Analysis of the Structural Mechanism of ATP Inhibition at the AAA1 Subunit of Cytoplasmic Dynein-1 Using a Chemical “Toolkit”

Dynein is a ~1.2 MDa cytoskeletal motor protein that carries organelles via retrograde transport in eukaryotic cells. The motor protein belongs to the ATPase family of proteins associated with diverse cellular activities and plays a critical role in transporting cargoes to the minus end of the microtubules. The motor domain of dynein possesses a hexameric head, where ATP hydrolysis occurs. The presented work analyzes the structure–activity relationship (SAR) of dynapyrazole A and B, as well as ciliobrevin A and D, in their various protonated states and their 46 analogues for their binding in the AAA1 subunit, the leading ATP hydrolytic site of the motor domain. This study exploits in silico methods to look at the analogues’ effects on the functionally essential subsites of the motor domain of dynein 1, since no similar experimental structural data are available. Ciliobrevin and its analogues bind to the ATP motifs of the AAA1, namely, the walker-A (W-A) or P-loop, the walker-B (W-B), and the sensor I and II. Ciliobrevin A shows a better binding affinity than its D analogue. Although the double bond in ciliobrevin A and D was expected to decrease the ligand potency, they show a better affinity to the AAA1 binding site than dynapyrazole A and B, lacking the bond. In addition, protonation of the nitrogen atom in ciliobrevin A and D, as well as dynapyrazole A and B, at the N9 site of ciliobrevin and the N7 of the latter increased their binding affinity. Exploring ciliobrevin A geometrical configuration suggests the E isomer has a superior binding profile over the Z due to binding at the critical ATP motifs. Utilizing the refined structure of the motor domain obtained through protein conformational search in this study exhibits that Arg1852 of the yeast cytoplasmic dynein could involve in the “glutamate switch” mechanism in cytoplasmic dynein 1 in lieu of the conserved Asn in AAA+ protein family.     

Thermoelastic damping in a micro-beam resonator using modified couple stress theory

In this paper, analytical expressions for the quality factor (QF) of thermoelastic damping (TED) applying modified couple stress theory (MCST) are presented for plane stress and strain conditions. For gold and nickel micro-beam resonators, which have a considerable length-scale parameter as case studies, the effect of the length-scale parameter on the QF of TED has been discussed in details. Results for the QF of TED show that when the beam thickness is close to the length-scale parameter of the material, the MCST diverges from the classical theory; otherwise, the two theories converge to each other. Also critical thickness variation due to applying MCST is studied.     

A novel method for the determination of cell infiltration into nanofiber scaffolds using image analysis for tissue engineering applications

One of the major themes in tissue engineering is scaffold fabrication. The porosity and pore size of scaffolds play a critical role in tissue engineering. Different methods are used to measure the porosity and pore size of scaffolds, although none can predict the cell infiltration for various cell sizes, shapes, and configurations. The aim of this study was to predict the cell infiltration of various cells with different sizes, shapes, and configurations through the use of image analysis. In this study, cell models were used to predict cell infiltration into nanofiber scaffolds. The results of this study showed that with increases in the cell size and the number of layers of nanofibers, the number of cells that could infiltrate the scaffolds decreased. In addition, the cell configuration had some effect on cell infiltration into the nanofiber scaffolds. © 2008 Wiley Periodicals, Inc. J Appl Polym Sci, 2009     

Restricting Lattice Flexibility in Polycrystalline Metal–Organic Framework Membranes for Carbon Capture

Although polycrystalline metal‐organic framework (MOF) membranes offer several advantages over other nanoporous membranes, thus far they have not yielded good CO₂ separation performance, crucial for energy‐efficient carbon capture. ZIF‐8, one of the most popular MOFs, has a crystallographically determined pore aperture of 0.34 nm, ideal for CO₂/N₂ and CO₂/CH₄ separation; however, its flexible lattice restricts the corresponding separation selectivities to below 5. A novel postsynthetic rapid heat treatment (RHT), implemented in a few seconds at 360 °C, which drastically improves the carbon capture performance of the ZIF‐8 membranes, is reported. Lattice stiffening is confirmed by the appearance of a temperature‐activated transport, attributed to a stronger interaction of gas molecules with the pore aperture, with activation energy increasing with the molecular size (CH₄ > CO₂ > H₂). Unprecedented CO₂/CH₄, CO₂/N₂, and H₂/CH₄ selectivities exceeding 30, 30, and 175, respectively, and complete blockage of C₃H₆, are achieved. Spectroscopic and X‐ray diffraction studies confirm that while the coordination environment and crystallinity are unaffected, lattice distortion and strain are incorporated in the ZIF‐8 lattice, increasing the lattice stiffness. Overall, RHT treatment is a facile and versatile technique that can vastly improve the gas‐separation performance of the MOF membranes.     

Voting Under Uncertainty: A Stochastic Framework for Analyzing Group Decision Making Problems

Water resources policy making often involves consideration of a broader scope of environmental, economic, and social issues. This inevitably complicates policy making since consensus among multiple stakeholders with different interests is needed to implement decisions. This work employs several practical and popular voting methods to solve a multi-stakeholder hydro-environmental management problem. Conventionally, voting methods or social choice rules have been applied for consensus development in small groups and elections. This work combines voting methods with a Monte-Carlo selection, in order to help with social choice making under uncertainty. This process is intended to aid decision-makers with understanding of the risks associated with potential decision alternatives. The Sacramento-San Joaquin Delta’s water export conflict is solved here as a benchmark problem to illustrate the proposed framework for social decision making and analysis under uncertainty.     

A unified benchmarking and model-based framework for building QoS-aware streaming media services

A number of technology and workload trends motivate us to consider the appropriate resource allocation mechanisms and policies for streaming media services in shared cluster environments. We present MediaGuard – a model-based infrastructure for building streaming media services – that can efficiently determine the fraction of server resources required to support a particular client request over its expected lifetime. The proposed solution is based on a unified cost function that uses a single value to reflect overall resource requirements such as the CPU, disk, memory, and bandwidth necessary to support a particular media stream based on its bit rate and whether it is likely to be served from memory or disk. We design a novel, time-segment-based memory model of a media server to efficiently determine in linear time whether a request will incur memory or disk access when given the history of previous accesses and the behavior of the server's main memory file buffer cache. Using the MediaGuard framework, we design two media services: (1) an efficient and accurate admission control service for streaming media servers that accounts for the impact of the server's main memory file buffer cache, and (2) a shared streaming media hosting service that can efficiently allocate the predefined shares of server resources to the hosted media services, while providing performance isolation and QoS guarantees among the hosted services. Our evaluation shows that, relative to a pessimistic admission control policy that assumes that all content must be served from disk, MediaGuard (as well as services that are built using it) deliver a factor of two improvement in server throughput.     

Effect of surface nanocrystallization on the microstructural and corrosion characteristics of AZ91D magnesium alloy

Surface distinct deformed layers with thicknesses up to 150 μm, with grain size in the top most surface is in the nanometer scale, were produced on AZ91D magnesium alloy using surface mechanical attrition treatment (SMAT). Effects of different ball size on the properties of the SMATed samples were investigated. The microstructural, grain size, hardness and roughness features of the treated surfaces were characterized using optical microscopy (OM), scanning electron microscopy (SEM), X-ray diffraction (XRD), micro-indenter and digital roughness meter, respectively. Corrosion behavior of the samples was evaluated using potentiodynamic polarization and electrochemical impedance spectroscopy (EIS) techniques. It is found that the ball diameter does not have a significant effect on the top surface grain size, but the thickness of the deformed layer increases with increase of ball size, from 50 μm for 2 mm balls to 150 μm for 5 mm balls. For all of the SMATed samples, the top surface microhardness value increased significantly and did not show any obvious change for samples treated with different balls. Corrosion studies show that the corrosion resistance of the sample treated with 2 mm balls is higher than that of those treated with 3 mm and 5 mm balls. This can be mainly attributed to the surface roughness and defects density of the samples, which are higher for the SMATed samples with 3 mm and 5 mm balls compared with that of sample SMATed with 2 mm balls.     

Electrospun composite nanofibers for tissue regeneration

Nanotechnology assists in the development of biocomposite nanofibrous scaffolds that can react positively to changes in the immediate cellular environment and stimulate specific regenerative events at molecular level to generate healthy tissues. Recently, electrospinning has gained huge momentum with greater accessibility of fabrication of composite, controlled and oriented nanofibers with sufficient porosity required for effective tissue regeneration. Current developments include the fabrication of nanofibrous scaffolds which can provide chemical, mechanical and biological signals to respond to the environmental stimuli. These nanofibers are fabricated by simple coating, blending of polymers/bioactive molecules or by surface modification methods. For obtaining optimized surface functionality, with specially designed architectures for the nanofibers (multi-layered, core-shell, aligned), electrospinning process has been modified and simultaneous 'electrospin-electrospraying' process is one of the most lately introduced technique in this perspective. Properties such as porosity, biodegradation and mechanical properties of composite electrospun nanofibers along with their utilization for nerve, cardiac, bone, skin, vascular and cartilage tissue engineering are discussed in this review. In order to locally deliver electrical stimulus and provide a physical template for cell proliferations, and to gain an external control on the level and duration of stimulation, electrically conducting polymeric nanofibers are also fabricated by electrospinning. Electrospun polypyrrole (PPy) and polyaniline (PAN) based scaffolds are the most extensively studied composite substrates for nerve and cardiac tissue engineering with or without electrical stimulations, and are discussed here. However, the major focus of ongoing and future research in regenerative medicine is to effectively exploit the pluripotent potential of Mesenchymal Stem Cell (MSC) differentiation on composite nanofibrous scaffolds for repair of organs.     

Electrospun conducting polymer nanofibers and electrical stimulation of nerve stem cells

Tissue engineering of nerve grafts requires synergistic combination of scaffolds and techniques to promote and direct neurite outgrowth across the lesion for effective nerve regeneration. In this study, we fabricated a composite polymeric scaffold which is conductive in nature by electrospinning and further performed electrical stimulation of nerve stem cells seeded on the electrospun nanofibers. Poly-L-lactide (PLLA) was blended with polyaniline (PANi) at a ratio of 85:15 and electrospun to obtain PLLA/PANi nanofibers with fiber diameters of 195 ± 30 nm. The morphology, chemical and mechanical properties of the electrospun PLLA and PLLA/PANi scaffolds were carried out by scanning electron microscopy (SEM), X-ray photo electron spectroscopy (XPS) and tensile instrument. The electrospun PLLA/PANi fibers showed a conductance of 3 × 10?? S by two-point probe measurement. In vitro electrical stimulation of the nerve stem cells cultured on PLLA/PANi scaffolds applied with an electric field of 100 mV/mm for a period of 60 min resulted in extended neurite outgrowth compared to the cells grown on non-stimulated scaffolds. Our studies further strengthen the implication of electrical stimulation of nerve stem cells on conducting polymeric scaffolds towards neurite elongation that could be effective for nerve tissue regeneration.     

Discovery of novel anticancer compounds based on a quinoxalinehydrazine pharmacophore

Quinoxalinehydrazines represent a novel class of compounds with excellent potency in a panel of cancer cell lines. A prototype compound, SC144, showed significant in vivo efficacy in mice xenograft models of human breast cancer cells. The subsequent structure-activity relationship study resulted in the discovery of SC161 with better potency in cancer cell lines. Further exploring the possible conformational space by a 10 ns molecular dynamics simulation as presented herein, resulted in various pharmacophore orientations. The trajectory analysis indicated that in most of the simulation time, the molecule stays favorably in a compact planarlike orientation. We therefore built a pharmacophore model based on the cluster containing the highest number of frames to represent the most probable orientation. The model was used to screen a subset of our small molecule database containing 350,000 compounds. We selected 35 compounds for the initial cytotoxicity screen. Seventeen compounds belonging to oxadiazolopyrazine and quinoline class displayed cytotoxicity in various cancer cell lines. Five of them, compounds 2, 6, 15, 16, and 19, all bearing an oxadiazolopyrazine scaffold, showed IC(50) values <3 muM in certain tumor cell lines. The most potent compound, 2, showed IC(50) values <2 muM in HCT116 p53(+/+), HCT116 p53(-/-), and HEY cells, and 8 muM in NIH3T3 cells. This study shows that conformational sampling of a lead small molecule followed by representative pharmacophore model development is an efficient approach for the rational design of novel anticancer agents with similar or better potency than the original lead but with different physicochemical properties.