Applications of capillary electrophoresis to environmentally interesting molecules and single-component combinatory libraries

Capillary Electrophoresis (CE) is a powerful analytical tool that has been applied to different areas. In this light, the separation of environmental interesting molecules with a novel type of running buffer additives and the application of CE to combinatorial libraries have been developed. Molecular modeling results are used to interpret the separation behavior. p-Carboxyethyl calix[n]arenes, a series of moderately water soluble, multiple charged macrocyclic compounds that possess a basket shape are added to the running buffer to separate native and substituted polycyclic aromatic hydrocarbons, amino alcohols and vitamers. The separations are based on the differential distribution of analytes between a running buffer phase, which is transported by electroosmotic flow, and an electrophoretically mediated calix[n]arene. The cavity size and geometry of the calix[n]arene are investigated to their separation performance. The influences of pH, organic solvent and field strength on elution range, capacity factors, efficiency, and selectivity are also studied. The potential utility of CE as analysis and biological activity screening method for rapid screening of single component combinatory libraries is demonstrated by mimicking a 5 x 5 drug matrix. Twenty-five compounds that include biotin are selected as the test analytes and avidin is treated as the biological activity screening reagent. Five mixtures of 9 components each are created at the diagonal of the matrix by pooling each component from the same column and row for rapid screening. After obtaining optimum separation conditions, affinity CE produces the locations of the potentially active components based on changes in peak area. Blind tests are conducted that successfully locate the active component(s). High speed, high resolving power and small sample consumption are unique advantages of CE over other analytical tools for this application

Synthesis of peptides with hydroxamic acid side chain appendages.

Chapter 1 detailed the synthesis method of hydroxamate peptides derivatives of pentapeptide Ac-PHSXX\\u27-N-NH2 by solid phase hydroxamate peptide synthesis method. The glutamic acid/aspartic acid side chain was modified to hydroxamic acid by on resin N-C coupling. The hydroxamate benzyl protecting group was removed during HF cleavage. In Chapter 2 a novel multiple hydroxamic acid peptide siderophore was prepared and the metal binding activity of these peptides was studied by ESI-MS and MS/MS. Siderophore peptide Ac-Gly1-Glu2(NHOH)-D-Pro3-Gly4-Glu5(NHOH)-D-Pro6-NH2 was found to have significant preference to Fe(III) over Zn(II) and Ni(II), while the natural peptide analogue Ac-Gly1-Glu2-D-Pro 3-Gly4-Glu5-D-Pro6-NH2 did not show any obvious preference in these metal ions. The study of these multi hydroxamate ligands metal coordination revealed that the C-terminal binding site (Glu5(NHOH)) has the stronger chelation capability than the N terminal (Glu2(NHOH)) metal binding site and the amide bonds between glutamic acid and proline were identified as the most fragile bonds by MS/MS study

Thymus Transcriptome Response to Avian Pathogenic E. coli (APEC) Infection

Colibacillosis, caused by avian pathogenic Escherichia coli (APEC), is responsible for multi-million dollar losses in the poultry industry every year in the United States. Therefore, it is important to understand the functional genomics of avian response to APEC, to find effective control strategies. The transcriptome characterizes genetic elements that are expressed. The thymus transcriptomes of 24 birds with known challenge status, necropsy day, and pathology level were sequenced using RNA-Seq. Many innate immune response pathways were significantly changed. Differentially expressed (DE) genes analysis showed APEC infection affected immune homeostasis through impairing the engagement of regulatory signal transduction pathways for T cell development. This study gives insight into T cell development and immune response under APEC infection. The DE gene analysis revealed gene networks that affect T cell development as well as immune homeostasis following APEC infection. These results add knowledge of host immune response to APEC infection

Mixture Transition Distribution Modelling of Multivariate Time Series of Discrete State Processes: With an Application to Modelling Flowering Synchronisation with Respect to Climate Dynamics

A new approach to assess synchronicity developed in this chapter is a novel bivariate extension of the generalised mixture transition distribution (MTDg) model (we coin this B-MTD). The aim of this chapter is to test MTDg an extended MTD with interactions model and its bivariate extension of MTD (B-MTD) to investigate synchrony of flowering of four Eucalypts species—E. leucoxylon, E. microcarpa, E. polyanthemos and E. tricarpa over a 31 year period. The mixture transition distribution (MTDg) is a method to estimate transition probabilities of high order Markov chains. Our B-MTD approach allows us the derive rules of thumb for synchrony and asynchrony between pairs of species, e.g. flowering of the four species. The latter B-MTD rules are based on transition probabilities between all possible on and off flowering states from previous to current time. We also apply MTDg modelling using lagged flowering states and climate covariates as predictors to model current flowering status (on/off) to assess synchronisation using residuals from the resultant models via our adaptation of Moran’s classic synchrony statistic. We compare these MTDg (with covariates)-based synchrony measures with our B-MTD results in addition to those from extended Kalman filter (EKF)-based residuals

Combined analysis of primary lymphoid tissues' transcriptomic response to extra-intestinal Escherichia coli (ExPEC) infection

AbstractAvian pathogenic Escherichia coli (APEC), an extraintestinal pathogenic E. coli (ExPEC), constitutes an animal health and a potential zoonotic risk. Most studies focus on the response of a single tissue to APEC infection. Understanding interactions among lymphoid tissues is of importance in controlling APEC infection. Therefore, we studied bone marrow, bursa, and thymus transcriptomes because of these tissues' crucial roles in development of pre-lymphocytes, B cells, and T cells, respectively. Using lesion scores of liver, pericardium, and air sacs, infected birds were classified as either resistant or susceptible. Little difference in gene expression was detected in resistant birds in bone marrow versus bursa or thymus, while there were large differences between tissues in susceptible birds. Phagosome, lysosome and cytokine interactions were strongly enhanced in thymus versus bone marrow in susceptible birds, and T cell receptor (TCR), cell cycle, and p53 signaling were significantly decreased. B cell receptor (BCR) was also significantly suppressed in bursa versus bone marrow in susceptible birds. This research provides novel insights into the complex developmental changes in gene expression occurring across the primary lymphoid organs and, therefore, serves as a foundation to understanding the cellular and molecular basis of host resistance to APEC infection

Marketing and Design in Organisational New Product Development: Early Evidence From New Zealand Manufacturing Firms

The multidisciplinary nature of organisational new product development (NPD) suggests that the development of successful new products is dependent upon the individual and combined efforts of various functions. Despite being recognised as two highly important disciplines in NPD, marketing and design have received little empirical examination of their roles in the NPD process and their effects on NPD outcome. In order to address this gap within the literature, the objectives of this thesis were to assess the presence of marketing and design in NPD, explore the nature of the marketing-design relationship, and examine the effects of marketing influence, design influence, and the level of marketing-design connectedness on NPD outcome. The study was set within the New Zealand context and data was collected via a web-based survey from 91 manufacturing firms that adopted both marketing and design in their NPD programmes. The results showed marketing and design to be two highly influential functions in NPD. Both functions were also found to be strongly involved in the NPD process. A positive relationship was found between marketing and design’s functional influence, which suggested the possibility of an interdependent relationship between the two disciplines. Finally, marketing and design were found to affect different aspects of NPD outcome, with marketing positively affecting product innovativeness, and design positively affecting process proficiency and financial performance. The research has implications for the future development of marketing, design, and NPD theories, as well as for managers seeking to improve their NPD activities through the alignment of their marketing and design functions

Piecewise frequency model for searches for long-transient gravitational waves from young neutron stars

In this work we characterise the performance of a new search technique designed to be sensitive to the remnants of binary neutron star systems. Sensitivity estimates of the new method on simulated data are competitive against those of other work. Previous searches for a gravitational-wave signal from a possible neutron star remnant of the binary neutron star merger event GW170817 have focused on short ($<500$~s) and long duration (2.5~hr -- 8~day) signals. To date, no such post-merger signal has been detected. We introduce a new piecewise model which has the flexibility to accurately follow gravitational-wave signals which are rapidly evolving in frequency, such as those which may be emitted from young neutron stars born from binary neutron star mergers or supernovae. We investigate the sensitivity and computational cost of this piecewise model when used in a fully coherent 1800-second $\mathcal{F}$-statistic search on simulated data containing possible signals from the GW170817 remnant. The sensitivity of the search using the piecewise model is determined using simulated data, with noise consistent with the LIGO second observing run. Across a 100--2000~Hz frequency band, the model achieves a peak sensitivity of $h_{\text{rss}}^{50\%} = 4.4 \times 10^{-23} \text{Hz}^{-1/2}$ at 200~Hz, competitive with other methods. The computational cost of conducting the search, over a bank of $1.1 \times 10^{12}$ templates, is estimated at 10 days running on 100 CPU's.Comment: 16 pages, 11 figures, 2 table

The development of a ε-polycaprolactone (PCL) scaffold for CNS repair

Potential treatment strategies for the repair of spinal cord injury (SCI) currently favour a combinatorial approach incorporating several factors, including exogenous cell transplantation and biocompatible scaffolds. The use of scaffolds for bridging the gap at the injury site is very appealing although there has been little investigation into CNS neural cell interaction and survival on such scaffolds before implantation. Previously we demonstrated that aligned micro-grooves 12.5-25 µm wide on ε-polycaprolactone (PCL) promoted aligned neurite orientation and supported myelination. In this study we identify the appropriate substrate and its topographical features required for the design of a 3D scaffold intended for transplantation in SCI. Using an established myelinating culture system of dissociated spinal cord cells, recapitulating many of the features of the intact spinal cord, we demonstrate that astrocytes plated on the topography secrete soluble factors(s) that delay oligodendrocyte differentiation but do not prevent myelination. However, as myelination does occur after a further 10-12 days in culture this does not prevent the use of PCL as a scaffold material as part of a combined strategy for the repair of SCI