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Probing Minor Groove Hydrogen Bonding Interactions between RB69 DNA Polymerase and DNA
Xia, Shuangluo,Christian, Thomas D.,Wang, Jimin,Konigsberg, William H. American Chemical Society 2012 Biochemistry Vol.51 No.21
<P>Minor groove hydrogen bonding (HB) interactions between DNA polymerases (pols) and N3 of purines or O2 of pyrimidines have been proposed to be essential for DNA synthesis from results obtained using various nucleoside analogues lacking the N3 or O2 contacts that interfered with primer extension. Because there has been no direct structural evidence to support this proposal, we decided to evaluate the contribution of minor groove HB interactions with family B pols. We have used RB69 DNA pol and 3-deaza-2′-deoxyadenosine (3DA), an analogue of 2-deoxyadenosine, which has the same HB pattern opposite T but with N3 replaced with a carbon atom. We then determined pre-steady-state kinetic parameters for the insertion of dAMP opposite dT using primer/templates (P/T)-containing 3DA. We also determined three structures of ternary complexes with 3DA at various positions in the duplex DNA substrate. We found that the incorporation efficiency of dAMP opposite dT decreased 10<SUP>2</SUP>–10<SUP>3</SUP>-fold even when only one minor groove HB interaction was missing. Our structures show that the HB pattern and base pair geometry of 3DA/dT is exactly the same as those of dA/dT, which makes 3DA an optimal analogue for probing minor groove HB interactions between a DNA polymerase and a nucleobase. In addition, our structures provide a rationale for the observed 10<SUP>2</SUP>–10<SUP>3</SUP>-fold decrease in the rate of nucleotide incorporation. The minor groove HB interactions between position <I>n</I> – 2 of the primer strand and RB69pol fix the rotomer conformations of the K706 and D621 side chains, as well as the position of metal ion A and its coordinating ligands, so that they are in the optinal orientation for DNA synthesis.</P><P><B>Graphic Abstract</B> <IMG SRC='http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/bichaw/2012/bichaw.2012.51.issue-21/bi300416z/production/images/medium/bi-2012-00416z_0006.gif'></P><P><A href='http://pubs.acs.org/doi/suppl/10.1021/bi300416z'>ACS Electronic Supporting Info</A></P>
Radiation damage in helium ion – irradiated reduced activation ferritic/martensitic steel
L.D. Xia,W.B. Liu,H.P. Liu,J.H. Zhang,H. Chen,Z.G. Yang,C. Zhang 한국원자력학회 2018 Nuclear Engineering and Technology Vol.50 No.1
Nanocrystalline reduced activation ferritic/martensitic (RAFM) steel samples were prepared using surfacemechanical attrition treatment (SMAT). Un-SMATed and SMATed reduced activation ferritic/martensitic samples were irradiated by helium ions at 200 C and 350 C with 2 dpa and 8 dpa, respectively,to investigate the effects of grain boundaries (GBs) and temperature on the formation of Hebubbles during irradiation. Experimental results show that He bubbles are preferentially trapped at GBsin all the irradiated samples. Bubble denuded zones are clearly observed near the GBs at 350 C, whereasthe bubble denuded zones are not obvious in the samples irradiated at 200 C. The average bubble sizeincreases and the bubble density decreases with an increasing irradiation temperature from 200 C to350 C. Both the average size and density of the bubbles increase with an increasing irradiation dose from2 dpa to 8 dpa. Bubbles with smaller size and lower density were observed in the SMATed samples butnot in the un-SMATed samples irradiated in the same conditions, which indicate t
Woo, H.J.,Kang, H.K.,Nguyen, T.T.H.,Kim, G.E.,Kim, Y.M.,Park, J.S.,Kim, D.,Cha, J.,Moon, Y.H.,Nam, S.H.,Xia, Y.m.,Kimura, A.,Kim, D. IPC Science and Technology Press ; Elsevier Scienc 2012 Enzyme and microbial technology Vol.51 No.6
Novel ampelopsin glucosides (AMPLS-Gs) were enzymatically synthesized and purified using a Sephadex LH-20 column. Each structure of the purified AMPLS-Gs was determined by nuclear magnetic resonance, and the ionic product of AMPLS-G1 was observed at m/z 505 (C<SUB>21</SUB>H<SUB>22</SUB>O<SUB>13</SUB>.Na)<SUP>+</SUP> using matrix-assisted laser desorption ionization time-of-flight mass spectrometry. AMPLS-G1 was identified as ampelopsin-4'-O-α-d-glucopyranoside. The optimum condition for AMPLS-G1, determined using response surface methodology, was 70mM ampelopsin, 150mM sucrose, and 1U/mL dextransucrase, which resulted in an AMPLS-G1 yield of 34g/L. The purified AMPLS-G1 displayed 89-fold increased water solubility and 14.5-fold browning resistance compared to those of AMPLS and competitive inhibition against tyrosinase with a K<SUB>i</SUB> value of 40.16μM. This value was smaller than that of AMPLS (K<SUB>i</SUB>=62.56μM) and much smaller than that of β-arbutin (K<SUB>i</SUB>=514.84μM), a commercial active ingredient of whitening cosmetics. These results indicate the potential of AMPLS and AMPLS-G1 as superior ingredients for functional cosmetics.
Yun, S.H.,Xia, L.,Edison, T.N.J.I.,Pandurangan, M.,Kim, D.H.,Kim, S.H.,Lee, Y.R. Elsevier Sequoia 2017 Sensors and actuators. B Chemical Vol.240 No.-
A novel ethylenediamine (EDA) based chemosensor 5 [dimethyl 2,2'-((3-oxocyclohex-1-ene-1,2-diyl)bis(azanediyl))dibenzoate] has been designed and synthesized for the turn on fluorescence sensing of Cu<SUP>2+</SUP> ions. The molecular geometry configuration of 5 is identified by X-ray diffraction and its corresponding orbital electron distributions are predicted by density functional theory (DFT). The probe 5 exhibits strong and selective complexing ability towards Cu<SUP>2+</SUP> over the other metal ions tested in both acetonitrile and aqueous solvent systems. MeCN-HEPES buffer system is more suitable for the selective fluorescence sensing of Cu<SUP>2+</SUP> ions. In addition, the lowest detection limit is 0.30μM for Cu<SUP>2+</SUP> ions. This probe has also been applied successfully for the confocal fluorescence imaging of MDCK cells. Therefore, this probe can be used in both the environmental and biological systems for the detection of Cu<SUP>2+</SUP>.
Development of the 3.7 GHz LHCD System on HL-2A
B. Lu,M. Huang,H. Zeng,X. Y. Bai,X. H. Mao,Z. H. Lu,J. Liang,Z. H. Kang,M. W. Wang,K. Feng,H. Wang,C. Wang,J. Q. Wang,S. Wei,T. Yao,Y. N. Bu,J. Feng,G. Y. Cheng,S. D. Song,D. H. Xia,J. Rao 한국물리학회 2014 THE JOURNAL OF THE KOREAN PHYSICAL SOCIETY Vol.65 No.8
A 2 MW-3.7 GHz lower hybrid current drive (LHCD) system is under development for physicsexperiments on the HL-2A device. The RF Power is generated by four TH2103A klystron amplifiersand propagates in the TE10 mode through WR284 waveguides. The transmission lines with a lengthof 20 m to 30 m are pressurized with 2 bars of nitrogen to decrease the possibility of arcing. Thelauncher, based on the passive-active multi-junction (PAM) concept, has been developed and iscurrently being realized. It was designed for a power spectrum peaked at Nk = 2.75 with goodcoupling properties over a wide range of plasma parameters. The four klystrons are fed by ahigh-voltage power supply (HVPS) based on the pulse step modulation (PSM) concept with a fastswitch-off time of less than ten μs. This system is expected to be in operation within 1 years and willexplore many international thermonuclear experimental reactor (ITER) related LH experiments inthe following years.
Radiation induced grain boundary segregation in ferritic/martensitic steels
Xia, L.D.,Ji, Y.Z.,Liu, W.B.,Chen, H.,Yang, Z.G.,Zhang, C.,Chen, L.Q. Korean Nuclear Society 2020 Nuclear Engineering and Technology Vol.52 No.1
The radiation induced segregation of Cr at grain boundaries (GBs) in Ferritic/Martensitic steels was modeled assuming vacancy and interstitialcy diffusion mechanisms. In particular, the dependence of segregation on temperature and grain boundary misorientation angle was analyzed. It is found that Cr enriches at grain boundaries at low temperatures primarily through the interstitialcy mechanism while depletes at high temperatures predominantly through the vacancy mechanism. There is a crossover from Cr enrichment to depletion at an intermediate temperature where the Cr:Fe vacancy and interstitialcy diffusion coefficient ratios intersect. The bell-shape Cr enrichment response is attributed to the decreasing void sinks inside the grains as temperature rises. It is also shown that low angle grain boundaries (LAGBs) and special Σ coincidence-site lattice (CSL) grain boundaries exhibit suppressed radiation induced segregation (RIS) response while high angle grain boundaries (HAGBs) have high RIS segregation. This different behavior is attributed to the variations in dislocation density at different grain boundaries.
Estimation of L-threonine requirements for Longyan laying ducks
Fouad, A.M.,Zhang, H.X.,Chen, W.,Xia, W.G.,Ruan, D.,Wang, S.,Zheng, C.T. Asian Australasian Association of Animal Productio 2017 Animal Bioscience Vol.30 No.2
Objective: A study was conducted to test six threonine (Thr) levels (0.39%, 0.44%, 0.49%, 0.54%, 0.59%, and 0.64%) to estimate the optimal dietary Thr requirements for Longyan laying ducks from 17 to 45 wk of age. Methods: Nine hundred Longyan ducks aged 17 wk were assigned randomly to the six dietary treatments, where each treatment comprised six replicate pens with 25 ducks per pen. Results: Increasing the Thr level enhanced egg production, egg weight, egg mass, and the feed conversion ratio (FCR) (linearly or quadratically; p<0.05). The Haugh unit score, yolk color, albumen height, and the weight, percentage, thickness, and breaking strength of the eggshell did not response to increases in the Thr levels, but the albumen weight and its proportion increased significantly (p<0.05), whereas the yolk weight and its proportion decreased significantly as the Thr levels increased. Conclusion: According to a regression model, the optimal Thr requirement for egg production, egg mass, and FCR in Longyan ducks is 0.57%, while 0.58% is the optimal level for egg weight from 17 to 45 wk of age.