No description available.

No description available.

No description available.

No description available.

No description available.

Otolin-1 is a collagenous, C1q domain-containing extracellular matrix protein that has been identified and characterized in the inner ear. Recently, mass spectrometry analysis of left ventricular cardiac tissue detected a peptide of Otolin-1. Experimental analysis confirms Otolin-1 is an insoluble protein present in the left ventricular extracellular matrix whose expression decreases dramatically post-myocardial infarction beginning at day 5 post-MI. The protein is localized to the gap junctions of cardiac myocytes, and depletion of protein levels in the infarcted region of the left ventricle shows strong association with ventricular dimensions, observed via echocardiography.

Matrix variate distributions present a innate way to model random matrices. Realiza- tions of random matrices are created by concurrently observing variables in different locations or at different time points. We use a finite mixture model composed of matrix variate normal densities to cluster matrix variate data. The matrix variate data was generated by accelerometers worn by children in a clinical study conducted at McMaster. Their acceleration along the three planes of motion over the course of seven days, forms their matrix variate data. We use the resulting clusters to verify existing group membership labels derived from a test of motor-skills proficiency used to assess the children’s locomotion. / Thesis / Master of Science (MSc)

An alternative gene therapy method, non-autologous somatic-gene therapy, is the use of a genetically modified universal cultured cell line that can be implanted into different allogeneic recipients. When used as recombinant cells in microcapsules, myoblasts possess several advantages over other cell types, namely their ability to terminally differentiate thus preventing overcrowding within the capsular space. However, encapsulated myoblasts demonstrate decreased proliferation and myogenic differentiation when compared to unencapsulated myoblasts due to the unnatural capsule environment. This study aims to improve the microcapsule environment by incorporating basic fibroblast growth factor (bFGF) and insulin-like growth factor-11 (IGF-11) and the extracellular matrix materials, collagen, laminin-1 and merosin (laminin-2) within the microcapsules in an attempt to mimic the natural surrounding required for myoblast growth and differentiation. While bFGF lead to significant increases in encapsulated myoblast proliferation, it did not appear to be an ideal choice for optimizing the microcapsule environment due to its inhibitory effect on differentiation and the relative cost in therapeutic delivery of proteins. Both merosin and the combination of laminin and merosin together provide a better alternative for increasing myoblast growth and survival within microcapsules since they have no apparent inhibitory effect on myogenic differentiation, and produce similar proliferative results seen when using bFGF. In terms of differentiation, the addition of IGF-11 to the microcapsules or the use of a myoblast cell line overexpressing IGF-11, aid in increasing the myogenic differentiation of encapsulated myoblasts, however, differentiation levels still do not approach those seen in unencapsulated myoblasts. The positive results obtained with the growth factors and matrix materials employed in this study are important steps towards the optimization of microcapsules by improving both the proliferation and differentiation of encapsulated myoblasts. However, more study is needed to elucidate possible solutions to the continued problem of decreased differentiation of myoblasts within APA microcapsules in order to achieve myogenic differentiation that is comparable to what is seen in unencapsulated myoblasts. / Thesis / Master of Science (MS)

Tetracycline molecules including doxycycline (DOX), consist of a group of broad-spectrum antibiotics. In addition, tetracyclines inhibit matrix metalloproteinase (MMPs) that contribute to tissue remodeling, inflammation, angiogenesis and are over-expressed in certain pathologies - such as Alzheimer’s disease, metastasis and diabetic foot ulcers (DFUs). Tetracyclines are hypothesized to inhibit MMPs through the chelation and sequestration of catalytic divalent ions such zinc and calcium. This inhibitory duality may be beneficial in pathologies that are characterized by MMP over-expression and prone to infection, such as DFUs. Compared to oral administration, topical DOX is an attractive route of administration for chronic wound healing as it may minimize the risks: associated antibiotic resistance; is being targeted directly to the wound bed. However, DOX is notoriously unstable in aqueous solution and common topical formulations. Liquid chromatography and mass spectrometry (LCMS) were employed to monitor stability using an in vitro MMP assay and an applicable E. coli anti-bacterial assay was assessed to quantify drug activity. 2 % (w/w) topical DOX demonstrated an acceptable stability 30 day when stored at 4 ºC. DOX inhibited MMP9 activity with an IC50 value of 48.27 μM. With respect to anti-bacterial activity, using cultured BL21 E.Coli and quantification of drug activity as an expression of colony forming units (CFUs) successfully reproduced the antimicrobial IC50 of doxycycline as 4.3 µM. Transdermal DOX has the potential to improve standard of care for DFUs, quality of life for the patient and reduce costs to the healthcare system. / Thesis / Master of Science (MSc) / Tetracyclines comprise of a group of broad-spectrum antibiotics; whose primary mechanism of action is inhibition of protein synthesis through binding of the bacterial ribosome. In addition, tetracyclines inhibit matrix metalloprotease (MMPs), zinc-dependent proteases that contribute to tissue remodeling, angiogenesis and are over-expressed in certain pathophysiologies such as diabetic foot ulcers (DFUs). The antibacterial mechanism of DOX on MMPs is reported and understood, however the inhibition is hypothesized to involve cation chelation. Thus, investigating this interaction is warranted to assist in developing a therapeutic for DFUs. A more logical product would involve direct topical application, such as a stable transdermal formulation of DOX.

Clustering and classification is the process of finding underlying group structure in heterogenous data. With the rise of the “big data” phenomenon, more complex data structures have made it so traditional clustering methods are oftentimes not advisable or feasible. This thesis presents methodology for analyzing three different examples of these more complex data types. The first is three-way (matrix variate) data, or data that come in the form of matrices. A large emphasis is placed on clustering skewed three-way data, and high dimensional three-way data. The second is click- stream data, which considers a user’s internet search patterns. Finally, co-clustering methodology is discussed for very high-dimensional two-way (multivariate) data. Parameter estimation for all these methods is based on the expectation maximization (EM) algorithm. Both simulated and real data are used for illustration. / Thesis / Doctor of Philosophy (PhD)