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.

Flexibility of short-strand RNA in aqueous solution as revealed by molecular dynamics simulation:are A′-RNA and A-RNA distinct conformational structures?

We use molecular dynamics simulations to compare the conformational structure and dynamics of a 21-base pair RNA sequence initially constructed according to the canonical A-RNA and A'-RNA forms in the presence of counterions and explicit water. Our study aims to add a dynamical perspective to the solid-state structural information that has been derived from X-ray data for these two characteristic forms of RNA. Analysis of the three main structural descriptors commonly used to differentiate between the two forms of RNA namely major groove width, inclination and the number of base pairs in a helical twist over a 30 ns simulation period reveals a flexible structure in aqueous solution with fluctuations in the values of these structural parameters encompassing the range between the two crystal forms and more. This provides evidence to suggest that the identification of distinct A-RNA and A'-RNA structures, while relevant in the crystalline form, may not be generally relevant in the context of RNA in the aqueous phase. The apparent structural flexibility observed in our simulations is likely to bear ramifications for the interactions of RNA with biological molecules (e.g. proteins) and non-biological molecules (e.g. non-viral gene delivery vectors). © CSIRO 2009.

The design and piloting of an eBusiness design studio

This paper describes the establishment and early use of an eBusiness Design Studio in Aston Business School at Aston University which is located in Birmingham in the UK. It was originally conceived as an R&D aid as much as a teaching resource. However the bulk of its use to date has been in the support of Masters level modules (courses) and this description will focus on that application in the first instance. We have less experience of its use in an R&D context but we will make some preliminary comments on this in a later section.

Reducible disulfide-based non-viral gene delivery systems

The design and synthesis of safe efficient non-viral vectors for gene delivery has attracted significant attention in recent years due primarily to the severe side-effect profile reported with the use of their viral counterparts. Previous experiments have revealed that the strong interaction between the carriers and nucleic acid may well hinder the release of the gene from the complex in the cytosol adversely affecting transfection efficiency. However, incorporating reducible disulfide bonds within the delivery systems themselves which are then cleaved in the glutathione-rich intracellular environment may help in solving this puzzle. This review focuses on recent development of these reducible carriers. The biological rationale and approaches to the synthesis of reducible vectors are discussed in detail. The in vitro and in vivo evaluations of reducible carriers are also summarized and it is evident that they offer a promising approach in non-viral gene delivery system design.

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.

Development of novel NMR pulse sequences

To elucidate the structures of orgamc molecules in solution using pulse FT NMR, heteronuclear pulse sequence experiments to probe carbon-13 (13C) and proton (1H) spin systems are invaluable. The one-dimensional insensitive nucleus detected PENDANT experiment finds popular use for structure determination via one-bond 13C-1H scalar couplings. PENDANT facilitates the desired increase in 13C signal-to-noise ratio, and unlike many other pulse sequence experiments (e.g., refocused INEPT and DEPT), allows the simultaneous detection of 13C quaternary nuclei. The tlrst chapter herein details the characterisation of PENDANT and the successful rectification of spectral anomalies that occur when it is used without proton broadband decoupling. Multiple-bond (long-range) l3C-1H scalar coupling correlations can yield important bonding information. When the molecule under scrutiny is devoid of proton spectral crowding, and more sensitive 'inverse' pulse sequence experiments are not available, one may use insensitive nucleus detected long-range selective one-dimensional correlation methods, rather than more time consuming and insensitive multidimensional analogues. To this end a novel long-range selective one-dimensional correlation pulse sequence experiment has been invented. Based on PENDANT, the new experiment is shown to rival the popular selective INEPT technique because it can determine the same correlations while simultaneously detecting isolated 13C quaternary nuclei. INEPT cannot facilitate this, potentially leaving other important quaternary nuclei undetected. The novel sequence has been modified further to yield a second novel experiment that simultaneously yields selective 13C transient nOe data. Consequently, the need to perform the two experiments back-to-back is conveniently removed, and the experimental time reduced. Finally, the SNARE pulse sequence was further developed. SNARE facilitates the reduction of experimental time by accelerating the relaxation of protons upon which pulse sequences, to which SNARE is appended, relies. It is shown, contrary to the original publication, that reiaxation time savings can be derived from negative nOes.

The percutaneous absorption of ionisable compounds

The effects of ionisation on transdermal drug delivery using excised human epidermis (HS) and silastic rubber (SR) as model permeation barriers were investigated in vitro using Franz-type absorption cells. Suspensions and solutions of salicylic acid (SA), the model ionogenic permeant, were used as donors and the variables studied were vehicle pH and trans-membrane pH-gradients. For solutions, the pH effect was related to the level of ionisation of the drug and the degree of saturation of the solution. With suspensions, the observed permeation rate was unaffected by pH. The penetration profiles through HS and SR were similar, although the overall flux through HS was about 70% of that observed through SR. Pretreatment of the membranes with various enhancer regimens, including oleic acid, Azone and N, N-dimethylamides in propylene glycol (PG) and isopropyl myristate (IPM) promoted the penetration of SA. SR was not a suitable model for enhancer pretreatment using IPM as a vehicle as the membrane was significantly disrupted by this vehicle. The results from comparable experiments with and without a trans-membrane pH-gradient did not have a significant effect upon flux or flux enhancement after pretreatment with the above enhancers. A theoretical model for the extraction coefficients of weak acids was derived using the partition coefficients of the ionised and unionised species, pH and pKa. This model was shown to account for the variation in overall partition of salicylic acid dependent upon pH and pKa. This model was shown to account for the variation in overall partition of salicylic acid dependent upon pH and pKa. The distribution of this solute between aqueous and oily phases, with and without added enhancer, was measured as a function of pH. The extraction coefficients determined were consistent with the model and showed that the behaviour of the system can be explained without referral to ion-pair mechanisms. Phosphonoacetate is an effective antiviral agent. However, as it is charged at physiological pH, its permeation across cell membranes is limited. To assess the improvement of the transport properties of this molecule, mono-, di- and tri-ester prodrugs were examined. These were assessed for stability and subsequent breakdown with respect to pH by HPLC. In vitro percutaneous absorption was observed using the triester, but not the ionic mono- or di-esters. The triester absorption could be potentiated using a range of enhancers with oleic acid being the most effective. Cyclodextrins (CD) have a role as absorption enhancers for peptide compounds across nasal epithelium. One potential mode of action is that CDs include these compounds, protect them from enzymic attack and thereby increase their residence time in the nasal epithelium. This study investigated the potential of CDs to protect ester prodrugs from enzymatic breakdown and prevent production of poorly transportable ionic species. Using a range of CD to ester molar ratios (10:1 to 2500:1) a small, but measurable, protection for the model esters (parabens) against esterase attack was observed. Possible mechanisms for this phenomenon are that CDs include the ester, making it unavailable for hydrolysis, the CDs may also affect the esterase in some way preventing access for the ester into the active site.

Gamma rays associated with neutron scattering in fusion reactor materials

The gamma-rays produced by the inelastic scattering of 14 MeV neutrons. in fusion reactor materials have been studied using a gamma-ray spectrometer employing a sodium iodide scintillation detector. The source neutrons are produced by the T(d,n)4He reaction using the SAMES accelerator at the University of Aston in Birmingham. In order to eliminate the large gamma-ray background and neutron signal due to the sensitivity of the sodium iodide detector to neutrons, the gamma-ray detector is heavily shielded and is used together with a particle time of flight discrimination system based on the associated particle time of flight method. The instant of production of a source neutron is determined by detecting the associated alpha-particle enabling discrimination between the neutrons and gamma-rays by their different time of flight times. The electronic system used for measuring the time of flight of the neutrons and gamrna-rays over the fixed flight path is described. The materials studied in this work were Lithium and Lead because of their importance as fuel breeding and shielding materials in conceptual fusion reactor designs. Several sample thicknesses were studied to determine the multiple scattering effects. The observed gamma-ray spectra from each sample at several scattering angles in the angular range Oº - 90° enabled absolute differential gamma-ray production cross-sections and angular distributions of the resolved gamma-rays from Lithium to be measured and compared with published data. For the Lead sample, the absolute differential gamma-ray production cross-sections for discrete 1 MeV ranges and the angular distributions were measured. The measured angular distributions of the present work and those on Iron from previous work are compared to the predictions of the Monte Carlo programme M.O.R.S.E. Good agreement was obtained between the experimental results and the theoretical predictions. In addition an empirical relation has been constructed which describes the multiple scattering effects by a single parameter and is capable of predicting the gamma-ray production cross-sections for the materials to an accuracy of ± 25%.

Voltage control on an uninhabited autonomous vehicle electrical distribution system

More-electric vehicle technology is becoming prevalent in a number of transportation systems because of its ability to improve efficiency and reduce costs. This paper examines the specific case of an Uninhabited Autonomous Vehicle (UAV), and the system topology and control elements required to achieve adequate dc distribution voltage bus regulation. Voltage control methods are investigated and a droop control scheme is implemented on the system. Simulation results are also presented.

The effects of the changing energy situation on demand for industrial heat exchangers

The Project arose during a period in which the World was still coming to terms with the effects and implications of the so called 'energy crisis' of 1973/74. Serck Heat Transfer is a manufacturer of heat exchangers which transfer heat between fluids of various sorts. As such the company felt that past and possible future changes in the energy situation could have an impact upon the demand for its products. The thesis represents the first attempt to examine the impact of changes in the energy situation (a major economic variable) on the long term demand for heat exchangers. The scope of the work was limited to the United Kingdom, this being the largest single market for Serek's products. The thesis analyses industrial heat exchanger markets and identifies those trends which are related to both the changing energy situation and the usage of heat exchangers. These trends have been interpreted In terms of projected values of heat exchanger demand. The projections cover the period 197S to the year 2000. Also examined in the thesis is the future energy situation both internationally and nationally and it is found that in the long term there will be increasing pressure on consumers to conserve energy through rising real prices. The possibility of a connection between energy consumption and heat exchanger demand is investigated and no significant correlation found. This appears to be because there are a number of determinants of demand besides energy related factors and also there is a wide diversity of individual markets for heat exchangers. Conclusions are that in all markets, bar one, the changing energy situation should lead to a higher level of heat exchanger demand than would otherwise be the case had the energy situation not changed. It is also pointed out that it is misleading to look at changes in one influence on the demand for a product and ignore others.

Evaluation of disinfecting procedures for aseptic transfer in hospital pharmacy departments

Current practice in National Health Service (NHS) hospitals employs 70% Industrial Methylated Spirit spray for surface disinfection of components required in Grade A pharmaceutical environments. This study seeks to investigate other agents and procedures that may provide more effective sanitisation. Several methods are available to test the efficacy of disinfectants against vegetative organisms. However, no methods currently available test the efficacy of disinfectants against spores on the hard surfaces encountered in the pharmacy aseptic processing environment. Therefore, a method has been developed to test the efficacy of disinfectants against spores, modified from British Standard 13697 and Association of Analytical Chemists standards. The testing procedure was used to evaluate alternative biocides and disinfection methods for transferring components into hospital pharmacy cleanrooms, and to determine which combinations of biocide and application method have the greatest efficacy against spores of Bacillus subtilis subspecies subtilis 168, Bacillus subtilis American Type Culture Collection (ATCC) 6633, and Bacillus pumilis ATCC 27142. Stainless steel carrier test plates were used to represent the hard surfaces in hospital pharmacy cleanrooms. Plates were inoculated with 10(7)-10(8) colony-forming units per milliliter (CFU/mL) and treated with the various biocide formulations, using different disinfection methods. Sporicidal activity was calculated as log reduction in CFU. Of the biocides tested, 6% hydrogen peroxide and a quaternary ammonium compound/chlorine dioxide combination were most effective compared to a Quat/biguanide, amphoteric surfactant, 70% v/v ethanol in deionised water and isopropyl alcohol in water for injection. Of the different application methods tested, spraying followed by wiping was the most effective, followed closely by wiping alone. Spraying alone was least effective.

Psychological risk factors for chronic post-surgical pain after inguinal hernia repair surgery:a prospective cohort study.

A significant proportion of patients experience chronic post-surgical pain (CPSP) following inguinal hernia surgery. Psychological models are useful in predicting acute pain after surgery, and in predicting the transition from acute to chronic pain in non-surgical contexts. This is a prospective cohort study to investigate psychological (cognitive and emotional) risk factors for CPSP after inguinal hernia surgery. Participants were asked to complete questionnaires before surgery and 1 week and 4 months after surgery. Data collected before surgery and 1 week after surgery were used to predict pain at 4 months. Psychological risk factors assessed included anxiety, depression, fear-avoidance, activity avoidance, catastrophizing, worry about the operation, activity expectations, perceived pain control and optimism. The study included 135 participants; follow-up questionnaires were returned by 119 (88.1%) and 115 (85.2%) participants at 1 week and 4 months after surgery respectively. The incidence of CPSP (pain at 4 months) was 39.5%. After controlling for age, body mass index and surgical variables (e.g. anaesthetic, type of surgery and mesh type used), lower pre-operative optimism was an independent risk factor for CPSP at 4 months; lower pre-operative optimism and lower perceived control over pain at 1 week after surgery predicted higher pain intensity at 4 months. No emotional variables were independently predictive of CPSP. Further research should target these cognitive variables in pre-operative psychological preparation for surgery. © 2011 European Federation of International Association for the Study of Pain Chapters.

Developing a knowledge-based perspective on coordination:the case of global software projects

We have attempted to bring together two areas which are challenging for both IS research and practice: forms of coordination and management of knowledge in the context of global, virtual software development projects. We developed a more comprehensive, knowledge-based model of how coordination can be achieved, and\illustrated the heuristic and explanatory power of the model when applied to global software projects experiencing different degrees of success. We first reviewed the literature on coordination and determined what is known about coordination of knowledge in global software projects. From this we developed a new, distinctive knowledge-based model of coordination, which was then employed to analyze two case studies of global software projects, at SAP and Baan, to illustrate the utility of the model.