Fluorescent microplate-based analysis of protein-DNA interactions I:immobilized protein

A simple protein-DNA interaction analysis has been developed using a high-affinity/high-specificity zinc finger protein. In essence, purified protein samples are immobilized directly onto the surface of microplate wells, and fluorescently labeled DNA is added in solution. After incubation and washing, bound DNA is detected in a standard microplate reader. The minimum sensitivity of the assay is approximately 0.2 nM DNA. Since the detection of bound DNA is noninvasive and the protein-DNA interaction is not disrupted during detection, iterative readings may be taken from the same well, after successive alterations in interaction conditions, if required. In this respect, the assay may therefore be considered real time and permits appropriate interaction conditions to be determined quantitatively. The assay format is ideally suited to investigate the interactions of purified unlabeled DNA binding proteins in a high-throughput format.

Fluorescent microplate-based analysis of protein-DNA interactions II:immobilized DNA

A simple protein-DNA interaction analysis has been developed using both a high-affinity/high-specificity zinc finger protein and a low-specificity zinc finger protein with nonspecific DNA binding capability. The latter protein is designed to mimic background binding by proteins generated in randomized or shuffled gene libraries. In essence, DNA is immobilized onto the surface of microplate wells via streptavidin capture, and green fluorescent protein (GFP)-labeled protein is added in solution as part of a crude cell lysate or protein mixture. After incubation and washing, bound protein is detected in a standard microplate reader. The minimum sensitivity of the assay is approximately 0.4 nM protein. The assay format is ideally suited to investigate the interactions of DNA binding proteins from within crude cell extracts and/or mixtures of proteins that may be encountered in protein libraries generated by codon randomization or gene shuffling.

Mathematical modelling and control of agitated extraction columns

Liquid-liquid extraction has long been known as a unit operation that plays an important role in industry. This process is well known for its complexity and sensitivity to operation conditions. This thesis presents an attempt to explore the dynamics and control of this process using a systematic approach and state of the art control system design techniques. The process was studied first experimentally under carefully selected. operation conditions, which resembles the ranges employed practically under stable and efficient conditions. Data were collected at steady state conditions using adequate sampling techniques for the dispersed and continuous phases as well as during the transients of the column with the aid of a computer-based online data logging system and online concentration analysis. A stagewise single stage backflow model was improved to mimic the dynamic operation of the column. The developed model accounts for the variation in hydrodynamics, mass transfer, and physical properties throughout the length of the column. End effects were treated by addition of stages at the column entrances. Two parameters were incorporated in the model namely; mass transfer weight factor to correct for the assumption of no mass transfer in the. settling zones at each stage and the backmixing coefficients to handle the axial dispersion phenomena encountered in the course of column operation. The parameters were estimated by minimizing the differences between the experimental and the model predicted concentration profiles at steady state conditions using non-linear optimisation technique. The estimated values were then correlated as functions of operating parameters and were incorporated in·the model equations. The model equations comprise a stiff differential~algebraic system. This system was solved using the GEAR ODE solver. The calculated concentration profiles were compared to those experimentally measured. A very good agreement of the two profiles was achieved within a percent relative error of ±2.S%. The developed rigorous dynamic model of the extraction column was used to derive linear time-invariant reduced-order models that relate the input variables (agitator speed, solvent feed flowrate and concentration, feed concentration and flowrate) to the output variables (raffinate concentration and extract concentration) using the asymptotic method of system identification. The reduced-order models were shown to be accurate in capturing the dynamic behaviour of the process with a maximum modelling prediction error of I %. The simplicity and accuracy of the derived reduced-order models allow for control system design and analysis of such complicated processes. The extraction column is a typical multivariable process with agitator speed and solvent feed flowrate considered as manipulative variables; raffinate concentration and extract concentration as controlled variables and the feeds concentration and feed flowrate as disturbance variables. The control system design of the extraction process was tackled as multi-loop decentralised SISO (Single Input Single Output) as well as centralised MIMO (Multi-Input Multi-Output) system using both conventional and model-based control techniques such as IMC (Internal Model Control) and MPC (Model Predictive Control). Control performance of each control scheme was. studied in terms of stability, speed of response, sensitivity to modelling errors (robustness), setpoint tracking capabilities and load rejection. For decentralised control, multiple loops were assigned to pair.each manipulated variable with each controlled variable according to the interaction analysis and other pairing criteria such as relative gain array (RGA), singular value analysis (SVD). Loops namely Rotor speed-Raffinate concentration and Solvent flowrate Extract concentration showed weak interaction. Multivariable MPC has shown more effective performance compared to other conventional techniques since it accounts for loops interaction, time delays, and input-output variables constraints.

Talking about depression:an analogue study of physician gender and communication style on patient disclosures

Objectives: To disentangle the effects of physician gender and patient-centered communication style on patients' oral engagement in depression care. Methods: Physician gender, physician race and communication style (high patient-centered (HPC) and low patient-centered (LPC)) were manipulated and presented as videotaped actors within a computer simulated medical visit to assess effects on analogue patient (AP) verbal responsiveness and care ratings. 307 APs (56% female; 70% African American) were randomly assigned to conditions and instructed to verbally respond to depression-related questions and indicate willingness to continue care. Disclosures were coded using Roter Interaction Analysis System (RIAS). Results: Both male and female APs talked more overall and conveyed more psychosocial and emotional talk to HPC gender discordant doctors (all p <.05). APs were more willing to continue treatment with gender-discordant HPC physicians (p <.05). No effects were evident in the LPC condition. Conclusions: Findings highlight a role for physician gender when considering active patient engagement in patient-centered depression care. This pattern suggests that there may be largely under-appreciated and consequential effects associated with patient expectations in regard to physician gender that these differ by patient gender. Practice implications: High patient-centeredness increases active patient engagement in depression care especially in gender discordant dyads. © 2014.

Modeling the peptide-T cell receptor interaction by the comparative molecular similarity indices analysis-soft independent modeling of class analogy technique

A set of 38 epitopes and 183 non-epitopes, which bind to alleles of the HLA-A3 supertype, was subjected to a combination of comparative molecular similarity indices analysis (CoMSIA) and soft independent modeling of class analogy (SIMCA). During the process of T cell recognition, T cell receptors (TCR) interact with the central section of the bound nonamer peptide; thus only positions 4−8 were considered in the study. The derived model distinguished 82% of the epitopes and 73% of the non-epitopes after cross-validation in five groups. The overall preference from the model is for polar amino acids with high electron density and the ability to form hydrogen bonds. These so-called “aggressive” amino acids are flanked by small-sized residues, which enable such residues to protrude from the binding cleft and take an active role in TCR-mediated T cell recognition. Combinations of “aggressive” and “passive” amino acids in the middle part of epitopes constitute a putative TCR binding motif

Long-range translational coupling in single-stranded RNA bacteriophages: an evolutionary analysis

In coliphage MS2 RNA a long-distance interaction (LDI) between an internal segment of the upstream coat gene and the start region of the replicase gene prevents initiation of replicase synthesis in the absence of coat gene translation. Elongating ribosomes break up the repressor LDI and thus activate the hidden initiation site. Expression studies on partial MS2 cDNA clones identified base pairing between 1427-1433 and 1738-1744, the so-called Min Jou (MJ) interaction, as the molecular basis for the long-range coupling mechanism. Here, we examine the biological significance of this interaction for the control of replicase gene translation. The LDI was disrupted by mutations in the 3'-side and the evolutionary adaptation was monitored upon phage passaging. Two categories of pseudorevertants emerged. The first type had restored the MJ interaction but not necessarily the native sequence. The pseudorevertants of the second type acquired a compensatory substitution some 80 nt downstream of the MJ interaction that stabilizes an adjacent LDI. In one examined case we confirmed that the second site mutations had restored coat-replicase translational coupling. Our results show the importance of translational control for fitness of the phage. They also reveal that the structure that buries the replicase start extends to structure elements bordering the MJ interaction.

Innovation, productivity and growth in US business services:a firm-level analysis

This paper examines the impact of innovation on the performance of US business service firms. We distinguish between different levels of innovation (new-to-market and new-to-firm) in our analysis, and allow explicitly for sample selection issues. Reflecting the literature, which highlights the importance of external interaction in service innovation, we pay particular attention to the role of external innovation linkages and their effect on business performance. We find that the presence of service innovation and its extent has a consistently positive effect on growth, but no effect on productivity. There is evidence that the growth effect of innovation can be attributed, at least in part, to the external linkages maintained by innovators in the process of innovation. External linkages have an overwhelmingly positive effect on (innovator) firm performance, regardless of whether innovation is measured as a discrete or continuous variable, and regardless of the level of innovation considered.

The lateral and ventromedial prefrontal cortex work as a dynamic integrated system:evidence from FMRI connectivity analysis

Recent functional magnetic resonance imaging (fMRI) investigations of the interaction between cognition and reward processing have found that the lateral prefrontal cortex (PFC) areas are preferentially activated to both increasing cognitive demand and reward level. Conversely, ventromedial PFC (VMPFC) areas show decreased activation to the same conditions, indicating a possible reciprocal relationship between cognitive and emotional processing regions. We report an fMRI study of a rewarded working memory task, in which we further explore how the relationship between reward and cognitive processing is mediated. We not only assess the integrity of reciprocal neural connections between the lateral PFC and VMPFC brain regions in different experimental contexts but also test whether additional cortical and subcortical regions influence this relationship. Psychophysiological interaction analyses were used as a measure of functional connectivity in order to characterize the influence of both cognitive and motivational variables on connectivity between the lateral PFC and the VMPFC. Psychophysiological interactions revealed negative functional connectivity between the lateral PFC and the VMPFC in the context of high memory load, and high memory load in tandem with a highly motivating context, but not in the context of reward alone. Physiophysiological interactions further indicated that the dorsal anterior cingulate and the caudate nucleus modulate this pathway. These findings provide evidence for a dynamic interplay between lateral PFC and VMPFC regions and are consistent with an emotional gating role for the VMPFC during cognitively demanding tasks. Our findings also support neuropsychological theories of mood disorders, which have long emphasized a dysfunctional relationship between emotion/motivational and cognitive processes in depression.

Interaction of liquid copper with sintered iron compacts

Interaction of liquid copper with sintered iron is important in brazing, liquid phase sintering and infiltration. In brazing, the penetration of liquid copper into the pores is to be `avoided', whereas in infiltration processes it is `encouraged', and in liquid phase sintering it should be `controlled' so that optimum mechanical properties are achieved. The main objective of the research is to model the interaction by studying the effect of the process variables on the mechanisms of copper interaction in Fe-Cu and Fe-Cu-C systems. This involves both theoretical and experimental considerations. Dilatometric investigations at 950, 1125 and 1200oC, together with metallographic analyses were carried out to clarify the copper growth phenomenon. It is shown that penetration of liquid copper into the iron grain boundaries is the major cause of dimensional changes. Infiltration profiles revealed that copper penetration between the iron interparticle contact points and along iron grain boundaries is a rapid process. The extent of copper penetration depends on the dihedral angle. Large dihedral angles hinder, and small angles promote copper penetration into the grain boundaries. Dihedral angle analysis shows that the addition of 0.6wt.% graphite reduces the number of zero dihedral angle from 27 to 3o and increases the mean dihedral angle from 9.8 to 41.5o. The dihedral angle was lowest at 1125oC and then increased to higher values as the system approached its equilibrium condition. Elementally mixed (E.M.) Fe-Cu compacts showed a rapid expansion at the copper melting point. However, graphite additions reduced compact growth by increasing the mean dihedral angle. In order to reduce the copper growth phenomenon, iron powder was coated with a thin layer of copper by an immersion coating (I.C.) technique. The dilatometric curves revealed an overall shrinkage in the I.C. compacts compared to their corresponding E.M. compacts. Multiple regression models showed that temperature had the most effect on dimensional changes and density had the most contributing effect upon the copper penetration area in the infiltrated powder metallurgy compacts.

Affect networks:a structural analysis of the relationship between work ties and job-related affect

The relationship between organizational networks and employees' affect was examined in 2 organizations. In Study 1, social network analysis of work ties and job-related affect for 259 employees showed that affect converged within work interaction groups. Similarity of affect between employees depended on the presence of work ties and structural equivalence. Affect was also related to the size and density of employees' work networks. Study 2 used a 10-week diary study of 31 employees to examine a merger of 2 organizational divisions and found that negative changes in employees' affect were related to having fewer cross-divisional ties and to experiencing greater reductions in network density. The findings suggest that affect permeates through and is shaped by organizational networks.

Institutional shifts in inter-municipal service delivery:an analysis of developments in eight Western European countries

Comparative research on inter-municipal cooperation in eight European countries shows that there is a great variety of institutional arrangements for cooperation across the different countries. Also, these arrangements tend to change over time in terms of the scope of cooperation among partners, their composition and the degree of organizational integration. This article describes and analyzes the variety of and shifts in institutional arrangements for a specific class of inter-municipal cooperation arrangements: those that are set up to provide for the joint delivery of public services. It is argued that specific arrangements are typically the outcomes of interaction between national institutional contexts,?environmental factors and local preferences.

Computer simulation of radio-frequency methane/hydrogen plasmas and their interaction with GaAs Surfaces

The following thesis describes the computer modelling of radio frequency capacitively coupled methane/hydrogen plasmas and the consequences for the reactive ion etching of (100) GaAs surfaces. In addition a range of etching experiments was undertaken over a matrix of pressure, power and methane concentration. The resulting surfaces were investigated using X-ray photoelectron spectroscopy and the results were discussed in terms of physical and chemical models of particle/surface interactions in addition to the predictions for energies, angles and relative fluxes to the substrate of the various plasma species. The model consisted of a Monte Carlo code which followed electrons and ions through the plasma and sheath potentials whilst taking account of collisions with background neutral gas molecules. The ionisation profile output from the electron module was used as input for the ionic module. Momentum scattering interactions of ions with gas molecules were investigated via different models and compared against results given by quantum mechanical code. The interactions were treated as central potential scattering events and the resulting neutral cascades were followed. The resulting predictions for ion energies at the cathode compared well to experimental ion energy distributions and this verified the particular form of the electrical potentials used and their applicability in the particular geometry plasma cell used in the etching experiments. The final code was used to investigate the effect of external plasma parameters on the mass distribution, energy and angles of all species impingent on the electrodes. Comparisons of electron energies in the plasma also agreed favourably with measurements made using a Langmuir electric probe. The surface analysis showed the surfaces all to be depleted in arsenic due to its preferential removal and the resultant Ga:As ratio in the surface was found to be directly linked to the etch rate. The etch rate was determined by the methane flux which was predicted by the code.

A three dimensional surface measurement and reconstruction system for respiratory function analysis

Respiration is a complex activity. If the relationship between all neurological and skeletomuscular interactions was perfectly understood, an accurate dynamic model of the respiratory system could be developed and the interaction between different inputs and outputs could be investigated in a straightforward fashion. Unfortunately, this is not the case and does not appear to be viable at this time. In addition, the provision of appropriate sensor signals for such a model would be a considerable invasive task. Useful quantitative information with respect to respiratory performance can be gained from non-invasive monitoring of chest and abdomen motion. Currently available devices are not well suited in application for spirometric measurement for ambulatory monitoring. A sensor matrix measurement technique is investigated to identify suitable sensing elements with which to base an upper body surface measurement device that monitors respiration. This thesis is divided into two main areas of investigation; model based and geometrical based surface plethysmography. In the first instance, chapter 2 deals with an array of tactile sensors that are used as progression of existing and previously investigated volumetric measurement schemes based on models of respiration. Chapter 3 details a non-model based geometrical approach to surface (and hence volumetric) profile measurement. Later sections of the thesis concentrate upon the development of a functioning prototype sensor array. To broaden the application area the study has been conducted as it would be fore a generically configured sensor array. In experimental form the system performance on group estimation compares favourably with existing system on volumetric performance. In addition provides continuous transient measurement of respiratory motion within an acceptable accuracy using approximately 20 sensing elements. Because of the potential size and complexity of the system it is possible to deploy it as a fully mobile ambulatory monitoring device, which may be used outside of the laboratory. It provides a means by which to isolate coupled physiological functions and thus allows individual contributions to be analysed separately. Thus facilitating greater understanding of respiratory physiology and diagnostic capabilities. The outcome of the study is the basis for a three-dimensional surface contour sensing system that is suitable for respiratory function monitoring and has the prospect with future development to be incorporated into a garment based clinical tool.

Design and development of a time of flight fast scattering spectrometer : a quantitative surface analysis technique and a new approach towards the experimental investigation of the surface particle interactions

A new surface analysis technique has been developed which has a number of benefits compared to conventional Low Energy Ion Scattering Spectrometry (LEISS). A major potential advantage arising from the absence of charge exchange complications is the possibility of quantification. The instrumentation that has been developed also offers the possibility of unique studies concerning the interaction between low energy ions and atoms and solid surfaces. From these studies it may also be possible, in principle, to generate sensitivity factors to quantify LEISS data. The instrumentation, which is referred to as a Time-of-Flight Fast Atom Scattering Spectrometer has been developed to investigate these conjecture in practice. The development, involved a number of modifications to an existing instrument, and allowed samples to be bombarded with a monoenergetic pulsed beam of either atoms or ions, and provided the capability to analyse the spectra of scattered atoms and ions separately. Further to this a system was designed and constructed to allow incident, exit and azimuthal angles of the particle beam to be varied independently. The key development was that of a pulsed, and mass filtered atom source; which was developed by a cyclic process of design, modelling and experimentation. Although it was possible to demonstrate the unique capabilities of the instrument, problems relating to surface contamination prevented the measurement of the neutralisation probabilities. However, these problems appear to be technical rather than scientific in nature, and could be readily resolved given the appropriate resources. Experimental spectra obtained from a number of samples demonstrate some fundamental differences between the scattered ion and neutral spectra. For practical non-ordered surfaces the ToF spectra are more complex than their LEISS counterparts. This is particularly true for helium scattering where it appears, in the absence of detailed computer simulation, that quantitative analysis is limited to ordered surfaces. Despite this limitation the ToFFASS instrument opens the way for quantitative analysis of the 'true' surface region to a wider range of surface materials.