Synthesis and expression of a gene encoding a 48-residue repeat in the Pseudomonas syringae ice nucleation protein

The aim of this work was to construct short analogues of the repetitive water-binding domain of the Pseudomonas syringae ice nucleation protein, InaZ. Structural analysis of these analogues might provide data pertaining to the protein-water contacts that underlie ice nucleation. An artificial gene coding for a 48-mer repeat sequence from InaZ was synthesized from four oligodeoxyribonucleotides and ligated into the expression vector, pGEX2T. The recombinant vector was cloned in Escherichia coli and a glutathione S-transferase fusion protein obtained. This fusion protein displayed a low level of ice-nucleating activity when tested by a droplet freezing assay. The fusion protein could be cleaved with thrombin, providing a means for future recovery of the 48-mer peptide in amounts suitable for structural analysis by nuclear magnetic resonance spectroscopy.

Work stressors, strains and hospital unit performance

Hospital employees who work in an environment with zero tolerance to error, face several stressors that may result in psychological, physiological, and behavioural strains, and subsequently, in suboptimal performance. This thesis includes two studies which investigate the stressor-to-strain-to-performance relationships in hospitals. The first study is a cross-sectional, multi-group investigation based on secondary data from 65,142 respondents in 172 acute/specialist UK NHS trusts. This model proposes that senior management leadership predicts social support and job design which, in turn, moderate stressors-to-strains across team structure. The results confirm the model's robustness. Regression analysis provides support for main effects and minimal support for moderation hypotheses. Therefore, based on its conclusions and inherent limitations, study one lays the framework for study two. The second study is a cross-sectional, multilevel investigation of the strain-reducing effects of social environment on externally-rated unit-level performance based on primary data from 1,137 employees in 136 units, in a hospital in Malta. The term "social environment" refers to the prediction of the moderator variables, which is to say, social support and decision latitude/control, by transformational leadership and team climate across hospital units. This study demonstrates that transformational leadership is positively associated with social support, whereas team climate is positively associated with both moderators. At the same time, it identifies a number of moderating effects which social support and decision latitude/control, both separately and together, had on specific stressor-to-strain relationships. The results show significant mediated stressor-to-strain-to-performance relationships. Furthermore, at the higher level, unit-level performance is positively associated with shared unit-level team climate and with unit-level vision, the latter being one of the five sub-dimension of transformational leadership. At the same time, performance is also positively related to both transformational leadership and team climate when the two constructs are tested together. Few studies have linked the buffering effects of the social environment in occupational stress with performance. Therefore, this research strives to make a significant contribution to the occupational stress and performance literature with a focus on hospital practice. Indeed, the study highlights the wide-ranging and far-reaching implications that these findings provide for theory, management, and practice.

Factors determining disease duration in Alzheimer's disease:a postmortem study of 103 cases using the Kaplan-Meier estimator and Cox regression

Factors associated with duration of dementia in a consecutive series of 103 Alzheimer's disease (AD) cases were studied using the Kaplan-Meier estimator and Cox regression analysis (proportional hazard model). Mean disease duration was 7.1 years (range: 6 weeks-30 years, standard deviation = 5.18); 25% of cases died within four years, 50% within 6.9 years, and 75% within 10 years. Familial AD cases (FAD) had a longer duration than sporadic cases (SAD), especially cases linked to presenilin (PSEN) genes. No significant differences in duration were associated with age, sex, or apolipoprotein E (Apo E) genotype. Duration was reduced in cases with arterial hypertension. Cox regression analysis suggested longer duration was associated with an earlier disease onset and increased senile plaque (SP) and neurofibrillary tangle (NFT) pathology in the orbital gyrus (OrG), CA1 sector of the hippocampus, and nucleus basalis of Meynert (NBM). The data suggest shorter disease duration in SAD and in cases with hypertensive comorbidity. In addition, degree of neuropathology did not influence survival, but spread of SP/NFT pathology into the frontal lobe, hippocampus, and basal forebrain was associated with longer disease duration. © 2014 R. A. Armstrong.

Explaining process and performance in the co-production of knowledge:a comparative analysis of collaborative research projects

Despite considerable and growing interest in the subject of academic researchers and practising managers jointly generating knowledge (which we term ‘co-production’), our searches of management literature revealed few articles based on primary data or multiple cases. Given the increasing commitment to co-production by academics, managers and those funding research, it seems important to strengthen the evidence base about practice and performance in co-production. Literature on collaborative research was reviewed to develop a framework to structure the analysis of this data and relate findings to the limited body of prior research on collaborative research practice and performance. This paper presents empirical data from four completed, large scale co-production projects. Despite major differences between the cases, we find that the key success factors and the indicators of performances are remarkably similar. We demonstrate many, complex influences between factors, between outcomes, and between factors and outcomes, and discuss the features that are distinctive to co-production. Our empirical findings are broadly consonant with prior literature, but go further in trying to understand success factors’ consequences for performance. A second contribution of this paper is the development of a conceptually and methodologically rigorous process for investigating collaborative research, linking process and performance. The paper closes with discussion of the study’s limitations and opportunities for further research.

The development of a wax layer on the interior wall of a circular pipe transporting heated oil

In this article we develop a simple model to describe the evolution of a depositional wax layer on the inner surface of a circular pipe transporting heated oil, which contains dissolved wax. When the outer pipe surface is cooled sufficiently, the growth of a wax layer is initiated on the inner pipe wall, and this evolves to a saturated steady state thickness. The model proposed is based on fundamental balances of heat flow from the oil, into the wax layer, and across the pipe wall. We present an analysis of the model, examine a relevant asymptotic limit in which the full details of the solution to the model are available and develop an efficient numerical method (based on the method of fundamental solutions) for producing approximations of the model solution. The mathematical structure of the model is that of a free boundary evolution problem of generalised Stefan type. © The Author, 2014.

The development of a wax layer on the interior wall of a circular pipe transporting heated oil

In this article we develop a simple model to describe the evolution of a depositional wax layer on the inner surface of a circular pipe transporting heated oil, which contains dissolved wax. When the outer pipe surface is cooled sufficiently, the growth of a wax layer is initiated on the inner pipe wall, and this evolves to a saturated steady state thickness. The model proposed is based on fundamental balances of heat flow from the oil, into the wax layer, and across the pipe wall. We present an analysis of the model, examine a relevant asymptotic limit in which the full details of the solution to the model are available and develop an efficient numerical method (based on the method of fundamental solutions) for producing approximations of the model solution. The mathematical structure of the model is that of a free boundary evolution problem of generalised Stefan type. © The Author, 2014.

BPROMPT:a consensus server for membrane protein prediction

Protein structure prediction is a cornerstone of bioinformatics research. Membrane proteins require their own prediction methods due to their intrinsically different composition. A variety of tools exist for topology prediction of membrane proteins, many of them available on the Internet. The server described in this paper, BPROMPT (Bayesian PRediction Of Membrane Protein Topology), uses a Bayesian Belief Network to combine the results of other prediction methods, providing a more accurate consensus prediction. Topology predictions with accuracies of 70% for prokaryotes and 53% for eukaryotes were achieved. BPROMPT can be accessed at http://www.jenner.ac.uk/BPROMPT.

Protein lipoxidation:detection strategies and challenges

Enzymatic and non-enzymatic lipid metabolism can give rise to reactive species that may covalently modify cellular or plasma proteins through a process known as lipoxidation. Under basal conditions, protein lipoxidation can contribute to normal cell homeostasis and participate in signaling or adaptive mechanisms, as exemplified by lipoxidation of Ras proteins or of the cytoskeletal protein vimentin, both of which behave as sensors of electrophilic species. Nevertheless, increased lipoxidation under pathological conditions may lead to deleterious effects on protein structure or aggregation. This can result in impaired degradation and accumulation of abnormally folded proteins contributing to pathophysiology, as may occur in neurodegenerative diseases. Identification of the protein targets of lipoxidation and its functional consequences under pathophysiological situations can unveil the modification patterns associated with the various outcomes, as well as preventive strategies or potential therapeutic targets. Given the wide structural variability of lipid moieties involved in lipoxidation, highly sensitive and specific methods for its detection are required. Derivatization of reactive carbonyl species is instrumental in the detection of adducts retaining carbonyl groups. In addition, use of tagged derivatives of electrophilic lipids enables enrichment of lipoxidized proteins or peptides. Ultimate confirmation of lipoxidation requires high resolution mass spectrometry approaches to unequivocally identify the adduct and the targeted residue. Moreover, rigorous validation of the targets identified and assessment of the functional consequences of these modifications are essential. Here we present an update on methods to approach the complex field of lipoxidation along with validation strategies and functional assays illustrated with well-studied lipoxidation targets.

Integer Programming Approach to HP Folding

One of the most widely studied protein structure prediction models is the hydrophobic-hydrophilic (HP) model, which explains the hydrophobic interaction and tries to maximize the number of contacts among hydrophobic amino-acids. In order to find a lower bound for the number of contacts, a number of heuristics have been proposed, but finding the optimal solution is still a challenge. In this research, we focus on creating a new integer programming model which is capable to provide tractable input for mixed-integer programming solvers, is general enough and allows relaxation with provable good upper bounds. Computational experiments using benchmark problems show that our formulation achieves these goals.

Redox control of protein degradation

Intracellular proteolysis is critical to maintain timely degradation of altered proteins including oxidized proteins. This review attempts to summarize the most relevant findings about oxidant protein modification, as well as the impact of reactive oxygen species on the proteolytic systems that regulate cell response to an oxidant environment: the ubiquitin-proteasome system (UPS), autophagy and the unfolded protein response (UPR). In the presence of an oxidant environment, these systems are critical to ensure proteostasis and cell survival. An example of altered degradation of oxidized proteins in pathology is provided for neurodegenerative diseases. Future work will determine if protein oxidation is a valid target to combat proteinopathies.

Protein modification and phospholipid oxidation

Phospholipid oxidation can generate reactive and electrophilic products that are capable of modifying proteins, especially at cysteine, lysine and histidine residues. Such lipoxidation reactions are known to alter protein structure and function, both with gain of function and loss of activity effects. As well as potential importance in the redox regulation of cell behaviour, lipoxidation products in plasma could also be useful biomarkers for stress conditions. Although studies with antibodies suggested the occurrence of lipoxidation adducts on ApoB-100, these products had not previously been characterized at a molecular level. We have developed new mass spectrometry-based approaches to detect and locate adducts of oxidized phospholipids in plasma proteins, as well as direct oxidation modifications of proteins, which avoid some of the problems typically encountered with database search engines leading to erroneous identifications of oxidative PTMs. This approach uses accurate mass extracted ion chromatograms (XICs) of fragment ions from peptides containing oxPTMs, and allows multiple modifications to be examined regardless of the protein that contains them. For example, a reporter ion at 184.074 Da/e corresponding to phosphocholine indicated the presence of oxidized phosphatidylcholine adducts, while 2 reporter ions at 100.078 and 82.025 Da/e were selective for allysine. ApoB-100-oxidized phospholipid adducts were detected even in healthy human samples, as well as LDL from patients with inflammatory disease. Lipidomic studies showed that more than 350 different species of lipid were present in LDL, and were altered in disease conditions. LDL clearly represents a very complex carrier system and one that offers a rich source of information about systemic conditions, with potential as indicators of oxidative damage in ageing or inflammatory diseases.

IUPHAR-DB:the IUPHAR database of G protein-coupled receptors and ion channels

The IUPHAR database (IUPHAR-DB) integrates peer-reviewed pharmacological, chemical, genetic, functional and anatomical information on the 354 nonsensory G protein-coupled receptors (GPCRs), 71 ligand-gated ion channel subunits and 141 voltage-gated-like ion channel subunits encoded by the human, rat and mouse genomes. These genes represent the targets of approximately one-third of currently approved drugs and are a major focus of drug discovery and development programs in the pharmaceutical industry. IUPHAR-DB provides a comprehensive description of the genes and their functions, with information on protein structure and interactions, ligands, expression patterns, signaling mechanisms, functional assays and biologically important receptor variants (e.g. single nucleotide polymorphisms and splice variants). In addition, the phenotypes resulting from altered gene expression (e.g. in genetically altered animals or in human genetic disorders) are described. The content of the database is peer reviewed by members of the International Union of Basic and Clinical Pharmacology Committee on Receptor Nomenclature and Drug Classification (NC-IUPHAR); the data are provided through manual curation of the primary literature by a network of over 60 subcommittees of NC-IUPHAR. Links to other bioinformatics resources, such as NCBI, Uniprot, HGNC and the rat and mouse genome databases are provided. IUPHAR-DB is freely available at http://www.iuphar-db.org. © 2008 The Author(s).

Detergent-free membrane protein purification

Membrane proteins are localised within a lipid bilayer; in order to purify them for functional and structural studies the first step must involve solubilising or extracting the protein from these lipids. To date this has been achieved using detergents which disrupt the bilayer and bind to the protein in the transmembrane region. However finding conditions for optimal extraction, without destabilising protein structure is time consuming and expensive. Here we present a recently-developed method using a styrene maleic acid (SMA) co-polymer instead of detergents. The SMA co-polymer extracts membrane proteins in a small disc of lipid bilayer which can be used for affinity chromatography purification, thus enabling the purification of membrane proteins while maintaining their native lipid bilayer environment.

The impacts of trade policy reforms on the Sri Lankan economy

This dissertation presents an analysis of the impacts of trade policy reforms in Sri Lanka. A Computable General Equilibrium (CGE) model is constructed with detailed description of the domestic production structure and foreign trade. The model is then used to investigate the effects of trade policy reforms on resource allocation and welfare.^ Prior to 1977, Sri Lanka maintained stringent control over its imports through rigid quantitative restrictions. A new economic policy reform package was introduced in 1977, and it shifted Sri Lanka's development strategy toward an export oriented policy regime. The shift of policy focus from a restrictive trade regime toward a more open trade regime is expected to have a significant impact on the volume of external trade, domestic production structure, allocation of resources, and social welfare.^ Simulations are carried out to assess the effects of three major policy reforms: (1) a devaluation of the Sri Lanka rupee, (2) a partial or a complete elimination of export duties, and (3) a devaluation-cum-removal of export duties.^ Simulation results indicate that the macroeconomic impact of a devaluation-cum-removal of export duties can be substantial. They also suggest that the resource-pull effects of a devaluation and a devaluation-cum-export duty removal policy are significant. However, the model shows that a devaluation combined with an export duty reduction is likely to be a superior strategy. ^

Development and validation of an instrument to predict online student success using faculty perceptions

Distance learning is growing and transforming educational institutions. The increasing use of distance learning by higher education institutions and particularly community colleges coupled with the higher level of student attrition in online courses than in traditional classrooms suggests that increased attention should be paid to factors that affect online student course completion. The purpose of the study was to develop and validate an instrument to predict community college online student course completion based on faculty perceptions, yielding a prediction model of online course completion rates. Social Presence and Media Richness theories were used to develop a theoretically-driven measure of online course completion. This research study involved surveying 311 community college faculty who taught at least one online course in the past 2 years. Email addresses of participating faculty were provided by two south Florida community colleges. Each participant was contacted through email, and a link to an Internet survey was given. The survey response rate was 63% (192 out of 303 available questionnaires). Data were analyzed through factor analysis, alpha reliability, and multiple regression. The exploratory factor analysis using principal component analysis with varimax rotation yielded a four-factor solution that accounted for 48.8% of the variance. Consistent with Social Presence theory, the factors with their percent of variance in parentheses were: immediacy (21.2%), technological immediacy (11.0%), online communication and interactivity (10.3%), and intimacy (6.3%). Internal consistency of the four factors was calculated using Cronbach's alpha (1951) with reliability coefficients ranging between .680 and .828. Multiple regression analysis yielded a model that significantly predicted 11% of the variance of the dependent variable, the percentage of student who completed the online course. As indicated in the literature (Johnson & Keil, 2002; Newberry, 2002), Media Richness theory appears to be closely related to Social Presence theory. However, elements from this theory did not emerge in the factor analysis.