Transmissible spongiform encephalopathy (TSE) strains are defined by their biological properties on transmission to wild-type mice, specifically by their characteristic incubation periods and patterns of vacuolar pathology (‘lesion profiles’) in the brain. Whilst a single TSE strain has been identified in variant Creutzfeldt-Jakob disease (vCJD), the phenotypic heterogeneity observed in sporadic CJD (sCJD) implies the existence of multiple strains of agent. These distinct strains are proposed to be enciphered by the different conformers of abnormal prion protein (PrP), recognised as different protease resistant PrP (PrPres) types by Western blotting (type 1 or type 2) and are thought to be substantially influenced by the different prion protein gene (PRNP) codon 129 polymorphism (MM, MV and VV). To test the relationship between disease phenotype and agent strain, this study carried out a full characterisation of the sCJD agent by primary transmission of brain tissue from 27 sCJD cases (comprising all six possible combinations of PRNP codon 129 genotype and PrPres type) in panels of wild-type mice using the standard strain typing properties of incubation period and lesion profiles, plus a full analysis of PrP in the mouse brain and the PrPres molecular subtypes present. Results were directly compared with the transmission characteristics of brain tissue from 10 vCJD cases. The characterisation of the agent strain in sCJD and vCJD was extended to include analysis of subsequent mouse-to-mouse passages. In an additional investigation, wild-type mice were experimentally challenged with a wide-range of lymphoid tissues, neural tissues and biological fluids from vCJD and sCJD patients in order to investigate the extent of peripheral involvement in CJD and to determine whether the agent is subject to any tissue-specific modifications. Analysis of all 27 sCJD sources demonstrated the existence of two strains of agent, one associated with the MM1/MV1 subgroups and the other associated with the MM2 subgroup, which could be distinguished by their transmission properties in the mice. The lack of transmission in mice challenged with VV1, MV2 and VV2 tissues provided evidence of at least one further sCJD strain. In contrast, all 10 vCJD sources resulted in consistent incubation periods and lesion profiles, suggesting that all 10 patients investigated were infected with the same strain of agent. Overall, the observation that PrPres type in sCJD and vCJD was maintained on transmission is consistent with the proposition that PrPres type plays a role in enciphering strain-specific information. Experimental transmissions from peripheral tissues extended the evidence for a peripheral infection in vCJD. However, comparison of incubation periods and lesion profiles from transmission of brain and peripheral tissues showed no evidence of tissue-specific modification in the biological properties of the agent. Furthermore, the detection of low levels of infectivity in a sCJD buffy coat sample provides supporting evidence for a peripheral involvement in sCJD. This study highlights the complex relationship between disease phenotype, PRNP codon 129 genotype, PrPres type and agent strain in sCJD and vCJD. Overall, this study confirms that multiple strains of agent are associated with sCJD, some of which successfully propagate in wild-type mice but none of which are identical to the agent responsible for vCJD. Importantly, the sCJD strains identified here by their biological properties partially correlated with the current sub-classification system for sCJD which is based on the clinical and pathological phenotype of the disease.

Protein-protein interactions (PPI’s) play important roles in biological systems. In particular, intra-protein interactions help create and maintain correctly folded protein states and mutations that result in misfolded states may be associated with significant changes in PPI behavior. Six unrelated protein systems with known structure files, each consisting of a wild-type and mutant strain, were studied using the computational algorithm OpenContact©. OpenContact© is a simple tool that can be used to rapidly identify or map interactions “hot-spots” in a protein and was, consequently, used in this study as a starting point to examine the potential or possible role of PPI’s on the behavior of mutated, misfolded proteins. Specific results include the observations of single chain protein systems exhibiting mutant strains with significantly stronger inter-atomic interactions as well as a surprising gain of secondary structure in the mutant state. These observations stood in contrast to multi-chain systems (proteins with more than two constituent chains) that appeared to display stronger inter-atomic interactions for the wild-type strains. Results also indicated a potential classification scheme for intra-protein interaction behavior in mutated states based on several criteria. It is important to note, however, that observations on PPI behavior presented need to be verified across a greater number of systems than those studied here before any such trends can be concretely established.

Systemic amyloidoses are a group of lethal diseases where proteins aggregate into fibrillar structures, called amyloid fibrils, that deposits throughout the body. Transthyretin (TTR) causes one type of amyloidosis, in which the aggregates mainly infiltrate nervous and cardiac tissue. Almost a hundred different mutations in the TTR gene are known to trigger the disease, but wild-type (wt) TTR is also incorporated into the fibrils, and may alone form amyloid. Patients with the TTRV30M mutation show, for unknown reasons, two clinical phenotypes. Some have an early onset of disease without cardiomyopathy while others have a late onset and cardiomyopathy. It has previously been described that amyloid fibrils formed from TTRV30M can have two different compositions; either with truncated molecules beside full-length TTR (type A) or only-full-length molecules (type B).  In this thesis, the clinical importance of the two types of amyloid fibrils was investigated. We found that the fibril composition types are correlated to the two clinical phenotypes seen among TTRV30M patients, with type A fibrils present in late onset patients and type B fibrils in early onset patients. The only treatment for hereditary TTR amyloidosis has been liver transplantation, whereby the liver producing the mutant TTR is replaced by an organ only producing wt protein. However, in some patients, cardiac symptoms progress post-transplantationally. We demonstrated that the propensity to incorporate wtTTR differs between fibril types and tissue types in TTRV30M patients, with cardiac amyloid of type A having the highest tendency. This offers an explanation to why particularly cardiac amyloidosis develops after transplantation, and suggests which patients that are at risk for such development. By examining patients with other mutations than TTRV30M, we showed that, in contrast to the general belief, a fibril composition with truncated TTR is very common and might even be the general rule. This may explain why TTRV30M patients often have a better outcome after liver transplantation than patients with other mutations. In conclusion, this thesis has contributed with one piece to the puzzle of understanding the differences in clinical phenotype and treatment response between TTR amyloidosis patients, by demonstrating corresponding differences at a molecular level.

Background: Clinical breakpoints and epidemiological cut-off values for N. gonorrhoeae azithromycin antimicrobial susceptibility testing have not been established. This study utilized existing minimum inhibitory concentration (MIC) data from CDC’s Gonococcal Isolate Surveillance Project (GISP) to establish epidemiological cut-off values for azithromycin and N. gonorrhoeae as determined by agar dilution. Methods: MIC distributions for the pooled dataset and each data year (2005-2012) were constructed. Epidemiological cut-off values were calculated using two methods. Method 1 considers the wild-type MIC distribution, the modal MIC for the distribution, and the inherent variability of the test (±1 twofold-dilution). Method 2 defines the epidemiological cut-off value as two twofold-dilutions higher than the MIC50. Results: Taking into consideration the wild-type MIC distributions and the inherent variability of the test, the epidemiological cut-off value chosen for the pooled dataset and each data year using Method 1 was ≤1.0 µg/mL. The MIC50 for the pooled dataset and each data year was 0.25 µg/mL. Two twofold-dilutions higher than the MIC50 (0.25 µg/mL) for the pooled dataset and each data year was 1.0 µg/mL. Discussion: The epidemiological cut-off values chosen using Methods 1 and 2 (≤1.0 µg/mL) were identical for the pooled dataset and each data year, indicating the epidemiological cut-off value has not changed from 2005-2012. The epidemiological cut-off value for N. gonorrhoeae azithromycin agar dilution antimicrobial susceptibility testing established during this study can be used to help set clinical breakpoints and identify isolates with reduced susceptibility to azithromycin.

The discovery that proprotein convertase subtilisin/kexin type 9 (PCSK9) mediates degradation of low-density lipoprotein receptors (LDLR) indicates a critical role in LDL metabolism. PCSK9 is a secreted protein that binds to the epidermal growth factor-like (EGF)-A domain of LDLR and directs the receptor for degradation in lysosomes by an unknown mechanism. A gain-of-function mutation, D374Y, increases binding to LDLR EGF-A >10-fold and is associated with a severe form of hypercholesterolemia in humans. Similar to previous studies, data obtained in my project has established that PCSK9 was capable of promoting robust LDLR degradation in liver-derived cell lines; however, minimal effects on LDLR levels were detected in several lines of fibroblast cells despite normal LDLR-dependent cellular uptake of PCSK9. Importantly, a PCSK9 degradation assay showed that 125I-labeled wild-type PCSK9 was internalized and degraded equally in both hepatic and fibroblast cells, indicating dissociation of wild-type PCSK9 from recycling LDLRs in fibroblasts. Moreover, PCSK9 recycling assays confirmed that no recycling of wild-type PCSK9 to the cell surface could be detected in fibroblast cells. In contrast, more than 60% of internalized PCSK9-D374Y recycled to the cell surface in these cells, and thus had reduced ability to direct the LDLR for lysosomal degradation despite persistent binding. Co-localization studies indicated that PCSK9-D374Y trafficked to both lysosomes and recycling compartments in fibroblast cells, whereas wild-type PCSK9 exclusively trafficked to lysosomes. We conclude that two factors diminish PCSK9 activity in fibroblast cells: i) an increased dissociation from the LDLR in early endosomal compartments, and ii) a decreased ability of bound PCSK9 to direct the LDLR to lysosomes for degradation. Finally, an LDLR variant that binds to PCSK9 in a Ca2+-independent manner could partially restore wild-type PCSK9 activity, but not PCSK9-D374Y activity, in fibroblast cells.

The discovery that proprotein convertase subtilisin/kexin type 9 (PCSK9) mediates degradation of low-density lipoprotein receptors (LDLR) indicates a critical role in LDL metabolism. PCSK9 is a secreted protein that binds to the epidermal growth factor-like (EGF)-A domain of LDLR and directs the receptor for degradation in lysosomes by an unknown mechanism. A gain-of-function mutation, D374Y, increases binding to LDLR EGF-A >10-fold and is associated with a severe form of hypercholesterolemia in humans. Similar to previous studies, data obtained in my project has established that PCSK9 was capable of promoting robust LDLR degradation in liver-derived cell lines; however, minimal effects on LDLR levels were detected in several lines of fibroblast cells despite normal LDLR-dependent cellular uptake of PCSK9. Importantly, a PCSK9 degradation assay showed that 125I-labeled wild-type PCSK9 was internalized and degraded equally in both hepatic and fibroblast cells, indicating dissociation of wild-type PCSK9 from recycling LDLRs in fibroblasts. Moreover, PCSK9 recycling assays confirmed that no recycling of wild-type PCSK9 to the cell surface could be detected in fibroblast cells. In contrast, more than 60% of internalized PCSK9-D374Y recycled to the cell surface in these cells, and thus had reduced ability to direct the LDLR for lysosomal degradation despite persistent binding. Co-localization studies indicated that PCSK9-D374Y trafficked to both lysosomes and recycling compartments in fibroblast cells, whereas wild-type PCSK9 exclusively trafficked to lysosomes. We conclude that two factors diminish PCSK9 activity in fibroblast cells: i) an increased dissociation from the LDLR in early endosomal compartments, and ii) a decreased ability of bound PCSK9 to direct the LDLR to lysosomes for degradation. Finally, an LDLR variant that binds to PCSK9 in a Ca2+-independent manner could partially restore wild-type PCSK9 activity, but not PCSK9-D374Y activity, in fibroblast cells.

No description available.

京都大学 / 新制・課程博士 / 博士(医学) / 甲第23780号 / 医博第4826号 / 新制||医||1057(附属図書館) / 京都大学大学院医学研究科医学専攻 / (主査)教授 村川 泰裕, 教授 武藤 学, 教授 滝田 順子 / 学位規則第4条第1項該当 / Doctor of Medical Science / Kyoto University / DFAM

Calmodulin is a highly conserved calcium ion binding protein expressed in all eukaryotic species. The 149 amino acid residues in the primary structure are organized in seven α helices with the highly flexible central α helix connecting the two non-cooperative domains of calmodulin. Each domain contains two EF-hand motifs to which calcium ions bind in a cooperative manner, hence the binding of four calcium ions saturate one calmodulin molecule. In the cardiovascular area calmodulin is involved in the activation of cardiac muscle contraction, and mutations that arise in the genetic sequence of the protein often have severe consequences. One such consequential mutation that can arise brings about the replacement of the highly conserved aspartic acid with glycine at position 130 in the amino acid sequence. In this research, the thermal and chemical stability within the C domain of the D130G variant of human calmodulin was investigated using a new method only requiring circular dichroism spectroscopic measurements. Affinity studies within the C domain of the D130G variant of human calmodulin were performed using fluorescence spectroscopy, and the ligands chosen for this purpose were trifluoperazine and p- HTMI. All analytical experiments were performed with the C domain of wild type human calmodulin as a reference. From the new method, it was concluded that the C domain of the D130G variant of human calmodulin has a slightly decreased stability in terms of Tm and Cm values compared to the C domain of wild type human calmodulin. The affinity analyses indicated that neither trifluoperazine nor p-HTMI discriminates between the C domain of the D130G variant of human calmodulin and the C domain of wild type human calmodulin in terms of dissociation constants. The pivotal outcome from this research is that the new method is applicable for determination of the stability parameters Tm and Cm of heat stable proteins.

This thesis focuses on the role and historical development of strategies of experimental domestication in scientific knowledge production, with a particular focus on the function of the laboratory strains known as 'wild types' in the model organism systems of classical genetics, where they play the role of standing in for the 'natural' instance of the species so that variation may be measured. As part of establishing how lab wild types came to assume this role, I have situated them within a much longer historical trajectory that tracks how changes in the manner that European intellectual traditions conceptualised the domestic-wild divide were linked to the development of new forms of scientific domestication and knowledge production. These new developments required that existing domesticating practices be intensified, expanded and analogised in order to better control, capture and comprehend 'wild' nature. My first two chapters introduce the domestic-wild divide by discussing both contemporary and ancient interpretations of it. In my third and fourth chapter, I explore the roots of the knowledge regime of European scientific domestication. I highlight Francis Bacon's campaign to use knowledge of domesticating practices to restore human dominion, before showing how Linnaeus later re-conceptualised the natural economy as an autonomous order and original order, with domestication reinterpreted as an artful transformation of nature requiring human maintenance to prevent reversion to its wild 'natural state'. I identify this idea of the wild as original and the domestic as derivative and artificially maintained as the basis of the original wild type concept. In my fifth chapter, I discuss Darwin's attempt to unite the domestic and wild under common laws of variation and selection, including his argument that reversion was simply a product of a return to ancestral conditions of existence. I observe that Darwin's theory of variation was problematic for the effort to bring wild nature under controlled conditions for study, so in my sixth and seventh chapters discuss how this difficulty was resolved, first by experimental naturalists both before and after Darwin who utilised vivaria and microscopes to bring pieces of nature indoors, and then by Weismann and Galton's sequestration of heredity, which helped persuade scientists that domestication was not in itself a cause of germinal variation. In my eighth and ninth chapter, I detail how sequestration led the early Mendelians de Vries and Bateson to assume that wild types could be brought into the lab from nature and purified into true-breeding strains. I discuss their differing atomist and interactionist perspectives on wild type, with de Vries favouring 'elementary species' as units of nature, whereas Bateson held wild types and mutants to represent normal and abnormal forms of the species respectively. In my last chapter, I cover the replacement of Bateson's interactionist genetics by the reductionist genetics of the Morgan group and argue that this led to a disintegration of wild types into their component genes. I conclude with a discussion of what wild type strains in classical genetics were meant to be representative of, and end by establishing that whilst these strains may not wholly be representative of their species, they are nonetheless useful tools for scientific knowledge production.