Diss. (sammanfattning) Umeå : Univ., 2004. / Härtill 3 uppsatser.

Thesis (M.S.)--University of Wisconsin, School of Nursing, 1973. / eContent provider-neutral record in process. Description based on print version record.

Thesis (Ph. D.)--University of Washington, 2001. / Vita. Includes bibliographical references (leaves 86-97).

Master of Science / Department of Statistics / Paul I. Nelson / A Bonferroni and an ordered P-value solution to the problem of controlling the experiment-wise Type I error rate are studied and compared in terms of actual size and power when carrying out correlated tests. Although both of these solutions can be used in a wide variety of settings, here they are only investigated in the context of multiple testing that specified pairwise comparisons of means, selected before data are collected, are all equal to zero in a completely randomized, balanced, one factor design where the data are independent random samples from normal distributions all having the same variance. Simulations indicate that both methods are very similar and effective in controlling experiment wise type error at a nominal rate of 0.05. Because the ordered P-value method has, almost uniformly, slightly greater power, it is my recommendation for use in the setting of this report.

This thesis investigates the functional consequences of neutralising the negative charges on the bacteriophage T7 antirestriction protein ocr. The ocr molecule is a small highly negatively charged, protein homodimer that mimics a short DNA duplex upon binding to the Type I Restriction Modification (RM) system. Thus, ocr facilitates phage infection by binding to and inactivating the host RM system. The aim of this study was to analyse the effect of reducing the negative charge on the ocr molecule by mutating the acidic residues of the protein. The ocr molecule (117 residues) is replete with Asp and Glu residues; each monomer of the homodimer contains 34 acidic residues. Our strategy was to begin with a synthetic gene in which all the acidic residues of ocr had been neutralised. This so called ‘positive ocr’ (or pocr) was used as a template to gradually reintroduce codons for acidic residues by adapting the ISOR strategy proposed by D.S.Tawfik. After each round of mutagenesis an average of 4-6 acidic residues were incorporated into pocr. In this fashion a series of mutant libraries in which acidic residues were progressively introduced into pocr was generated. A high-throughput in vivo selection assay was developed and validated by assessing the antirestriction behaviour of a number of mutants of the DNA mimic proteins wtOcr and Orf18 ArdA. Further to this, selective screening of the libraries allowed us to select clones that displayed antirestriction activity. These mutants were purified and in vitro characterisation confirmed these mutants as displaying the minimum number of acidic residues deemed critical for the activity of ocr. This in vitro process effectively simulated the evolution of the charge mimicry of ocr. Moreover, we were able to tune the high-throughput assay to different selection criteria in order to elucidate various levels of functionality and unexpected changes in phenotype. This approach enables us to map the “in vitro” evolution of ocr to identify acidic residues that are required for protein expression, solubility and function proceeding to a fully functional antirestriction protein.

The increase in waste heat after consuming energy or burning fossil fuels is an issue environmentally and economically. Thermoelectric (TE) materials are developed to use in various applications because of their ability in converting waste heat into electricity. However, the applications are limited due to a low efficiency of materials, and research on thermoelectric materials is an on-going project for future use. Type-I clathrates are one of the TE materials which are studied in depth since the proposal of Slack’s PGEC (Phonon-Glass-Electron-Crystal) concept in 1995 due to their excellent thermoelectric properties. In this study, development and optimization of quaternary type-I clathrates will be the focus because double substitution often leads to better figure-of-merit, ZT, but it hasn’t really been studied. Higher ZT value is necessary because the energy conversion efficiency of TE materials is depending on the ZT value along with a larger temperature difference. Addition of lanthanoid elements as 2nd guest atoms to the main type-I clathrate structure, realized in Ba8Ga16Ge30, will be attempted to form quaternary compounds. The formation of the quaternary clathrates will be analyzed through powder X-ray diffraction, single crystal analysis and energy dispersive X-ray analysis. Also, as the performance of TE materials is examined through the figure of merit, ZT = TS²σ/κ, various techniques will be used to determine the Seebeck coefficient, the electrical conductivity and the thermal conductivity. The quaternary clathrates, Ba8-xLnxGa16Ge30 and Ba8-xLnxGa16+xGe30-x, where Ln = La, Ce and Eu were synthesized from the pure elements in stoichiometric ratios at 1000°C with slow cooling to room temperature. The products were then annealed at 600°C to acquire homogeneous samples for analyses. The various compositions of lanthanoid were intercalated into the structure of clathrates, which resulted in the quaternary clathrates with homogeneity. The crystal structure of quaternary clathrates with the space group of Pm-3n exhibited the same structure type as the ternary clathrates. The successfully formed products were refined with Rietveld refinements to understand their structures. The Eu containing clathrates crystallized with a lattice parameter a = 10.78251(6) Å, V = 1253.60(2) ų, for x = 0.3. The Ce containing clathrates also adopted the same space group with a lattice parameter a = 10.77331(6) Å, V = 1250.40(2) ų, for x = 0.3. The La containing clathrates formed with a lattice parameter a = 10.78494(6) Å, V = 1254.45(2) ų, for x = 0.3. Between 0.2 and 1.0 lanthanoid elements per formula unit were substituted with decreasing amount of barium where the actual amount of Ln in clathrates was lower than nominal amount. All these quaternary clathrates were found to be n-type semiconductors as determined through the Seebeck coefficient and electrical conductivity measurements.

Reproduction de : Thèse de doctorat : cMicrobiologie et biocatalyse industrielles : Toulouse, INPT : 2007. / Titre provenant de l'écran-titre. Bibliogr. 236 réf.

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The increase in waste heat after consuming energy or burning fossil fuels is an issue environmentally and economically. Thermoelectric (TE) materials are developed to use in various applications because of their ability in converting waste heat into electricity. However, the applications are limited due to a low efficiency of materials, and research on thermoelectric materials is an on-going project for future use. Type-I clathrates are one of the TE materials which are studied in depth since the proposal of Slack’s PGEC (Phonon-Glass-Electron-Crystal) concept in 1995 due to their excellent thermoelectric properties. In this study, development and optimization of quaternary type-I clathrates will be the focus because double substitution often leads to better figure-of-merit, ZT, but it hasn’t really been studied. Higher ZT value is necessary because the energy conversion efficiency of TE materials is depending on the ZT value along with a larger temperature difference. Addition of lanthanoid elements as 2nd guest atoms to the main type-I clathrate structure, realized in Ba8Ga16Ge30, will be attempted to form quaternary compounds. The formation of the quaternary clathrates will be analyzed through powder X-ray diffraction, single crystal analysis and energy dispersive X-ray analysis. Also, as the performance of TE materials is examined through the figure of merit, ZT = TS²σ/κ, various techniques will be used to determine the Seebeck coefficient, the electrical conductivity and the thermal conductivity. The quaternary clathrates, Ba8-xLnxGa16Ge30 and Ba8-xLnxGa16+xGe30-x, where Ln = La, Ce and Eu were synthesized from the pure elements in stoichiometric ratios at 1000°C with slow cooling to room temperature. The products were then annealed at 600°C to acquire homogeneous samples for analyses. The various compositions of lanthanoid were intercalated into the structure of clathrates, which resulted in the quaternary clathrates with homogeneity. The crystal structure of quaternary clathrates with the space group of Pm-3n exhibited the same structure type as the ternary clathrates. The successfully formed products were refined with Rietveld refinements to understand their structures. The Eu containing clathrates crystallized with a lattice parameter a = 10.78251(6) Å, V = 1253.60(2) ų, for x = 0.3. The Ce containing clathrates also adopted the same space group with a lattice parameter a = 10.77331(6) Å, V = 1250.40(2) ų, for x = 0.3. The La containing clathrates formed with a lattice parameter a = 10.78494(6) Å, V = 1254.45(2) ų, for x = 0.3. Between 0.2 and 1.0 lanthanoid elements per formula unit were substituted with decreasing amount of barium where the actual amount of Ln in clathrates was lower than nominal amount. All these quaternary clathrates were found to be n-type semiconductors as determined through the Seebeck coefficient and electrical conductivity measurements.

Aging is amongst the strongest risk factors for neurodegenerative disease and elevated Type I interferon (IFN) signaling has been associated with both normal aging and central nervous system (CNS) diseases. Type I IFN is normally produced by nucleated cells in response to the detection of viral pathogen associated molecular patterns (PAMPs) by pathogen recognition receptors (PRRs). More recently it has been appreciated that Type I IFNs are also produced in response to endogenous stimuli, in the absence of viral pathogens. While Type I IFN signaling has been shown to be elevated in human and murine brains during normal aging, the underlying cause was unknown. Here we demonstrate by flow cytometry that aging results in increased size and numbers of mitochondria in the murine brain. Despite identifying increased mitochondrial number and mitochondrial DNA content, we found no change to mitochondrially-encoded transcripts, suggesting either deficits in mitophagy or augmented biogenesis due to insufficient oxidative phosphorylation. Interestingly, mitochondrial numbers correlated with elevated Type I IFN signaling in aging, linking mitochondria to the age-dependent innate immune response in the CNS. Using genetically engineered mice, we excluded roles for two critical innate immune pathways, STING and IRAK4, in the age-dependent increase in Type I IFN signaling in the brain. Notably, we subsequently identified a mitochondrially restricted innate immune protein, mitochondrial antiviral signaling (MAVS) as an essential molecular mediator of the age-dependent Type I IFN response; MAVS deficiency in aged mice restored Type I IFN signaling in the CNS to the levels observed in adult wildtype mice. Further, using intracerebroventricular (icv) administration of antisense oligonucleotides (ASO) as an orthogonal approach, we reduced MAVS transcript and protein expression within the CNS and thereby reduced Type I IFN signaling. Our data demonstrate a specific and selective role of MAVS expression in the CNS in Type I IFN signaling in aging. To investigate the relationship between mitochondrial aging and MAVS activation, we isolated cytoplasmic and mitochondrial RNA from young and aged animals as MAVS is most studied for its response to RNA ligands. Upon transfection into reporter cells, we found that mitochondrial RNA, but not cytoplasmic RNA, from both young and aged mice was sufficient to induce Type I IFN reporter activity in a MAVS-dependent manner. Furthermore, we attempted to mimic the increase of mitochondria observed in the aging CNS by transferring mitochondria from young and aged animals to recipient cells. Mitochondrial transfer also induced MAVS-dependent Type I IFN signaling in wildtype, but not MAVS null, mouse embryonic fibroblasts (MEFs). Collectively, our findings suggest that the accumulation of mitochondria in aging serves as a robust source of MAVS pathway ligands and implicate a novel link between mitochondrial aging and MAVS-mediated innate immune signaling in the CNS.