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“Nuclear genes encode most mitochondrial proteins, and their mutations cause diverse and debilitating clinical disorders. To date, 1,200 of these mitochondrial genes have been recorded, while no standardized catalog exists of the associated clinical phenotypes. Such a catalog would be useful to develop methods to WH-4-023 analyze human phenotypic data, to determine genotype-phenotype relations among many genes and diseases, and to support the clinical diagnosis of mitochondrial disorders. Here we establish a clinical phenotype catalog of 174 mitochondrial disease genes and study associations of diseases and genes. Phenotypic features such as clinical signs and symptoms were manually annotated from full-text medical articles and classified based on the hierarchical MeSH ontology. This classification of phenotypic features of each gene allowed for the comparison of diseases between different genes. In turn, we were then able to measure the phenotypic associations of disease PD98059 MAPK inhibitor genes for which we calculated a quantitative value that is based on their shared phenotypic features. The results showed that genes sharing more similar phenotypes have a stronger tendency for functional interactions, proving the
usefulness of phenotype similarity values in disease gene network analysis. We then constructed a functional network of mitochondrial genes and discovered a higher connectivity for non-disease than for disease genes, and a tendency of disease genes to interact with each other. Utilizing these differences, we propose 168 candidate genes that resemble the characteristic interaction patterns of mitochondrial disease genes. Through their network associations, the candidates are further prioritized for the study of specific disorders such as optic neuropathies and Parkinson disease. Most mitochondrial disease
phenotypes involve several clinical categories including neurologic, metabolic, and gastrointestinal disorders, which might indicate the effects of gene defects within the mitochondrial system. The accompanying Taselisib chemical structure knowledgebase (http://www.mitophenome.org/) supports the study of clinical diseases and associated genes.”
“We took a model created by the molecular dynamics (MD) simulation with a semiempirical potential as a target system and explored how its amorphous structure and a few other properties depend on the simulation method. We found that if the cooling rate is too high, 10(13)-10(14) K/s, the system has no time to adjust its structure to the change in temperature/density. Since this cooling corresponds to a typical ab initio MD simulation, this brings into doubt that an equilibrium glass structure can be obtained using ab initio MD simulation. We also used the target partial pair correlation functions (PPCFs) to explore a possibility to create the atomic models from diffraction data alone.