Extracting quantitative structural parameters for disordered polymers from neutron scattering data

The organization of non-crystalline polymeric materials at a local level, namely on a spatial scale between a few and 100 a, is still unclear in many respects. The determination of the local structure in terms of the configuration and conformation of the polymer chain and of the packing characteristics of the chain in the bulk material represents a challenging problem. Data from wide-angle diffraction experiments are very difficult to interpret due to the very large amount of information that they carry, that is the large number of correlations present in the diffraction patterns.We describe new approaches that permit a detailed analysis of the complex neutron diffraction patterns characterizing polymer melts and glasses. The coupling of different computer modelling strategies with neutron scattering data over a wide Q range allows the extraction of detailed quantitative information on the structural arrangements of the materials of interest. Proceeding from modelling routes as diverse as force field calculations, single-chain modelling and reverse Monte Carlo, we show the successes and pitfalls of each approach in describing model systems, which illustrate the need to attack the data analysis problem simultaneously from several fronts.

Evaluation and comparison of SYBR Green I Real-Time PCR and TaqMan Real-Time PCR methods for quantitative assay of Listeria monocytogenes in nutrient broth and milk

Specific traditional plate count method and real-time PCR systems based on SYBR Green I and TaqMan technologies using a specific primer pair and probe for amplification of iap-gene were used for quantitative assay of Listeria monocytogenes in seven decimal serial dilution series of nutrient broth and milk samples containing 1.58 to 1.58×107 cfu /ml and the real-time PCR methods were compared with the plate count method with respect to accuracy and sensitivity. In this study, the plate count method was performed using surface-plating of 0.1 ml of each sample on Palcam Agar. The lowest detectable level for this method was 1.58×10 cfu/ml for both nutrient broth and milk samples. Using purified DNA as a template for generation of standard curves, as few as four copies of the iap-gene could be detected per reaction with both real-time PCR assays, indicating that they were highly sensitive. When these real-time PCR assays were applied to quantification of L. monocytogenes in decimal serial dilution series of nutrient broth and milk samples, 3.16×10 to 3.16×105 copies per reaction (equals to 1.58×103 to 1.58×107 cfu/ml L. monocytogenes) were detectable. As logarithmic cycles, for Plate Count and both molecular assays, the quantitative results of the detectable steps were similar to the inoculation levels.

In vitro evaluation of the fermentation properties and potential prebiotic activity of caprine cheese whey oligosaccharides in batch culture systems

The prebiotic effect of oligosaccharides recovered and purified from caprine whey, was evaluated by in vitro fermentation under anaerobic conditions using batch cultures at 37ºC with human faeces. Effects on key gut bacterial groups were monitored over 24h by fluorescence in situ hybridisation (FISH), which was used to determine a quantitative prebiotic index score. Production of short-chain fatty acids (SCFAs) as fermentation end products was analysed by high-performance liquid chromatography (HPLC). Growth of Bifidobacterium spp was significantly higher (p ≥ 0.05) with the purified oligosaccharides compared to the negative control. Lactic and propionic acids were the main SCFAs produced. Antimicrobial activity of the oligosaccharides was also tested, revealing no inhibition though a decrease in Staphylococcus aureus and Escherichia coli growth. These findings indicate that naturally extracted oligosaccharides from caprine whey could be used as new and valuable source of prebiotics.

A global quantitative synthesis of local and landscape effects on wild bee pollinators in agroecosystems

Bees provide essential pollination services that are potentially affected both by local farm management and the surrounding landscape. To better understand these different factors, we modelled the relative effects of landscape composition (nesting and floral resources within foraging distances), landscape configuration (patch shape, interpatch connectivity and habitat aggregation) and farm management (organic vs. conventional and local-scale field diversity), and their interactions, on wild bee abundance and richness for 39 crop systems globally. Bee abundance and richness were higher in diversified and organic fields and in landscapes comprising more high-quality habitats; bee richness on conventional fields with low diversity benefited most from high-quality surrounding land cover. Landscape configuration effects were weak. Bee responses varied slightly by biome. Our synthesis reveals that pollinator persistence will depend on both the maintenance of high-quality habitats around farms and on local management practices that may offset impacts of intensive monoculture agriculture.

Antipathogenic activity of probiotics against Salmonella Typhimurium and Clostridium difficile in anaerobic batch culture systems: is it due to synergies in probiotic mixtures or the specificity of single strains?

Probiotics are currently being investigated for prevention of infections caused by enteric pathogens. The aim of this in vitro study was to evaluate the influence of three single probiotics: Lactobacillus casei NCIMB 30185 (PXN 37), Lactobacillus acidophilus NCIMB 30184 (PXN 35), Bifidobacterium breve NCIMB 30180 (PXN 25) and a probiotic mixture containing the above strains plus twelve other strains belonging to the Lactobacillus, Bifidobacterium, Lactococcus, Streptococcus and Bacillus genera on the survival of Salmonella Typhimurium and Clostridium difficile using pH-controlled anaerobic batch cultures containing mixed fecal bacteria. Changes in relevant bacterial groups and effects of probiotic addition on survival of the two pathogens were assessed over 24 h. Quantitative analysis of bacterial populations revealed that there was a significant increase in lactobacilli and/or bifidobacteria numbers, depending on probiotic addition, compared with the control (no added probiotic). There was also a significant reduction in S. Typhimurium and C. difficile numbers in the presence of certain probiotics compared with controls. Of the probiotic treatments, two single strains namely L. casei NCIMB 30185 (PXN 37), and B. breve NCIMB 30180 (PXN 25) were the most potent in reducing the numbers of S. Typhimurium and C. difficile. In addition, the supplementation with probiotics into the systems influenced some fermentations parameters. Acetate was found in the largest concentrations in all vessels and lactate and formate were generally detected in higher amounts in vessels with probiotic addition compared to controls.

Participatory research approaches in the development of improved management practices in indigenous chickens production systems with smallholder farmers in Kenya

This thesis is concerned with development of improved management practices in indigenous chicken production systems in a research process that includes participatory approaches with smallholder farmers and other stakeholders in Kenya. The research process involved a wide range of activities that included on-station experiments, field surveys, stakeholder consultations in workshops, seminars and visits, and on-farm farmer participatory research to evaluate the effect of some improved management interventions on production performance of indigenous chickens. The participatory research was greatly informed from collective experiences and lessons of the previous activities. The on-station studies focused on hatching, growth and nutritional characteristics of the indigenous chickens. Four research publications from these studies are included in this thesis. Quantitative statistical analyses were applied and they involved use of growth models estimated with non-linear regressions for the growth characteristics, chi-square determinations to investigate differences among different reciprocal crosses of indigenous chickens and general linear models and covariance determination for the nutrition study. The on-station studies brought greater understanding of performance and production characteristics of indigenous chickens and the influence of management practices on these characteristics. The field surveys and stakeholder consultations helped in understanding the overarching issues affecting the productivity of the indigenous chickens systems and their place in the livelihoods of smallholder farmers. These activities created strong networking opportunities with stakeholders from a wide spectrum. The on-farm farmer participatory research involved selection of 200 farmers in five regions followed by training and introduction of interventions on improved management practices which included housing, vaccination, deworming and feed supplementation. Implementation and monitoring was mainly done by individual farmers continuously for close to one and half years. Six quarterly visits to the farms were made by the research team to monitor and provide support for on-going project activities. The data collected has been analysed for 5 consecutive 3-monthly periods. Descriptive and inferential statistics were applied to analyse the data collected involving treatment applications, production characteristics and flock demography characteristics. Out of the 200 farmers initially selected, 173 had records on treatment applications and flock demography characteristics while 127 farmers had records on production characteristics. The demographic analysis with a dissimilarity index of flock size produced 7 distinct farm groups from among the 173 farms. Two of these farm groups were represented in similar numbers in each of the five regions. The research process also involved a number of dissemination and communication strategies that have brought the process and project outcomes into the domain of accessibility by wider readership locally and globally. These include workshops, seminars, field visits and consultations, local and international conferences, electronic conferencing, publications and personal communication via emailing and conventional posting. A number of research and development proposals were also developed based on the knowledge and experiences gained from the research process. The thesis captures the research process activities and outcomes in 8 chapters which include in ascending order – introduction, theoretical concepts underpinning FPR, research methodology and process, on-station research output, FPR descriptive statistical analysis, FPR inferential statistical analysis on production characteristics, FPR demographic analysis and conclusions. Various research approaches both quantitative and qualitative have been applied in the research process indicating the possibilities and importance of combining both systems for greater understanding of issues being studied. In our case, participatory studies of the improved management of indigenous chickens indicates their potential importance as livelihood assets for poor people.

Bollène-2002 experiment: radar quantitative precipitation estimation in the Cévennes–Vivarais region, France

The Bollène-2002 Experiment was aimed at developing the use of a radar volume-scanning strategy for conducting radar rainfall estimations in the mountainous regions of France. A developmental radar processing system, called Traitements Régionalisés et Adaptatifs de Données Radar pour l’Hydrologie (Regionalized and Adaptive Radar Data Processing for Hydrological Applications), has been built and several algorithms were specifically produced as part of this project. These algorithms include 1) a clutter identification technique based on the pulse-to-pulse variability of reflectivity Z for noncoherent radar, 2) a coupled procedure for determining a rain partition between convective and widespread rainfall R and the associated normalized vertical profiles of reflectivity, and 3) a method for calculating reflectivity at ground level from reflectivities measured aloft. Several radar processing strategies, including nonadaptive, time-adaptive, and space–time-adaptive variants, have been implemented to assess the performance of these new algorithms. Reference rainfall data were derived from a careful analysis of rain gauge datasets furnished by the Cévennes–Vivarais Mediterranean Hydrometeorological Observatory. The assessment criteria for five intense and long-lasting Mediterranean rain events have proven that good quantitative precipitation estimates can be obtained from radar data alone within 100-km range by using well-sited, well-maintained radar systems and sophisticated, physically based data-processing systems. The basic requirements entail performing accurate electronic calibration and stability verification, determining the radar detection domain, achieving efficient clutter elimination, and capturing the vertical structure(s) of reflectivity for the target event. Radar performance was shown to depend on type of rainfall, with better results obtained with deep convective rain systems (Nash coefficients of roughly 0.90 for point radar–rain gauge comparisons at the event time step), as opposed to shallow convective and frontal rain systems (Nash coefficients in the 0.6–0.8 range). In comparison with time-adaptive strategies, the space–time-adaptive strategy yields a very significant reduction in the radar–rain gauge bias while the level of scatter remains basically unchanged. Because the Z–R relationships have not been optimized in this study, results are attributed to an improved processing of spatial variations in the vertical profile of reflectivity. The two main recommendations for future work consist of adapting the rain separation method for radar network operations and documenting Z–R relationships conditional on rainfall type.

Modelling capability and affordance as properties of human/machine resource systems

Understanding how and why the capability of one set of business resources, its structural arrangements and mechanisms compared to another works can provide competitive advantage in terms of new business processes and product and service development. However, most business models of capability are descriptive and lack formal modelling language to qualitatively and quantifiably compare capabilities, Gibson’s theory of affordance, the potential for action, provides a formal basis for a more robust and quantitative model, but most formal affordance models are complex and abstract and lack support for real-world applications. We aim to understand the ‘how’ and ‘why’ of business capability, by developing a quantitative and qualitative model that underpins earlier work on Capability-Affordance Modelling – CAM. This paper integrates an affordance based capability model and the formalism of Coloured Petri Nets to develop a simulation model. Using the model, we show how capability depends on the space time path of interacting resources, the mechanism of transition and specific critical affordance factors relating to the values of the variables for resources, people and physical objects. We show how the model can identify the capabilities of resources to enable the capability to inject a drug and anaesthetise a patient.

In vitro evaluation of the fermentation properties and potential probiotic activity of Lactobacillus plantarum C4 in batch culture systems

Lactobacillus plantarum C4 has been tested in in vitro pH-controlled anaerobic faecal batch cultures as compared to Lactobacillus rhamnosus GG to determine changes caused to the composition of faecal bacteria. Effects upon major groups of the microbiota and levels of short-chain fatty acids (SCFA) were assessed over 24 h. Concomitantly, hydrophobic character and ability of both bacterial cells to adhere in vitro to Caco-2 cells were investigated. Quantitative analysis of bacterial populations revealed that there was a significant increase in Lactobacillus/Enterococcus numbers in vessels with probiotic supplemented with fructooligosaccharides (FOS), compared to the negative control. L. plantarum C4 showed to have more hydrophilic behaviour and fulfilled better adhesive properties, compared to L. rhamnosus GG. Thus, L. plantarum C4 can modulate the intestinal microbiota in vitro, promoting changes in some numerically and metabolically relevant microbial populations and shifts in the production of SCFA.

Quantitative single-molecule localization microscopy combined with rule-based modeling reveals ligand-induced TNF-R1 reorganization toward higher-order oligomers

We report on the assembly of tumor necrosis factor receptor 1 (TNF-R1) prior to ligand activation and its ligand-induced reorganization at the cell membrane. We apply single-molecule localization microscopy to obtain quantitative information on receptor cluster sizes and copy numbers. Our data suggest a dimeric pre-assembly of TNF-R1, as well as receptor reorganization toward higher oligomeric states with stable populations comprising three to six TNF-R1. Our experimental results directly serve as input parameters for computational modeling of the ligand-receptor interaction. Simulations corroborate the experimental finding of higher-order oligomeric states. This work is a first demonstration how quantitative, super-resolution and advanced microscopy can be used for systems biology approaches at the single-molecule and single-cell level.

Regulation of early steps of GPVI signal transduction by phosphatases: a systems biology approach

We present a data-driven mathematical model of a key initiating step in platelet activation, a central process in the prevention of bleeding following Injury. In vascular disease, this process is activated inappropriately and causes thrombosis, heart attacks and stroke. The collagen receptor GPVI is the primary trigger for platelet activation at sites of injury. Understanding the complex molecular mechanisms initiated by this receptor is important for development of more effective antithrombotic medicines. In this work we developed a series of nonlinear ordinary differential equation models that are direct representations of biological hypotheses surrounding the initial steps in GPVI-stimulated signal transduction. At each stage model simulations were compared to our own quantitative, high-temporal experimental data that guides further experimental design, data collection and model refinement. Much is known about the linear forward reactions within platelet signalling pathways but knowledge of the roles of putative reverse reactions are poorly understood. An initial model, that includes a simple constitutively active phosphatase, was unable to explain experimental data. Model revisions, incorporating a complex pathway of interactions (and specifically the phosphatase TULA-2), provided a good description of the experimental data both based on observations of phosphorylation in samples from one donor and in those of a wider population. Our model was used to investigate the levels of proteins involved in regulating the pathway and the effect of low GPVI levels that have been associated with disease. Results indicate a clear separation in healthy and GPVI deficient states in respect of the signalling cascade dynamics associated with Syk tyrosine phosphorylation and activation. Our approach reveals the central importance of this negative feedback pathway that results in the temporal regulation of a specific class of protein tyrosine phosphatases in controlling the rate, and therefore extent, of GPVI-stimulated platelet activation.