understanding of inflammatory and allergy related diseases.
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Encoding Abrupt and Uniform Dopant Profiles in Vapor-Liquid-Solid Nanowires by Suppressing the Reservoir Effect of the Liquid Catalyst.
ACS Nano
PUBLISHED: 11-04-2014
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Semiconductor nanowires (NWs) are often synthesized by the vapor-liquid-solid (VLS) mechanism, a process in which a liquid droplet-supplied with precursors in the vapor phase-catalyzes the growth of a solid, crystalline NW. By changing the supply of precursors, the NW composition can be altered as it grows to create axial heterostructures, which are applicable to a range of technologies. The abruptness of the heterojunction is mediated by the liquid catalyst, which can act as a reservoir of material and impose a lower limit on the junction width. Here, we demonstrate that this "reservoir effect" is not a fundamental limitation and can be suppressed by selection of specific VLS reaction conditions. For Au-catalyzed Si NWs doped with P, we evaluate dopant profiles under a variety of synthetic conditions using a combination of elemental imaging with energy-dispersive X-ray spectroscopy and dopant-dependent wet-chemical etching. We observe a diameter-dependent reservoir effect under most conditions. However, at sufficiently slow NW growth rates (?250 nm/min) and low reactor pressures (?40 Torr), the dopant profiles are diameter independent and radially uniform with abrupt, sub-10 nm axial transitions. A kinetic model of NW doping, including the microscopic processes of (1) P incorporation into the liquid catalyst, (2) P evaporation from the catalyst, and (3) P crystallization in the Si NW, quantitatively explains the results and shows that suppression of the reservoir effect can be achieved when P evaporation is much faster than P crystallization. We expect similar reaction conditions can be developed for other NW systems and will facilitate the development of NW-based technologies that require uniform and abrupt heterostructures.
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Neutron emission measurement at the HL-2A tokamak device with a liquid scintillation detector.
Rev Sci Instrum
PUBLISHED: 11-03-2014
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Neutron emission measurement at the HL-2A tokamak device with a liquid scintillation detector is described. The detector was placed at a location with little structure material in the field of view, and equipped with a gain monitoring system which could provide the possibility to evaluate the gain variation as well as to correct for the detector response. Time trace of the neutron emissivity was obtained and it was consistent with the result of a standard (235)U fission chamber. During the plasma discharge the neutron yield could vary by about four orders of magnitude and the fluctuation of the detector gain was up to about 6%. Pulse height spectrum of the liquid scintillation detector was constructed and corrected with the aid of the gain monitoring system, and the correction was found to be essential for the assessment of the neutron energy spectrum. This successful measurement offered experience and confidence for the application of liquid scintillation detectors in the upcoming neutron camera system.
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Polyribosomes Are Molecular 3D Nanoprinters That Orchestrate the Assembly of Vault Particles.
ACS Nano
PUBLISHED: 10-31-2014
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Ribosomes are molecular machines that function in polyribosome complexes to translate genetic information, guide the synthesis of polypeptides, and modulate the folding of nascent proteins. Here, we report a surprising function for polyribosomes as a result of a systematic examination of the assembly of a large ribonucleoprotein complex, the vault particle. Structural and functional evidence points to a model of vault assembly whereby the polyribosome acts like a 3D nanoprinter to direct the ordered translation and assembly of the multi-subunit vault homopolymer, a process which we refer to as polyribosome templating. Structure-based mutagenesis and cell-free in vitro expression studies further demonstrated the critical importance of the polyribosome in vault assembly. Polyribosome templating prevents chaos by ensuring efficiency and order in the production of large homopolymeric protein structures in the crowded cellular environment and might explain the origin of many polyribosome-associated molecular assemblies inside the cell.
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[Influence of ozone on snap bean under ambient air in two sites of northern China].
Huan Jing Ke Xue
PUBLISHED: 10-24-2014
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Tropospheric ozone (O3) has been assumed the most phytotoxic air pollutant and the snap bean (Phaseolus vulgaris L.) is known to be an ozone-sensitive species. Two genotypes (R123, ozone-tolerance, S156, ozone-sensitivity) of snap bean were explored in three places. The objective of this study was to evaluate whether the snap bean was influenced under the current ambient ozone concentration. The findings indicated that the leaves of bean grown at Research Center for Eco-Environmental Sciences (RCEES), Chinese Academy of Sciences and ChangPing showed visible ozone symptoms under the ambient ozone concentration, and the averaged ozone injury proportion in S156 was 23.5% higher than R123 during the entire growth season. The ozone damage to the snap bean depends on the plant growing stages. The injury symptoms appeared just after flowering, increased from the stages of flowering to pod formation, and reached the maximum at the stages of pod maturation. The ratio of S156/R123 in pod yield was 0.48, and 0.24 and 0.73 in the RCEES, ChangPing and Harbin, respectively. The ratio close to 1 was assumed that the plant growth is not affected by ozone, and the lower ratio is, the more damage caused by ozone. Obviously, the current ambient ozone concentration of Beijing area has significantly caused the yield loss of snap bean.
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Effects of 5?fluorouracil and class III phosphoinositide 3?kinase small interfering RNA combination therapy on SGC7901 human gastric cancer cells.
Mol Med Rep
PUBLISHED: 10-01-2014
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The aim of the present study was to investigate the effects of small interfering RNA?mediated inhibition of Class III phosphoinositide 3?kinase (PI3K) signal transduction on the proliferation, apoptosis and autophagy of SGC7901 gastric cancer cells. The present study also aimed to examine the contribution of autophagic inhibition to the antitumor effects of 5?fluorouracil (5?FU). A PI3K(III)?RNA interference (i)?green fluorescent protein (GFP) recombinant replication adenovirus (AD) and the negative control (NC)?RNAi?GFP control AD were constructed and infected into SGC7901 cells. A methyl thiazolyl tetrazolium assay was used to determine the growth rate of the SGC7901 cells. Immunofluorescent staining was used to detect microtubule?associated protein 1 light chain 3 expression. The mitochondrial membrane potential was measured using the JC?1 fluorescent probe. Autophagic expression was monitored with MDC staining and transmission electron microscopy. The results revealed that following combination treatment of the SGC7901 gastric cancer cells with 5?FU + PI3K(III)?RNAi?AD, the optical density absorbance values at 24, 48 and 72 h were 0.17±1.64, 0.13±4.64 and 0.11±3.56%, respectively, with cell viability inhibition ratios of 45.89±6.67, 72.57±9.48 and 87.51±4.65%, respectively. As compared with the other treatment groups, the inhibition rate in the combined treatment group was significantly higher (P<0.05). The percentages of the cells with green fluorescence in the combined treatment group were 74.4±3.86 (24 h), 82.3±1.84 (48 h) and 92.5±1.1% (72 h), which were larger than those of the other groups. The percentage of cells with green fluorescence became larger, which indicated that the mitochondrion membrane potential had been reduced to a greater extent. MDC staining revealed that the number of autophagic vacuoles in the cells (measured at 24, 48 and 72 h) decreased gradually with time, with more autophagic vacuoles observed in the cells in the control group at 24 h than those in the other treatment groups. Fewest autophagic vacuoles were identified in the combined treatment group. Using a fluorescence microscope, the immune fluorescence expression of microtubule?associated proteins 1A/1B light chain 3A, which is the specific protein of autophagy, in the combined treatment group was observed to be significantly downregulated, as compared with the other groups. As determined by transmission electron microscopic observation of the SGC7901 gastric cancer cells, the degree of autophagy in the combined treatment group was significantly reduced, as compared with that of the other treatment groups. In conclusion, following combined treatment with 5?FU and an inhibitor of class III PI3K signal transduction, the proliferation of SGC7901 cells was significantly suppressed, the mitochondrion membrane potentials were significantly reduced and the expression levels of autophagic markers were significantly downregulated.
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Modification-dependent restriction endonuclease, MspJI, flips 5-methylcytosine out of the DNA helix.
Nucleic Acids Res.
PUBLISHED: 09-27-2014
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MspJI belongs to a family of restriction enzymes that cleave DNA containing 5-methylcytosine (5mC) or 5-hydroxymethylcytosine (5hmC). MspJI is specific for the sequence 5(h)mC-N-N-G or A and cleaves with some variability 9/13 nucleotides downstream. Earlier, we reported the crystal structure of MspJI without DNA and proposed how it might recognize this sequence and catalyze cleavage. Here we report its co-crystal structure with a 27-base pair oligonucleotide containing 5mC. This structure confirms that MspJI acts as a homotetramer and that the modified cytosine is flipped from the DNA helix into an SRA-like-binding pocket. We expected the structure to reveal two DNA molecules bound specifically to the tetramer and engaged with the enzyme's two DNA-cleavage sites. A coincidence of crystal packing precluded this organization, however. We found that each DNA molecule interacted with two adjacent tetramers, binding one specifically and the other non-specifically. The latter interaction, which prevented cleavage-site engagement, also involved base flipping and might represent the sequence-interrogation phase that precedes specific recognition. MspJI is unusual in that DNA molecules are recognized and cleaved by different subunits. Such interchange of function might explain how other complex multimeric restriction enzymes act.
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Wilms tumor protein recognizes 5-carboxylcytosine within a specific DNA sequence.
Genes Dev.
PUBLISHED: 09-25-2014
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In mammalian DNA, cytosine occurs in several chemical forms, including unmodified cytosine (C), 5-methylcytosine (5mC), 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC). 5mC is a major epigenetic signal that acts to regulate gene expression. 5hmC, 5fC, and 5caC are oxidized derivatives that might also act as distinct epigenetic signals. We investigated the response of the zinc finger DNA-binding domains of transcription factors early growth response protein 1 (Egr1) and Wilms tumor protein 1 (WT1) to different forms of modified cytosine within their recognition sequence, 5'-GCG(T/G)GGGCG-3'. Both displayed high affinity for the sequence when C or 5mC was present and much reduced affinity when 5hmC or 5fC was present, indicating that they differentiate primarily oxidized C from unoxidized C, rather than methylated C from unmethylated C. 5caC affected the two proteins differently, abolishing binding by Egr1 but not by WT1. We ascribe this difference to electrostatic interactions in the binding sites. In Egr1, a negatively charged glutamate conflicts with the negatively charged carboxylate of 5caC, whereas the corresponding glutamine of WT1 interacts with this group favorably. Our analyses shows that zinc finger proteins (and their splice variants) can respond in modulated ways to alternative modifications within their binding sequence.
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[Application of HLAMatchmaker analysis eplets mismatch of renal transplant matching].
Zhongguo Ying Yong Sheng Li Xue Za Zhi
PUBLISHED: 09-24-2014
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Eplets mismatch based on HLAMatchmaker software evaluates the clinical application of kidney transplantation.
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[Effects of amino acid on growth and secondary metabolites contents of adventitious roots of Tripterygium wilfordii].
Zhongguo Zhong Yao Za Zhi
PUBLISHED: 09-24-2014
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The adventitious root of Tripterygium wilfordii was used as experiment material to study effects of various concentration of aspartic acid, isoleucine, cysteine and arginine in MS medium on the growth and triptolide, wilforgine, wilforine contents of the adventitious roots. The results showed that compared with the control, supplemented with 0.25 mmol x L(-1) aspartic acid at 3rd week, the growth of the adventitious roots only accounted for 80%, but the content of triptolide of the adventitious roots and the medium was 1.36, 1.30 times, the content of wilforgine was 1.16, 1.37 times, the content of wilforine was 1.22, 1.63 times, respectively. At 3rd week 0.05 mmol x L(-1) isoleucine, the growth of adventitious roots was 97.3%, wilforgine of adventitious roots and medium 1.02, 1.27 times, wilforine 1.36 times and 1.15 times. At 1st week 0.25 mmol x L(-1) cysteine, the growth of the adventitious roots comprised 77.5% of the control, while content of triptolide of adventitious roots reached 1.87 times. At 2nd week 1.00 mmol x L(-1) cysteine, the growth of adventitious roots was 44.6% of the control, the content of wilforine in medium was 2.97 times. At 3rd week 0.50 mmol x L(-1) arginine, the growth of adventitious roots was 124.2%, the content of wilforgine and wilforine was 1.3, 1.4 times, respectively.
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Concise synthesis of 2,4-disubstituted thiazoles from ?-azido disulfides and carboxylic acids or anhydrides: asymmetric synthesis of cystothiazole C.
Org. Biomol. Chem.
PUBLISHED: 09-17-2014
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A novel and efficient method for the one-pot synthesis of 2,4-disubstituted thiazoles from carboxylic acids or anhydrides is presented. Based on this new method, the total synthesis of the bis-2,4-disubstituted bis(thiazoles) natural product cystothiazole C is also presented.
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[Effect of electroacupuncture stimulation of "Fenglong" (ST 40) on expression of inflammatory cytokines of celiac macrophages in hyperlipidemia rats].
Zhen Ci Yan Jiu
PUBLISHED: 09-16-2014
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To observe the effect of electroacupuncture (EA) stimulation of "Fenglong" (ST 40) on celiac inflammatory factors in rats with hyperlipemia (HLP), so as to reveal its mechanism underlying improvement of HLP.
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A Green Approach for Preparing Doped TiO2 Single Crystals.
ACS Appl Mater Interfaces
PUBLISHED: 09-16-2014
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Doped TiO2 with metal, nonmetal, and rare earth elements has shown a great potential in energy and environmental applications, but it is difficult to dope well-defined TiO2 single crystals (SCs) with {001} exposed facet due to their high crystallinity. In this work, we developed a green and general approach to prepare the {001}-exposed TiO2 SCs doped with various elements, on the basis of recycling the wasted ethylene glycol electrolyte from the anodic oxidation for TiO2 nanotube preparation. All six representative elements (i.e., metal, nonmetal, and rare earth types) could be successfully doped into the TiO2 SCs without breaking their single-crystalline structure and exposed high-energy facet. The electronic properties of the doped TiO2 SCs were significantly improved. All the doped TiO2 SCs exhibited a superior photoactivity under visible-light irradiation for degrading rhodamine B, a typical organic pollutant. The prepared doped TiO2 SCs have a promising potential in environmental and energy applications.
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Reduced graphene oxide supported palladium nanoparticles via photoassisted citrate reduction for enhanced electrocatalytic activities.
ACS Appl Mater Interfaces
PUBLISHED: 09-02-2014
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Reduced graphene oxide (rGO) supported palladium nanoparticles (Pd NPs) with a size of ?3 nm were synthesized using one-pot photoassisted citrate reduction. This synthetic approach allows for the formation and assembly of Pd NPs onto the rGO surface with a desired size and can be readily used for other metal NP preparation. The prepared rGO-Pd exhibited 5.2 times higher mass activity for ethanol oxidation reaction than the commercial platinum/carbon (Pt/C). In the oxygen reduction reaction tests, rGO-Pd exhibited comparable activity compared with Pt/C and maintained its high performance after 4000 cycles of potential sweep. These results demonstrate that our synthetic approach is effective for preparing graphene-supported metal NPs with excellent activity and stability in ethanol oxidation and oxygen reduction reactions.
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Theoretical insights into the reductive metabolism of CCl4 by cytochrome P450 enzymes and the CCl4-dependent suicidal inactivation of P450.
Dalton Trans
PUBLISHED: 08-29-2014
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The anaerobic metabolism of CCl4 by P450 enzymes was investigated using quantum chemical calculations. It was found that under anaerobic conditions, the substrate CCl4 might undergo one or two subsequent one-electron reductions to generate different reactive metabolites, trichloromethyl radical (?CCl3) and dichlorocarbene (:CCl2) respectively. Meanwhile, it was the reduced ferrous haem complex rather than the unreduced ferric haem complex that could directly achieve such reductions. Based on the formation of the former reactive metabolite, a further one-electron reduction could take place with the assistance of a proton to yield the latter reactive species, i.e., a further reductive dechloridation of ?CCl3 could take place via a novel SE3 mechanism. In addition, the ?CCl3 species was capable of binding covalently to the meso-carbon atom of the prosthetic group, leading to the suicidal destruction of P450 enzymes. Whereas the :CCl2 species was involved in the CCl4-dependent reversible P450 inhibition as its hydrolysis product, CO, but was not significantly involved in the CCl4-dependent irreversible P450 destruction. It is obvious that the reductive metabolism of CCl4 to reactive intermediates by P450 enzymes is an essential prerequisite for its toxicity.
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Quantitative determination of metformin, glyburide and its metabolites in plasma and urine of pregnant patients by LC-MS/MS.
Biomed. Chromatogr.
PUBLISHED: 08-27-2014
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This report describes the development and validation of an LC-MS/MS method for the quantitative determination of glyburide (GLB), its five metabolites (M1, M2a, M2b, M3 and M4) and metformin (MET) in plasma and urine of pregnant patients under treatment with a combination of the two medications. The extraction recovery of the analytes from plasma samples was 87-99%, and that from urine samples was 85-95%. The differences in retention times among the analytes and the wide range of the concentrations of the medications and their metabolites in plasma and urine patient samples required the development of three LC methods. The lower limit of quantitation (LLOQ) of the analytes in plasma samples was as follows: GLB, 1.02 ng/mL; its five metabolites, 0.100-0.113 ng/mL; and MET, 4.95 ng/mL. The LLOQ in urine samples was 0.0594 ng/mL for GLB, 0.984-1.02 ng/mL for its five metabolites and 30.0 µg/mL for MET. The relative deviation of this method was <14% for intra-day and inter-day assays in plasma and urine samples, and the accuracy was 86-114% in plasma, and 94-105% in urine. The method described in this report was successfully utilized for determining the concentrations of the two medications in patient plasma and urine. Copyright © 2014 John Wiley & Sons, Ltd.
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Engineering the interfaces of ITO@Cu2S nanowire arrays toward efficient and stable counter electrodes for quantum-dot-sensitized solar cells.
ACS Appl Mater Interfaces
PUBLISHED: 08-27-2014
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Among the issues that restrict the power conversion efficiency (PCE) of quantum-dot-sensitized solar cells (QDSSCs), insufficient catalytic activity and stability of counter electrodes (CEs) are critical but challenging ones. The state-of-the-art Cu/Cu2S CEs still suffer from mechanical instability and uncertainty due to the reaction of copper and electrolyte. Herein, ITO@Cu2S core-shell nanowire arrays were developed to fabricate CEs for QDSSCs, which have no such issues in Cu/Cu2S CEs. These nanowire arrays exhibited small charge transfer resistance and sheet resistance, and provided more active catalytic sites and easy accessibility for electrolyte due to the three-dimensional structure upon use as CEs. More interestingly, it was found that the interface of ITO/Cu2S significantly affected the performance of ITO@Cu2S nanowire array CEs. By varying synthetic methods, a series of ITO@Cu2S nanowire arrays were prepared to investigate the influence of ITO/Cu2S interface on their performance. The results showed that ITO@Cu2S nanowire array CEs with a continuous Cu2S nanocrystal shell fabricated via an improved cation exchange route exhibited excellent and thickness-dependent performance. The PCE of corresponding QDSSCs increased by 11.6 and 16.5% compared to that with the discrete Cu2S nanocrystal and the classic Cu/Cu2S CE, respectively, indicating its promising potential as a new type of CE for QDSSCs.
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The role of telomeres and telomerase in hematologic malignancies and hematopoietic stem cell transplantation.
J Hematol Oncol
PUBLISHED: 08-20-2014
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Telomeres are specific nucleoprotein structures at the ends of eukaryotic chromosomes. Telomeres and telomere-associated proteins maintain genome stability by protecting the ends of chromosomes from fusion and degradation. In normal somatic cells, the length of the telomeres gradually becomes shortened with cell division. In tumor cells, the shortening of telomeres length is accelerated under the increased proliferation pressure. However, it will be maintained at an extremely short length as the result of activation of telomerase. Significantly shortened telomeres, activation of telomerase, and altered expression of telomere-associated proteins are common features of various hematologic malignancies and are related with progression or chemotherapy resistance in these diseases. In patients who have received hematopoietic stem cell transplantation (HSCT), the telomere length and the telomerase activity of the engrafted donor cells have a significant influence on HSCT outcomes. Transplantation-related factors should be taken into consideration because of their impacts on telomere homeostasis. As activation of telomerase is widespread in tumor cells, it has been employed as a target point in the treatment of neoplastic hematologic disorders. In this review, the characteristics and roles of telomeres and telomerase both in hematologic malignancies and in HSCT will be summarized. The current status of telomerase-targeted therapies utilized in the treatment of hematologic malignancies will also be reviewed.
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Analytic derivative couplings for spin-flip configuration interaction singles and spin-flip time-dependent density functional theory.
J Chem Phys
PUBLISHED: 08-20-2014
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We revisit the calculation of analytic derivative couplings for configuration interaction singles (CIS), and derive and implement these couplings for its spin-flip variant for the first time. Our algorithm is closely related to the CIS analytic energy gradient algorithm and should be straightforward to implement in any quantum chemistry code that has CIS analytic energy gradients. The additional cost of evaluating the derivative couplings is small in comparison to the cost of evaluating the gradients for the two electronic states in question. Incorporation of an exchange-correlation term provides an ad hoc extension of this formalism to time-dependent density functional theory within the Tamm-Dancoff approximation, without the need to invoke quadratic response theory or evaluate third derivatives of the exchange-correlation functional. Application to several different conical intersections in ethylene demonstrates that minimum-energy crossing points along conical seams can be located at substantially reduced cost when analytic derivative couplings are employed, as compared to use of a branching-plane updating algorithm that does not require these couplings. Application to H3 near its D(3h) geometry demonstrates that correct topology is obtained in the vicinity of a conical intersection involving a degenerate ground state.
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Myeloid-Specific Blockade of Notch Signaling by RBP-J Knockout Attenuates Spinal Cord Injury Accompanied by Compromised Inflammation Response in Mice.
Mol. Neurobiol.
PUBLISHED: 08-19-2014
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The outcome of spinal cord injury (SCI) is determined by both neural cell-intrinsic survival pathways and tissue microenvironment-derived signals. Macrophages dominating the inflammatory responses in SCI possess both destructive and reparative potentials, according to their activation status. Notch signaling is involved in both cell survival and macrophage-mediated inflammation, but a comprehensive role of Notch signaling in SCI has been elusive. In this study, we compared the effects of general Notch blockade by a pharmaceutical ?-secretase inhibitor (GSI) and myeloid-specific Notch signal disruption by recombination signal binding protein J? (RBP-J) knockout on SCI. The administration of Notch signal inhibitor GSI resulted in worsened hind limb locomotion and exacerbated inflammation. However, mice lacking RBP-J, the critical transcription factor mediating signals from all four mammalian Notch receptors, in myeloid lineage displayed promoted functional recovery, attenuated glial scar formation, improved neuronal survival and axon regrowth, and mitigated inflammatory response after SCI. These benefits were accompanied by enhanced AKT activation in the lesion area after SCI. These findings demonstrate that abrogating Notch signal in myeloid cells ameliorates inflammation response post-SCI and promotes functional recovery, but general pharmaceutical Notch interception has opposite effects. Therefore, clinical intervention of Notch signaling in SCI needs to pinpoint myeloid lineage to avoid the counteractive effects of global inhibition.
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Labeled protein recognition at a membrane bilayer interface by embedded synthetic receptors.
Langmuir
PUBLISHED: 08-19-2014
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Self-folding deep cavitands embedded in a supported lipid bilayer are capable of recognizing suitably labeled proteins at the bilayer interface. The addition of a choline derived binding "handle" to a number of different proteins allows their selective noncovalent recognition, with association constants on the order of 10(5) M(-1). The proteins are displayed at the water:bilayer interface, and a single binding handle allows recognition of the large, charged protein by a small molecule synthetic receptor via complementary shape and charge interactions.
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DJ-1: a promising marker in metastatic uveal melanoma.
J. Cancer Res. Clin. Oncol.
PUBLISHED: 08-17-2014
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Overexpression of DJ-1 was associated with metastatic uveal melanoma (UM). The purpose of this study was to evaluate the potential of serum DJ-1 as a biomarker for metastasis of uveal melanoma.
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Design, synthesis and fungicidal activities of some novel pyrazole derivatives.
Molecules
PUBLISHED: 08-07-2014
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In order to discover new compounds with good fungicidal activities, 32 pyrazole derivatives were designed and synthesized. The structures of the target compounds were confirmed by 1H-NMR, 13C-NMR, and high-resolution electrospray ionization mass spectrometry (HR-ESI-MS), and their fungicidal activities against Botrytis cinerea, Rhizoctonia solani Kuhn, Valsa mali Miyabe et Yamada, Thanatephorus cucumeris (Frank) Donk, Fusarium oxysporum (S-chl) f.sp. cucumerinum Owen, and Fusarium graminearum Schw were tested. The bioassay results indicated that most of the derivatives exhibited considerable antifungal activities, especially compound 26 containing a p-trifluoromethyl- phenyl moiety showed the highest activity, with EC50 values of 2.432, 2.182, 1.787, 1.638, 6.986, and 6.043 ?g/mL against B. cinerea, R. solani, V. mali, T. cucumeris, F. oxysporum, and F. graminearum, respectively. Moreover, the activities of compounds such as compounds 27-32 were enhanced by introducing isothiocyanate and carboxamide moieties to the 5-position of the pyrazole ring.
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Role of the cerebrospinal fluid-contacting nucleus in the descending inhibition of spinal pain transmission.
Exp. Neurol.
PUBLISHED: 08-06-2014
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The brainstem is well recognized as a critical site for integrating descending modulatory systems that both inhibit and facilitate pain at the level of the spinal cord. The cerebrospinal fluid-contacting nucleus (CSF-contacting nucleus) distributes and localizes in the ventral periaqueductal central gray of the brainstem. Although emerging lines of evidence suggest that the CSF-contacting nucleus may be closely linked to transduction and regulation of pain signals, the definitive role of the CSF-contacting nucleus in pain modulation remains poorly understood. In the present study, we determined the role of the CSF-contacting nucleus in rat nocifensive behaviors after persistent pain by targeted ablation of the CSF-contacting nucleus in the brainstem using the cholera toxin subunit B-saporin (CB-SAP), a cytotoxin coupled to cholera toxin subunit B. Compared with CB/SAP, CB-SAP induced complete ablation of the CSF-contacting nucleus, and the CB-SAP-treated rats showed hypersensitivity in responses to acute nociceptive stimulation, and exacerbated spontaneous nocifensive responses induced by formalin, thermal hyperalgesia and mechanical allodynia induced by plantar incision. Furthermore, immunohistochemical experiments showed that the CSF-contacting nucleus was a cluster of 5-HT-containing neurons in the brainstem, and the spinal projection of serotonergic axons originating from the CSF-contacting nucleus constituted the descending 5-HT pathway to the spinal cord. CB-SAP induced significant downregulation of 5-HT in the spinal dorsal horn, and intrathecal injection of 5-HT significantly reversed hypersensitivity in responses to acute nociceptive stimulation in the CB-SAP-treated rats. These results indicate that the CSF-contacting nucleus 5-HT pathway is an important component of the endogenous descending inhibitory system in the control of spinal nociceptive transmission.
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Controllable atmospheric pressure growth of mono-layer, bi-layer and tri-layer graphene.
Chem. Commun. (Camb.)
PUBLISHED: 08-06-2014
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Here we report a three-step growth method for high-quality mono-layer, bi-layer and tri-layer graphene with coverage ~90% at atmospheric pressure. The growth temperature and gas flow rate have been found to be the key factors. This method would be of great importance for the large scale production of graphene with defined thickness.
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Rapid in situ detection of ultratrace 2,4-dinitrotoluene solids by a sandwiched paper-like electrochemical sensor.
Anal. Chem.
PUBLISHED: 08-05-2014
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This work reported the rapid in situ detection of ultratrace 2,4-dinitrotoluene (DNT) solids on various substrates by a sandwiched paper-like electrochemical sensor. The sensor, prepared by a simple electroless deposition method without using special instruments, possessed a unique thin-film structure of an insulated polyvinylidene fluoride (PVDF) membrane in between two gold (Au) conducting layers. The resulting gold-PVDF sandwich (GPVDFS) array exhibited excellent flexibility, porosity and electrochemical performance as a highly integrated dual-electrode sensor platform. The infiltration of nonvolatile ionic liquid (IL) electrolytes containing ferrocene (Fc) into the GPVDFS array produced a paper-like electrochemical sensor, which can directly detect ultratrace DNT solids on various substrate surfaces (e.g., plant leaves, gloves and metal knives) with detection limit as low as 0.33 ng/mm(2). The critical role of Fc in the detection of DNT at this dual-electrode sensor was explored. The compensating electrochemical oxidation of Fc at the counter/reference electrode was found to be essential to the reduction of DNT at the working electrode when IL electrolytes were employed. The present work thus demonstrated the promising applications of paper-based porous electrode arrays in developing IL-based electrochemical sensors for the in situ detection of analyte solids in complicated environments.
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Serum protein S9, SOD3 and MMP9 as new diagnostic biomarkers for pulmonary tuberculosis by iTRAQ-coupled two-dimensional LC-MS/MS.
Proteomics
PUBLISHED: 07-31-2014
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This study aimed to discover the novel non-invasive biomarkers for the diagnosis of pulmonary tuberculosis (TB). We applied iTRAQ 2D LC-MS/MS technique to investigate protein profiles in patients with pulmonary TB and other lung diseases. A total of 34 differentially expressed proteins (24 up-regulated proteins and 10 down-regulated proteins) were identified in the serum of pulmonary TB patients. Significant differences in protein S100-A9 (S100A9), extracellular superoxide dismutase [Cu-Zn] (SOD3), and matrix metalloproteinase 9 (MMP9) were found between pulmonary TB and other lung diseases by ELISA. Correlations analysis revealed that the serum concentration of MMP9 in the pulmonary TB was in moderate correlation with SOD3 (r = 0.581) and S100A9 (r = 0.471), while SOD3 was in weak correlation with S100A9 (r = 0.287). The combination of serum S100A9, SOD3, and MMP9 levels could achieve 92.5% sensitivity and 95% specificity to discriminate between pulmonary TB and healthy controls, 90% sensitivity and 87.5% specificity to discriminate between pulmonary TB and pneumonia, and 85% sensitivity and 92.5% specificity to discriminate between pulmonary TB and lung cancer, respectively. The results showed that S100A9, SOD3, and MMP9 may be potential diagnostic biomarkers for pulmonary TB, and provided experimental basis for the diagnosis of pulmonary TB. This article is protected by copyright. All rights reserved.
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Expression of acid-sensing ion channels in nucleus pulposus cells of the human intervertebral disk is regulated by non-steroid anti-inflammatory drugs.
Acta Biochim. Biophys. Sin. (Shanghai)
PUBLISHED: 07-30-2014
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Non-steroid anti-inflammatory drugs (NSAIDs) are generally used in the treatment of inflammation and pain through cyclooxygenase (COX) inhibition. Mounting evidence has indicated additional COX-independent targets for NSAIDs including acid-sensing ion channels (ASICs) 1a and 3. However, detailed function and mechanism of ASICs still remain largely elusive. In this study, the impact of NSAIDs on ASICs in nucleus pulposus cells of the human intervertebral disk was investigated. Nucleus pulposus cells were isolated and cultured from protruded disk tissues of 40 patients. It was shown that ASIC1a and ASIC3 were expressed and functional in these cells by analyzing proton-gated currents after ASIC inhibition. We further investigated the neuroprotective capacity of ibuprofen (a COX inhibitor), psalmotoxin-1 (PcTX1, a tarantula toxin specific for homomeric ASIC1a), and amiloride (a classic inhibitor of the epithelial sodium channel ENaC/DEG family to which ASICs belong). PcTX1-containing venom has been shown to be comparable with amiloride in its neuroprotective features in rodent models of ischemia. Taken together, our data showed that amiloride, PcTX1, and ibuprofen decreased ASIC protein expression and thereby exerted protective effects from ASIC inhibition-mediated cell damage.
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The Carboxy-Terminal Domain of ROS1 Is Essential for 5-Methylcytosine DNA Glycosylase Activity.
J. Mol. Biol.
PUBLISHED: 07-24-2014
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Arabidopsis thaliana repressor of silencing 1 (ROS1) is a multi-domain bifunctional DNA glycosylase/lyase, which excises 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) as well as thymine and 5-hydroxymethyluracil (i.e., the deamination products of 5mC and 5hmC) when paired with a guanine, leaving an apyrimidinic (AP) site that is subsequently incised by the lyase activity. ROS1 is slow in base excision and fast in AP lyase activity, indicating that the recognition of pyrimidine modifications might be a rate-limiting step. In the C-terminal half, the enzyme harbors a helix-hairpin-helix DNA glycosylase domain followed by a unique C-terminal domain. We show that the isolated glycosylase domain is inactive for base excision but retains partial AP lyase activity. Addition of the C-terminal domain restores the base excision activity and increases the AP lyase activity as well. Furthermore, the two domains remain tightly associated and can be co-purified by chromatography. We suggest that the C-terminal domain of ROS1 is indispensable for the 5mC DNA glycosylase activity of ROS1.
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Effects and mechanisms of transcutaneous electroacupuncture on chemotherapy-induced nausea and vomiting.
Evid Based Complement Alternat Med
PUBLISHED: 07-17-2014
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Nausea and vomiting are one of the major complications of chemotherapy for cancers. The aim of this study is to investigate the emetic effects and mechanisms involving serotonin and dopamine of needleless transcutaneous electroacupuncture (TEA) at Neiguan (PC6) and Jianshi (PC5) on chemotherapy-induced nausea and vomiting in patients with cancers. Seventy-two patients with chemotherapy were randomly divided into sham-TEA group (sham-TEA, n = 34) and TEA group (n = 38). TEA was performed at PC 6 and PC 5 (1?h, bid) in combination with granisetron. Sham-TEA was delivered at nonacupoints using the same parameters. We found the following. (1) In the acute phase, the conventional antiemetic therapy using Ondansetron effectively reduced nausea and vomiting; the addition of TEA did not show any additive effects. In the delayed phase, however, TEA significantly increased the rate of complete control (P < 0.01) and reduced the nausea score (P < 0.05), compared with sham-TEA. (2) TEA significantly reduced serum levels of 5-HT and dopamine in comparison with sham-TEA. Those results demonstrate that needleless transcutaneous electroacupuncture at PC6 using a watch-size digital stimulator improves emesis and reduces nausea in the delayed phase of chemotherapy in patients with cancers. This antiemetic effect is possibly mediated via mechanisms involving serotonin and dopamine.
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[Effects of electroacupuncture at "Fenglong" (ST 40) on formation of macrophage-derived foam cell and efflux of cholesterol in hyperlipidemia rats].
Zhongguo Zhen Jiu
PUBLISHED: 07-16-2014
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To explore action mechanism of electroacupuncture (EA) at "Fenglong" (ST 40) for treatment of hyperlipidemia.
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Ectopic DNMT3L triggers assembly of a repressive complex for retroviral silencing in somatic cells.
J. Virol.
PUBLISHED: 07-02-2014
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Mammalian genomes are replete with retrotransposable elements, including endogenous retroviruses. DNA methyltransferase 3-like (DNMT3L) is an epigenetic regulator expressed in prospermatogonia, growing oocytes, and embryonic stem (ES) cells. Here, we demonstrate that DNMT3L enhances the interaction of repressive epigenetic modifiers, including histone deacetylase 1 (HDAC1), SET domain, bifurcated 1 (SETDB1), DNA methyltransferase 3A (DNMT3A), and tripartite motif-containing protein 28 (TRIM28; also known as TIF1? and KAP1) in ES cells and orchestrates retroviral silencing activity with TRIM28 through mechanisms including, but not limited to, de novo DNA methylation. Ectopic expression of DNMT3L in somatic cells causes methylation-independent retroviral silencing activity by recruitment of the TRIM28/HDAC1/SETDB1/DNMT3A/DNMT3L complex to newly integrated Moloney murine leukemia virus (Mo-MuLV) proviral DNA. Concurrent with this recruitment, we also observed the accumulation of histone H3 lysine 9 trimethylation (H3K9me3) and heterochromatin protein 1 gamma (HP1?), as well as reduced H3K9 and H3K27 acetylation at Mo-MuLV proviral sequences. Ectopic expression of DNMT3L in late-passage mouse embryonic fibroblasts (MEFs) recruited cytoplasmically localized HDAC1 to the nucleus. The formation of this epigenetic modifying complex requires interaction of DNMT3L with DNMT3A as well as with histone H3. In fetal testes at embryonic day 17.5, endogenous DNMT3L also enhanced the binding among TRIM28, DNMT3A, SETDB1, and HDAC1. We propose that DNMT3L may be involved in initiating a cascade of repressive epigenetic modifications by assisting in the preparation of a chromatin context that further attracts DNMT3A-DNMT3L binding and installs longer-term DNA methylation marks at newly integrated retroviruses.
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Mechanism of A pH-induced Peptide Inserting into a POPC Bilayer: A Molecular Dynamic Study.
Curr Pharm Biotechnol
PUBLISHED: 06-24-2014
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Membrane insertion peptides have been developed in recent years and serve as cargos to deliver small molecules into cells. A class of membrane insertion peptides is the so called pH-induced peptides (pHLIPs), which are able to insert into membrane when the environment pH is acidic. Despite a number of experimental studies, the insertion process as well as the penetration mechanism is still worth study with computational methods. Thus, we performed molecular dynamics simulations in this study to elucidate the detailed penetration process and mechanism. Both protonated and unprotonated peptides are employed to interact with a POPCs bilayer. By analyzing the trajectory of the simulation, the peptide travelling across membrane is expected to take milliseconds or seconds. While the peptide penetrating through the POPC bilayer boundary is much faster (several nanoseconds). More importantly, the elaborate energies between a peptide and water molecules, the energies between a peptide and POPCs have been analyzed throughout the simulation time correspondingly. A constant decrease of interaction energies have been observed for peptide-water interaction in the protonated condition. At last, we employ the statistics of hydrogen bonds to explain the penetration mechanism tentatively. For the protonated system, the decrease of hydrogen bonds of peptide-water and the increase of hydrogen bonds of peptide- POPCs have been considered as the main driven force for the peptide insertion.
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Fumigant activity of eleven essential oil compounds and their selected binary mixtures against Culex pipiens pallens (Diptera: Culicidae).
Parasitol. Res.
PUBLISHED: 06-02-2014
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To seek natural products for the development of environment friendly mosquito control agents, fumigant activity of eleven essential oil compounds and the joint action of the active compounds were evaluated against Culex pipiens pallens adults. Fumigant bioassay demonstrated that carvacrol exhibited the highest fumigant activity followed by thymol and l-perillaldehyde, with LC50 values of 0.26, 0.28, and 0.34 mg/L air, respectively. Among the binary mixtures of four compounds with preferable performance, only the binary mixture of carvacrol and thymol (1:1, w/w) displayed a synergistic effect with the co-toxicity coefficient (CTC) value of 174.1 and LC50 value of 0.16 mg/L air. Furthermore, the actual efficacy of the binary mixture at 300 mg/mat (KT50?=?7.9, 15.8, and 22.0 min after 0, 2, and 4 h of preliminary heating, respectively) was comparable with that of d-allethrin at 30 mg/mat (KT50?=?8.7, 17.9, and 21.2 min after 0, 2, and 4 h of preliminary heating, respectively) tested in vaporizing mats by the glass chamber method (70?×?70?×?70 cm). These results revealed that carvacrol, thymol, and their binary mixture have potential for the development of natural fumigants for adult mosquito control.
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A theoretical analysis of the phosphorescence efficiencies of Cu(i) complexes.
Dalton Trans
PUBLISHED: 05-23-2014
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We herein report a theoretical analysis using density functional theory (DFT) and time-dependent DFT (TDDFT) to study the electronic structures and photophysical properties of mixed-ligand Cu(i) complexes. An evaluation of the non-radiative and radiative decay rate constants (knr and kr) is presented. It is found that large spin-orbit coupling (SOC) matrix elements do not necessarily result in large values of kr. Introducing the POP (bis[2-(diphenylphosphino)phenyl]ether) ligand instead of a pair of PPh3 (triphenylphosphine) ligands, it is found that the ether linkage plays an important role in governing the quantum efficiency of the studied complexes. However, the balance between hole injection and electron acceptance, which leads to the quantum yield of [Cu(dmp)(POP)](+) being close to that of [Cu(dbp)(POP)](+), is another important factor in tuning the quantum efficiency. A thorough understanding of the effect of the coordinating ligand on the photophysical behavior of a transition metal complex is desirable for the rational synthesis of highly phosphorescent materials.
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Screening and identification of potential biomarkers and establishment of the diagnostic serum proteomic model for the Traditional Chinese Medicine Syndromes of tuberculosis.
J Ethnopharmacol
PUBLISHED: 05-07-2014
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Chemotherapy is the mainstay of modern tuberculosis (TB) control. Traditional Chinese Medicine (TCM) can enhance the effect of anti-TB drug, promote the absorption of the foci in the lung and reduce drug toxicity. In TCM, the determination of treatment is based on ZHENG (also called TCM syndrome). To establish a diagnostic model by using proteomics technology in order to identify potential biomarkers for TCM syndromes of TB.
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Generation of naive induced pluripotent stem cells from rhesus monkey fibroblasts.
Cell Stem Cell
PUBLISHED: 04-28-2014
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Conventional embryonic stem cells (ESCs) or induced pluripotent stem cells (iPSCs) derived from primates resemble mouse epiblast stem cells, raising an intriguing question regarding whether the naive pluripotent state resembling mouse embryonic stem cells (mESCs) exists in primates and how to capture it in vitro. Here we identified several specific signaling modulators that are sufficient to generate rhesus monkey fibroblast-derived iPSCs with the features of naive pluripotency in terms of growth properties, gene expression profiles, self-renewal signaling, X-reactivation, and the potential to generate cross-species chimeric embryos. Interestingly, together with recent reports of naive human pluripotent stem cells, our findings suggest several conserved signaling pathways shared with rodents and specific to primates, providing significant insights for acquiring naive pluripotency from other species. In addition, the derivation of rhesus monkey naive iPSCs also provides a valuable cell source for use in preclinical research and disease modeling.
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Theoretical investigation on remote-control photocycloreversion of dithienylethene driven by azobenzene chromophores.
Spectrochim Acta A Mol Biomol Spectrosc
PUBLISHED: 04-26-2014
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When adding two azobenzene chromophores on a dithienylethene molecule, the irradiation at 450nm can effectively arouse the cycloreversion reaction of the ring-closed dithienylethene. We investigated the frontier molecular orbitals and absorption properties of such series of molecules and inferred the mechanism of the ring-opening reaction. The 450nm light sensed by the side azobenzene groups can excite the whole molecule to a high excited state, and through electronic transition and energy transfer the active electron may centre on the dithienylethene ring part, then the ring-opening happens. While for the ring-open form, the energy of the 450nm light is not high enough to promote the electron to the exact molecular orbital occupying the central dithienylethene ring, so it cannot cause the ring-closing reaction.
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The molecular configuration of a DOPA/ST monolayer at the air-water interface: a molecular dynamics study.
Phys Chem Chem Phys
PUBLISHED: 04-15-2014
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In this study, surface pressure-area isotherms for N-stearoyldopamine (DOPA) and 4-stearylcatechol (ST) monolayers are obtained by means of molecular dynamics simulations and compared to experimental isotherms. The difference between DOPA and ST is an amide group, which is present in the alkyl tails of DOPA molecules. We find a large difference between the isotherms for DOPA and ST monolayers. Upon using TIP4P/2005 for water and OPLS force fields for the organic material and a relatively large system size, the simulated results are found to be consistent with experiments. With molecular dynamics simulations, the configurations of molecules in the monolayers can be directly analyzed. When the surface pressure is high, a regular molecular orientation is observed for ST molecules, whereas regular orientations are only observed in local domains for DOPA molecules. The differences between DOPA and ST monolayers are attributed to the amide groups in DOPA molecules, which are useful for both steric effects and the formation of hydrogen bonds in the DOPA monolayers. This study clearly demonstrates that hydrogen bonds, due to the presence of the amide group in DOPA, are the cause of the disorder in its Langmuir monolayers. Thus, the conclusion may be helpful in making ordered organic monolayers in the future.
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Theoretical investigation and design of high-efficiency dithiafulvenyl-based sensitizers for dye-sensitized solar cells: the impacts of elongating ?-spacers and rigidifying dithiophene.
Phys Chem Chem Phys
PUBLISHED: 04-12-2014
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DSSCs have been extensively investigated in the past decade, and the search for more efficient dyes for DSSCs remains challenging. In this work we discuss the influences of elongating ?-spacers and rigidifying dithiophene on the performance of dithiafulvenyl (DTF)-based organic dyes using density functional theory (DFT) and time-dependent DFT methods. We show that systematically elongating the ?-spacer of the DTF-2P dye by increasing the number of thiophene groups tends to red-shift the absorption peak and broaden the absorption range, thus improving the light-harvesting efficiency of DTF-2P-T and DTF-2P-2T. Furthermore, among the three dyes, DTF-2P-T would have the best performance because it performs nicely on the key parameters including the electron injection driving force (D), the light-harvesting efficiency (LHE), and the shift of the TiO2 conduction band (?Ecb). In particular, DTF-2P-2T has a larger LHE despite the smaller D and ?Ecb compared with DTF-2P-T. Having realized the great merits of modification on ?-spacers, afterwards, we designed a novel dye by rigidifying the dithiophene moiety of DTF-2P-2T. The resulting dye is proven to be very promising to challenge the conversion efficiency 8.29% of DTF-2P-T due to the improved ?Ecb and LHE. Our theoretical studies are expected to provide valuable insights into the molecular design of novel DTF-based dyes for the optimization of DSSC.
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SPECT and near-infrared fluorescence imaging of breast cancer with a neuropilin-1-targeting peptide.
J Control Release
PUBLISHED: 04-10-2014
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Breast cancer is the most common malignant cancer and is the leading cause of cancer death among females. Molecular imaging is a promising approach for the early detection and staging of breast cancer as well as for assessing therapeutic responses. Tumor-targeting peptides are effective targeting vehicles for molecular imaging. Here, we identified a breast cancer-targeting peptide CLKADKAKC (CK3) contains a cryptic C-end rule motif that may mediate its binding to neuropilin-1 (NRP-1), an attractive therapeutic target which expression was associated with poor outcome of the patients with breast cancer. Phage CK3 bound to NRP-1-positive breast cancer cells, which could be inhibited by peptide CK3 in a dose-dependent manner or by knock-down NRP-1 expression. Consistently, NRP-1 overexpression in cells increased the binding of phage CK3. Furthermore, peptide CK3 co-localized with NRP-1. Importantly, unlike previously reported NRP-1-targeting peptides with exposed C-end rule motifs, peptide CK3 did not penetrate into lungs and heart in vivo, which could make it more clinically applicable. Single-photon emission CT (SPECT) and near-infrared fluorescence (NIRF) imaging showed enrichment of peptide CK3 to the xenograft tumors in nude mice. In conclusion, as a novel NRP-1-targeting peptide, peptide CK3 could be used for breast cancer molecular imaging, which may represent a new avenue for breast cancer diagnostics, staging and assessments of therapeutic response.
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Molecular simulation investigation on the interaction between barrier-to-autointegration factor or its Gly25Glu mutant and DNA.
J Mol Model
PUBLISHED: 04-09-2014
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In order to understand the binding mechanism between Barrier-to-autointegration factor (BAF) and DNA, two DNA:BAF complexes with wild type (WT) BAF and its Gly25Glu point mutate type (MT) were generated by molecular docking on the basis of the crystal structures of BAF (PDB code: 2ODG, chain A) and DNA (PDB code: 2BZF, chain B and C). Then, molecular dynamics (MD) simulations were performed on the two docked structures, as well as BAF (WT) and BAF (MT). The results show that monomer BAF is more flexible than BAF in DNA:BAF complex, suggesting that DNA is effective to stabilize conformation of BAF, which is in good agreement with the experimental results. Besides, the mutated Glu25 in DNA:BAF (MT) can change the BAF conformation to some extent. With deeper investigation on the DNA:BAF structures, the hydrogen bonds are found to make great contribution to the interaction between DNA and BAF. The hydrogen bonds in DNA:BAF (MT) are fewer than those in DNA:BAF (WT), indicating that the Gly25Glu mutation in BAF has an important effect on the hydrogen bonds in the DNA:BAF complex. Besides, the binding free energy in DNA:BAF (MT) is also higher than that in DNA:BAF (WT). It results from the influence of Glu25 side chain on the orientation of Lys6 and Lys33 in the interface between DNA and BAF. The binding free energy of Lys72, another key residue, decreases a lot in DNA:BAF (MT) anomalously. The decreasing energy causes the destruction of hydrophobic pocket in the binding site between DNA and BAF (MT). Our results are helpful for further experimental investigations.
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Structural/electronic properties and reaction energies of a series of mono- and bis-uranyl dihalides equatorially coordinated by N/O ligands.
J Mol Model
PUBLISHED: 03-25-2014
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Monometallic (UO2)(X)2(L)3 (L?=?pyridine (py), X?=?F (1), Cl (2), Br (3) and I (4); L?=?tetrahydrofuran (thf), X?=?Cl (5); L?=?pyrrole (pl), X?=?Cl (6)) as well as bimetallic [(UO2)(?2-X)(X)(L)2]2 (L?=?py, X?=?F (7), Cl (8), Br (9) and I (10); L?=?thf, X?=?Cl (11); L?=?pl, X?=?Cl (12); ? 2?=?doubly bridged) were examined using relativistic density functional theory. With changing from F, Cl, Br to I irregardless of in mono- or bis-uranyl complexes, bond lengths of U?=?O were calculated to be decreasing, resulting from strengthening of axial U?=?O bonds while weakening equatorial X???U coordination. This is further evidenced by calculated bond orders of U?=?O and stretching vibrational frequencies. A similar situation was is found in 2, 5 and 6 as well as in 8, 11 and 12, where N/O ligands are varied but the chlorine atoms are retained. The present study reveals that all these complexes have U(f)-character low-lying unoccupied orbitals, and their ?*(U?=?O) antibonds are located on higher-energy orbitals. Complex 1 was calculated to show ?(U?=?O) bonding character for HOMO, and pyridine-character for other occupied orbitals; the fluorine ligand occurs in a relatively low-energy region. In contrast, the ?(p) characters of heavier halogen atoms significantly contribute to most frontier molecular orbitals of 2, 3 and 4. Unlike this electronic feature of 2, complexes 5 and 6 exhibit mainly thf and pyrrole characters, respectively, for their high-lying occupied orbitals. Electronic structures of bisuranyl complexes 7-12, albeit a little more complicated, are revealed to be similar to those of the corresponding monouranyl complexes. Finally, energies of formation reactions of the above complexes were calculated and compared with available experimental results.
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Theoretical studies on the interaction of ruthenium sensitizers and redox couple in different deprotonation situations.
J Phys Chem A
PUBLISHED: 03-12-2014
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We report a DFT study of interaction between the Ru complex sensitizer [Ru(dcbpy)2(NCS)2: dcbpy = 4,4'-dicarboxy-2,2'-bipyridyl] (N3) and iodide ion under the influence of different deprotonation situations. There are two kinds of interaction mechanisms: iodide ion interacts with metal-center Ru atom or carboxyl, derived from the natural charge distribution analysis. The calculation indicated that there were several stable intermedium forms in different deprotonation degree. The stability of these intermedium forms would be perturbed gradually while the number of eliminated protons increased. It can be predicted that in the initial period of absorption and injection as well as the dissolve process where the deprotonation was demanded, the dye will not attacked by the iodide ion in solution extensively. Additionally, dye with more carboxyls will reduce the activity of redox reaction and more obstacles are required to be overcome before or during the redox reaction. The comparison of natural charge between isolate N3 and N3 with iodide ion intermedium (N3I(-)) showed the iodide ion attacking made the charge contribute on N3 molecule more negative, nevertheless the N3I(-) still has ability to attract another iodide ion. The attacking of iodide ion will also influence the electronic transition and absorption properties through the analysis of the frontier molecular orbitals and the densities of states. The results reported in this paper give us the guidance to carry out the further investigations about the dye regeneration process.
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Fosfomycin induced structural change in fosfomycin resistance kinases FomA: molecular dynamics and molecular docking studies.
J Mol Model
PUBLISHED: 03-10-2014
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Fosfomycin resistance kinases FomA, one of the key enzymes responsible for bacterial resistances to fosfomycin, has gained much attention recently due to the raising public concern for multi-drug resistant bacteria. Using molecular docking followed by molecular dynamics simulations, our group illustrated the process of fosfomycin induced conformational change of FomA. The detailed roles of the catalytic residues (Lys18, His58 and Thr210) during the formation of the enzyme-substrate complex were shown in our research. The organization functions of Gly53, Gly54, Ile61 and Leu75 were also highlighted. Furthermore, the cation-? interaction between Arg62 and Trp207 was observed and speculated to play an auxiliary role in the conformation change process of the enzyme. This detailed molecular level illustration of the formation of FomA·ATP·Mg·Fosfomycin complex could provide insight for both anti-biotic discovery and improvement of fosfomycin in the future.
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Accurate simulation of geometry, singlet-singlet and triplet-singlet excitation of cyclometalated iridium(III) complex.
J Mol Model
PUBLISHED: 03-05-2014
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In the current contribution, we present a critical study of the theoretical protocol used for the determination of the electronic spectra properties of luminescent cyclometalated iridium(III) complex, [Ir(III)(ppy)?H?dcbpy]? (where, ppy = 2-phenylpyridine, H?dcbpy = 2,2'-bipyridine-4,4'-dicarboxylic acid), considered as a representative example of the various problems related to the prediction of electronic spectra of transition metal complex. The choice of the exchange-correlation functional is crucial for the validity of the conclusions that would be drawn from the numerical results. The influence of the exchange-correlation on geometry parameter and absorption/emission band, the role of solvent effects on time-dependent density function theory (TD-DFT) calculations, as well as the importance of the chosen proper procedure to optimize triplet excited geometry, have been thus examined in detail. From the obtained results, some general conclusions and guidelines are presented: i) PBE0 functional is the most accurate in prediction of ground state geometry; ii) the well-established B3LYP, B3P86, PBE0, and X3LYP have similar accuracy in calculation of absorption spectrum; and iii) the hybrid approach TD-DFT//CIS gives out excellent agreement in the evaluation of triplet excitation energy.
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Ultrafast self-healing of polymer toward strength restoration.
ACS Appl Mater Interfaces
PUBLISHED: 02-20-2014
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Self-healing materials should take effect immediately following crack generation in principle, but the speed of autonomic recovery of mechanical properties through either extrinsic or intrinsic healing strategy reported so far is not that fast. Mostly, a couple of hours are taken for reaching steady state or maximum healing. To accelerate the healing process, the authors of this work make use of antimony pentafluoride as instant hardener of epoxy and successfully encapsulate the highly active antimony pentafluoride-ethanol complex in terms of hollow silica spheres. Accordingly, self-healing agent based on microencapsulated antimony pentafluoride-ethanol complex and epoxy monomer is developed. Epoxy material with the embedded healant capsules can thus be healed within a few seconds, as demonstrated by impact and fatigue tests. It is believed that the outcome presented here might help to move the self-healing technique closer to practical application, especially when the engineering significance of epoxy material is concerned.
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Activation of spinal phosphatidylinositol 3-kinase/protein kinase B mediates pain behavior induced by plantar incision in mice.
Exp. Neurol.
PUBLISHED: 01-25-2014
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The etiology of postoperative pain may be different from antigen-induced inflammatory pain and neuropathic pain. However, central neural plasticity plays a key role in incision pain. It is also known that phosphatidylinositol 3-kinase (PI3K) and protein kinase B/Akt (PKB/Akt) are widely expressed in laminae I-IV of the spinal horn and play a critical role in spinal central sensitization. In the present study, we explored the role of PI3K and Akt in incision pain behaviors. Plantar incision induced a time-dependent activation of spinal PI3K-p110? and Akt, while activated Akt and PI3K-p110? were localized in spinal neurons or microglias, but not in astrocytes. Pre-treatment with PI3K inhibitors, wortmannin or LY294002 prevented the activation of Akt brought on by plantar incision in a dose-dependent manner. In addition, inhibition of spinal PI3K signaling pathway prevented pain behaviors (dose-dependent) and spinal Fos protein expression caused by plantar incision. These data demonstrated that PI3K signaling mediated pain behaviors caused by plantar incision in mice.
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Insights into the phosphatase and the synthase activities of human bisphosphoglycerate mutase: a quantum mechanics/molecular mechanics simulation.
Phys Chem Chem Phys
PUBLISHED: 01-21-2014
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Bisphosphoglycerate mutase (BPGM) is a multi-activity enzyme. Its main function is to synthesize the 2,3-bisphosphoglycerate, the allosteric effector of hemoglobin. This enzyme can also catalyze the 2,3-bisphosphoglycerate to the 3-phosphoglycerate. In this study, the reaction mechanisms of both the phosphatase and the synthase activities of human bisphosphoglycerate mutase were theoretically calculated by using the quantum mechanics/molecular mechanics method based on the metadynamics and umbrella sampling simulations. The simulation results not only show the free energy curve of the phosphatase and the synthase reactions, but also reveal the important role of some residues in the active site. Additionally, the energy barriers of the two reactions indicate that the activity of the synthase in human bisphosphoglycerate mutase is much higher than that of the phosphatase. The estimated reaction barriers are consistent with the experimental data. Therefore, our work can give important information to understand the catalytic mechanism of the bisphosphoglycerate mutase family.
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Exploring the mechanism how Marburg virus VP35 recognizes and binds dsRNA by molecular dynamics simulations and free energy calculations.
Biopolymers
PUBLISHED: 01-16-2014
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Filoviruses often cause terrible infectious disease which has not been successfully dealt with pharmacologically. All filoviruses encode a unique protein termed VP35 which can mask doubled-stranded RNA to deactivate interferon. The interface of VP35-dsRNA would be a feasible target for structure-based antiviral agent design. To explore the essence of VP35-dsRNA interaction, molecular dynamics simulation combined with MM-GBSA calculations were performed on Marburg virus VP35-dsRNA complex and several mutational complexes. The energetic analysis indicates that nonpolar interactions provide the main driving force for the binding process. Although the intermolecular electrostatic interactions play important roles in VP35-dsRNA interaction, the whole polar interactions are unfavorable for binding which result in a low binding affinity. Compared with wild type VP35, the studied mutants F228A, R271A, and K298A have obviously reduced binding free energies with dsRNA reflecting in the reduction of polar or nonpolar interactions. The results also indicate that the loss of binding affinity for one dsRNA strand would abolish the total binding affinity. Three important residues Arg271, Arg294, and Lys298 which makes the largest contribution for binding in VP35 lose their binding affinity significantly in mutants. The uncovering of VP35-dsRNA recognition mechanism will provide some insights for development of antiviral drug. © 2014 Wiley Periodicals, Inc. Biopolymers 101: 849-860, 2014.
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Mutation and low pH effect on the stability as well as unfolding kinetics of transthyretin dimer.
Biophys. Chem.
PUBLISHED: 01-10-2014
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Transthyretin (TTR) dissociation and aggregation appear to cause several amyloid diseases. TTR dimer is an important intermediate that is hard to be observed from the biological experiments. To date, the molecular origin and the structural motifs for TTR dimer dissociation, as well as the unfolding process have not been rationalized at atomic resolution. To this end, we have investigated the effect of low pH and mutation L55P on stability as well as the unfolding pathway of TTR dimer using constant pH molecular dynamics simulations. The result shows that acidic environment results in loose TTR dimer structure. Mutation L55P causes the disruption of strand D and makes the CE-loop very flexible. In acidic conditions, dimeric L55P mutant exhibits notable conformation changes and an evident trend to separate. Our work shows that the movements of strand C and the loops nearby are the beginning of the unfolding process. In addition, hydrogen bond network at the interface of the two monomers plays a part in stabilizing TTR dimer. The dynamic investigation on TTR dimer provides important insights into the structure-function relationships of TTR, and rationalizes the structural origin for the tendency of unfolding and changes of structure that occur upon introduction of mutation and pH along the TTR dimer dissociation and unfolding process.
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Structure of a Naegleria Tet-like dioxygenase in complex with 5-methylcytosine DNA.
Nature
PUBLISHED: 01-07-2014
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Cytosine residues in mammalian DNA occur in five forms: cytosine (C), 5-methylcytosine (5mC), 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC). The ten-eleven translocation (Tet) dioxygenases convert 5mC to 5hmC, 5fC and 5caC in three consecutive, Fe(II)- and ?-ketoglutarate-dependent oxidation reactions. The Tet family of dioxygenases is widely distributed across the tree of life, including in the heterolobosean amoeboflagellate Naegleria gruberi. The genome of Naegleria encodes homologues of mammalian DNA methyltransferase and Tet proteins. Here we study biochemically and structurally one of the Naegleria Tet-like proteins (NgTet1), which shares significant sequence conservation (approximately 14% identity or 39% similarity) with mammalian Tet1. Like mammalian Tet proteins, NgTet1 acts on 5mC and generates 5hmC, 5fC and 5caC. The crystal structure of NgTet1 in complex with DNA containing a 5mCpG site revealed that NgTet1 uses a base-flipping mechanism to access 5mC. The DNA is contacted from the minor groove and bent towards the major groove. The flipped 5mC is positioned in the active-site pocket with planar stacking contacts, Watson-Crick polar hydrogen bonds and van der Waals interactions specific for 5mC. The sequence conservation between NgTet1 and mammalian Tet1, including residues involved in structural integrity and functional significance, suggests structural conservation across phyla.
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A high-throughput gene disruption methodology for the entomopathogenic fungus Metarhizium robertsii.
PLoS ONE
PUBLISHED: 01-01-2014
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Systematic gene disruption is a direct way to interrogate a fungal genome to functionally characterize the full suite of genes involved in various biological processes. Metarhizium robertsii is extraordinarily versatile, and it is a pathogen of arthropods, a saprophyte and a beneficial colonizer of rhizospheres. Thus, M. robertsii can be used as a representative to simultaneously study several major lifestyles that are not shared by the "model" fungi Saccharomyces cerevisiae and Neurospora crassa; a systematic genetic analysis of M. robertsii will benefit studies in other fungi. In order to systematically disrupt genes in M. robertsii, we developed a high-throughput gene disruption methodology, which includes two technologies. One is the modified OSCAR-based, high-throughput construction of gene disruption plasmids. This technology involves two donor plasmids (pA-Bar-OSCAR with the herbicide resistance genes Bar and pA-Sur-OSCAR with another herbicide resistance gene Sur) and a recipient binary plasmid pPK2-OSCAR-GFP that was produced by replacing the Bar cassette in pPK2-bar-GFP with a ccdB cassette and recombination recognition sites. Using this technology, a gene disruption plasmid can be constructed in one cloning step in two days. The other is a highly efficient gene disruption technology based on homologous recombination using a Ku70 deletion mutant (?MrKu70) as the recipient strain. The deletion of MrKu70, a gene encoding a key component involved in nonhomologous end-joining DNA repair in fungi, dramatically increases the gene disruption efficiency. The frequency of disrupting the conidiation-associated gene Cag8 in ?MrKu70 was 93% compared to 7% in the wild-type strain. Since ?MrKu70 is not different from the wild-type strain in development, pathogenicity and tolerance to various abiotic stresses, it can be used as a recipient strain for a systematic gene disruption project to characterize the whole suite of genes involved in the biological processes of M. robertsii.
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Comprehensive molecular diagnosis of Bardet-Biedl syndrome by high-throughput targeted exome sequencing.
PLoS ONE
PUBLISHED: 01-01-2014
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Bardet-Biedl syndrome (BBS) is an autosomal recessive disorder with significant genetic heterogeneity. BBS is linked to mutations in 17 genes, which contain more than 200 coding exons. Currently, BBS is diagnosed by direct DNA sequencing for mutations in these genes, which because of the large genomic screening region is both time-consuming and expensive. In order to develop a practical method for the clinic diagnosis of BBS, we have developed a high-throughput targeted exome sequencing (TES) for genetic diagnosis. Five typical BBS patients were recruited and screened for mutations in a total of 144 known genes responsible for inherited retinal diseases, a hallmark symptom of BBS. The genomic DNA of these patients and their families were subjected to high-throughput DNA re-sequencing. Deep bioinformatics analysis was carried out to filter the massive sequencing data, which were further confirmed through co-segregation analysis. TES successfully revealed mutations in BBS genes in each patient and family member. Six pathological mutations, including five novel mutations, were revealed in the genes BBS2, MKKS, ARL6, MKS1. This study represents the first report of targeted exome sequencing in BBS patients and demonstrates that high-throughput TES is an accurate and rapid method for the genetic diagnosis of BBS.
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[Study on optimal model of hypothetical work injury insurance scheme].
Zhonghua Lao Dong Wei Sheng Zhi Ye Bing Za Zhi
PUBLISHED: 12-28-2013
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To explore an optimal model of hypothetical work injury insurance scheme, which is in line with the wishes of workers, based on the problems in the implementation of work injury insurance in China and to provide useful information for relevant policy makers.
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Formononetin induces the mitochondrial apoptosis pathway in prostate cancer cells via downregulation of the IGF-1/IGF-1R signaling pathway.
Pharm Biol
PUBLISHED: 12-24-2013
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Abstract Context: Formononetin, an isoflavone, can inhibit the proliferation of cancer cells, including those of the prostate. However, its antitumor mechanism remains unclear. Aim: To investigate whether the insulin-like growth factor 1 (IGF-1)/insulin-like growth factor 1 receptor (IGF-1?R) signaling pathway mediates the formononetin antitumor effect on prostate cancer cells. Materials and methods: The viability of PC-3 cells was measured by MTT assay 48?h after formononetin treatment (25, 50 and 100??M). Formononetin-induced cell apoptosis was measured by Hoechst 33258 staining and flow cytometry. Expression of Bax mRNA was detected by real-time PCR, and the expression levels of Bax and IGF-1?R proteins were detected by western blots. Results: At concentrations >12.5??M, formononetin significantly inhibited the proliferation of human prostate cancer cells. Formononetin increased Bax mRNA and protein expression levels and decreased the expression levels of pIGF-1?R protein in a dose-dependent manner. Conclusion: High concentrations of formononetin-induced apoptosis in androgen-independent prostate cancer cells through inhibition of the IGF-1/IGF-1?R pathway.
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A new topology of the HK97-like fold revealed in Bordetella bacteriophage by cryoEM at 3.5 A resolution.
Elife
PUBLISHED: 12-19-2013
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Bacteriophage BPP-1 infects and kills Bordetella species that cause whooping cough. Its diversity-generating retroelement (DGR) provides a naturally occurring phage-display system, but engineering efforts are hampered without atomic structures. Here, we report a cryo electron microscopy structure of the BPP-1 head at 3.5 Å resolution. Our atomic model shows two of the three protein folds representing major viral lineages: jellyroll for its cement protein (CP) and HK97-like (Johnson) for its major capsid protein (MCP). Strikingly, the fold topology of MCP is permuted non-circularly from the Johnson fold topology previously seen in viral and cellular proteins. We illustrate that the new topology is likely the only feasible alternative of the old topology. ?-sheet augmentation and electrostatic interactions contribute to the formation of non-covalent chainmail in BPP-1, unlike covalent inter-protein linkages of the HK97 chainmail. Despite these complex interactions, the termini of both CP and MCP are ideally positioned for DGR-based phage-display engineering. DOI: http://dx.doi.org/10.7554/eLife.01299.001.
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ITO@Cu2S Tunnel Junction Nanowire Arrays as Efficient Counter Electrode for Quantum-Dot-Sensitized Solar Cells.
Nano Lett.
PUBLISHED: 12-18-2013
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Quantum-dot-sensitized solar cell (QDSSC) has been considered as an alternative to new generation photovoltaics, but it still presents very low power conversion efficiency. Besides the continuous effort on improving photoanodes and electrolytes, the focused investigation on charge transfer at interfaces and the rational design for counter electrodes (CEs) are recently receiving much attention. Herein, core-shell nanowire arrays with tin-doped indium oxide (ITO) nanowire core and Cu2S nanocrystal shell (ITO@Cu2S) were dedicatedly designed and fabricated as new efficient CEs for QDSSCs in order to improve charge collection and transport and to avoid the intrinsic issue of copper dissolution in popular and most efficient Cu/Cu2S CEs. The high-quality tunnel junctions formed between n-type ITO nanowires and p-type Cu2S nanocrystals led to the considerable decrease in sheet resistance and charge transfer resistance and thus facilitated the electron transport during the operation of QDSSCs. The three-dimensional structure of nanowire arrays provided high surface area for more active catalytic sites and easy accessibility for an electrolyte. As a result, the power conversion efficiency of QDSSCs with the designed ITO@Cu2S CEs increased by 84.5 and 33.5% compared to that with planar Au and Cu2S CEs, respectively.
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Role of chaperone-mediated autophagy in degrading Huntingtons disease-associated huntingtin protein.
Acta Biochim. Biophys. Sin. (Shanghai)
PUBLISHED: 12-08-2013
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Mutant N-terminal huntingtin (Htt) protein resulting from Huntingtons disease (HD) with expanded polyglutamine accumulates and forms aggregates in vulnerable neurons. Both ubiquitin proteasomal and autophagic pathways contribute to the degradation of mutant Htt. Here, we focus on the involvement of chaperone-mediated autophagy (CMA), a selective form of autophagy in the clearance of Htt. Selective catabolism in CMA is conferred by the presence of a KFERQ-like targeting motif in the substrates, by which molecular chaperones recognize the hydrophobic surfaces of the misfolded substrates, and transfer them to the lysosomal membrane protein type-2A, LAMP-2A. The substrates are taken into the lysosomes through LAMP-2A and are rapidly degraded by the lysosomal enzymes. Taken together, we summarize the recent evidence to elucidate that Htt is also a potential substrate of CMA. We propose that the manipulation of CMA could be a therapeutic strategy for HD.
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[Three-dimensional finite-element analysis of maxillary protraction based on labiolingual appliance].
Hua Xi Kou Qiang Yi Xue Za Zhi
PUBLISHED: 12-05-2013
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This study aims to analyze the biomechanical effects of four sutures that are related to maxillary growth during a maxillary protraction treatment cycle based on labiolingual appliance.
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DNA recognition of 5-carboxylcytosine by a zfp57 mutant at an atomic resolution of 0.97 Å.
Biochemistry
PUBLISHED: 11-20-2013
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The Zfp57 gene encodes a KRAB (Krüppel-associated box) domain-containing C2H2 zinc finger transcription factor that is expressed in early development. Zfp57 protein recognizes methylated CpG dinucleotide within GCGGCA elements at multiple imprinting control regions. In the previously determined structure of the mouse Zfp57 DNA-binding domain in complex with DNA containing 5-methylcytosine (5mC), the side chains of Arg178 and Glu182 contact the methyl group via hydrophobic and van der Waals interactions. We examined the role of Glu182 in recognition of 5mC by mutagenesis. The majority of mutants examined lose selectivity of methylated (5mC) over unmodified (C) and oxidative derivatives, 5-hydroxymethylcytosine, 5-formylcytosine, and 5-carboxylcytosine (5caC), suggesting that the side chain of Glu182 (the size and the charge) is dispensable for methyl group recognition but negatively impacts the binding of unmodified cytosine as well as oxidized derivatives of 5mC to achieve 5mC selectivity. Substitution of Glu182 with its corresponding amide (E182Q) had no effect on methylated DNA binding but gained significant binding affinity for 5caC DNA, resulting in a binding affinity for 5caC DNA comparable to that of the wild-type protein for 5mC. We show structurally that the uncharged amide group of E182Q interacts favorably with the carboxylate group of 5caC. Furthermore, introducing a positively charged arginine at position 182 resulted in a mutant (E182R) having higher selectivity for the negatively charged 5caC.
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Molecular Dynamic Investigations of the Mutational Effects on Structural Characteristics and Tunnel Geometry in CYP17A1.
J Chem Inf Model
PUBLISHED: 11-18-2013
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Cytochrome P450 (CYP) 17A1 is a dual-function monooxygenase with a critical role in the synthesis of many human steroid hormones. The enzyme is an important target for the treatment of breast and prostate cancers that proliferate in response to estrogens and androgens. Despite the ample experimental mutagenesis data, the molecular origin and the structural motifs for the enzymatic activities deficiencies have not been rationalized at the atomic resolution. To this end, we have investigated the effects on structural characteristics and tunnel geometry upon single point mutations in CYP17A1. The MD simulation results combined with PMF calculations and MM-GBSA calculations render an "access mechanism" which encapsulates the effects of mutations on the changes in both structural flexibility and tunnel dynamics, bridging the gap between the theory and the experimentally observed results of enzymatic activity decrease. The underlying molecular mechanism of the heterogeneities in open/closed conformational changes, as well as the wider opening of their respective major tunnels between wt17A1 and two mutants, may be attributed to the closer distances of hydrophobic residues or the disruption of a hydrophobic core. The knowledge of ligand binding characteristics and key residues contributions could guide future experimental and computational work on CYPs so that desirable changes in their enzymatic activities may be achieved. The present study provides important insights into the structure-function relationships of CYP17A1 protein, which could contribute to further understanding about 17-hydroxylase deficiencies and may also improve the understanding of polycystic ovary disease.
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Cooperative thermodynamic control of selectivity in the self-assembly of rare Earth metal-ligand helices.
J. Am. Chem. Soc.
PUBLISHED: 11-15-2013
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Metal-selective self-assembly with rare-earth cations is possible with suitable rigid, symmetrical bis-tridentate ligands. Kinetically controlled formation is initially observed, with smaller cations preferentially incorporated. Over time, the more thermodynamically favorable complexes with larger metals are formed. This thermodynamic control is a cooperative supramolecular phenomenon and only occurs upon multiple-metal-based self-assembly: single-metal ML3 analogues do not show reversible selectivity. The selectivity is dependent on small variations in lanthanide ionic radius and occurs despite identical coordination-ligand coordination geometries and minor size differences in the rare-earth metals.
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Optical absorptance measurement of an individual multiwall carbon nanotube using a T type thermal probe method.
Rev Sci Instrum
PUBLISHED: 11-05-2013
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Optical absorptance is an important property of carbon nanotubes for practical applications but has rarely been accurately measured. We developed a T type thermal probe method to measure the optical absorptance of an individual multiwall carbon nanotube. In this method, one end of the carbon nanotube (CNT) is attached to the center of a platinum nanofilm in a T shape and the Pt nanofilm acts as a thermometer. A laser beam irradiates at the CNT and the absorbed laser power can be determined by measuring the average temperature rise of the Pt nanofilm based on the temperature dependence of the electric resistance. Experimental results showed that a 100-nm-diameter multiwall CNT could absorb 13.2% of the 514-nm-wavelength laser power with the laser spot diameter being 1 ?m. This method is useful for determining the optical absorptance of CNTs and other one-dimensional nanostructures such as Si/Ge nanowires for various optical wavelengths in their photovoltaic, photoelectrolysis and other optical applications.
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The discovery and identification of a candidate proteomic biomarker of active tuberculosis.
BMC Infect. Dis.
PUBLISHED: 10-15-2013
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Noninvasive and convenient biomarkers for early diagnosis of tuberculosis (TB) remain an urgent need. The aim of this study was to discover and identify potential biomarkers specific for TB.
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Synthesis of 1,4-Bis(phenylethynyl)benzenes and Their Application as Blue Phase Liquid Crystal Composition.
Int J Mol Sci
PUBLISHED: 09-14-2013
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A number of 1,4-bis(phenylethynyl)benzene derivatives (BPEBs) and their analogues with different numbers of side-substitute fluorine atoms on benzene rings, and alkyl chains, ethoxyl groups, fluorine atoms and trifluoromethyl groups as the end groups have been synthesized. The effects of the different substituents on their properties such as thermal behavior of melting point and clearing point, the temperature of nematic phase, optical anisotropy and dielectric anisotropy have been well investigated, and it has been found that some BPEBs have a wide range of the nematic phase temperature with high optical anisotropy (?n) and acceptable dielectric anisotropy (??), which have been applied as the crucial compositions to constitute a liquid crystal mixture having the properties of ?? = 29.0 and ?n = 0.283 at 25 °C. With the addition of the chiral dopant to the obtained liquid crystal mixture, blue phase liquid crystal with a blue phase temperature range of 8 °C has been achieved.
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Exploring the molecular basis of dsRNA recognition by Mss116p using molecular dynamics simulations and free-energy calculations.
Langmuir
PUBLISHED: 08-22-2013
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DEAD-box proteins are the largest family of helicase that are important in nearly all aspects of RNA metabolism. However, it is unclear how these proteins recognize and bind RNA. Here, we present a detailed analysis of the related DEAD-box protein Mss116p-RNA interaction, using molecular dynamics simulations with MM-GBSA calculations. The energetic analysis indicates that the two strands of double strands RNA (dsRNA) are recognized asymmetrically by Mss116p. The strand 1 of dsRNA provides the main binding affinity. Meanwhile, the nonpolar interaction provides the main driving force for the binding process. Although the contribution of polar interaction is small, it is vital in stabilizing the protein-RNA interaction. Compared with the wild type Mss116p, two studied mutants Q412A and D441A have obviously reduced binding free energies with dsRNA because of the decreasing of polar interaction. Three important residues Lys409, Arg415 and Arg438 lose their binding affinity significantly in mutants. In conclusion, these results complement previous experiments to advance comprehensive understanding of Mss116p-dsRNA interaction. The results also would provide support for the application of similar approaches to the understanding of other DEAD-box protein-RNA complexes.
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Molecular dynamics simulation of a DOPA/ST monolayer on the Au(111) surface.
Phys Chem Chem Phys
PUBLISHED: 08-13-2013
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In order to study the influence of molecular structure on the formation of a monolayer, two molecules have been considered, namely N-stearoyldopamine (DOPA) and 4-stearyl-catechol (ST). The difference between these two molecules is the amide group in DOPA. By investigating these monolayers at different surface areas per molecule, the molecular configurations of a DOPA/ST monolayer on the Au(111) surface were obtained. We conclude that for both kinds of molecules, the ?-interaction between the catechol group and the Au(111) surface is important. Compared to experimental results, the catechol groups are found either parallel or perpendicular to the Au(111) surface in MD simulation. The difference between DOPA and ST systems is that when there are fewer molecules on the Au(111) surface, in the DOPA system, the amount of catechol groups perpendicular with their hydroxyls orienting towards the surface is less than that of the ST system. Further analysis of catechol groups and amide groups indicates that various kinds of hydrogen bonds formed in the DOPA system have a profound influence on the structure and regularity of the monolayer.
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Tailoring the LCST of PNIPAAM-b-PLA-b-PNIPAAM Triblock Copolymers via Stereocomplexation.
Macromol Rapid Commun
PUBLISHED: 08-06-2013
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Poly(N-isopropylacrylamide)-block-poly(l-lactic acid)-block-poly(N-isopropylacrylamide) (PNIPAAM-b-PLLA-b-PNIPAAM) and PNIPAAM-b-PDLA-b-PNIPAAM triblock copolymers with varying polylactic acid (PLA) lengths are synthesized using a combination of ring-opening polymerization and atom-transfer radical polymerization. Results of (1) H NMR and gel permeation chromatography analyses show that the copolymers have a well-defined triblock structure and the PLA segment lengths can be readily controlled with monomer feed ratio. Stereocomplexation between the enantiomeric PLA segments is confirmed with differential scanning calorimetry and wide-angle X-ray scattering. Dynamic light scattering experiments show that (1) the LCST of PNIPAAM in water could be tailored from 32 °C up to 38.5 °C by increasing the length of PLA segments and mixing copolymers of similar molecular weight with enantiomeric PLA segments to induce stereocomplexation, and (2) the LCST of each mixed copolymer system could be tailored within a 2-3 °C range of body temperature by manipulating the ratio of the enantiomeric copolymers in solution.
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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.