• Title/Summary/Keyword: Molecular dynamic

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Movement of Rhizobia Inside Tobacco and Lifestyle Alternation from Endophytes to Free-Living Rhizobia on Leaves

  • Ji, Kui-Xian;Chi, Feng;Yang, Ming-Feng;Shen, Shi-Hua;Jing, Yu-Xiang;Dazzo, Frank B.;Cheng, Hai-Ping
    • Journal of Microbiology and Biotechnology
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    • v.20 no.2
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    • pp.238-244
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    • 2010
  • Rhizobia are well-known for their ability to infect and nodulate legume roots, forming a nitrogen-fixing symbiosis of agricultural importance. In addition, recent studies have shown that rhizobia can colonize roots and aerial plant tissues of rice as a model plant of the Graminaceae family. Here we show that rhizobia can invade tobacco, a model plant belonging to the Solanaceae family. Inoculation of seedling. roots with five GFP-tagged rhizobial species followed by microscopy and viable plating analyses indicated their colonization of the surface and interior of the whole vegetative plant. Blockage of ascending epiphytic migration by coating the hypocotyls with Vaseline showed that the endophytic rhizobia can exit the leaf interior through stomata and colonize the external phyllosphere habitat. These studies indicate rhizobia can colonize both below- and above-ground tissues of tobacco using a dynamic invasion process that involves both epiphytic and endophytic lifestyles.

Kinetic analysis of 64Cu-NODAGA-gluco-E[c(RGDfK)]2 for a tumor angiogenesis PET tracer

  • Choi, Jae Yong;Park, Ji-Ae;Kim, Jung Young;Lee, Ji Woong;Lee, Minkyung;Shin, Un Chol;Kang, Joo Hyun;An, Gwang Il;Lee, Kyo Chul;Ryu, Young Hoon;Kim, Kyeong Min
    • Journal of Radiopharmaceuticals and Molecular Probes
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    • v.2 no.2
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    • pp.108-112
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    • 2016
  • Molecular imaging with the radiolabeled RGD peptides for ${\alpha}_v{\beta}_3$ integrin has been an increasing interest for tumor diagnosis and the treatment monitoring. Recently, $^{64}Cu$-NODAGA-gluco-E[c(RGDfK)]$_2$ was developed for quantification of ${\alpha}_v{\beta}_3$ integrin and its biological properties was elucidated. To better understand the molecular process in vivo, we performed the kinetic analysis for the $^{64}Cu$-NODAGA-gluco-E[c(RGDfK)]$_2$. After preparation of a radiotracer, dynamic PET images were obtained in the U87MG xenograft mice for 60 min (n = 6). Binding potential values were estimated from the 3-tissue compartment model, reference Logan and simplified reference tissue model. In the early time frame (0-20 min), the liver, kidney, intestine, urinary bladder and tumor were visualized but these uptakes were diminished as time went by. The tumors showed a good contrast at 40 min after administration. $^{64}Cu$-NODAGA-gluco-E[c(RGDfK)]$_2$ showed the 2-fold uptake in the tumor compared with that in the muscle. The parametric maps for binding values also provide the higher tumor-to-background contrast than the static images. A binding value obtained from the 3-tissue compartment model was comparable to other modeling methods. From these results, we conclude that $^{64}Cu$-NODAGA-gluco-E[c(RGDfK)]$_2$ may be a promising PET radiotracer for the evaluation of angiogenesis.

DNA Condensation and Delivery in 293 Cells Using Low Molecular Weight Chitosan/gene Nano-complex (저분자량 키토산/유전자 나노콤플렉스 제조 및 이를 이용한 293 세포로의 전달)

  • Pang, Shi-Won;Jang, Yangsoo;Kim, Jung-Hyun;Kim, Woo-Sik
    • Korean Chemical Engineering Research
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    • v.43 no.2
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    • pp.313-317
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    • 2005
  • Synthetic gene carriers such as poly-cationic polymers easily form complexes with plasmid DNA which contains negative charge. Chitosan is a polysaccharide that demonstrates much potential as a gene delivery system. The ability of depolymerized chitosan to condense DNA was determined using electrophoresis. Dynamic laser scattering and scanning electron microscopy were used to examine the size and the morphology of the chitosan/DNA complex. Parameters such as chitosan molecular weight and charge density influenced the complex size and the DNA amount condensed with chitosan. The cell viabilities in the presence of chitosan ranged between 84-108% of the control in all experiments. Gene expression efficacy using chitosan/DNA complex was enhanced in 293 cells relative to that using naked DNA, although it was lower than that using lipofecamine. Transfection efficacy using low molecular weight chitosan (Mw=8,517) was higher than those of the control and the other chitosan (MW=4,078). The low molecular weight chitosan (MW=8,517) with a high charge density (18.32 mV) fulfilled the requirements for a suitable model gene delivery system with respect to the condensing ability of DNA, complex formation, and transfection efficacy.

Transient Response of The Optimal Taper-Flat Head Slider in Magnetic Storage Devices

  • Arayavongkul, R.;Mongkolwongrojn, M.
    • 제어로봇시스템학회:학술대회논문집
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    • 2004.08a
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    • pp.990-994
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    • 2004
  • This paper presents a method to predict the transient characteristic of the air lubricated slider head in a hard disk drive by using optimization technique. The time dependent modified Reynolds equation based on the molecular slip flow approximation equations was used to describe the fluid flow within the air bearing and the implicit finite difference scheme is applied to calculate the pressure distribution under the slider head. The exhaustive search combined with the Broyden-Fletcher-Goldfarb-Shanno method were employed to obtain optimum design variables which are taper angle, rail width and taper length in order to keep the forces and moments acting on the slider head in dynamic equilibrium. The results show that the optimal head slider of the magnetic head has good stability characteristic that can reach the steady state within 0.5 microsecond.

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Molecular Dynamics Simulations of Small n-Alkane Clusters in a Mesoscopic Solvent

  • Ko, Seo-Young;Lee, Song-Hi
    • Bulletin of the Korean Chemical Society
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    • v.24 no.6
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    • pp.771-776
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    • 2003
  • The structural and dynamic properties of small n-alkane clusters embedded in a mesoscopic solvent are investigated. The solvent interactions are taken into account through a multi-particle collision operator that conserves mass, momentum and energy and the solvent dynamics is updated at discrete time intervals. The cluster molecules interact among themselves and with the solvent molecules through intermolecular forces. The properties of n-heptane and n-decane clusters interacting with the mesoscopic solvent molecules through repulsive Lennard-Jones interactions are studied as a function of the number of the mesoscopic solvent molecules. Modifications of both the cluster and solvent structure as a result of cluster-solvent interactions are considered. The cluster-solvent interactions also affect the dynamics of the small n-alkane clusters.

Molecular Dynamics Study on Oxygen Ions Diffusion of Gd-doped Ceria (Gd-doped Ceria의 산소이온 확산에 대한 분자동력학법 연구)

  • 강은태;김희승
    • Journal of the Korean Ceramic Society
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    • v.38 no.8
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    • pp.698-704
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    • 2001
  • Doped ceria의 전기전도도는 도핑 원소의 종류와 양에 큰 의존성을 가지고 특정 조성에서 최대 전도도 값을 가지며 높은 dopant 농도에서는 전기전도도는 감소한다. 이런 현상은 dopant와 산소 빈자리 사이의 회합 형성과 관련이 있다고 알려져 있다. 그러나 Gd 이온이 도핑된 ceria의 경우 주된 회합종이 (2G $d_{Ce}$ $V_{o}$ )인지 (G $e_{Ce}$ $V_{o}$ ) 인지는 명확하게 알려져 있지 않다. 본 연구에서는 회합분포가 전기전도도에 미치는 영향을 연구하기 위해 결함의 회합종과 분포가 다른 3가지 경우에 대해서 시뮬레이션을 행하였다. 분자동력학법을 이용하여 다양한 온도와 다른 회합분포의 경우에 대해 산소 확산계수가 계산되어졌으며, 계산된 산소 확산계수는 실험적으로 결정된 bulk 전도도로부터 얻어진 산소 확산계수와 비교되어졌다. 그 결과 (2G $d_{Ce}$ $V_{o}$ )와 (G $e_{Ce}$ $V_{o}$ ) 회합이 공존하며 이들이 통계학적으로 이항 분포를 가지는 경우가 실험적으로 보고된 값과 가장 일치하는 결과를 얻을 수 있었다.

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Mechanism, Function and Regulation of Microtubule-Dependent Microtubule Amplification in Mitosis

  • Zhu, Hui;Fang, Kayleen;Fang, Guowei
    • Molecules and Cells
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    • v.27 no.1
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    • pp.1-3
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    • 2009
  • Mitotic spindle mediates the segregation of chromosomes in the cell cycle and the proper function of the spindle is crucial to the high fidelity of chromosome segregation and to the stability of the genome. Nucleation of microtubules (MTs) from centrosomes and chromatin represents two well-characterized pathways essential for the assembly of a dynamic spindle in mitosis. Recently, we identified a third MT nucleation pathway, in which existing MTs in the spindle act as a template to promote the nucleation and polymerization of MTs, thereby efficiently amplifying MTs in the spindle. We will review here our current understanding on the molecular mechanism, the physiological function and the cell-cycle regulation of MT amplification.

Chemical synthesis of processable conducting polyaniline derivative with free amine functional groups

  • Kar, Pradip
    • Advances in materials Research
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    • v.3 no.2
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    • pp.117-128
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    • 2014
  • Processable conducting polyaniline derivative with free amine functional groups was successfully synthesized from the monomer o-phenylenediamine in aqueous hydrochloric acid medium using ammonium persulfate as an oxidative initiator. The synthesized poly(o-phenylenediamine) (PoPD) in critical condition was found to be completely soluble in common organic solvents like dimethyl sulfoxide, N,N-dimethyl formamide etc. From the intrinsic viscosity measurement, the optimum condition for the polymerization was established. The polymer was characterized by ultraviolet visible spectroscopy, Fourier transform infrared spectroscopy, proton magnetic resonance spectroscopy ($^1HNMR$) and thermogravimetric (TGA) analyses. The weight average molecular weights of the synthesized polymers were determined by the dynamic light scattering (DLS) method. From the spectroscopic analysis the structure was found to resemble that of polyaniline derivative with free amine functional groups attached to ortho/meta position in the phenyl ring. However, very little ladder unit was also present with in the polymer chain. The moderate thermal stability of the synthesized polymer could be found from the TGA analysis. The average DC conductivity of $2.8{\times}10^{-4}S/cm$ was observed for the synthesized polymer pellet after doping with hydrochloric acid.

Nanoporous graphene oxide membrane and its application in molecular sieving

  • Fatemi, S. Mahmood;Arabieh, Masoud;Sepehrian, Hamid
    • Carbon letters
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    • v.16 no.3
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    • pp.183-191
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    • 2015
  • Gas transport through graphene-derived membranes has gained much interest recently due to its promising potential in filtration and separation applications. In this work, we explore Kr-85 gas radionuclide sequestration from natural air in nanoporous graphene oxide membranes in which different sizes and geometries of pores were modeled on the graphene oxide sheet. This was done using atomistic simulations considering mean-squared displacement, diffusion coefficient, number of crossed species of gases through nanoporous graphene oxide, and flow through interlayer galleries. The results showed that the gas features have the densest adsorbed zone in nanoporous graphene oxide, compared with a graphene membrane, and that graphene oxide was more favorable than graphene for Kr separation. The aim of this paper is to show that for the well-defined pore size called P-7, it is possible to separate Kr-85 from a gas mixture containing Kr-85, O2 and N2. The results would benefit the oil industry among others.

Roles of YAP in mediating endothelial cell junctional stability and vascular remodeling

  • Choi, Hyun-Jung;Kwon, Young-Guen
    • BMB Reports
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    • v.48 no.8
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    • pp.429-430
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    • 2015
  • Angiogenesis is a complex process involving dynamic interaction of various cell to cell interactions. Endothelial cell interactions regulated by growth factors, inflammatory cytokines, or hemodynamic stress are critical for balancing vascular quiescence and activation. Yes-associated protein (YAP), an effector of Hippo signaling, is known to play significant roles in maintaining cellular homeostasis. However, its role in endothelial cells for angiogenic regulation remains relatively unexplored. We demonstrated the critical role of YAP in vascular endothelial cells and elucidated the underlying molecular mechanisms involved in angiogenic regulation of YAP. YAP was expressed in active angiogenic regions where endothelial cell junctions were relatively loosened. Consistently, YAP subcellular localization and activity were regulated by VE-cadherin-mediated PI3K/Akt pathway. YAP thereby regulated endothelial sprouting via angiopoietin-2 expression. These results provide an insight into a model of coordinating endothelial junctional stability and angiogenic activation through YAP. [BMB Reports 2015; 48(8): 429-430]