The Experts below are selected from a list of 6033 Experts worldwide ranked by ideXlab platform
Tamar Schlick - One of the best experts on this subject based on the ideXlab platform.
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Crucial role of Dynamic Linker histone binding and divalent ions for DNA accessibility and gene regulation revealed by mesoscale modeling of oligonucleosomes.
Nucleic acids research, 2012Co-Authors: Rosana Collepardo-guevara, Tamar SchlickAbstract:Monte Carlo simulations of a mesoscale model of oligonucleosomes are analyzed to examine the role of Dynamic-Linker histone (LH) binding/unbinding in high monovalent salt with divalent ions, and to further interpret noted chromatin fiber softening by Dynamic LH in monovalent salt conditions. We find that divalent ions produce a fiber stiffening effect that competes with, but does not overshadow, the dramatic softening triggered by Dynamic-LH behavior. Indeed, we find that in typical in vivo conditions, Dynamic-LH binding/unbinding reduces fiber stiffening dramatically (by a factor of almost 5, as measured by the elasticity modulus) compared with rigidly fixed LH, and also the force needed to initiate chromatin unfolding, making it consistent with those of molecular motors. Our data also show that, during unfolding, divalent ions together with LHs induce Linker-DNA bending and DNA–DNA repulsion screening, which guarantee formation of heteromorphic superbeads-on-a-string structures that combine regions of loose and compact fiber independently of the characteristics of the LH–core bond. These structures might be important for gene regulation as they expose regions of the DNA selectively. Dynamic control of LH binding/unbinding, either globally or locally, in the presence of divalent ions, might constitute a mechanism for regulation of gene expression.
Jonathan Cook - One of the best experts on this subject based on the ideXlab platform.
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towards a service based middleware layer for runtime environments
ACM Symposium on Applied Computing, 2008Co-Authors: Abdulmalik Algahmi, Jonathan CookAbstract:Natively compiled, binary-code application programs are typically thought of as executing on the "raw" operating system. However, they do in fact utilize a bare-bones middleware layer---the Dynamic Linker. This paper presents a service-based view of an expanded run-time environment in which the current Dynamic Linker is only a core service, and other middleware-type services are available to the application and its components (shared libraries). This paper then describes a prototype implementation of such an environment, called SBRT, or Service-Based Run-Time. SBRT also contains a unified event-based interface that allows for customized middleware services by means of an extension mechanism.
Wang Zhe Guo - One of the best experts on this subject based on the ideXlab platform.
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ghcfe1a a Dynamic Linker between the er network and actin cytoskeleton plays an important role in cotton fibre cell initiation and elongation
Journal of Experimental Botany, 2015Co-Authors: Haihai Wang, Zhidi Feng, Xiaowei Niu, Caiping Cai, Zhaosheng Kong, Tianzhe Zhang, Xinyu Wang, Se Wang, Wang Zhe GuoAbstract:Fibre cell initiation and elongation is critical for cotton fibre development. However, little is known about the regulation of initiation and elongation during fibre cell development. Here, the regulatory role of a novel protein GhCFE1A was uncovered. GhCFE1A is preferentially expressed at initiation and rapid elongation stages during fibre development; in addition, much higher expression of GhCFE1A was detected at the fibre initiation stage in fi br eless cotton mutants than in the fibre-bearing TM-1 wild-type. Importantly, overexpression of GhCFE1A in cotton not only delayed fibre cell elongation but also significantly reduced the density of lint and fuzz fibre initials and stem trichomes. Yeast two-hybrid assay showed that GhCFE1A interacted with several actin proteins, and the interaction was further confirmed by co-sedimentation assay. Interestingly, a subcellular localization assay showed that GhCFE1A resided on the cortical endoplasmic reticulum (ER) network and co-localized with actin cables. Moreover, the density of F-actin filaments was shown to be reduced in GhCFE1A-overexpressing fibres at the rapid elongation stage compared with the wild-type control. Taken together, the results demonstrate that GhCFE1A probably functions as a Dynamic Linker between the actin cytoskeleton and the ER network, and plays an important role in fibre cell initiation and elongation during cotton fibre development.
Rosana Collepardo-guevara - One of the best experts on this subject based on the ideXlab platform.
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Crucial role of Dynamic Linker histone binding and divalent ions for DNA accessibility and gene regulation revealed by mesoscale modeling of oligonucleosomes.
Nucleic acids research, 2012Co-Authors: Rosana Collepardo-guevara, Tamar SchlickAbstract:Monte Carlo simulations of a mesoscale model of oligonucleosomes are analyzed to examine the role of Dynamic-Linker histone (LH) binding/unbinding in high monovalent salt with divalent ions, and to further interpret noted chromatin fiber softening by Dynamic LH in monovalent salt conditions. We find that divalent ions produce a fiber stiffening effect that competes with, but does not overshadow, the dramatic softening triggered by Dynamic-LH behavior. Indeed, we find that in typical in vivo conditions, Dynamic-LH binding/unbinding reduces fiber stiffening dramatically (by a factor of almost 5, as measured by the elasticity modulus) compared with rigidly fixed LH, and also the force needed to initiate chromatin unfolding, making it consistent with those of molecular motors. Our data also show that, during unfolding, divalent ions together with LHs induce Linker-DNA bending and DNA–DNA repulsion screening, which guarantee formation of heteromorphic superbeads-on-a-string structures that combine regions of loose and compact fiber independently of the characteristics of the LH–core bond. These structures might be important for gene regulation as they expose regions of the DNA selectively. Dynamic control of LH binding/unbinding, either globally or locally, in the presence of divalent ions, might constitute a mechanism for regulation of gene expression.
Tatchamapan Yoskamtorn - One of the best experts on this subject based on the ideXlab platform.
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Structural and Dynamic studies of Zr-based metal-organic frameworks toward external stimuli
2021Co-Authors: Tatchamapan YoskamtornAbstract:Advanced studies of structures and Dynamics of functional materials based on metal-organic frameworks (MOFs) showing exceptional stimuli-driven properties is of strong current interest for the design of next-generation smart materials, especially for sorption-based applications such as gas storage, energy storage, controlled drug delivery, and molecular sensing, to name but a few. State-of-the-art diffraction and spectroscopy in conjunction with theoretical calculations are one of the most powerful approaches to achieve these detailed analyses at a molecular level. This thesis aims to study mechanistic aspects of stimuli-responsive behaviours responsible for a distinctive stepwise ammonia (NH3) adsorption in the defect-rich Zr-based metal-organic frameworks (MOFs), namely UiO-67 and its isostructural UiO-bpydc, both experimentally and computationally. In Chapter 3, high-resolution neutron and synchrotron diffractions along with Rietveld refinement and density functional theory (DFT) calculations have been used to characterise the binding domains and the interactions of NH3/ND3 with defect-rich UiO-67 and UiO-bpydc containing biphenyl dicarboxylate and bipyridine dicarboxylate Linkers, respectively. The results establish that the dramatic alteration of stepwise adsorption processes is closely associated with hydrogen bonding network between NH3/ND3 and the frameworks at the disordered/defective trigonal and lozenge pore windows of the materials without significant change in pore volume and unit cell parameters. Specifically, UiO-bpydc is possible to make stronger and more extensive hydrogen bonding using pyridine sites of the Linker than in UiO-67. These molecular controls lead to stimulus-tailoring properties such as gate-controlled porosity by Dynamic Linker flipping, disorder, and structural rigidity which are further confirmed by temperature-dependence of in situ structural analyses accompanied with guest-induced rotational motions of the organic Linkers studied by DFT in Chapter 4. To get deeper insights into the interesting NH3-induced stepwise adsorption, the Dynamic features of the MOF-NH3 systems have been further investigated by using advanced inelastic neutron scattering (INS), quasi-elastic neutron scattering (QENS) in conjunction with theoretical calculations. Guest-induced Linker stiffening reflected by the suppression of lattice motions of the host frameworks upon NH3 adsorption is achieved, which exhibits greater effect in the UiO-bpydc case. More excitingly, analysis of INS difference spectra reveals heterogeneous Dynamics of the trapped NH3 depending on MOF functionality and gas loading. For the UiO-67, the well-ordered NH3 molecules primarily adsorbed at μ3-OH have more feasibility to undergo progressive interactions with the incoming NH3 molecules, signifying its more accessible porous structure for NH3 inclusion due to the lack of guest-stimulated pore blocking conversely observed in the UiO-bpydc. QENS study elucidates negligible mobility of NH3 in both MOFs at the lowest dosage, indicative of the similar localised diffusion caused by strongly bound NH3 at the μ3-OH sites of the hosts. On the other hand, the NH3 diffusivities in these frameworks become distinct at higher NH3 uptake where the stepped adsorption occurs. This observation points toward the confined NH3 molecules experiencing a diversity of either pore environments or host-guest interactions
