Physical Sciences and Mathematics Commons^™

Biological Sequence Simulation For Testing Complex Evolutionary Hypotheses: Indel-Seq-Gen Version 2.0, Cory L. Strope

Department of Computer Science and Engineering: Dissertations, Theses, and Student Research

Reconstructing the evolutionary history of biological sequences will provide a better understanding of mechanisms of sequence divergence and functional evolution. Long-term sequence evolution includes not only substitutions of residues but also more dynamic changes such as insertion, deletion, and long-range rearrangements. Such dynamic changes make reconstructing sequence evolution history difficult and affect the accuracy of molecular evolutionary methods, such as multiple sequence alignments (MSAs) and phylogenetic methods. In order to test the accuracy of these methods, benchmark datasets are required. However, currently available benchmark datasets have limitations in their sizes and evolutionary histories of the included sequences are unknown. These …

Exchange Coupling At Cobalt/ Nickel Oxide Interfaces, Andrew G. Baruth

Department of Physics and Astronomy: Dissertations, Theses, and Student Research

Spin arrangement at interfaces in layered magnetic materials is of vital importance to the emerging field of spintronics. Knowledge of how and why the interfacial spins behave in a certain way will aid in the development of future magnetic-based memories.

Much exploration has taken place in the interlayer exchange coupling (IEC) of ferromagnetic heterostructures with in-plane anisotropy. Only recently has it become apparent that to achieve the goals of increased areal density in magnetic memory a push for exploring magnetic materials with perpendicular magnetic anisotropy (PMA) must occur. An interesting and promising candidate for such a magnetic system is [Co/Pt]/NiO/[Co/Pt], …

N- And C-Terminal Domains In Human Holocarboxylase Synthetase Participate In Substrate Recognition, Yousef I. Hassan, Hideaki Moriyama, Lars J. Olsen, Xin Bi, Janos Zempleni

Hideaki Moriyama Publications

Holocarboxylase synthetase (HCS) catalyzes the binding of the vitamin biotin to carboxylases and histones. Carboxylases mediate essential steps in macronutrient metabolism. For example, propionyl- CoA carboxylase (PCC) catalyzes the carboxylation of propionyl-CoA in the metabolism of oddchain fatty acids. HCS comprises four putative domains, i.e., the N-terminus, the biotin transfer/ATP binding domain, a putative linker domain, and the C-terminus. Both N- and C-termini are essential for biotinylation of carboxylases by HCS, but the exact functions of these two domains in enzyme catalysis are unknown. Here we tested the hypothesis that N- and C-termini play roles in substrate recognition by HCS. …