Application and development of advanced Lorentz microscopy techniques for the study of magnetic nanostructures

Understanding the magnetic structure and behaviour of domain walls has attracted recent attention in both academia and industry as it is of fundamental importance for the development of magnetic storage media. At the University of Glasgow we specialise in direct magnetic imaging through Lorentz electron microscopy. This PhD project presents an investigation into the development of magnetic imaging methods in the TEM and their application in imaging narrow domain walls in multilayer magnetic structures. Lorentz microscopy techniques are limited in quantitative magnetic imaging as this generally requires using scanning imaging modes which limits the capability of imaging dynamic processes. The first imaging method developed in this study is a phase gradient technique with the aim of producing quantitative magnetic contrast proportional to the magnetic induction of the sample whilst maintaining a live imaging mode. This method uses a specifically engineered, semi-electron-transparent graded wedge aperture to controllably perturb intensity in the back focal plane. The results of this study found that this method could produce magnetic contrast proportional to the sample induction, however the required gradient of the wedge aperture made this contrast close to the noise level with large associated errors. In the second part of this study we investigated the development of a technique aimed at gaining sub-microsecond temporal resolution within TEMs based on streak imaging. We are using ramped pulsed magnetic fields, applied across nanowire samples to both induce magnetic behaviour and detect the electron beam across the detector with respect to time. We are coupling this with a novel pixelated detector on the TEM in the form of a Medipix/Timepix chip capable of microsecond exposure times without adding noise. Running this detector in integral mode and allowing for practical limitations such as experiment time and aperture stability, the resultant streak images were taken in Fresnel, Foucault and low angle diffraction imaging modes. We found that while this method is theoretically viable, the limiting factor was the contrast of the magnetic signal in the streak and therefore the total image counts. Domain walls (DWs) in synthetic antiferromagnetically (SAF) coupled films patterned as nanowires offer exciting possibilities; the domain walls in these multilayers have narrower widths and reduced magnetostatic energy compared to those in single layer nanowires. In this study Co90Fe10/Ru/Co90Fe10 films were used to investigate the existence and structure of these walls. Nanowires were fabricated in these films and the DW structure was studied with respect to both wire width and varying magnetic layer thickness. It was found that while the DW structure does not appear to vary with the range of wire widths used, it changed significantly with varying thickness. The narrow DWs were observed to form only in samples with an unbalanced ratio of 1:25 : 1 or below; 1:75 : 1 and 2 : 1 samples were both observed to form transverse domain walls

MODELING RATIOS WITH POTENTIAL ZERO-INFLATION TO ASSESS SOIL NEMATODE COMMUNITY STRUCTURE

The southern root-knot nematode (SRKN) and the weedy perennials, yellow nutsedge (YNS) and purple nutsedge (PNS) are simultaneously-occurring pests in the irrigated agricultural soils of southern New Mexico. Previous research has characterized SRKN, YNS and PNS as a mutually beneficial pest complex and has shown their enhanced population growth and survival when they occur together. In addition, it was shown that the density of nutsedge in a field could be used as a predictor of SRKN juveniles in the soil. In addition to SRKN, which is the most harmful of the plant parasitic nematodes, in southern New Mexico other species or categories of nematodes were identified and counted. Some of them are not as damaging to crop plants as SRKN, and some of them may be essential for soil health. The nematode species could be grouped into categories according to trophic level (what nematodes eat) and herbivore feeding behavior (how herbivore nematodes eat). Then three ratios of counts each were calculated for trophic and feeding behavior categories to investigate the soil nematode community structure. These proportions were modeled as functions of the weed hosts YNS and PNS by generalized linear regression models using the logit link function and three distributions: the Binomial, Zero-Inflated Binomial (ZIB) and Binomial Hurdle (BH). The latter two were used to account for potential high proportions of zeroes in the data. Formulas for the probability mass functions and moments were developed for the ZIB and BH. The SAS NLMIXED procedure was used to fit models for each of three sampling dates (May, July and September) in the two years of an alfalfa field study. General results showed that the Binomial generally provided the best fit, indicating lower zero-inflation than expected, but that ZIB and BH are often comparable. Importance of YNS and PNS predictors varied over sample dates and ratios. Specific results for one selected ratio illustrate the differences in estimated probabilities between Binomial, ZIB and BH distributions as YNS counts increase

Development of Vortex Bioreactor Technology for Decentralised Water Treatment

The vortex bioreactor (VBR) is a simple decentralised water treatment system (DeWaTS) that sits at the interface between swirl flow, biotechnology and chemical engineering. The device utilises swirl flow and suspended activated beads to achieve downstream water processing and has been tested for applications including centrifugal-driven separation, pathogen neutralisation and metal absorption. The VBR was optimised for the treatment of faecally contaminated effluents in the developing world, and the design features related to the key challenges faced by the wastewater industry are highlighted here. The VBR has two aspects that can be modified to generate different reactor conditions: the impeller, where the swirl flow is modified through alterations of rotation speed, and impeller geometry and the suspended activated beads, which facilitate mixing and alter the reactor surface area. Data from testing for some of the different applications mentioned above are presented here, and future planned developments for the technology are discussed

Co-production of bio-oil and propylene through the hydrothermal liquefaction of polyhydroxybutyrate producing cyanobacteria

A polyhydroxybutyrate (PHB) producing cyanobacteria was converted through hydrothermal liquefaction (HTL) into propylene and a bio-oil suitable for advanced biofuel production. HTL of model compounds demonstrated that in contrast to proteins and carbohydrates, no synergistic effects were detected when converting PHB in the presence of algae. Subsequently, Synechocystis cf. salina, which had accumulated 7.5wt% PHB was converted via HTL (15% dry weight loading, 340°C). The reaction gave an overall propylene yield of 2.6%, higher than that obtained from the model compounds, in addition to a bio-oil with a low nitrogen content of 4.6%. No propylene was recovered from the alternative non-PHB producing cyanobacterial strains screened, suggesting that PHB is the source of propylene. PHB producing microorganisms could therefore be used as a feedstock for a biorefinery to produce polypropylene and advanced biofuels, with the level of propylene being proportional to the accumulated amount of PHB

OmniMapFree: A unified tool to visualise and explore sequenced genomes

<p>Abstract</p> <p>• Background</p> <p>Acquiring and exploring whole genome sequence information for a species under investigation is now a routine experimental approach. On most genome browsers, typically, only the DNA sequence, EST support, motif search results, and GO annotations are displayed. However, for many species, a growing volume of additional experimental information is available but this is rarely searchable within the landscape of the entire genome.</p> <p>• Results</p> <p>We have developed a generic software which permits users to view a single genome in entirety either within its chromosome or supercontig context within a single window. This software permits the genome to be displayed at any scales and with any features. Different data types and data sets are displayed onto the genome, which have been acquired from other types of studies including classical genetics, forward and reverse genetics, transcriptomics, proteomics and improved annotation from alternative sources. In each display, different types of information can be overlapped, then retrieved in the desired combinations and scales and used in follow up analyses. The displays generated are of publication quality.</p> <p>• Conclusions</p> <p>OmniMapFree provides a unified, versatile and easy-to-use software tool for studying a single genome in association with all the other datasets and data types available for the organism.</p

Engineering The Unicellular Alga Phaeodactylum tricornutum For High-Value Plant Triterpenoid Production

Plant triterpenoids constitute a diverse class of organic compounds that play a major role in development, plant defense and environmental interaction. Several triterpenes have demonstrated potential as pharmaceuticals. One example is betulin, which has shown promise as a pharmaceutical precursor for the treatment of certain cancers and HIV. Major challenges for triterpenoid commercialization include their low production levels and their cost‐effective purification from the complex mixtures present in their natural hosts. Therefore, attempts to produce these compounds in industrially relevant microbial systems such as bacteria and yeasts have attracted great interest. Here we report the production of the triterpenes betulin and its precursor lupeol in the photosynthetic diatom Phaeodactylum tricornutum, a unicellular eukaryotic alga. This was achieved by introducing three plant enzymes in the microalga: a Lotus japonicus oxidosqualene cyclase and a Medicago truncatula cytochrome P450 along with its native reductase. The introduction of the L. japonicus oxidosqualene cyclase perturbed the mRNA expression levels of the native mevalonate and sterol biosynthesis pathway. The best performing strains were selected and grown in a 550L pilot scale photobioreactor facility. To our knowledge, this is the most extensive pathway engineering undertaken in a diatom and the first time that a sapogenin has been artificially produced in a microalga, demonstrating the feasibility of the photo‐bio‐production of more complex high‐value, metabolites in microalgae

Search for a new gauge boson in the A′A' Experiment (APEX)

We present a search at Jefferson Laboratory for new forces mediated by sub-GeV vector bosons with weak coupling $\alpha'$ to electrons. Such a particle $A'$ can be produced in electron-nucleus fixed-target scattering and then decay to an $e^+e^-$ pair, producing a narrow resonance in the QED trident spectrum. Using APEX test run data, we searched in the mass range 175--250 MeV, found no evidence for an $A'\to e^+e^-$ reaction, and set an upper limit of $\alpha'/\alpha \simeq 10^{-6}$. Our findings demonstrate that fixed-target searches can explore a new, wide, and important range of masses and couplings for sub-GeV forces.Comment: 5 pages, 5 figures, references adde

PHI-base update: additions to the pathogen–host interaction database

The pathogen–host interaction database (PHI-base) is a web-accessible database that catalogues experimentally verified pathogenicity, virulence and effector genes from bacterial, fungal and Oomycete pathogens, which infect human, animal, plant, insect, fish and fungal hosts. Plant endophytes are also included. PHI-base is therefore an invaluable resource for the discovery of genes in medically and agronomically important pathogens, which may be potential targets for chemical intervention. The database is freely accessible to both academic and non-academic users. This publication describes recent additions to the database and both current and future applications. The number of fields that characterize PHI-base entries has almost doubled. Important additional fields deal with new experimental methods, strain information, pathogenicity islands and external references that link the database to external resources, for example, gene ontology terms and Locus IDs. Another important addition is the inclusion of anti-infectives and their target genes that makes it possible to predict the compounds, that may interact with newly identified virulence factors. In parallel, the curation process has been improved and now involves several external experts. On the technical side, several new search tools have been provided and the database is also now distributed in XML format. PHI-base is available at: http://www.phi-base.org/

Evolution of age and length at maturation of Alaskan salmon under size-selective harvest

Spatial and temporal trends and variation in life-history traits, including age and length at maturation, can be influenced by environmental and anthropogenic processes, including size-selective exploitation. Spawning adults in many wild Alaskan sockeye salmon populations have become shorter at a given age over the past half-century, but their age composition has not changed. These fish have been exploited by a gillnet fishery since the late 1800s that has tended to remove the larger fish. Using a rare, long-term dataset, we estimated probabilistic maturation reaction norms (PMRNs) for males and females in nine populations in two basins and correlated these changes with fishery size selection and intensity to determine whether such selection contributed to microevolutionary changes in maturation length. PMRN midpoints decreased in six of nine populations for both sexes, consistent with the harvest. These results support the hypothesis that environmental changes in the ocean (likely from competition) combined with adaptive microevolution (decreased PMRNs) have produced the observed life-history patterns. PMRNs did not decrease in all populations, and we documented differences in magnitude and consistency of size selection and exploitation rates among populations. Incorporating evolutionary considerations and tracking further changes in life-history traits can support continued sustainable exploitation and productivity in these and other exploited natural resources