The cellular prion protein (PrPC) is unique amongst mammalian proteins in that it not only has the capacity to aggregate (in the form of scrapie PrP; PrPSc) and cause neuronal degeneration, but can also act as an independent vector for the transmission of disease from one individual to another of the same or, in some instances, other species. Since the discovery of PrPC nearly thirty years ago, two salient questions have remained largely unanswered, namely, (i) what is the normal function of the cellular protein in the central nervous system, and (ii) what is/are the factor(s) involved in the misfolding of PrPC into PrPSc? To shed light on aspects of these questions, we undertook a discovery-based interactome investigation of PrPC in mouse neuroblastoma cells (Chapter 2), and among the candidate interactors, identified two members of the ZIP family of zinc transporters (ZIP6 and ZIP10) as possessing a PrP-like domain. Detailed analyses revealed that the LIV-1 subfamily of ZIP transporters (to which ZIPs 6 and 10 belong) are in fact the evolutionary ancestors of prions (Chapter 3). We were further able to demonstrate that PrPC likely emerged from a ZIP ancestor molecule nearly half-a-billion years ago via a retrotransposition event (Chapter 4). Moreover, biochemical investigations on ZIP10, as a model LIV-1 ZIP transporter, demonstrated that the ectodomain shedding of ZIP10 observed in prion-infected mice resembles a cellular response to transition metal starvation and suggested that prion disease in mice might phenocopy a transition metal starvation status (Chapter 5). These studies have opened a new angle to study prion biology in health and disease. Biochemical investigations on other LIV-1 ZIPs and attempts at the structural elucidation of the PrP-like domain of LIV-1 ZIP proteins are ongoing and have not been included in this thesis.

SUR2A is a member of the ABC transporter superfamily. SUR2A mediated regulation of KATP channels is essential as mutations in the nucleotide binding domains (NBDs) of SUR2A are associated with cardiovascular disorders. Studies of eukaryotic NBDs, such as SUR2A, are hindered by low solubility of the isolated domain. We hypothesized that the solubility of heterologously expressed SUR2A NBDs depends on the definition of the domain boundaries. Boundaries were initially predicted using a combination of a structure-based sequence alignment and homology modeling, and subsequently verified by testing the solubility of five SUR2A NBD1 constructs with different N- or C-terminal boundaries. The boundaries of SUR2A NBD1 essential for solubility were identified. CD and NMR data indicate that SUR2A NBD1 is folded. Our method may be applied as a general method for developing suitable constructs of other NBDs of ABC proteins such as SUR isoforms, SUR2B and SUR2C, and the vacuolar transporter, Ycf1p.

ATP-sensitive potassium (KATP) channels have crucial roles in several biological processes. KATP channels possess four regulatory sulfonylurea receptors. The SUR proteins are members of the ubiquitous ATP-binding cassette (ABC) superfamily. However, unlike most ABC proteins, SURs do not transport substrates but function strictly as regulators of KATP channel activity. Currently, studies into the molecular basis by which various mutations in SUR2A cause disease are highly limited. This is primarily a consequence of poor solubility of isolated SUR2A NBDs, as is typical for many eukaryotic NBDs. By employing structure-based sequence alignments and biophysical studies, we determined domain boundaries for SUR2A NBD1 that enabled, for the first time, NMR studies of NBD1. Our biophysical studies demonstrate that the isolated SUR2A NBD1 is folded and exhibits differential dynamics upon ATP binding activity. Additional studies are now possible to examine the effects of disease-causing mutations on structure, dynamics, and interactions of NBD1.

SUR2A is a member of the ABC transporter superfamily. SUR2A mediated regulation of KATP channels is essential as mutations in the nucleotide binding domains (NBDs) of SUR2A are associated with cardiovascular disorders. Studies of eukaryotic NBDs, such as SUR2A, are hindered by low solubility of the isolated domain. We hypothesized that the solubility of heterologously expressed SUR2A NBDs depends on the definition of the domain boundaries. Boundaries were initially predicted using a combination of a structure-based sequence alignment and homology modeling, and subsequently verified by testing the solubility of five SUR2A NBD1 constructs with different N- or C-terminal boundaries. The boundaries of SUR2A NBD1 essential for solubility were identified. CD and NMR data indicate that SUR2A NBD1 is folded. Our method may be applied as a general method for developing suitable constructs of other NBDs of ABC proteins such as SUR isoforms, SUR2B and SUR2C, and the vacuolar transporter, Ycf1p.

ATP-sensitive potassium (KATP) channels have crucial roles in several biological processes. KATP channels possess four regulatory sulfonylurea receptors. The SUR proteins are members of the ubiquitous ATP-binding cassette (ABC) superfamily. However, unlike most ABC proteins, SURs do not transport substrates but function strictly as regulators of KATP channel activity. Currently, studies into the molecular basis by which various mutations in SUR2A cause disease are highly limited. This is primarily a consequence of poor solubility of isolated SUR2A NBDs, as is typical for many eukaryotic NBDs. By employing structure-based sequence alignments and biophysical studies, we determined domain boundaries for SUR2A NBD1 that enabled, for the first time, NMR studies of NBD1. Our biophysical studies demonstrate that the isolated SUR2A NBD1 is folded and exhibits differential dynamics upon ATP binding activity. Additional studies are now possible to examine the effects of disease-causing mutations on structure, dynamics, and interactions of NBD1.

The protein SiaA (Streptococcal iron acquisition) is involved in heme uptake in the bacterium Streptococcus pyogenes. It is difficult to obtain this protein in its fully holo form (completely loaded with heme). To increase the concentration of heme in the growing cell, we added ä-aminolevulinic acid (ALA) and ferrous sulfate (FeSO4), precursors of heme, to the growth media. Neither increasing the concentration of heme in vivo, nor growth at lower temperature for longer times, increased the production of holoprotein. The classical method of measuring the concentration of heme in a newly discovered heme protein is cumbersome. We have developed an improved method, which gives a solution that is more stable and has a cleaner spectrum. With further development, this new technique may replace the classical assay. Background information on S. pyogenes, SiaA, ABC transporters, heme biosynthesis, and the pyridine hemochrome assay are described.

Lignin is a key component of plant secondary cell walls, providing strength to the plant and allowing water transport. Lignin is a polymer of monolignols that are synthesized in the cell and transported into the cellulose rich cell wall. The primary goal of this thesis is to understand the mechanism(s) of monolignol deposition during xylogenesis. The currently accepted theory is that monolignols are exported by Golgi-mediated vesicle delivery to the secondary cell wall. When this theory was re-examined using cryofixed developing pine, quantitative autoradiography showed that monolignols did not accumulate in Golgi but were rapidly translocated from cytosol to cell wall. This suggests alternative mechanisms, such as membrane transporters, work in monolignol export. ATP binding cassette (ABC) transporters were chosen because they transport other secondary metabolites and some ABC transporter encoding genes are highly expressed in lignifying cells. Four candidate ABC transporters were selected in Arabidopsis (ABCB11, ABCB14, ABCB15 from the ABCB/MDR subfamily and ABCG33 from the ABCG/PDR subfamily) and shown to have overlapping, high vasculature expression patterns. Mutants with T-DNA insertions in single ABC transporter genes had no change in lignification of inflorescence stems. However, a reduced polar auxin transport phenotype was detected in mutants of ABCB11, ABCB14 and ABCB15. An additional approach was the use of inhibitors of ABC transporters. A new assay, which was developed to quantify lignification in primary xylem of Arabidopsis roots, demonstrated that ABC inhibitors did not change lignin deposition. Monolignols are exported and polymerized in the polysaccharide matrix of the cell wall, which includes hemicelluloses that may organize monolignols during polymerization. Since diverse lignified cell types are enriched in either G- or S-lignin, I hypothesized that this pattern could reflect different hemicellulose distributions, which was examined using antibody labeling of xylans or mannans in hybrid poplar xylem. While xylans were generally distributed in all secondary cell walls, mannans were enriched in fibers but not in the ray and vessel walls. In summary, during secondary cell wall deposition, monolignols are exported by unknown transporter(s) rather than Golgi vesicles. In developing poplar wood, the monolignols are deposited into diverse hemicellulose domains in different cell types.

Transporters dynamically expressed at the mammary gland transport critical nutrients into the breast milk of nursing mothers to meet the nutritional demands of the suckling infant. However, xenobiotics may interact with these transporters to potentially alter the nutrient composition of milk and compromise neonatal nutrition. The aim of the present study was to quantitatively evaluate the constitutive expression of various nutrient transporters in whole mammary gland tissue and mammary epithelial organoids (MEO) isolated from female Sprague-Dawley rats at various stages of pregnancy, lactation, and involution. Furthermore, the studys aim was to determine if appropriately cultured mammary epithelial organoids (MEO) maintain in vivo transporter expression to lay down critical groundwork for the development of an in vitro screening tool assessing xenobiotic-nutrient transporter interactions. The following transporters were evaluated using quantitative real-time reverse transcription polymerase chain reaction (QRT-PCR): multidrug resistance protein (Mdr) 1a, 1b; multidrug resistance-like protein (Mrp) 1; organic cation transporter (Oct) 1; organic cation/carnitine transporter (Octn) 1, 2, and 3; concentrative nucleoside transporter (Cnt) 1, 2, and 3; equilibrative nucleoside transporter (Ent) 1, 2, and 3; nucleobase transporter (Ncbt) 1 and 2; oligopeptide transporter (Pept) 1 and 2; methotrexate carrier (Mtx) 1; divalent metal transporter (Dmt) 1; and the milk protein ?-casein. Transporter expression patterns in MEO differed from whole tissue for ?-actin, Mdr1a, Mdr1b, Oct1, Octn3, Ent3, Cnt1, Cnt3, Ncbt1, Pept2, Mtx1, and ?-casein. This brings into question whether whole mammary gland tissue is truly appropriate for an understanding of transporter expression in the mammary epithelium. Nevertheless, four general transporter expression patterns emerged in isolated MEO: decline throughout lactation (Mdr1a, Mdr1b, Mrp1 & Dmt1), increase throughout lactation (Cnt1 & Octn3), increase in early lactation (Oct1, Octn2, Ent1, Cnt2, Cnt3, Pept2 & Mtx1) and constant expression throughout lactation (Octn1, Ent2, Ent3, Ncbt1, Ncbt2 & Pept1). These expression patterns will provide insight into the critical windows of nutrient delivery to the breast milk to provide adequate nutritional stimuli to the suckling infant. Furthermore, MEO cultured in an extracellular matrix-rich environment maintained transporter expression at the mRNA level, which underscores the potential of the primary MEO in vitro model system as a screening tool for xenobiotic-transporter interactions at the mammary gland. Transporter expression patterns in MEO were unique for each transporter evaluated. This information accompanied by an in vitro screening tool may allow for predictions of xenobiotic interference with breast milk composition to help safeguard infant health.

Zinc (Zn) is an essential micronutrient for the growth and development of all organisms. Zinc deficiency is a widespread micronutrient disorder worldwide, which reduces crop yields and the nutritive value of the grain. Understanding the process of zinc absorption and translocation in crop is essential for this purpose. Zinc is taken up by plants and translocated within plants through high-affinity zinc transporter proteins embedded in the plasma membrane. The Zn transporters are induced under Zn deficiency, and it is speculated that the expression levels of some of zinc transporters are critical for improved tolerance to low zinc. A number of Zn transporters have been cloned from higher plants including rice and Arabidopsis, but little has been done in barley and wheat. This project aims to investigate genes involveld in zinc efficiency mechanism by complementation analysis in yeast, which is double mutant of zinc-transporters, using cDNA expression library from a most zinc efficient barley cultivar, Tokak-157.

Queueing network-based approximation models were developed to evaluate the performance of fixed-route material-handling systems supporting a multiple workcenter manufacturing facility. In this research, we develop analytical models for fixed-route material-handling systems from two different perspectives: the workcenters?? point of view and the transporters?? point of view. The state-dependent nature of the transportation time is considered here for more accurate analytical approximation models for material-handling systems. Also, an analytical methodology is developed for analytical descriptions of the impact of several different vehicledispatching policies for material-handling systems. Two different types of vehicledispatching policies are considered. Those are workcenter-initiated vehicle dispatching rules and vehicle-initiated vehicle dispatching rules. For the workcenterinitiated vehicle dispatching rule, the Closest Transporter Allocation Rule (CTAR) was used to assign empty transporters to jobs needing to be moved between various workcenters. On the other hand, four different vehicle-initiated vehicle dispatching rules, Shortest Distance Dispatching Rule (SDR), Time Limit/Shortest DistanceDispatching Rule (TL/SDR), First-Come First-Serve Dispatching Rule (FCFSR), Longest Distance Dispatching Rule (LDR), are used to select job requests from workcenters when a transporter is available. From the models with a queue space limit of one at each workcenter and one transporter, two different types of extensions are considered. First, the queue space limit at each workcenter is increased from one to two while the number of transporters remains at one. Second, the number of transporters in the system is also increased from one to two while maintaining the queue space limit of one at each workcenter. Finally, using a simulation approach, we modified the Nearest Neighbor (NN) heuristic dispatching procedure for multi-load transporters proposed by Tanchoco and Co (1994) and tested for a fixed-route material-handling system. The effects of our modified NN and the original NN transporter dispatching procedures on the system performance measures, such as WIP or Cycle Time were investigated and we demonstrated that the modified NN heuristic dispatching procedure performs better than the original NN procedure in terms of these system performance measures.