Doctor of Philosophy

dissertationThis work focuses on the study of low-magnetic field (<10mT) magnetoresistance effects of organic polymer diodes based on the n-conjugated polymer MEH-PPV in presence of oscillating magnetic fields in the radio frequency range. In these conditions, the combination of static and ac fields can magnetic resonantly influence the electronspin degree of freedom of localized charge-carrier states. As long as bipolar injection conditions influence the net current of the polymer diode, magnetic-resonance changes of the charge carrier spin state can affect spin-dependent charge carrier recombination rates and therefore the material's conductivity. Since the observed spin-dependent recombination currents are governed by the charge carrier pair's spin-permutation symmetry, magnetoresistance measurements under ac drive allow for the electrical detection of magnetic resonance under very low magnetic field conditions where inductive magnetic resonance detection schemes fail due to a lack of spin polarization. In this thesis, this effect was utilized for two effects. Firstly, for the exploration of a magnetic resonance regime where the driving field B 1 approaches the same magnitude as the static magnetic field B0. When Bi approaches B0, a regime where magnetic resonance effects become nonlinear emerges and interesting collective spin-phenomena occur. This includes spin-cooperativity, where the resonantlydriven spin ensemble assumes a macroscopically collective state. Experiments are presented that tested and confirmed previous theoretical predictions. When B}~B0, the emerging spin-cooperativity of recombining polaron pairs in organic semiconductors can be observed through magnetoresistance measurements. The experiments confirmed the theory in all aspects and demonstrated the emergence of the spin-Dicke effect. Secondly, for the exploration of whether magnetic resonantly-controlled spindependent currents can be used for magnetometry of inhomogeneous magnetic fields. This work is a continuation of the previously introduced idea to utilize spin-dependent charge carrier recombination in organic semiconductors for an absolute low-magnetic field magnetometry that is robust against fluctuating environmental conditions. The work focuses on the measurement of magnetic field distributions in gradient magnetic fields. It is shown that organic semiconductor-based magnetic resonance magnetometers can reveal magnetic field distributions. However, this measurement approach can be compromised by inductive resonance artifacts introduced by the large-bandwidth RF stripline resonators needed to operate the magnetometer

An examination of the molecular mechanisms controlling the tissue accumulation of conjugated linoleic acid (CLA) in cattle

End of project reportLong chain n-3 polyunsaturated fatty acids (n-3 PUFA) and conjugated linoleic acid (CLA) have demonstrable and potential human health benefits in terms of preventing cancer, diabetes, chronic inflammation, obesity and coronary heart disease. Supplementation of cattle diets with a blend of oils rich in n-3 PUFA and linoleic acid have a synergistic effect on the accumulation of ruminal and tissue concentrations of trans vaccenic acid (TVA), the main substrate for ?-9 desaturase which is responsible for de novo tissue synthesis of the cis 9, trans 11 isomer of CLA. This dietary strategy translates into increases in milk concentrations of CLA in dairy cows; however, concentrations in the muscle of beef animals have not always been increased. There is an apparent paradox in that n-3 PUFA supplementation enhances ruminal synthesis of trans-vaccenic acid (TVA), but then inhibits its conversion to CLA possibly through altering the activity of ?-9 desaturase. Recently, the promoter regions of the bovine ?- 9 desaturase gene has been isolated and analysed and has been shown to contain a conserved PUFA response region

Investigating students seriousness during selected conceptual inventory surveys

Conceptual inventory surveys are routinely used in education research to identify student learning needs and assess instructional practices. Students might not fully engage with these instruments because of the low stakes attached to them. This paper explores tests that can be used to estimate the percentage of students in a population who might not have taken such surveys seriously. These three seriousness tests are the pattern recognition test, the easy questions test, and the uncommon answers test. These three tests are applied to sets of students who were assessed either by the Force Concept Inventory, the Conceptual Survey of Electricity and Magnetism, or the Brief Electricity and Magnetism Assessment. The results of our investigation are compared to computer simulated populations of random answers.Comment: 8 pages; submitted to Phys Rev PE

Global gene expression in endometrium of high and low fertility heifers during the mid-luteal phase of the estrous cycle

peer-reviewedBackground In both beef and dairy cattle, the majority of early embryo loss occurs within the first 14 days following insemination. During this time-period, embryos are completely dependent on their maternal uterine environment for development, growth and ultimately survival, therefore an optimum uterine environment is critical to their survival. The objective of this study was to investigate whether differences in endometrial gene expression during the mid-luteal phase of the estrous cycle exist between crossbred beef heifers ranked as either high (HF) or low fertility (LF) (following four rounds of artificial insemination (AI)) using the Affymetrix® 23 K Bovine Gene Chip. Results Conception rates for each of the four rounds of AI were within a normal range: 70–73.3%. Microarray analysis of endometrial tissue collected on day 7 of the estrous cycle detected 419 differentially expressed genes (DEG) between HF (n = 6) and LF (n = 6) animals. The main gene pathways affected were, cellular growth and proliferation, angiogenesis, lipid metabolism, cellular and tissue morphology and development, inflammation and metabolic exchange. DEG included, FST, SLC45A2, MMP19, FADS1 and GALNT6. Conclusions This study highlights, some of the molecular mechanisms potentially controlling uterine endometrial function during the mid-luteal phase of the estrous cycle, which may contribute to uterine endometrial mediated impaired fertility in cattle. Differentially expressed genes are potential candidate genes for the identification of genetic variation influencing cow fertility, which may be incorporated into future breeding programmes.Teagasc Walsh Fellowship Programm

Investigating intra-host and intra-herd sequence diversity of foot-and-mouth disease virus

Due to the poor-fidelity of the enzymes involved in RNA genome replication, foot-and-mouth disease (FMD) virus samples comprise of unique polymorphic populations. In this study, deep sequencing was utilised to characterise the diversity of FMD virus (FMDV) populations in 6 infected cattle present on a single farm during the series of outbreaks in the UK in 2007. A novel RT–PCR method was developed to amplify a 7.6 kb nucleotide fragment encompassing the polyprotein coding region of the FMDV genome. Illumina sequencing of each sample identified the fine polymorphic structures at each nucleotide position, from consensus level changes to variants present at a 0.24% frequency. These data were used to investigate population dynamics of FMDV at both herd and host levels, evaluate the impact of host on the viral swarm structure and to identify transmission links with viruses recovered from other farms in the same series of outbreaks. In 7 samples, from 6 different animals, a total of 5 consensus level variants were identified, in addition to 104 sub-consensus variants of which 22 were shared between 2 or more animals. Further analysis revealed differences in swarm structures from samples derived from the same animal suggesting the presence of distinct viral populations evolving independently at different lesion sites within the same infected animal

Host reticulocytes provide metabolic reservoirs that can be exploited by malaria parasites

Human malaria parasites proliferate in different erythroid cell types during infection. Whilst Plasmodium vivax exhibits a strong preference for immature reticulocytes, the more pathogenic P. falciparum primarily infects mature erythrocytes. In order to assess if these two cell types offer different growth conditions and relate them to parasite preference, we compared the metabolomes of human and rodent reticulocytes with those of their mature erythrocyte counterparts. Reticulocytes were found to have a more complex, enriched metabolic profile than mature erythrocytes and a higher level of metabolic overlap between reticulocyte resident parasite stages and their host cell. This redundancy was assessed by generating a panel of mutants of the rodent malaria parasite P. berghei with defects in intermediary carbon metabolism (ICM) and pyrimidine biosynthesis known to be important for P. falciparum growth and survival in vitro in mature erythrocytes. P. berghei ICM mutants (pbpepc-, phosphoenolpyruvate carboxylase and pbmdh-, malate dehydrogenase) multiplied in reticulocytes and committed to sexual development like wild type parasites. However, P. berghei pyrimidine biosynthesis mutants (pboprt-, orotate phosphoribosyltransferase and pbompdc-, orotidine 5′-monophosphate decarboxylase) were restricted to growth in the youngest forms of reticulocytes and had a severe slow growth phenotype in part resulting from reduced merozoite production. The pbpepc-, pboprt- and pbompdc- mutants retained virulence in mice implying that malaria parasites can partially salvage pyrimidines but failed to complete differentiation to various stages in mosquitoes. These findings suggest that species-specific differences in Plasmodium host cell tropism result in marked differences in the necessity for parasite intrinsic metabolism. These data have implications for drug design when targeting mature erythrocyte or reticulocyte resident parasites

Controls on the rheological properties of peridotite at a palaeosubduction interface: A transect across the base of the Oman-UAE ophiolite

Studies of experimentally deformed rocks and small-scale natural shear zones have demonstrated that volumetrically minor phases can control strain localisation by limiting grain growth and promoting grain-size sensitive deformation mechanisms. These small-scale studies are often used to infer a critical role for minor phases in the development of plate boundaries. However, the role of minor phases in strain localisation at an actual plate boundary remains to be tested by direct observation. In order to test the hypothesis that minor phases control strain localisation at plate boundaries, we conducted microstructural analyses of peridotite samples collected along a ~1 km transect across the base of the Oman-United Arab Emirates (UAE) ophiolite. The base of the ophiolite is marked by the Semail thrust, which represents the now exhumed contact between subducted oceanic crust and the overlying mantle wedge. As such, the base of the ophiolite provides the opportunity to directly examine a former plate boundary. Our results demonstrate that the mean olivine grain size is inversely proportional to the abundance of minor phases (primarily orthopyroxene, as well as clinopyroxene, hornblende, and spinel), consistent with suppression of grain growth by grain-boundary pinning. Our results also reveal that mean olivine grain size is proportional to CPO strength (both of which generally decrease towards the metamorphic sole), suggesting that the fraction of strain produced by different deformation mechanisms varied spatially. Experimentally-derived flow laws indicate that under the inferred deformation conditions, the viscosity of olivine was grain-size sensitive. As such, grain size, and thereby the abundance of minor phases, influenced viscosity during subduction-related deformation along the base of the mantle wedge. We calculate an order of magnitude decrease in the viscosity of olivine towards the base of the ophiolite, which suggests strain was localized near the subduction interface. Our data indicate that this rheological weakening was primarily the result of more abundant minor phases near the base of the ophiolite. Our interpretations are consistent with those of previous studies on experimentally deformed rocks and smaller-scale natural shear zones that indicate minor phases can exert the primary control on strain localisation. However, our study demonstrates for the first time that minor phases can control strain localisation at the scales relevant to a major plate boundar

Structural and metamorphic architecture of the Zanskar Himalaya, Suru Valley region, NW India: Implications for the evolution of the Himalayan metamorphic core

New 1:50,000-scale geological mapping in the Zanskar Himalaya of NW India, covering 2,400 km2, is integrated with structural and petrographic analysis to document the evolution and key tectonometamorphic relationships within the Himalayan metamorphic core. The integrated dataset constrains the regional three-dimensional geology and relationships between lithostratigraphy, folds, faults, deformation fabrics, metamorphic isograds, and growth of porphyroblasts within the context of five main deformation phases. Following the initial collision of India and Asia, NW−SE-oriented deformation is recorded by D1 (greenschist-facies) fabrics and D2 (greenschist- to amphibolite-facies) fabrics. D2 represents the main tectonometamorphic deformation phase associated with crustal thickening and produced the dominant regional penetrative fabric through crenulation and transposition of D1 fabrics. Thrust-sense D2 fabrics were reactivated during D3 as the Greater Himalayan Sequence was exhumed along the normal-sense Zanskar Shear Zone, which is part of the South Tibetan Detachment System. D3 fabrics, associated with movement on the Zanskar Shear Zone, were temporally continuous with crenulation and mesoscale folding, recording progressive kilometer-scale backfolding and backthrusting toward the NE between the Greater Himalayan Sequence−Tethyan Himalayan Sequence and the adjacent Indus Suture Zone. Finally, D4 and D5 are recorded as kilometer-scale open folding of older planar and linear structures. The orientation of mineral isograd surfaces ranges from subparallel to oblique with respect to D2 planar structural elements. The growth of pelitic and metabasic peak metamorphic phases from greenschist to upper-amphibolite facies is synchronous with or postdates D2 fabrics. D3 fabrics wrap thermal peak porphyroblasts and realign linear mineral phases. Tectonic thinning adjacent to D3 normal faults is documented by reduced structural spacing of isograds and alignment of isograd surfaces parallel to the faults. D4 and D5 structures modify the trace of all regional metamorphic isograds. Collectively, these observations imply that the thermal peak of metamorphism was reached after the main phase of deformation (D2), and predated movement on the Zanskar Shear Zone (D3). The results document numerous classical elements of collisional orogenesis, including implied clockwise P-T paths, polyphase deformation, and a complete Barrovian metamorphic isograd sequence supplemented by complementary metabasic isograds. The Zanskar Himalaya, unlike other areas of the Himalayan metamorphic core, records metamorphic conditions primarily attained following substantial crustal thickening rather than during subsequent decompression and exhumation. The reduced expression and/or discontinuous nature of exhuming fault systems, which produces variable levels of crustal exposure, may account for this lateral heterogeneity across the mountain belt. Deciphering the complex kinematics of continental tectonics requires the integration of observations and data over large length scales and a range of structural levels

High Resolution Chandra Spectroscopy of Gamma Cassiopeia (B0.5IVe)

gamma Cas has long been famous for its unique hard X-ray characteristics. We report herein on a 53 ks Chandra HETGS observation of this target. An inspection of our spectrum shows that it is quite atypical for a massive star, with abnormally weak Fe XXV, XXVI lines, Ly-alpha lines of H-like species from Fe XVII, XXIII, XXIV, S XVI, Si XIV, Mg XII, Ne X, O VII, VIII, and N VII. Also, line ratios of the rif-triplet of for a few He-like ions XVII are consistent with the dominance of collisional atomic processes. Yet, the presence of Fe and Si fluorescence K features indicates that photoionization also occurs in nearby cold gas. The line profiles indicate a mean velocity at rest and a broadening of 500 km/s. A global fitting analysis of the line and continuum spectrum finds that there are 3-4 plasma emission components. The dominant hot (12 keV) component and has a Fe abundance of 0.22 solar. Some fraction of this component (10-30%) is heavily absorbed. The other 2-3 components, with temperatures 0.1, 0.4, 3 keV, are "warm," have a nearly solar composition, a lower column absorption, and are responsible for most other emission lines. The strength of the fluorescence features and the dual-column absorption model for the hot plasma component suggest the presence near the hot sites of a cold gas structure with a column density of 10^23 cm^-2. Since this value is consistent with theoretical estimates of the vertical disk column of this star, these attributes suggest that the X-rays originate near the star or disk. It is possible that the Fe anomaly in the hot component is related to the First Ionization Potential effect found in coronal structures around active cool stars. This would be yet another indication that the X-rays -rays are produced in the immediate vicinity of the Be star.Comment: 32 pages, 4 figures (Fig. 3 colorized.) To be published in 01/10/04 Astrophysical Journal, Main Journal; included figures and updated formattin

Birth delivery method affects expression of immune genes in lung and jejunum tissue of neonatal beef calves

peer-reviewedBackground Caesarean section is a routine veterinary obstetrical procedure employed to alleviate dystocia in cattle. However, CS, particularly before the onset of labour, is known to negatively affect neonatal respiration and metabolic adaptation in humans, though there is little published information for cattle. The aim of this study was to investigate the effect of elective caesarean section (ECS) or normal trans-vaginal (TV) delivery, on lung and jejunal gene expression profiles of neonatal calves. Results Paternal half-sib Angus calves (gestation length 278 + 1.8 d) were delivered either transvaginally (TV; n = 8) or by elective caesarean section (ECS; n = 9) and immediately euthanized. Lung and jejunum epithelial tissue was isolated and snap frozen. Total RNA was extracted using Trizol reagent and reverse transcribed to generate cDNA. For lung tissue, primers were designed to target genes involved in immunity, surfactant production, cellular detoxification, membrane transport and mucin production. Primers for jejunum tissue were chosen to target mucin production, immunoglobulin uptake, cortisol reaction and membrane trafficking. Quantitative real-time PCR reactions were performed and data were statistically analysed using mixed models ANOVA. In lung tissue the expression of five genes were affected (p < 0.05) by delivery method. Four of these genes were present at lower (LAP, CYP1A1, SCN11α and SCN11β) and one (MUC5AC) at higher abundance in ECS compared with TV calves. In jejunal tissue, expression of TNFα, Il-1β and 1 l-6 was higher in ECS compared with TV calves. Conclusions This novel study shows that ECS delivery affects the expression of key genes involved in the efficiency of the pulmonary liquid to air transition at birth, and may lead to an increased inflammatory response in jejunal tissue, which could compromise colostral immunoglobulin absorption. These findings are important to our understanding of the viability and management of neonatal calves born through ECS