The discovery of biomarkers for Parkinson's disease (PD) is challenging due to the heterogeneous nature of this disorder, and a poor correlation between the underlying pathology and the clinically expressed phenotype. An ideal biomarker would inform on PD-relevant pathological changes via an easily assayed biological characteristic, which reliably tracks clinical symptoms. Human dermal (skin) fibroblasts are accessible peripheral cells that constitute a patient-specific system, which potentially recapitulates the PD chronological and epigenetic aging history. Here, we compared primary skin fibroblasts obtained from individuals diagnosed with late-onset sporadic PD, and healthy age-matched controls. These fibroblasts were studied from fundamental viewpoints of growth and morphology, as well as redox, mitochondrial, and autophagic function. It was observed that fibroblasts from PD subjects had higher growth rates, and appeared distinctly different in terms of morphology and spatial organization in culture, compared to control cells. It was also found that the PD fibroblasts exhibited significantly compromised mitochondrial structure and function when assessed via morphological and oxidative phosphorylation assays. Additionally, a striking increase in baseline macroautophagy levels was seen in cells from PD subjects. Exposure of the skin fibroblasts to physiologically relevant stress, specifically ultraviolet irradiation (UVA), further exaggerated the autophagic dysfunction in the PD cells. Moreover, the PD fibroblasts accumulated higher levels of reactive oxygen species (ROS) coupled with lower cell viability upon UVA treatment. In essence, these studies highlight primary skin fibroblasts as a patient-relevant model that captures fundamental PD molecular mechanisms, and supports their potential utility to develop diagnostic and prognostic biomarkers for the disease.

A real-time application is designed as a set of tasks with specific timing attributes and constraints. These tasks can be categorized as periodic, sporadic or aperiodic, based on the timing attributes that are specified for them which in turn define their runtime behaviors. To ensure correct execution and behavior of the task set at runtime, the scheduler of the underlying operating system should take into account the type of each task (i.e.,  periodic, sporadic, aperiodic). This is important so that the scheduler can schedule the task set in a predictable way and be able to allocate CPU time to each task appropriately in order for them to achieve their timing constraints. ENEA OSE is a real-time operating system with fixed priority preemptive scheduling policy which is used heavily in embedded systems, such as telecommunication systems developed by Ericsson. While OSE allows for specification of priority levels for tasks and schedules them accordingly, it can not distinguish between different types of tasks. This thesis work investigates mechanisms to build a scheduler on top of OSE, which can identify three types of real-time tasks and schedule them in a more predictable way. The scheduler can also monitor behavior of task set at run-time and invoke violation handlers if time constraints of a task are violated. The scheduler is implemented on OSE5.5 soft kernel. It identifies periodic, aperiodic and sporadic tasks. Sporadic and aperiodic tasks can be interrupt driven or program driven. The scheduler implements EDF and RMS as scheduling policy of periodic tasks. Sporadic and aperiodic tasks can be scheduled using polling server or background scheme. Schedules generated by the scheduler  deviate from expected timing behavior due to scheduling overhead. Approaches to reduce deviation are suggested as future extension of thesis work. Usability of the scheduler can be increased by extending the scheduler to support other scheduling algorithm in addition to RMS and EDF. / CHESS

Final publication is available at http://www.cell.com/cell-stem-cell/abstract/S1934-5909(13)00012-X / 京都大学 / 0048 / 新制・課程博士 / 博士(医学) / 甲第19622号 / 医博第4129号 / 新制||医||1015(附属図書館) / 32658 / 京都大学大学院医学研究科医学専攻 / (主査)教授 高橋 淳, 教授 伊佐 正, 教授 YOUSSEFIAN Shohab / 学位規則第4条第1項該当 / Doctor of Medical Science / Kyoto University / DFAM

Strong Gelfand pairs describe a relation between a group and a subgroup, using a relation between inner products of their characters. We find all strong Gelfand pairs of the dihedral and dicyclic groups, and several of the sporadic groups. We provide some results for the strong Gelfand pairs of the affine linear groups, in addition to the exceptional classical groups $\mathrm{Sp}_4(q)$ for $q$ a power of $2$.

Lymphangioleiomyomatosis (LAM) is a rare lung disease recognized by abnormal growth of smooth muscle cells proliferating in lungs parenchyma, developing benign tumors, migrating to the other organs, and ultimately leading to respiratory failure and death. Despite existing literature mainly on clinical aspects of LAM, there is a gap of literature in regards to the knowledge, attitude, and lifestyle practices (KAPs) of LAM patients and their effects on their quality of life. The purpose of this quantitative study was to investigate the KAPs of the sporadic LAM patients as measured by the Bristol Chronic Obstructive Pulmonary Disease Knowledge Questionnaire, Beliefs and Behavior Questionnaire, Determinants of Lifestyle Behavior Questionnaire; these KAPs were then analyzed for their relationship to quality of life reports as measured by the St George’s Quality of Life Questionnaire. Transtheoretical model (TTM) was used to describe the relationship among the variables. The data were collected through online survey questionnaires from 143 sporadic LAM patients registered at the LAM Foundation. Pearson’s correlations and linear regression were used to analyze the data. The results of the analysis showed that there was a significant positive relationship between attitude, lifestyle practices, and quality of life and a negative relationship between knowledge and quality of life. The outcome achieved by this study and its implication on social change identifies the need to initiate more study-specific KAPs within LAM populations, including individuals with tuberous sclerosis complex LAM. The results could also encourage the LAM community as well as other stakeholders to implement programs, workshops, and interventions that could promote and enhance quality of life.

ALS is an often lethal disease involving degeneration of motor neurons in the brain and spinal cord. Current treatments only extend life by several months, and novel therapies are needed. We combined RNA-Sequencing, systems biology analyses, and molecular biology assays to elucidate sporadic ALS group-specific differences in postmortem cervical spinal sections (7 sALS and 8 control samples) that may be relevant to disease pathology. >55 million 2X150 RNA-sequencing reads per sample were generated and processed. In Chapter 2, we used bioinformatics tools to identify nuclear differentially expressed genes (DEGs) between our two groups. Further, we used Weighted Gene Co-Expression Network Analysis to identify gene co-expression networks associated with disease status. Qiagen’s Ingenuity Pathway Analysis revealed our sALS group-specific DEGs and a sALS group-specific gene co-expression network were associated with inflammatory processes and TNF-α signaling. Further, TNFAIP2 was identified as a sALS group-specific upregulated DEG and a network hub gene within that network. We hypothesized TNFAIP2’s upregulation in our ALS samples reflected increased TNF-α signaling and that TNFAIP2 promoted motor neuron death via TNF superfamily apoptotic pathways. Transient overexpression of TNFAIP2 decreased cell viability in both neural stem cells and induced pluripotent stem cell-derived motor neurons. Further, inhibition of activated caspase 9 (a protein necessary for TNF superfamily mitochondrial-mediated apoptosis) reversed this effect in neural stem cells. In Chapters 3 and 4, we used bioinformatics tools to identify sALS group-specifc mitochondrial DEGs and differentially used exons (DUEs). Qiagen’s Ingenuity Pathway Analysis revealed our sALS group-specific DUEs were associated with cholesterol biosynthesis.

[Truncated abstract] Sporadic inclusion body myositis (sIBM) is a chronic inflammatory disease that is the most common myopathy in individuals above the age of 50 in the Caucasian population. sIBM is characterised by cytotoxic immune infiltration of skeletal muscle, consisting primarily of CD8+ T-cells and macrophages, as well as a degenerative process, with muscle fibre vacuolation and intracellular filamentous inclusions. The pathogenesis of sIBM is likely to involve a complex interaction between genetic and environmental factors. Whilst the physiological and pathological characteristics of sIBM have been clearly identified, the exact origin and genetic basis of the disease remains unknown. A number of studies show that sIBM is associated with alleles of the major histocompatibility complex (MHC) on chromosome 6p21.3 and specifically with two ancestral haplotypes (AH) in Caucasians – the 8.1AH, defined by HLA-B*0801, HLA-DRB1*0301 and the 35.2AH, defined by HLA-B*3501, HLA-DRB1*0101. Mapping studies subsequently showed that sIBM susceptibility likely originates from a 389kb region of the MHC, spanning from centromeric of PBX2 to telomeric of HLA-DRB1. The central hypothesis of this thesis was that susceptibility to sIBM is conferred by a single allele found within a region defined using the 8.1AH, which is also carried by other haplotypes associated with sIBM. Three patient cohorts from Australia, the U.S.A and Japan were studied. ... Of the 32 alleles genotyped, none were found in all susceptibility haplotypes and one was common, but not unique, to the 8.1AH, 7.2AH and 52.1AH. Five SNPs were also found in two of the three haplotypes, although none were specific to the sIBM susceptibility haplotypes. These data suggest that the 8.1AH is likely to carry an sIBM susceptibility allele independent of the 35.2AH, 7.2AH and 52.1AH. Based on the possible mechanism of action in cellular differentiation and its location within the 8.1AH-defined sIBM susceptibility region reported in 2004, NOTCH4 was a strong candidate for conferring sIBM susceptibility. NOTCH4 coding region polymorphisms were thus investigated in a Caucasian patient cohort to assess any possible role in sIBM susceptibility. While the frequency of some alleles were increased in sIBM patients, the strong linkage disequilibrium throughout the MHC prevented confirmation of any alleles as playing a direct role in sIBM. The 8.1AH-derived sIBM susceptibility region was further refined using recombination mapping. This approach used markers characterised against multiple haplotypes to genotype patients carrying part of the 8.1AH to locate a common, overlapping susceptibility region. Recombination mapping of patients revealed a common overlapping region of the 8.1AH, extending from BTNL2 to HLA-DRB3. The results of the study indicate that 8.1AH-derived susceptibility for sIBM is likely to originate from a 172kb region encompassing HLA-DRA, HLA-DRB3 and part of BTNL2. These genes warrant further investigation in future studies.

This thesis demonstrates an alternative, concise but informative, method for representing group elements, which will prove particularly useful for the sporadic groups. It explains the theory behind symmetric presentations, and describes the algorithm for working with elements represented in this manner.

Protein product tumor suppressor PALB2 gene plays a major role in pathway of DNA repair of double-strand breaks throught the homologous recombination mechanism. Significance of its pathogenic variants in hereditary forms of breast cancer in BRCA1/2- negative patients in families with multiple breast cancers may be in the Czech Republic comparable with the BRCA2 gene. A role of the PALB2 gene in sporadic breast cancer occurence, which represent 90 - 95 % of all cancers, is still unknown. This thesis focuses on inactivation pathway of tumor suppressor PALB2 in the sporadic breast cancer by a mechanism of allelic loss detecting by loss of heterozygosity (LOH) of corresponding microsatellite markers and hypermethylation of promoter region as the most common mechanisms of inactivation tumor suppressors in early tumorigenesis. In a group of 51 nonselected patients with sporadic breast cancer we found four samples with PALB2 locus allelic loss. These samples were analyzed for somatic mutations. No mutation was found. There is no evidence of promotor hypermethylation in any of the samples. Our data suggest a role of the PALB2 gene inactivation in a minority group of sporadic breast cancers.

Colorectal carcinoma (CRC) is one of the most prevalent malignancies in the Czech Republic. In general, there are two molecular pathways leading to CRC: one is characterized by chromosomal instability, the other by the deficiency in DNA mismatch repair (MMR) genes. MutL homologue 1 (MLH1) gene, a member of the MMR gene-family, represents a key component of the MMR system, responsible for recognition of nucleotide mismatches occurring during DNA replication, and for the recruitment of repair proteins to correct the replication errors. According to literature, somatic mutations in MMR genes, and MLH1 in particular, hallmark sporadic, MMR deficient, CRC cases. We aimed at analyzing somatic events in MLH1 gene and the determination of microsatellite instability (MSI) status in 99 DNA samples from 96 patients with sporadic CRC. Mutations were screened by high resolution melting (HRM) curve analysis. Positive cases in each run were subsequently verified by automated sequencing. Mainly gene variants were found in MLH1 gene: We discovered two new variants, one in exon 2 at position c. 204 C>G, p. Ile68Met (98 C/C, 1C/G) and the other in exon 11 at position c. 973 C>T, p. Arg325Trp (98 C/C, 1 C/T). Only the latter variant c. 973 C>T was identified as somatic mutation. All other variants found in MLH1 gene...