Structure, dynamics, and energetics of siRNA-cationic vector complexation:a molecular dynamics study

The design and synthesis of safe and efficient nonviral vectors for gene delivery has attracted significant attention in recent years. Previous experiments have revealed that the charge density of a polycation (the carrier) plays a crucial role in complexation and the release of the gene from the complex in the cytosol. In this work, we adopt an atomistic molecular dynamics simulation approach to study the complexation of short strand duplex RNA with six cationic carrier systems of varying charge and surface topology. The simulations reveal detailed molecular-level pictures of the structures and dynamics of the RNA-polycation complexes. Estimates for the binding free energy indicate that electrostatic contributions are dominant followed by van der Waals interactions. The binding free energy between the 8(+)polymers and the RNA is found to be larger than that of the 4(+)polymers, in general agreement with previously published data. Because reliable binding free energies provide an effective index of the ability of the polycationic carrier to bind the nucleic acid and also carry implications for the process of gene release within the cytosol, these novel simulations have the potential to provide us with a much better understanding of key mechanistic aspects of gene-polycation complexation and thereby advance the rational design of nonviral gene delivery systems.

Structure and dynamics of multiple cationic vectors-siRNA complexation by all-atomic molecular dynamics simulations

Understanding the molecular mechanism of gene condensation is a key component to rationalizing gene delivery phenomena, including functional properties such as the stability of the gene-vector complex and the intracellular release of the gene. In this work, we adopt an atomistic molecular dynamics simulation approach to study the complexation of short strand duplex RNA with four cationic carrier systems of varying charge and surface topology at different charge ratios. At lower charge ratios, polymers bind quite effectively to siRNA, while at high charge ratios, the complexes are saturated and there are free polymers that are unable to associate with RNA. We also observed reduced fluctuations in RNA structures when complexed with multiple polymers in solution as compared to both free siRNA in water and the single polymer complexes. These novel simulations provide a much better understanding of key mechanistic aspects of gene-polycation complexation and thereby advance progress toward rational design of nonviral gene delivery systems.

The effect of pH on PAMAM dendrimer-siRNA complexation:endosomal considerations as determined by molecular dynamics simulation

Intracellular degradation of genes, most notably within the endo-lysosomal compartment is considered a significant barrier to (non-viral) gene delivery in vivo. Previous reports based on in vitro studies claim that carriers possessing a mixture of primary, secondary and tertiary amines are able to buffer the acidic environment within the endosome, allowing for timely release of their contents, leading to higher transfection rates. In this report, we adopt an atomistic molecular dynamics (MD) simulation approach, comparing the complexation of 21-bp siRNA with low-generation polyamidoamine (PAMAM) dendrimers (G0 and G1) at both neutral and acidic pHs, the latter of which mimics the degradative environment within maturing 'late-endosomes'. Our simulations reveal that the time taken for the dendrimer-gene complex (dendriplex) to reach equilibrium is appreciably longer at low pH and this is accompanied by more compact packaging of the dendriplex, as compared to simulations performed at neutral pH. We also note larger absolute values of calculated binding free energies of the dendriplex at low pH, indicating a higher dendrimer-nucleic acid affinity in comparison with neutral pH. These novel simulations provide a more detailed understanding of low molecular-weight polymer-siRNA behavior, mimicking the endosomal environment and provide input of direct relevance to the "proton sponge theory", thereby advancing the rational design of non-viral gene delivery systems.

All-fiber polarization interference filters based on 45°-tilted fiber gratings

We report all-fiber polarization interference filters, known as Lyot and Lyot-Ohman filters, based on alternative concatenation of UV-inscribed fiber gratings with structure tilted at 45° and polarization maintaining (PM) fiber cavities. Such filters generate comb-like transmission of linear polarization output. The free spectral range (FSR) of a single-stage (Lyot) filter is PM fiber cavity length dependent, as a 20 cm long cavity showed a 26.6 nm FSR while the 40 cm one exhibited a 14.8 nm FSR. Furthermore, we have theoretically and experimentally demonstrated all-fiber 2-stage and 3-stage Lyot-Ohman filters, giving more freedom in tailoring the transmission characteristics.

The Kinematics of interference mechanisms in certain machining operations

The mechanism of "Helical Interference" in milled slots is examined and a coherent theory for the geometry of such surfaces is presented. An examination of the relevant literature shows a fragmented approach to the problem owing to its normally destructive nature, so a complete analysis is developed for slots of constant lead, thus giving a united and exact theory for many different setting parameters and a range of cutter shapes. For the first time, a theory is developed to explain the "Interference Surface" generated in variable lead slots for cylindrical work and attention is drawn to other practical surfaces, such as cones, where variable leads are encountered. Although generally outside the scope of this work, an introductory analysis of these cases is considered in order to develop the cylindrical theory. Special emphasis is laid upon practical areas where the interference mechanism can be used constructively and its application as the rake face of a cutting tool is discussed. A theory of rake angle for such cutting tools is given for commonly used planes, and relative variations in calculated rake angle between planes is examined. Practical tests are conducted to validate both constant lead and variable lead theories and some design improvements to the conventional dividing head are suggested in order to manufacture variable lead workpieces, by use of a "superposed" rotation. A prototype machine is manufactured and its kinematic principle given for both linear and non-linearly varying superposed rotations. Practical workpieces of the former type are manufactured and compared with analytical predictions,while theoretical curves are generated for non-linear workpieces and then compared with those of linear geometry. Finally suggestions are made for the application of these principles to the manufacture of spiral bevel gears, using the "Interference Surface" along a cone as the tooth form.

Hydrotalcite intercalated siRNA:computational characterization of the interlayer environment

Using molecular dynamics (MD) simulations, we explore the structural and dynamical properties of siRNA within the intercalated environment of a Mg:Al 2:1 Layered Double Hydroxide (LDH) nanoparticle. An ab initio force field (Condensed-phase Optimized Molecular Potentials for Atomistic Simulation Studies: COMPASS) is used for the MD simulations of the hybrid organic-inorganic systems. The structure, arrangement, mobility, close contacts and hydrogen bonds associated with the intercalated RNA are examined and contrasted with those of the isolated RNA. Computed powder X-ray diffraction patterns are also compared with related LDH-DNA experiments. As a method of probing whether the intercalated environment approximates the crystalline or rather the aqueous state, we explore the stability of the principle parameters (e.g., the major groove width) that differentiate both A- and A'- crystalline forms of siRNA and contrast this with recent findings for the same siRNA simulated in water. We find the crystalline forms remain structurally distinct when intercalated, whereas this is not the case in water. Implications for the stability of hybrid LDH-RNA systems are discussed.

Electromagnetic interference from variable speed motor drives

A methodology is presented which can be used to produce the level of electromagnetic interference, in the form of conducted and radiated emissions, from variable speed drives, the drive that was modelled being a Eurotherm 583 drive. The conducted emissions are predicted using an accurate circuit model of the drive and its associated equipment. The circuit model was constructed from a number of different areas, these being: the power electronics of the drive, the line impedance stabilising network used during the experimental work to measure the conducted emissions, a model of an induction motor assuming near zero load, an accurate model of the shielded cable which connected the drive to the motor, and finally the parasitic capacitances that were present in the drive modelled. The conducted emissions were predicted with an error of +/-6dB over the frequency range 150kHz to 16MHz, which compares well with the limits set in the standards which specify a frequency range of 150kHz to 30MHz. The conducted emissions model was also used to predict the current and voltage sources which were used to predict the radiated emissions from the drive. Two methods for the prediction of the radiated emissions from the drive were investigated, the first being two-dimensional finite element analysis and the second three-dimensional transmission line matrix modelling. The finite element model took account of the features of the drive that were considered to produce the majority of the radiation, these features being the switching of the IGBT's in the inverter, the shielded cable which connected the drive to the motor as well as some of the cables that were present in the drive.The model also took account of the structure of the test rig used to measure the radiated emissions. It was found that the majority of the radiation produced came from the shielded cable and the common mode currents that were flowing in the shield, and that it was feasible to model the radiation from the drive by only modelling the shielded cable. The radiated emissions were correctly predicted in the frequency range 30MHz to 200MHz with an error of +10dB/-6dB. The transmission line matrix method modelled the shielded cable which connected the drive to the motor and also took account of the architecture of the test rig. Only limited simulations were performed using the transmission line matrix model as it was found to be a very slow method and not an ideal solution to the problem. However the limited results obtained were comparable, to within 5%, to the results obtained using the finite element model.

A network coding based interference cancelation scheme for wireless ad hoc networks

The performance of wireless networks is limited by multiple access interference (MAI) in the traditional communication approach where the interfered signals of the concurrent transmissions are treated as noise. In this paper, we treat the interfered signals from a new perspective on the basis of additive electromagnetic (EM) waves and propose a network coding based interference cancelation (NCIC) scheme. In the proposed scheme, adjacent nodes can transmit simultaneously with careful scheduling; therefore, network performance will not be limited by the MAI. Additionally we design a space segmentation method for general wireless ad hoc networks, which organizes network into clusters with regular shapes (e.g., square and hexagon) to reduce the number of relay nodes. The segmentation methodworks with the scheduling scheme and can help achieve better scalability and reduced complexity. We derive accurate analytic models for the probability of connectivity between two adjacent cluster heads which is important for successful information relay. We proved that with the proposed NCIC scheme, the transmission efficiency can be improved by at least 50% for general wireless networks as compared to the traditional interference avoidance schemes. Numeric results also show the space segmentation is feasible and effective. Finally we propose and discuss a method to implement the NCIC scheme in a practical orthogonal frequency division multiplexing (OFDM) communications networks. Copyright © 2009 John Wiley & Sons, Ltd.

Studying membrane trafficking in the worm C. elegans by RNA interference

A powerful approach to gain understanding of molecular machinery responsible for membrane trafficking is through inactivation of gene function by RNA interference (RNAi). RNAi-mediated gene silencing occurs when a double-stranded RNA is introduced into cells and targets a complementary mRNA for degradation. The subsequent lack of mRNA prevents the synthesis of the corresponding protein and ultimately causes depletion of a particular gene product from the cell. The effects of such depletion can then by analyzed by functional, morphological, and biochemical assays. RNAi-mediated knockdowns of numerous gene products in cultured cells of mammalian and other species origins have provided significant new insight into traffic regulation and represent standard approaches in current cell biology. However, RNAi in the multicellular nematode Caenorhabditis elegans model allows RNAi studies within the context of a whole organism, and thus provides an unprecedented opportunity to explore effects of specific trafficking regulators within the context of distinct developmental stages and diverse cell types. In addition, various transgenic C. elegans strains have been developed that express marker proteins tagged with fluorescent proteins to facilitate the analysis of trafficking within the secretory and endocytic pathways. This chapter provides a detailed description of a basic RNAi approach that can be used to analyze the function of any gene of interest in secretory and endosomal trafficking in C. elegans. © 2013 Elsevier Inc.

The embodied nature of spatial perspective taking:embodied transformation versus sensorimotor interference

Humans are able to mentally adopt the spatial perspective of others and understand the world from their point of view. We propose that spatial perspective taking (SPT) could have developed from the physical alignment of perspectives. This would support the notion that others have put forward claiming that SPT is an embodied cognitive process. We investigated this issue by contrasting several accounts in terms of the assumed processes and the nature of the embodiment. In a series of four experiments we found substantial evidence that the transformations during SPT comprise large parts of the body schema, which we did not observe for object rotation. We further conclude that the embodiment of SPT is best conceptualised as the self-initiated emulation of a body movement, supporting the notion of endogenous motoric embodiment. Overall our results are much more in agreement with an ‘embodied’ transformation account than with the notion of sensorimotor interference. Finally we discuss our findings in terms of SPT as a possible evolutionary stepping stone towards more complex alignments of socio-cognitive perspectives.

Disturbing visual working memory:electrophysiological evidence for a role of the prefrontal cortex in recovery from interference

Single cell recordings in monkeys support the notion that the lateral prefrontal cortex (PFC) controls reactivation of visual working memory representations when rehearsal is disrupted. In contrast, recent fMRI findings yielded a double dissociation for PFC and the medial temporal lobe (MTL) in a letter working memory task. PFC was engaged in interference protection during reactivation while MTL was prominently involved in the retrieval of the letter representations. We present event-related potential data (ERP) that support PFC involvement in the top-down control of reactivation during a visual working memory task with endogenously triggered recovery after visual interference. A differentiating view is proposed for the role of PFC in working memory with respect to endogenous/exogenous control and to stimulus type. General implications for binding and retention mechanisms are discussed.

Statistical model of OFDMA cellular networks uplink interference using lognormal distribution

In this letter, we propose an analytical approach to model uplink intercell interference (ICI) in hexagonal grid based orthogonal frequency division multiple access (OFMDA) cellular networks. The key idea is that the uplink ICI from individual cells is approximated with a lognormal distribution with statistical parameters being determined analytically. Accordingly, the aggregated uplink ICI is approximated with another lognormal distribution and its statistical parameters can be determined from those of individual cells using Fenton-Wilkson method. Analytic expressions of uplink ICI are derived with two traditional frequency reuse schemes, namely integer frequency reuse schemes with factor 1 (IFR-1) and factor 3 (IFR-3). Uplink fractional power control and lognormal shadowing are modeled. System performances in terms of signal to interference plus noise ratio (SINR) and spectrum efficiency are also derived. The proposed model has been validated by simulations. © 2013 IEEE.

Broadband tunable all-fiber polarization interference filter based on 45° tilted fiber gratings

We have theoretically and experimentally designed and demonstrated an all-fiber polarization interference filter (AFPIF), which is formed by a polarization-maintaining (PM) fiber cavity structure utilizing two 45° tilted fiber gratings (45°-TFGs) inscribed by UV laser on the PM fiber. Such a filter could generate modulated transmission of linear polarization status. It has been revealed that the modulation depth of the transmission depends on the coupling angle between the 45°-TFGs and the PM fiber cavity. When the two 45°-TFGs in PM fiber are oriented at 45° to the principal axis of the PM fiber cavity, the maximum modulation depth is achievable. Due to the thermal effect on birefringence of the PM fiber, the AFPIF can be tuned over a broad wavelength range just by simple thermal tuning of the cavity. The experiment results show that the temperature tuning sensitivity is proportional to the length ratio of the PM fiber cavity under heating. For 18 and 40 cm long cavities with 6 cm part under heating, the thermal tuning sensitivities are 0.616 and 0.31 nm/° C, respectively, which are almost two orders of magnitude higher than normal fiber Bragg gratings. © 1983-2012 IEEE.