Attenuation of macrophage IL-10 responses by HIV-1

HIV-1 infection of monocyte derived macrophages (MDM) attenuates innate immune IL-10 transcriptional responses, resulting in increased inflammation. I sought to identify the host and virus determinants of this effect to provide novel insights into HIV-associated immune dysfunction and the mechanisms that regulate IL-10 responses. I established a protocol in which THP-1 cells can be differentiated to a macrophage like phenotype able to generate innate immune IL-10 responses and confirmed that this was attenuated by HIV 1. I found that at least one of the HIV accessory genes vpr or vpu were necessary for IL-10 attenuation in THP-1s, but not in MDMs. I focussed my remaining experiments on MDMs in which I also introduced single cell analysis using RNA fluorescence in situ hybridisation. In this model, neither HIV 1 accessory proteins nor productive HIV 1 infection was necessary for attenuation of IL-10. Instead I found that HIV 1 RNA was necessary and sufficient for this phenotype. TLR8-binding HIV 1 RNA motifs and a synthetic TLR8 ligand recapitulated attenuation of macrophage IL-10 responses, implicating a role for TLR8. This interaction would be expected to lead to induction of type I interferons (IFN). Consistent with this, type I IFN attenuated IL-10 responses and its effect was reversed by blocking the type I IFN receptor. However, in the same model, HIV 1 did not induce IFN responses and HIV 1 attenuation of IL-10 was not reversed by IFN receptor blockade. In addition, transient exposure to HIV-1 achieved sustained attenuation of macrophage IL-10 responses. My data support a model in which incoming HIV-1 RNA interacts with TLR8, leading to specific transcriptional regulation of IL-10 independently of IFN induction, most likely via epigenetic mechanisms. These data reveal a novel pathway for adaptation of innate immune responses and a potential mechanism for immune activation in HIV-1 infection due to deficient IL-10 immunoregulation

Capacity of elements of Banach algebras

As its name suggests, this thesis is an account of the recent theory of the capacity of elements of Banach algebras. The first chapter contains a summary of the background theory, other than fundamentals, used, and consists mainly of perturbation theory of linear operators and certain properties (Jf strictly singular operators. This chapter relies heavily on the work of T„ Kato, both in his own papers and the book by S. Goldberg "Unbounded Linear Operators". Chapter 2 introduces the notion of capacity, following Halmos in his paper "Capacity in Banach algebras", and several small new results are proved, and counterexamples given, to tidy up "loose ends". The question of the capacity of the sum of two quasialgebraic elements (i.e. ones with capacity zero) is raised, and a partial solution given. The perturbation theory of Chapter 1 is applied to show the equality of the capacity of the spectrum and the Fredholn spectrum of an operator on a Banach space, whence it is shown that if J is a closed two-sided ideal of B(x) containing only Riesz operators, then perturbation by an element of J leaves the capacity invariant; this is true, in particular, for compact operators. A converse theorem is proved for Hilbert space, Chapter 3 introduces the new concept of the joint capacity of an r-tuple of elements cf a commutative Banach algebra, and develops the theory of this notion, Much of the theory parallels, xn a weaker form, that of the original concept, but there are significant differences. Finally, a perturbation theorem, similar to the original one is proved for the joint capacity

The Mesostigmatid Mite Protogamasellus mica, an Effective Predator of Free-Living and Plant-Parasitic Nematodes

Protogamasellus mica was extracted from a sugarcane field in Australia and cultured on bacterial-feeding nematodes. Studies with various nematodes in laboratory arenas showed that one mite and its progeny reduced nematode numbers by between 26 and 50 nematodes/day. A bacterivore (Mesorhabditis sp.), a fungivore (Aphelenchus avenae), and two plant parasites (root-knot nematode, Meloidogyne javanica and root-lesion nematode, Pratylenchus zeae) were all reduced at much the same rate despite the fact that the nematodes are quite different in size and motility and belong to different trophic groups. When sugarcane was grown in the greenhouse for 8 wk, stunt nematode (Tylenchorhynchus annulatus), a plant parasite that feeds ectoparasitically on roots, was almost eliminated from pots inoculated with the mite, and numbers of microbivores and root-lesion nematode were markedly reduced. Huge reductions in nematode populations were also observed when mites were added to microcosms containing small quantities of defaunated soil. These results show that P. mica multiplies rapidly when nematodes are available as a food source and has the capacity to play a role in regulating populations of both plant-parasitic and free-living nematodes. Future research should focus on understanding the crop and soil management practices required to enable this mite and other predatory species to thrive

Oxidation of carbon compounds by Methylococcus capsulatus

The effect of various potential Inhibitors on methane oxidation was tested on whole-cell suspensions of Methylococcus capsulatus (strain Texas) (TRMC ) and Methylococcus capsulatus (strain Bath) (MC). Methane oxidation by TRMC was specifically inhibited by a large number of metal-chelating/binding agents and suggested the involvement of a metal ion(s) with the methane mono -oxygenase. The whole-cell results of MC showed a much more restricted specific inhibitor pattern for methane oxidation, which was confirmed by cell-free studies. The inhibitor pattern of MC was compared with that of TRMC and with reported patterns for other methane-utilisers. The effect of a number of acetylenic compounds on methane oxidation by MC was tested and the results discussed. The substrate specificity of the methane mono-oxygenase from MC was determined and found to be very non-specific. It catalysed the oxidation of various substituted methane derivatives, including methanol. C₁ -C₈ n-alkanes were hydroxylated to the corresponding 1- and 2-alcohols, carbon monoxide to carbon dioxide, terminal alkenes to the corresponding 1, 2-epoxides and internal alkenes to a variety of products. Ethers, alicyclic, aromatic and heterocyclic compounds were also oxidised. The significance of the various oxidations are discussed. Only NADPH could replace NADH as electron donor for methane mono-oxygenase activity. The subject of non-growth substrate oxidation by micro-organisms is discussed and the terminology of the area critically reviewed. Whole-cell oxidation studies with MC revealed five fortuitously oxidised non-growth substrates (chloromethane, bromomethane, dimethyl ether, ethene and propene) and seven cometabolic non-growth substrates (carbon monoxide, diethyl ether, ethane, propane, but-1 -ene, cis but-2-ene and trans but-2-ene). From these, dimethyl ether, bromomethane and carbon monoxide were selected to study in detail their effect on cellular metabolism of MC. During the oxidation studies it was suspected that an NAD(P)⁺ -linked aldehyde dehydrogenase was present. Confirmative tests proved positive. Activity in crude cell-free extracts was lost on dialysis, but could be restored by supplementing with inactive, heat-treated extract. The non-dialysable, heat-sensitive component was isolated and purified. The heat-stable component/co-factor was presumed to be a low molecular weight protein or polypeptide. The enzymic potential for an NAD(P)⁺ -linked cyclic scheme for the complete oxidation of formaldehyde was detected in crude cell- free extracts of MC. The relative Importance of the different formaldehyde oxidation systems found is discussed

g you The direct determination of haplotypes from extended regions of genomic DNA

Background: One of the major obstacles to the exploitation of genetic variation in human medicine, veterinary medicine, and animal breeding is the difficulty in defining haplotypes in unrelated individuals. Results: We have developed a Multiplex Double Amplification Refractory Mutation System combined with Solid Phase PCR on Fluorescently labelled beads. The process is inherently amenable to automation. It provides a high degree of internal Quality Control, as each PCR product is represented in duplicate on the bead array, and each SNP is tested against multiple partners. This technique can resolve very complex genotypes into their constituent haplotypes; it defined all the alleles at 60 SNP in exon 2 of the ovine DRB1 MHC locus in a sample of 109 rams. These 60 SNP formed 33 DRB1 exon 2 alleles; two of which had not been previously identified; although both of them have been independently confirmed. Conclusion: This technique has the same resolution as allele specific sequencing. Sequencing has the advantage of identifying novel polymorphic sites but where all SNP sites have been identified this novel procedure can resolve all alleles and haplotypes and identify novel combinations of polymorphisms. This method is similar in price to direct sequencing and provides a low cost system for direct haplotyping of extended DNA sequence

Landslide Inventory, Susceptibility, Frequency and Hazard zoning in the Wollongong and wider Sydney Basin Area

The University of Wollongong Landslide Research Team has been working on the development of GIS-based Landslide Inventory, Susceptibility and Hazard Zoning projects for over 15 years. To undertake the zoning work we use knowledge-based methods including Data Mining techniques which are facilitated within a GIS framework. This work is ongoing, and as with this paper, there are two main aims; firstly for those smaller sub-regions of Sydney where considerable data have been obtained and the landslide inventory development is comprehensive, increasingly more reliable modelling, analysis and synthesis is being done, and secondly, for the entire 31,000km2 geological extent of the Sydney Basin region where the available data are relatively small scale and the process of developing the landslide inventory is in the early stages, preliminary studies which are described as ‘proof of concept’ have been completed and are reported herein. The most advanced sub-region is a large portion of the Illawarra Escarpment within the Wollongong Local Government Area (LGA). Another advanced sub-region is the Picton area within the Wollondilly LGA. All the while, input data is being refined and improved in particular with the advent of Airborne Laser Scan derived DEM’s and the ongoing development and populating of Landslide Inventories. In tandem with refined input data, computing capabilities are also rapidly evolving and this is enabling ever growing terrain modelling capacity. With higher resolution input data for the Sydney Basin project, including a more rigorous Landslide Inventory which is already well under development, higher resolution geology information and possibly even a better or more recent DEM, the regional yet large scale GIS-based Susceptibility modelling outcomes are likely to be suitable for use at Local Government Planning levels. Furthermore, susceptibility modelling at a national scale to identify preliminary or ‘first pass’ binary type (i.e., in/out) areas for further assessment is also achievable in the very near future

Determination of the optimal number of clusters in harmonic data classification

In many of clustering algorithms, such as K-means and Fuzzy C-mean, the value of the expected numbers of clusters is often needed in advance as an input parameter to the algorithm. Other clustering algorithms estimate this number as the clustering process progresses using various heuristic techniques; however such techniques can also lead to a local minima within the solution space without finding the optimum number of clusters. In this paper, a method has been developed to determine the optimum number of clusters in power quality monitoring data using a data mining algorithm based on the minimum message length technique. The proposed method was tested using data from known number of clusters with randomly generated data points, with data from a simulation of a power system, and with power quality data from an actual harmonic monitoring system in a distribution system in Australia. The results from the tests confirm the effectiveness of the proposed method in finding the optimum number of clusters

Application of MML to motor skills acquisition

Study on modeling human psychomotor behaviour based on tracked motion data is reported. The motion data is acquired through various integrated inertial sensors, and represented as Euler angles and accelerations. The Minimum Message Length (MML) algorithm is used to identify frames of intrinsic segmentations and to acquire a classification basis for unsupervised machine learning. The classification model can ultimately be deployed in recognizing certain skilled behaviors. The prior results are analyzed as FSMs\u27 (Finite State Machines) to extract the potential rules underlying behaviors. The progress made so far and plan for further work is reported

Human behaviour recognition with segmented inertial data

The development and recent advancements of integrated inertial sensors has afforded substantive new possibilities for the acquisition and study of complex human motor skills and ultimately their imitation within robotic systems. This paper describes continuing work on kinetic models that are derived through unsupervised learning from a continuous stream of signals, including Euler angles and accelerations in three spatial dimensions, acquired from motions of a human arm. An intrinsic classification algorithm, MML (Minimum Message Length encoding) is used to segment the complex data, formulating a Gaussian Mixture Model of the dynamic modes it represents. Subsequent representation and analysis as FSM (Finite State Machines) has found distinguishing and consistent sequences of modes that persist across both, a variety of tasks as well as multiple candidates. An exemplary “standard” sequence for each behaviour can be abstracted from a corpus of suitable data and in turn utilised together with alignment techniques to identify behaviours of new sequences, as well as detail the homologous extent between each. The progress in contrast to previous work and future objectives are discussed

Identification of Load Power Quality Characteristics using Data Mining

The rapid increase in computer technology and the availability of large scale power quality monitoring data should now motivate distribution network service providers to attempt to extract information that may otherwise remain hidden within the recorded data. Such information may be critical for identification and diagnoses of power quality disturbance problems, prediction of system abnormalities or failure, and alarming of critical system situations. Data mining tools are an obvious candidate for assisting in such analysis of large scale power quality monitoring data. This paper describes a method of applying unsupervised and supervised learning strategies of data mining in power quality data analysis. Firstly underlying classes in harmonic data from medium and low voltage (MV/LV) distribution systems were identified using clustering. Secondly the link analysis is used to merge the obtained clusters into supergroups. The characteristics of these super-groups are discovered using various algorithms for classification techniques. Finally the a priori algorithm of association rules is used to find the correlation between the harmonic currents and voltages at different sites (substation, residential, commercial and industrial) for the interconnected supergroups