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

Comparing Various Machine Learning Statistical Methods Using Variable Differentials to Predict College Basketball

The purpose of this Senior Honors Project is to research, study, and demonstrate newfound knowledge of various machine learning statistical techniques that are not covered in the University of Akron’s statistics major curriculum. This report will be an overview of three machine-learning methods that were used to predict NCAA Basketball results, specifically, the March Madness tournament. The variables used for these methods, models, and tests will include numerous variables kept throughout the season for each team, along with a couple variables that are used by the selection committee when tournament teams are being picked. The end goal is to find out which machine learning method populates the most successful bracket by using key differential statistics between teams and variables of past tournament winners using Neural Network, Boosted Decision Trees, and Naïve Bayes methodologies

Supply Management and Price Ceilings on Production Quota Values: Future or Folly?

This paper examines and contrasts two policies instituted by the Dairy Farmers of Ontario (DFO) in reaction to the escalation of production quota values on the provincial quota exchange, which regulates the transfer of dairy production quota among producers in the province of Ontario.Supply Management, DFO, Production Quota, Provincial Quota Exchange, Price ceiling, Progressive Transfer Assessment, Agricultural and Food Policy, Livestock Production/Industries, Production Economics,

Characterization of shielding effectiveness for metallic enclosures

This topic discusses and verifies an equation for estimating the shielding effectiveness of metallic enclosures through the use of numerical simulations. Using ideas from Bethe\u27s Theory of Diffraction by Small Holes , a previous student from the Missouri S&T Electromagnetic Compatibility Laboratory developed an equation that would yield an envelope prediction for the worst-case EMI from an aperture array backed by an over-moded cavity. Min Li (PhDEE \u2799) used results from measurements, simulations, and physics-based equations to formulate a simple equation that would predict these EMI levels. The main purpose of this thesis is to revisit this work and determine when and why this prediction fails, if at all. Broadband FDTD simulations are used to first evaluate several simple models of aperture arrays in an infinite PEC sheet. With a sound understanding of this scenario, the simulations are then extended to the more realistic PEC enclosures. In the end, the shielding effectiveness of aperture arrays excited by both uniform plane waves at normal incidence and over-moded cavities can be predicted to within 3dB, so long as the dimensions of the apertures remain less than [lambda]/6 --Abstract, page ii

Searching the World-Wide-Web using nucleotide and peptide sequences

*Background:* No approaches have yet been developed to allow instant searching of the World-Wide-Web by just entering a string of sequence data. Though general search engines can be tuned to accept ‘processed’ queries, the burden of preparing such ‘search strings’ simply defeats the purpose of quickly locating highly relevant information. Unlike ‘sequence similarity’ searches that employ dedicated algorithms (like BLAST) to compare an input sequence from defined databases, a direct ‘sequence based’ search simply locates quick and relevant information about a blunt piece of nucleotide or peptide sequence. This approach is particularly invaluable to all biomedical researchers who would often like to enter a sequence and quickly locate any pertinent information before proceeding to carry out detailed sequence alignment. 

*Results:* Here, we describe the theory and implementation of a web-based front-end for a search engine, like Google, which accepts sequence fragments and interactively retrieves a collection of highly relevant links and documents, in real-time. e.g. flat files like patent records, privately hosted sequence documents and regular databases. 

*Conclusions:* The importance of this simple yet highly relevant tool will be evident when with a little bit of tweaking, the tool can be engineered to carry out searches on all kinds of hosted documents in the World-Wide-Web.

*Availability:* Instaseq is free web based service that can be accessed by visiting the following hyperlink on the WWW
http://instaseq.georgetown.edu 
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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

On the development of flight-test equipment in relation to the aircraft spin

A review of the development of flight test equipment throughout aviation history is presented, focusing specifically on the stall spin. The primitive, yet, ingenious solutions devised in the early twentieth century by the pioneers of this field, paved the way for the advancement in knowledge of the complex aerodynamic properties inherent during a spin. Both in Britain and the US, the dangers associated with stalling and spinning were acknowledged shortly after the birth of aviation, with pilots and academics alike seeking to investigate the causes. Initially, the goal was to design safer aircraft, with more predictable handling, dynamic manoeuvrability, and precise controllability. Both nations were able to independently develop equipment packs which were to become standard for airborne investigations of the spin and other manoeuvres in the following years. These early studies laid the foundations on which we're still building today, now using state-of-the-art technology to enhance our knowledge of spin dynamics ever further