The thresholding problem is important in today’s data-rich research scenario. A threshold is a well-defined point in the data distribution beyond which the data is highly likely to have scientific meaning. The selection of threshold is crucial since it heavily influences any downstream analysis and inferences made there from. A legitimate threshold is one that is not arbitrary but scientifically well grounded, data-dependent and best segregates the information-rich and noisy sections of data. Although the thresholding problem is not restricted to any particular field of study, little research has been done. This study investigates the problem in context of network-based analysis of transcriptomic data. Six conceptually diverse algorithms – based on number of maximal cliques, correlations of control spots with genes, top 1% of correlations, spectral graph clustering, Bonferroni correction of p-values and statistical power – are used to threshold the gene correlation matrices of three time-series microarray datasets and tested for stability and validity. Stability or reliability of the first four algorithms towards thresholding is tested upon block bootstrapping of arrays in the datasets and comparing the estimated thresholds against the bootstrap threshold distributions. Validity of thresholding algorithms is tested by comparison of the estimated thresholds against threshold based on biological information. Thresholds based on the modular basis of gene networks are concluded to perform better both in terms of stability as well as validity. Future challenges to research the problem have been identified. Although the study utilizes transcriptomic data for analysis, we assert its applicability to thresholding across various fields.

Vitronectin is a multifunctional glycoprotein involved in regulation of such processes as hemostasis, cell migration, immunity, and tumor metastasis. Many of its functions require interaction with various binding partners. One such partner, plasminogen activator inhibitor-type 1 (PAI-1), belongs to the serine protease inhibitor (serpin) superfamily of proteins. PAI-1 helps regulate hemostasis by affecting blood clot breakdown, and helps regulate cell migration and tissue remodeling by affecting extracellular matrix digestion. Our laboratory is pursuing structural information on vitronectin and the complex formed between vitronectin and PAI-1. To this end, the work presented in this thesis focuses on two aims: characterizing the interaction of vitronectin and PAI-1 with metal ions, and developing reagents to be used in structural studies of vitronectin. We have used electron paramagnetic resonance (EPR) spectroscopy to study metal binding by vitronectin and PAI-1. We have tested vitronectin and PAI-1 for binding of Mn2+ and Cu2+, and also established the feasibility of studying protein-Cu2+ interaction in solution by EPR, using bovine serum albumin (BSA) and Cu2+. In another set of experiments, we have used activity assays to assess the effect of metal ions on PAI-1 activity and on stabilization of PAI-1 by vitronectin. Regarding reagents, we have expressed and purified active, perdeuterated PAI-1, which can be used in complex with vitronectin in neutron scattering and NMR experiments. We characterized several monoclonal antibodies to vitronectin, and identified one suitable for use in co-crystallization screens. These accomplishments will aid in development of a more detailed picture of the interaction between vitronectin and PAI-1.

The recent completion of the sequencing of several species of the <em>Shewanella</em> genus provides a unique opportunity for comparative genomics studies. We chose the first 10 fully sequenced Shewanella genomes to investigate the evolution of signal transduction proteins (ST). ST is a universal and highly regulated system, and as a very well-studied system provides an excellent starting point for investigation. Furthermore, Shewanella have been shown to have a large number of two-component systems and diguanylate cyclases relative to their genome size. In this study we investigate the evolution of signal transduction across several Shewanella strains by utilizing a domainlevel approach for determining homology and orthology of the parent proteins. Proteins were broken down into their constituent domains and domain sized sequences and compared using a reciprocal best BLAST hit approach to determine homology between all of the species. Analysis of homologous domains and proteins revealed several levels of conservation and a core group of signal transduction proteins common to all members. Further analysis of domain homology provided putative annotations of previously unrecognized sequences and highlighted deficiencies in specific Pfam domain models. Analysis of paralogous domains and proteins showed agreement with 16s rRNA based estimates of evolution, although the position of S. oneidensis MR-1 was novel.

Thesis (doctoral)--Universität Göttingen, 1967.

Inaug.-diss.--München. / "Literatur-verzeichnis": p. 89-[91].

Thesis (Th. M.)--Dallas Theological Seminary, 2003. / Includes bibliographical references (leaves 62-67).

Issued also as thesis, Universit́e de Paris.

Issued also as Diss. - Zürich. / "Literatur": p. xx-xxv.

Thesis--Copenhagen.

The editor's proefschrift--Utrecht. / Text in Latin and Dutch; four versions, according to two Latin and two early Dutch manuscripts. Issued also as Neerlandica Traiectina, v. 10. Includes bibliographical references.