Unlocking the M13 (F1) virion : investigation into the role of pIII C domain of F specific filamentous bacteriophage in infection : a thesis presented in partial fulfillment of the requirements for the degree of Master of Science in Biochemistry at Massey University, Palmerston North, New Zealand

Filamentous phage adsorb to the host cells by binding of the N2 domain of pIII to the tip of the F pilus. Binding of N1 domain of pIII to the secondary receptor (Tol A), triggers the opening of the virion by a poorly understood mechanism. Filamentous phage assembly is a secretion-like process. The assembly is terminated and virion released from the membranes by C domain of pIII. Because the infection is a reversal of assembly, it can be hypothesized that the C domain of pIII plays an active role in the infection. To test this hypothesis, we have set up a system in which virions carried a mixture of two types of mutant pIII molecules: i) functional N1N2 domains fused to a short C domain that can be incorporated but cannot terminate assembly and release the phage from the membrane: ii) C domain only, which can terminate phage assembly, but lacks the receptor-binding domains N1N2. The infectivity of the particles was as low as 0.21% that of the positive control setup in which virions carried a mixture of wild-type pIII and C domain. Therefore, a functional C domain covalently linked to the receptor domain N1N2 is required for infection. These findings suggest that simple binding of N1 domain of pIII to the periplasmic receptor TolA is not sufficient for infection. Rather, this interaction may, via functional C domain of pIII, trigger a conformational change required for the downstream events which result in the virion uncoating and DNA entry. To add further weight to this model, a "microphage" producing system was designed to produce short phage particles suitable for Cryo-EM structural analysis

Maximal information component analysis: a novel non-linear network analysis method.

BackgroundNetwork construction and analysis algorithms provide scientists with the ability to sift through high-throughput biological outputs, such as transcription microarrays, for small groups of genes (modules) that are relevant for further research. Most of these algorithms ignore the important role of non-linear interactions in the data, and the ability for genes to operate in multiple functional groups at once, despite clear evidence for both of these phenomena in observed biological systems.ResultsWe have created a novel co-expression network analysis algorithm that incorporates both of these principles by combining the information-theoretic association measure of the maximal information coefficient (MIC) with an Interaction Component Model. We evaluate the performance of this approach on two datasets collected from a large panel of mice, one from macrophages and the other from liver by comparing the two measures based on a measure of module entropy, Gene Ontology (GO) enrichment, and scale-free topology (SFT) fit. Our algorithm outperforms a widely used co-expression analysis method, weighted gene co-expression network analysis (WGCNA), in the macrophage data, while returning comparable results in the liver dataset when using these criteria. We demonstrate that the macrophage data has more non-linear interactions than the liver dataset, which may explain the increased performance of our method, termed Maximal Information Component Analysis (MICA) in that case.ConclusionsIn making our network algorithm more accurately reflect known biological principles, we are able to generate modules with improved relevance, particularly in networks with confounding factors such as gene by environment interactions

CFD simulation of flow around angle of attack and sideslip angle vanes on a BAe Jetstream 3102 - Part 1

CFD modelling techniques are exploited to investigate the local velocity field around angle of attack and sideslip angle sensors fitted to the nose of a modified BAe Jetstream 3102 small airliner. Analysis of the flow angularity at the vane locations has allowed the vanes response to varying flight conditions to be predicted and errors in the readings to be quantified. Subsequently, a more accurate calibration of the system is applied to the current configuration on the Jetstream, and a better understanding of the position error with respect to the vane locations is obtained. The above aircraft was acquired by Cranfield University in 2003 with subsequent flow angle vane modifications taking place in 2005. The aircraft is currently in operation with the National Flying Laboratory Centre (NFLC) for research and demonstration purposes

68Ga-DOTATATE PET Identifies Residual Myocardial Inflammation and Bone Marrow Activation After Myocardial Infarction.

Myocardial infarction (MI) healing occurs in two phases: first an inflammatory phase, where clearance of necrotic debris occurs, followed by a reparative phase characterized by angiogenesis, granulation tissue formation and attempts to repair the extracellular matrix. While efficient healing relies on co-ordinated mobilization of monocytes to the damaged myocardium, with resolution of the acute inflammatory response by ~10-14 days, excessive inflammation impairs myocardial salvage and promotes adverse cardiac remodelling

Returning to play after prolonged training restrictions in professional collision sports

The COVID-19 pandemic in 2020 has resulted in widespread training disruption in many sports. Some athletes have access to facilities and equipment, whilst others have limited or no access, severely limiting their training practices. A primary concern is that the maintenance of key physical qualities (e.g., strength, power, high-speed running ability, acceleration, deceleration and change of direction), game-specific contact skills (e.g., tackling) and decision-making ability, are challenged, impacting on performance and injury risk on resumption of training and competition. In extended periods of reduced training, without targeted intervention, changes in body composition and function can be profound. However, there are strategies that can dramatically mitigate potential losses, including resistance training to failure with lighter loads, plyometric training, exposure to high-speed running to ensure appropriate hamstring conditioning, and nutritional intervention. Athletes may require psychological support given the challenges associated with isolation and a change in regular training routine. Whilst training restrictions may result in a decrease in some physical and psychological qualities, athletes can return in a positive state following an enforced period of rest and recovery. On return to training, the focus should be on progression of all aspects of training, taking into account the status of individual athletes

The Matsu Wheel: A Cloud-Based Framework for Efficient Analysis and Reanalysis of Earth Satellite Imagery

Project Matsu is a collaboration between the Open Commons Consortium and NASA focused on developing open source technology for cloud-based processing of Earth satellite imagery with practical applications to aid in natural disaster detection and relief. Project Matsu has developed an open source cloud-based infrastructure to process, analyze, and reanalyze large collections of hyperspectral satellite image data using OpenStack, Hadoop, MapReduce and related technologies. We describe a framework for efficient analysis of large amounts of data called the Matsu "Wheel." The Matsu Wheel is currently used to process incoming hyperspectral satellite data produced daily by NASA's Earth Observing-1 (EO-1) satellite. The framework allows batches of analytics, scanning for new data, to be applied to data as it flows in. In the Matsu Wheel, the data only need to be accessed and preprocessed once, regardless of the number or types of analytics, which can easily be slotted into the existing framework. The Matsu Wheel system provides a significantly more efficient use of computational resources over alternative methods when the data are large, have high-volume throughput, may require heavy preprocessing, and are typically used for many types of analysis. We also describe our preliminary Wheel analytics, including an anomaly detector for rare spectral signatures or thermal anomalies in hyperspectral data and a land cover classifier that can be used for water and flood detection. Each of these analytics can generate visual reports accessible via the web for the public and interested decision makers. The result products of the analytics are also made accessible through an Open Geospatial Compliant (OGC)-compliant Web Map Service (WMS) for further distribution. The Matsu Wheel allows many shared data services to be performed together to efficiently use resources for processing hyperspectral satellite image data and other, e.g., large environmental datasets that may be analyzed for many purposes

A crossover randomised controlled trial of oral mandibular advancement devices for obstructive sleep apnoea-hypopnoea (TOMADO)

Rationale Mandibular advancement devices (MADs) are used to treat obstructive sleep apnoea-hypopnoea syndrome (OSAHS) but evidence is lacking regarding their clinical and cost-effectiveness in less severe disease. Objectives To compare clinical- and cost-effectiveness of a range of MADs against no treatment in mild to moderate OSAHS. Measurements and methods This open-label, randomised, controlled, crossover trial was undertaken at a UK sleep centre. Adults with Apnoea-Hypopnoea Index (AHI) 5–<30/h and Epworth Sleepiness Scale (ESS) score ≥9 underwent 6 weeks of treatment with three nonadjustable MADs: self-moulded (SleepPro 1; SP1); semi-bespoke (SleepPro 2; SP2); fully-bespoke MAD (bMAD); and 4 weeks no treatment. Primary outcome was AHI scored by a polysomnographer blinded to treatment. Secondary outcomes included ESS, quality of life, resource use and cost. Main results 90 patients were randomised and 83 were analysed. All devices reduced AHI compared with no treatment by 26% (95% CI 11% to 38%, p=0.001) for SP1, 33% (95% CI 24% to 41%) for SP2 and 36% (95% CI 24% to 45%, p<0.001) for bMAD. ESS was 1.51 (95% CI 0.73 to 2.29, p<0.001, SP1) to 2.37 (95% CI 1.53 to 3.22, p<0.001, bMAD) lower than no treatment (p<0.001 for all). Compliance was lower for SP1, which was the least preferred treatment at trial exit. All devices were cost-effective compared with no treatment at a £20 000/quality-adjusted life year (QALY) threshold. SP2 was the most cost-effective up to £39 800/QALY. Conclusions Non-adjustable MADs achieve clinically important improvements in mild to moderate OSAHS and are cost-effective

Quantum teleportation on a photonic chip

Quantum teleportation is a fundamental concept in quantum physics which now finds important applications at the heart of quantum technology including quantum relays, quantum repeaters and linear optics quantum computing (LOQC). Photonic implementations have largely focussed on achieving long distance teleportation due to its suitability for decoherence-free communication. Teleportation also plays a vital role in the scalability of photonic quantum computing, for which large linear optical networks will likely require an integrated architecture. Here we report the first demonstration of quantum teleportation in which all key parts - entanglement preparation, Bell-state analysis and quantum state tomography - are performed on a reconfigurable integrated photonic chip. We also show that a novel element-wise characterisation method is critical to mitigate component errors, a key technique which will become increasingly important as integrated circuits reach higher complexities necessary for quantum enhanced operation.Comment: Originally submitted version - refer to online journal for accepted manuscript; Nature Photonics (2014