Improved processing of microarray data using image reconstruction techniques

Spotted cDNA microarray data analysis suffers from various problems such as noise from a variety of sources, missing data, inconsistency, and, of course, the presence of outliers. This paper introduces a new method that dramatically reduces the noise when processing the original image data. The proposed approach recreates the microarray slide image, as it would have been with all the genes removed. By subtracting this background recreation from the original, the gene ratios can be calculated with more precision and less influence from outliers and other artifacts that would normally make the analysis of this data more difficult. The new technique is also beneficial, as it does not rely on the accurate fitting of a region to each gene, with its only requirement being an approximate coordinate. In experiments conducted, the new method was tested against one of the mainstream methods of processing spotted microarray images. Our method is shown to produce much less variation in gene measurements. This evidence is supported by clustering results that show a marked improvement in accuracy

Identification of Novel Pesticides for Use against Glasshouse Invertebrate Pests in UK Tomatoes and Peppers

To inform current and future pesticide availability to glasshouse vegetable growers, the current project trialled more than twenty products, including existing industry standards, against four key pests of glasshouse tomatoes and bell peppers. These included experimental conventional chemical pesticides as well as alternative biopesticide and biorational products based on phytochemicals, microbials and physically-acting substances. The results suggest that certain biopesticide products, particularly botanicals, provide good levels of pest control, with the same being true of experimental conventional chemical pesticides not yet recommended for use against these pests on these crops. Efforts are on-going to ensure that results of the current project translate to industry benefit via new pesticide approvals

Elastic Properties of Hydrogrossular Garnet and Implications for Water in the Upper Mantle

The single-crystal elastic properties of a hydrous silicate garnet, hibschite (Ca_3Al_2(SiO_4)_(1.72)(H_4O_4)_(1.28)), were measured using Brillouin spectroscopic techniques. The adiabatic bulk modulus of hibschite, K_s = 99.8±1.0 GPa, and the shear modulus, μ = 64.3±0.5 GPa, are 40% lower than the bulk and shear moduli for anhydrous grossular garnet Ca_3Al_2(SiO_4)_3. This increased compressibility of hydrogarnet is attributed to increased hydrogen bonding with pressure in the H_4O_4 tetrahedron. Density considerations indicate that hydrogarnet is likely to be stable relative to an assemblage with H_2O as a separate phase throughout the upper mantle and probably the transition zone. Assuming garnet to be the sole repository for mantle water, the seismic wave velocities of a “wet” eclogitic layer are 6–8% lower than those of dry eclogite. A hydrated eclogitic layer several times thicker than the oceanic crust would probably be required for a water-rich region of the mantle to be seismologically detectable. Lesser quantities of mantle water than those implied by the above scenario may be invisible to seismic techniques

Stock assessment of the Australian east coast tailor (Pomatomus saltatrix) fishery

Tailor is a highly migratory fish with an iconic, mainly beach-based fishery on the Australian east coast. There is a pronounced annual, close-inshore run of large schools of tailor from New South Wales, where the fishery peaks in April–June, to Queensland where the Fraser Island fishery at the northern end of the run peaks in August–September. The commercial sector of the fishery developed over the first half of the 20th century while the recreational beach line sector grew strongly from the late 1940s, facilitated by rapid developments in recreational beach-fishing gear. The recreational sector appeared to have had a pronounced peak in both harvest size and fishing effort in the mid-1990s, after which both the recreational and commercial sectors experienced big falls driven largely by cultural change. Recreational participation rates and fishing effort fell sharply while fishery management implemented measures such as bag limits on the recreational sector and harvest limits and spatial restrictions on the commercial sector. Information on the tailor fishery is relatively rich in fish length-frequency and ageing data, although data quality greatly improved from the mid-1990s with the introduction of scientific sampling methods. Prior to that time there were no reliable fish ageing data and most length-frequency data came from tagging experiments. The eastern Australian stock of tailor mainly consists of young fish with not many surviving beyond four years of age. The oldest fish aged by Fisheries Queensland’s monitoring team were just under seven years of age

Studies on an endotoxin produced by Pseudomonas aeruginosa

The Introduction to the thesis is devoted to a review of the principal methods which have been used in the extraction of the extraction of the endotoxins or somatic antigens of Gram negative bacteria, and the chemical nature of those substance. The part played by the lipid portion of the complex in the biological activity is discussed along with the effect on the biological activity of chemical modification of endotoxins. The experimental work is in two main sections. In the first of these, the isolation, purification and properties of the ondotoxin from Pseudomonas aeruginosa are described and the results discussed. The ondotoxin was isolated as a lipopolysaccharide by a procedure which involved heating acetone-dried bacterial cells with aqueous phenol, followed by dialysis and high speed centrifugation of the aqueous extract. The lipopolysaccharide was shown to contain galactose, glucose, galactosamine, glucosamine and an aldohoptooe. The lipid portion obtained after short acid hydrolysis contained other-soluble and chloroform-soluble fractions in both of which glucosamine, several amino acids and a series of fatty acids were detected. The lipopolysaccharide was shown to be antigenic and highly pyrogenic when injected into rabbits, and to be toxic to rabbits and mice. The second experimental section is concerned with the effect of a combination of trichloracetic acid and phenol extraction on the Pseoudomonas aerpginosa cells. Cold trichloracetic acid extraction by the Boivin technique gave a low yield of endotoxin, but it was found that the rosidue after trichloracetic acid extraction could be treated with hot aqueous phenol to give appreciable amounts of an endotoxic material which was similar to the ondotoxin obtained by direct treatment of the cells with hot phenol, but which was free from contaminating nucleic acid. By the use of the combined extraction technique, nucleic acid-free lipopolysaucharides were also obtained in good yield from proteus vulgaris and Escherichia coli. It was also found that the maintenance of low temperature during the trichloracotic acid extraction was not essential when using the double extraction method to obtain nucleic acid-free lipopolysaccharides. A farther series of experiments showed that even after multiple extraction with cold trichioracetic acid, a considerable amount of endotoxin remained unextracted and could be obtained from the residue by treatment with hot phenol

Dynamic electrophysiological connectomics

The human brain can be divided into multiple areas, each responsible for different aspects of behaviour. For a century we have been developing techniques to non-invasively map these areas and their associated functions, a discipline now known as neuroimaging. In recent years the field has undergone a paradigm shift to investigate how the brain communicates with itself; it is widely regarded that healthy brain function relies upon efficient connectivity between different functional areas, and the neuroimaging field has been revolutionised by our ability to estimate this connectivity. Studies into communication between spatially separate locations in the brain have revealed a series of robust functional networks which govern mental processes. However these studies have been based on the temporal averaging of minutes or even hours of data to give us a generalised ’snapshot’ of connectivity. Increasing evidence shows us that these connections are dynamic in space, time and frequency and so the next generation of of neuroimaging methods, which capture this 5-dimensional connectivity will prove to be key tools in the investigation of brain networks and ultimately their breakdown in disease. In this thesis we introduce novel methods to capture non-stationarity using magnetoencephalography (MEG), an imaging modality which measures the changes in extracranial magnetic fields associated with neuronal current flow. MEG is a direct measurement of neural activity and has an excellent temporal resolution, which makes it attractive for non-invasively tracking dynamic functional connections. However there are many technical limitations which can confound assessment of functional connectivity which have to be addressed. In Chapters 2 and 3 we introduce the theory behind MEG; specifically how it is possible to measure the femtoTelsa changes in magnetic field generated by the brain and how to project these data to generate a 3-dimensional picture of current in the brain. Chapter 4 reviews some of popular methods of assessing functional connectivity and how to control for the influence of artefactual functional connections erroneously produced during source projection. Chapter 5 introduces a pipeline to assess functional connections across time, space and frequency and in Chapter 6 we apply this pipeline to show that resting state networks, measured using ’static’ metrics are in fact comprised of a series of rapidly forming and dissolving subnetwork connections. Finally, Chapter 7 introduces a pipeline to track dynamic network behaviour simultaneously across the entire brain volume and shows that networks can be characterised by their temporal signatures of connectivity

Dynamic electrophysiological connectomics

The human brain can be divided into multiple areas, each responsible for different aspects of behaviour. For a century we have been developing techniques to non-invasively map these areas and their associated functions, a discipline now known as neuroimaging. In recent years the field has undergone a paradigm shift to investigate how the brain communicates with itself; it is widely regarded that healthy brain function relies upon efficient connectivity between different functional areas, and the neuroimaging field has been revolutionised by our ability to estimate this connectivity. Studies into communication between spatially separate locations in the brain have revealed a series of robust functional networks which govern mental processes. However these studies have been based on the temporal averaging of minutes or even hours of data to give us a generalised ’snapshot’ of connectivity. Increasing evidence shows us that these connections are dynamic in space, time and frequency and so the next generation of of neuroimaging methods, which capture this 5-dimensional connectivity will prove to be key tools in the investigation of brain networks and ultimately their breakdown in disease. In this thesis we introduce novel methods to capture non-stationarity using magnetoencephalography (MEG), an imaging modality which measures the changes in extracranial magnetic fields associated with neuronal current flow. MEG is a direct measurement of neural activity and has an excellent temporal resolution, which makes it attractive for non-invasively tracking dynamic functional connections. However there are many technical limitations which can confound assessment of functional connectivity which have to be addressed. In Chapters 2 and 3 we introduce the theory behind MEG; specifically how it is possible to measure the femtoTelsa changes in magnetic field generated by the brain and how to project these data to generate a 3-dimensional picture of current in the brain. Chapter 4 reviews some of popular methods of assessing functional connectivity and how to control for the influence of artefactual functional connections erroneously produced during source projection. Chapter 5 introduces a pipeline to assess functional connections across time, space and frequency and in Chapter 6 we apply this pipeline to show that resting state networks, measured using ’static’ metrics are in fact comprised of a series of rapidly forming and dissolving subnetwork connections. Finally, Chapter 7 introduces a pipeline to track dynamic network behaviour simultaneously across the entire brain volume and shows that networks can be characterised by their temporal signatures of connectivity