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Thesis (doctoral)--Helsinki University of Technology, 2004. / Includes bibliographical references. Also available on the World Wide Web.

No description available.

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The ultimate intent of this research program is to produce nanosized magnetic tunneling junctions, and to study the physical properties of such devices. The physical phenomena of nanosized tunneling junctions are significantly different than that of currently popular micro-sized junctions. There is a considerable amount of work that must be done prior to producing these new junctions to ensure that good measurements can be carried out once the structures have been built. This thesis describes the efforts taken to design a measurement platform that will accurately measure tunneling magnetoresistance (TMR) in nanosized Magneto-tunneling Junctions (MTJ). The testing done with this system at various stages throughout the design and testing process confirm the expectations for the performance of the system. Voltage-current measurements can be performed on objects ranging from a few nanometers in size to micrometer sized. Traditional micro-sized MTJs have not been excluded in this design.

The passage of fluid, ions and macromolecules across the epithelium is controlled primarily by epithelial tight junctions. Altered epithelial permeability is associated with lung disease, and barrier function is impaired by the Th2 cytokine IL-13. This thesis investigates the signalling pathways involved in the modulation of the epithelial barrier by IL-13 stimulation. Initial experiments demonstrated that the human sub-bronchial epithelial cell line Calu-3 could be easily manipulated when grown using an air-liquid culture system. Expression of various key tight junction proteins was demonstrated, as well as a high trans-epithelial resistance (TER) for up to 7 days. Stimulation with IL-13 resulted in a decrease in TER compared with controls and this decrease was shown to be prevented with the PI3K inhibitor ZSTK474. IL-13 did not increase paracellular permeability of the epithelial monolayer to FITC-dextran from the apical to the basolateral chamber and ZSTK474 did not influence FITC-dextran flux. Immunocytochemistry showed that the expression of the tight junction protein claudin 2 was increased by IL-13 stimulation and this change in expression was shown to be PI3K dependent with the PI3K inhibitor ZSKT474 preventing the increase. Further studies were carried out in an attempt to uncover the PI3K isoform responsible for the effects seen on both the TER and the TJ expression. It was shown that inhibition of the p110α isoform with PIK75 mimicked the result observed with the pan-PI3K inhibitor ZSTK474 and prevented the IL-13-induced claudin 2 upregulation. However none of the PI3K isoform inhibitiors showed the prevention of TER, as shown by the pan PI3K inhibitor ZSTK474. The role of STAT6 in TJ modulation was shown to be similar to that of PI3K, in that inhibition of STAT6 had a positive effect on the epithelial barrier by preventing the IL-13-induced TER decrease and the increase in the expression of claudin 2. In addition, both PI3K inhibition and STAT6 inhibition demonstrated effects on basal TER and claudin 2 expression, indicating that both pathways are involved in maintenance of epithelial barrier integrity.

Four-stranded DNA junctions (also known as Holliday junctions) are structural intermediates involved in a growing number of biological processes including DNA repair, genetic recombination, and viral integration. Although previous studies have focused on understanding the conformational variability and sequence-dependent formation of Holliday junctions in solution there have been relatively few insights into junction structure at the atomic level. Recent crystallographic studies have demonstrated that the more compact stacked-X junction form has an antiparallel alignment of DNA strands and standard Watson-Crick base pairs across the central crossover region. Junction formation within this crystallographic system was seen to be dependent on a common trinucleotide sequence motif ("ACC-triplet" at the 6th, 7th and 8th positions of the decanucleotide sequence d(CCnnnN₆N₇N₈GG)) containing a series of stabilizing direct and solvent-mediated hydrogen bonding interactions. This thesis addresses questions concerning the nucleotide sequence-dependent formation and conformational variability of DNA Holliday junctions as determined by single crystal x-ray diffraction. We have used the modified bases 2,6-diaminopurine and inosine to demonstrate that minor groove interactions adjacent to the trinucleotide junction core are not major contributors to overall conformation. In addition, incorporation of guanine into the sixth position of this core does not have a significant effect on junction geometry. Meanwhile, incorporation of 5-bromouracil into the eighth position perturbs the geometry in terms of the interduplex angle as well as the defined conformational variables, J[subscript roll] and J[subscript slide]. These novel junction structures demonstrate that the nucleotide sequence within the central core generates a position specific relationship between molecular interactions at the junction crossover and overall structural geometry. A systematic crystallographic screen of the trinucleotide core region is presented here as an unbiased, comprehensive, search for sequences that stabilize junctions. As the result of this screen, we can extend the core sequence motif to 'N₆Y₇C₈' where N₆ is an adenine, guanine, or cytosine nucleotide and Y₇ is either a cytosine or thymine (if N₆ = adenine) nucleotide. Using these novel junction structures, we demonstrate that base sequence within the central core has a significant effect on the overall geometry of the junction. Thus, this central region of the structure may serve as a linchpin for determining the local and global conformation and overall variability of the four-stranded DNA Holliday junction. These observations raise some interesting questions regarding the importance of this core region in biological processes such as genetic recombination. / Graduation date: 2005

Thesis (M. Phil.)--University of Hong Kong, 2002. / Includes bibliographical references (leaves 102-107).