The establishment of the Border Industrialization Program (BIP) between Mexico and the United States in 1965 led to the creation of free-trade zone assembly factories--or maquiladoras--along Mexico's Northern border and in the interior. Thousands of Mexican women have since entered the industrial export sector as maquiladora workers, and make up the majority of unskilled and semi-skilled assemblers in electronic and apparel maquila plants. This paper agues that maquiladora managers' preference for women is the result of an unquestioning belief in the gender-specific traits of women--such as dexterity, docility, patience--and well-calculated hiring and personnel policies, which have been designed not only to take advantage of the patriarchal system in Mexico and women's weaker social, political and economic position, but to maintain and control women's qualities of "cheapness", "docility", and "productivity", to the advantage of business.

The construction process of the functional macronucleus in certain types of ciliates is known as the ciliate gene assembly process. It consists of a massive amount of DNA excision from the micronucleus and the rearrangement of the rest of the DNA sequences (in the case of stichotrichous ciliates). While several computational models have tried to represent certain parts of the gene assembly process, the real process remains not completely understood. In this research, a new formal model called the Computational 2JLP model is introduced based on the recent biological 2JLP model. For justifying the formal model, a simulation is created and tested with real data. Several parameters are introduced in the model that are used to test ambiguities or edge cases of the biological model. Parameters are systematically tested from the simulation to try to find their optimal values. Interestingly, a negative correlation is found between a parameter (which is used to filter out scnRNAs that are similar to IES specific sequences from the macronucleus) and the outcome of the simulation. It indicates that if a scnRNA consists of both an MDS and IES, then from the perspective of maximizing the outcome of the simulation, it is desirable to filter out this scnRNA. The simulator successfully performs the gene assembly process whether the inputs are scrambled or unscrambled DNA sequences. It is desirable for this model to serve as a foundation for future computational and mathematical study, and to help inform and refine the biological model.

No description available.

No description available.

The Type 2 Secretion System (T2SS) is responsible for the transport of toxins and enzymes across the outer membrane of many Gram-negative bacteria. A crucial component of the T2SS is a large pore, composed of a multimer of EpsD, named the secretin. This pore inserts in the outer membrane with the assistance of a pilotin (EpsS) or assembly factors (EpsAB), both of which are present within the genome of Vibrio cholerae. The goal of this study was to determine whether or not both assembly mechanisms operate on the same secretin assembly in V. cholerae. Protease deficient mutants generated from an insertion transposon library in V. cholerae epsAB were analyzed. The transposon was found to disrupt the operon encoding VC1702 and epsS. Mutant strains of V. cholerae were constructed or obtained that are deficient in epsA, epsB, epsC, and epsS. Double mutants were constructed that were deficient in epsA and epsS or epsB and epsS. These mutants were tested for assembly of the secretin and secretion of lipase, protease, and cholera toxin. The epsA and epsB mutants have slightly reduced levels of secretion and secretin assembly, while the levels in the pilotin mutant are drastically reduced. The double mutants had little to no assembly, and secretion was reduced to the levels of the control mutant epsC. In an attempt to restore function epsAB was over-expressed in all strains. It successfully complemented the epsA and epsB mutants, and restored levels of secretion to epsS levels in the double mutant, epsAS. In a similar manner to epsAB complementation, epsS was over-expressed. It was found to require the preceding gene VC1702 to complement. The operon, encoding both epsS and VC1702, could complement both epsA and epsS mutations and over-expression increased secretin assembly and secretion to levels greater than wild-type levels. Lastly, a phylogenomic analysis demonstrates that the EpsAB protein complex is found in most orders of the gamma proteobacteria and is ancestral. The pilotins appear to be a late acquisition as they are only found in the family Enterobacteriales.

This thesis is an experimental investigation on the binding of self-assembling peptides to oligodeoxynucleotides (ODNs) and the characterization of the resulting peptide-ODN complexes/aggregates, the first key step in the development of a peptide-based gene delivery system. Effects of pH, charge distribution along the peptide backbone, and oligonucleotide sequences on the peptide-ODN binding were investigated by a series of physicochemical methods. UV-Vis absorption and fluorescence anisotropy experiments demonstrate that aggregates are formed after mixing the peptide and ODN in aqueous solution. The aggregates in solution can be centrifuged out. Based on this property, the fraction of ODNs incorporated in the peptide-ODN aggregates can be obtained by comparing the UV-Vis absorption of the solution before and after centrifugation. Binding isotherms are generated by a binding density function analysis of the UV absorbance results. The binding parameters are extracted from the analysis of the binding isotherms based on the McGhee and von Hippel model. Equilibrium binding parameter studies show that the binding of two self-assembling peptides, EAK16-II and EAK 16-IV, to model single and double-stranded ODNs at pH 4 is stronger than at pH 7, and that no binding occurs at pH 11. These results demonstrate that electrostatic interactions play an important role in the EAK-ODN binding because EAKs are more positively charged at low pH. EAKs bind more strongly to dG16 than to the other ODN sequences dC16 and dGC16. This demonstrates that the hydrogen bond might be involved because they promote the binding of the lysine residues of the peptide to dG16 to a greater extent than to dC16. The charge distribution along the peptides is found to have an effect on the binding. EAK16-IV, whose positively charged residues are clustered at one end of the peptide, binds to the ODNs more strongly than EAK16-II, whose positively charged residues are distributed throughout the peptide chain, at the same pH. The binding process of EAKs to the ODNs was investigated by fluorescence anisotropy and static light scattering experiments. The results show that individual EAK and ODN molecules complex first, followed by the aggregation of these complexes into large aggregates. The nature of the resulting peptide-ODN complexes/aggregates is examined by UV-Vis absorption, fluorescence anisotropy, and PAGE experiments. The results demonstrate that free EAK, free ODNs, and small EAK-ODN complexes, which can not be centrifuged out, exist in the supernatant, and that large aggregates are collected in the pellets after centrifugation of the solution. The size of the resulting EAK-ODN complexes/aggregates measured by AFM and DLS is around a few hundreds of nanometers at low EAK concentrations. The accessibility of the ODNs to the quencher in the solution is reduced by 40 % and 60 % after binding to EAK16-II and EAK16-IV, respectively, as determined by fluorescence quenching experiments on EAK-ODN mixture solutions. An ODN protection from Exonuclease 1 degradation is provided by the EAK16-II or EAK16-IV matrix when they are mixed with the ODNs at pH 4. However, the ODNs are protected to a much lower degree when the EAK-ODN aggregates are prepared at pH 7. The EAK-ODN aggregates prepared at pH 7 are found to dissociate more easily than those prepared at pH 4 when they are incubated with exonuclease I solution at pH 9.5. These results suggest that the ODN protection afforded by the EAK-ODN aggregates is correlated with their structural stability after being incubated with the nuclease solution. The stability of the EAK-ODN aggregates after dilution is determined by UV-Vis absorption. No detectable dissociation of the aggregates is observed over 20 hrs after a 5- and 10-fold dilution of the solution in the same buffer used for their preparation. The EAK-ODN aggregates remain stable after the solutions are centrifuged, and re-dissolved in fresh buffer solutions. The ability of an EAK matix to protect ODNs from nuclease degradation together with its biocompatibility and low-toxicity suggests that EAK self-assembling peptides could be used as carriers for gene delivery.

Advances in software engineering and programming languages have had an impact on productivity, time to market, comprehension, maintenance, and evolution of software. Low-level systems have been largely overlooked in this arena, not only because of their complexities, but also the "bare bones'" culture of this domain. This dissertation investigates the program comprehension needs of two stakeholder groups using different assembly languages: a mainframe development group and a malware analysis group. Exploratory interviews and surveys suggest that the groups' needs may be similar at a high-level. However, a detailed study involving requirements elicitation and case studies, reveals that the truth is much more complicated. As a proof of concept, we have created the AVA (Assembly Visualization and Analysis) framework, which is independent of the underlying assembly language. Despite this independence, tools within AVA could not be applied with equal efficacy, even just within these two groups. This dissertation shows that there exist fundamental differences not only in the highly-specialized nature of each group's work, but also in the assembly languages themselves. This reality necessitates a disjoint set of tools that cannot be consolidated into a universally applicable framework. / Graduate / 0984 / jebaldwin@gmail.com

The field of nanotechnology has enabled scientists to perform fascinating engineering manipulations of biological substrates. Systems of DNA are now able to perform algorithmic computations by way of constructing biological modules composed of DNA macromolecules and using laboratory techniques available to biological sciences. The tile assembly model is an established model of biomolecular computing: using properties of DNA macromolecules to define constructions of self-assembling biological systems. The existing tile assembly model uses the concept of DNA tiles conceptually shaped as squares and exposes the tiles to carefully controlled biological conditions. The result is that under this process we can design and create these systems to compute solutions to algorithmic problems. Hexagons are the only two-dimensional regular polygon other than squares that can tile a plane infinitely leaving no space uncovered, where only translations of the initial polygon is allowed. Therefore hexagon-shaped DNA tiles can be defined to cover a planar surface, with the notable difference of six adjacent tiles per position versus the four adjacent neighbours in traditional four sided tiles. In this thesis, we will define a generalization of the tile assembly model that supports six-sided DNA tiles, in addition to the traditional four sides. We will introduce a problem known as the 0-1 Knapsack problem that is currently unsolved with square tiles. Moreover, a solution to the problem was attempted by tile assembly model researchers, however we show there is an error in their solution. After we analyze their solution and discover the shortcomings of square tiles under those constraints, we then show this fault is not applicable to hexagon tiles. Therefore, we show that the 0-1 Knapsack problem is solvable using hexagon shaped tiles.

Computing has reached a point where it is visible in almost every aspect of one’s daily activities. Consider, for example, a typical household. There will be a desktop computer, game console, tablet computer, and smartphones built using different types of processors and instruction sets. To support the pervasive and heterogeneous nature of computing there has been many advances in programming languages, hardware features, and increasingly complex software systems. One task that is shared by all people who work with software is the need to develop a concrete understanding of foreign code so that tasks such as bug fixing, feature implementation, and security audits can be conducted. To do this tools are needed to help present the code in a manner that is conducive to comprehension and allows for knowledge to be transferred. Current tools for program comprehension are aimed at high-level languages and do not provide a platform for assembly code comprehension that is extensible both in terms of the supported environment as well as the supported analysis. This thesis presents ICE, an Integrated Comprehension Environment, that is de- veloped to support comprehension of assembly code while remaining extensible. ICE is designed to receive data from external tools, such as disassemblers and debuggers, which is then presented in a series of visualizations: Cartographer, Tracks, and a Control Flow Graph. Cartographer displays an interactive function call graph while Tracks displays a navigable sequence diagram. Support for new visualizations is provided through the extensible implementation enabling analysts to develop visual- izations tailored to their needs. Evaluation of ICE is completed through a series of case studies that demonstrate different aspects of ICE relative to currently available tools. / Graduate / 0984 / dpucsek@uvic.ca

Advances in software engineering and programming languages have had an impact on productivity, time to market, comprehension, maintenance, and evolution of software. Low-level systems have been largely overlooked in this arena, not only because of their complexities, but also the "bare bones'" culture of this domain. This dissertation investigates the program comprehension needs of two stakeholder groups using different assembly languages: a mainframe development group and a malware analysis group. Exploratory interviews and surveys suggest that the groups' needs may be similar at a high-level. However, a detailed study involving requirements elicitation and case studies, reveals that the truth is much more complicated. As a proof of concept, we have created the AVA (Assembly Visualization and Analysis) framework, which is independent of the underlying assembly language. Despite this independence, tools within AVA could not be applied with equal efficacy, even just within these two groups. This dissertation shows that there exist fundamental differences not only in the highly-specialized nature of each group's work, but also in the assembly languages themselves. This reality necessitates a disjoint set of tools that cannot be consolidated into a universally applicable framework. / Graduate / 0984 / jebaldwin@gmail.com