A new spice-like modeling tool for bio- and electro- acoustic systems including thermoviscous effects

International audienceA dedicated toolbox has been developed within ASYGN a recent software tool that simulates aVLSI circuits at a high-level of modeling. It accounts in both time- and frequency- domain for the specific feature of bio- and electro- acoustic systems especially when some of the constituting elements are very thin or narrow. The models correspond to systems of complex equations in which some of the complex coefficients can be frequency dependent. Results are solved and viewed in real time. The tool was developed to introduce some improvement in the model of the auditory system of the cricket. In 2007 Reeve et al. designed and tested an electrical equivalent circuit based on Michelsen 1994. The latter results from two major simplification namely the absence of thermoviscous effects and of any acoustical role of a septum located in the middle of a transverse acoustic trachea. Thanks to the weak couplings the model can be subdivided into independent elements such as tubes, cavities or membranes simply connected together. Thermoviscous effects and the role of the medial septum can now be fully investigated. Our results were first validated using Matlab. Our model reveals interesting feature compared to its historical counterpart

Development of a human mitochondrial oligonucleotide microarray (h-MitoArray) and gene expression analysis of fibroblast cell lines from 13 patients with isolated F1Fo ATP synthase deficiency

<p>Abstract</p> <p>Background</p> <p>To strengthen research and differential diagnostics of mitochondrial disorders, we constructed and validated an oligonucleotide microarray (h-MitoArray) allowing expression analysis of 1632 human genes involved in mitochondrial biology, cell cycle regulation, signal transduction and apoptosis. Using h-MitoArray we analyzed gene expression profiles in 9 control and 13 fibroblast cell lines from patients with F₁F_oATP synthase deficiency consisting of 2 patients with mt9205ΔTA microdeletion and a genetically heterogeneous group of 11 patients with not yet characterized nuclear defects. Analysing gene expression profiles, we attempted to classify patients into expected defect specific subgroups, and subsequently reveal group specific compensatory changes, identify potential phenotype causing pathways and define candidate disease causing genes.</p> <p>Results</p> <p>Molecular studies, in combination with unsupervised clustering methods, defined three subgroups of patient cell lines – M group with mtDNA mutation and N1 and N2 groups with nuclear defect. Comparison of expression profiles and functional annotation, gene enrichment and pathway analyses of differentially expressed genes revealed in the M group a transcription profile suggestive of synchronized suppression of mitochondrial biogenesis and G1/S arrest. The N1 group showed elevated expression of complex I and reduced expression of complexes III, V, and V-type ATP synthase subunit genes, reduced expression of genes involved in phosphorylation dependent signaling along MAPK, Jak-STAT, JNK, and p38 MAP kinase pathways, signs of activated apoptosis and oxidative stress resembling phenotype of premature senescent fibroblasts. No specific functionally meaningful changes, except of signs of activated apoptosis, were detected in the N2 group. Evaluation of individual gene expression profiles confirmed already known <it>ATP6/ATP8 </it>defect in patients from the M group and indicated several candidate disease causing genes for nuclear defects.</p> <p>Conclusion</p> <p>Our analysis showed that deficiency in the ATP synthase protein complex amount is generally accompanied by only minor changes in expression of ATP synthase related genes. It also suggested that the site (mtDNA vs nuclear DNA) and the severity (ATP synthase content) of the underlying defect have diverse effects on cellular gene expression phenotypes, which warrants further investigation of cell cycle regulatory and signal transduction pathways in other OXPHOS disorders and related pharmacological models.</p