Biological transport is an essential phenomenon for the living systems. A mechanistic investigation of biological transport processes is highly important for the characterization of physiological and cellular events, the design and functioning of several biomedical devices and the development of new therapies. To investigate the physical-chemical details of this phenomenon, concerted efforts of both experiments and theory are necessary. Motor proteins constitute a major portion of the active transport in the living cell. However, the actual mechanism of how chemical energy is converted into their directed motion has still remained obscure. Recent experiments on motor proteins have been producing exciting results that have motivated theoretical studies. In order to provide deep insight onto motor protein's mechanochemical coupling we have used stochastic modeling based on discrete-state chemical kinetic model. Such models enable us to (1) resolve the contradiction between experimental observations on heterodimeric kinesins and highly popular hand-over-hand mechanism, (2) take into account the free energy landscape modification of individual motor domains due to interdomain interaction, (3) recognize the effect of spatial fluctuations on biochemical properties of molecular motors, and (4) calculate the dynamical properties such as velocities, dispersions of complex biochemical pathways. We have also initiated the investigation of the dynamics of coupled motor assemblies using stochastic modeling. Furthermore, an extensive Monte Carlo lattice simulation based study on facilitated search process of DNA-binding proteins is presented. This simulation shows that the accelerated search compared to pure Smoluchowski limit can be achieved even in the case where the one-dimensional diffusion is order of magnitude slower than the three-dimensional diffusion. We also show that facilitated search is not only the manifestation of dimensionality reduction but correlation times play a crucial role in the overall search times. Finally, a more general field of stochastic processes, namely first-passage time process is investigated. Explicit expressions of important properties, such as splitting probailities and mean first-passage times, that are relevant to (but not limited to) biological transport, are derived for several complex systems.

The human wildtype p53 tumor suppressor gene is found in two different forms, p53 Arginine and p53 Proline. This difference results in a substitution of a proline for an arginine at codon 72 producing the polymorphism. Knowing that apoptosis and cell cycle arrest are the two main functions of p53, the objective of this project was to determine the difference in the capacity of these allelic variants of p53 to induce apoptosis and/or cell cycle arrest in two different experimental model systems. The first experimental system was composed of non-transformed 10(1) cells and the second one was transformed Saos-2 cells. In the first experimental system, the two wildtype forms of p53 induced cell cycle arrest at the same level and did not induce apoptosis. On the other hand, in transformed cells, both p53Arg and p53Pro induced apoptosis at similar levels. No cell cycle arrest activity has been detected in Saos-2 cells. In conclusion, this study suggests that the induction of cell cycle arrest or apoptosis depends more on the cell type than on the type of the p53 protein. Also, the intensity of cell cycle arrest or apoptosis is independent of which allelic variant of p53 is present under the experimental conditions used in this study.

Despite a century of research, the evolutionary origin of angiosperms remains uncertain. Morphological studies have identified the gnetophytes as the sister group of angiosperms mainly because of the similar organization of their reproductive structures. Molecular studies have been ambiguous as to whether these two groups are closely related. Study of the development of seed plant reproductive structures can help to untangle this issue. Here, I report the cloning of five MARS-box floral homeotic gene homologues from the gnetophyte Ephedra andina. Three of these genes belong to AG, AGL6 and TM3 subfamilies. These monophyletic groups comprise angiosperm as well as conifer homologues. Phylogenetic analysis of the plant MADS-box gene family reveals that within subfamilies, Ephedra genes always form subclades with other gymnosperm genes to the exclusion of all angiosperm genes. These results suggest that gnetophytes are more closely related to conifers than to angiosperms.

Thesis (Ph. D.)--University of Hong Kong, 2007. / Also available online.

Diss. (sammanfattning) Stockholm : Karol. inst., 2003. / Härtill 5 uppsatser.

Dissertation (Ph.D.).--University of Texas Graduate School of Biomedical Sciences at San Antonio, 2007. / Vita. Includes bibliographical references.

Thesis (Ph.D.). / Written for the Dept. of Pharmacology and Therapeutics. Title from title page of PDF (viewed 2008/07/23). Includes bibliographical references.

Thesis (Ph. D.)--University of Missouri-Columbia, 2007. / The entire dissertation/thesis text is included in the research.pdf file; the official abstract appears in the short.pdf file (which also appears in the research.pdf); a non-technical general description, or public abstract, appears in the public.pdf file. Vita. "August 2007" Includes bibliographical references.

Thesis (Ph.D.)--University of Missouri-Columbia, 2006. / The entire dissertation/thesis text is included in the research.pdf file; the official abstract appears in the short.pdf file (which also appears in the research.pdf); a non-technical general description, or public abstract, appears in the public.pdf file. Title from title screen of research.pdf file (viewed on April 27, 2009) Vita. Includes bibliographical references.

Thesis (Ph. D.)--University of Oklahoma. / Includes bibliographical references.