分裂酵母の網羅的メタボローム解析

広島大学(Hiroshima University)博士(理学)Doctor of Sciencedoctora

Shaft seals and stuffing boxes of pumps

Čerpadla jsou nedílnou součástí průmyslu, zemědělství, ale také běžného života. Jedním z hlavních prvků, které mají vliv na správnou funkci a spolehlivost těchto strojů jsou hřídelové ucpávky a těsnění. Tato práce se v první části zabývá jednotlivými druhy hřídelových ucpávek a těsnění, jejich konstrukčním provedením, aplikací, funkcí a používanými materiály. V druhé části je dimenzována vhodná ucpávka pro vybrané čerpadlo.Pumps are an integral part of industry, agriculture, but also everyday life. One of the main elements that affect the proper function and reliability of these machines are shaft seals and gaskets. The first part of this work deals with individual types of shaft seals and gaskets, their design, application, function and used materials. In the second part, a suitable seal for the selected pump is dimensioned.

MZmine 2: Modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data

<p>Abstract</p> <p>Background</p> <p>Mass spectrometry (MS) coupled with online separation methods is commonly applied for differential and quantitative profiling of biological samples in metabolomic as well as proteomic research. Such approaches are used for systems biology, functional genomics, and biomarker discovery, among others. An ongoing challenge of these molecular profiling approaches, however, is the development of better data processing methods. Here we introduce a new generation of a popular open-source data processing toolbox, MZmine 2.</p> <p>Results</p> <p>A key concept of the MZmine 2 software design is the strict separation of core functionality and data processing modules, with emphasis on easy usability and support for high-resolution spectra processing. Data processing modules take advantage of embedded visualization tools, allowing for immediate previews of parameter settings. Newly introduced functionality includes the identification of peaks using online databases, MSⁿdata support, improved isotope pattern support, scatter plot visualization, and a new method for peak list alignment based on the random sample consensus (RANSAC) algorithm. The performance of the RANSAC alignment was evaluated using synthetic datasets as well as actual experimental data, and the results were compared to those obtained using other alignment algorithms.</p> <p>Conclusions</p> <p>MZmine 2 is freely available under a GNU GPL license and can be obtained from the project website at: <url>http://mzmine.sourceforge.net/</url>. The current version of MZmine 2 is suitable for processing large batches of data and has been applied to both targeted and non-targeted metabolomic analyses.</p

Genetic regulation of mitotic competence in G0quiescent cells

Quiescent (G0 phase) cells must maintain mitotic competence (MC) to restart the cell cycle. This is essential for reproduction in unicellular organisms and also for development and cell replacement in higher organisms. Recently, suppression of MC has gained attention as a possible therapeutic strategy for cancer. Using a Schizosaccharomyces pombe deletion-mutant library, we identified 85 genes required to maintain MC during the G0 phase induced by nitrogen deprivation. G0 cells must recycle proteins and RNA, governed by anabolism, catabolism, transport, and availability of small molecules such as antioxidants. Protein phosphatases are also essential to maintain MC. In particular, Nem1-Spo7 protects the nucleus from autophagy by regulating Ned1, a lipin. These genes, designated GZE (G-Zero Essential) genes, reveal the landscape of genetic regulation of MC

Genetic defects in SAPK signalling, chromatin regulation, vesicle transport and CoA-related lipid metabolism are rescued by rapamycin in fission yeast

Rapamycin inhibits TOR (target of rapamycin) kinase, and is being used clinically to treat various diseases ranging from cancers to fibrodysplasia ossificans progressiva. To understand rapamycin mechanisms of action more comprehensively, 1014 temperature-sensitive (ts) fission yeast (Schizosaccharomyces pombe) mutants were screened in order to isolate strains in which the ts phenotype was rescued by rapamycin. Rapamycin-rescued 45 strains, among which 12 genes responsible for temperature sensitivity were identified. These genes are involved in stress-activated protein kinase (SAPK) signalling, chromatin regulation, vesicle transport, and CoA- and mevalonate-related lipid metabolism. Subsequent metabolome analyses revealed that rapamycin upregulated stress-responsive metabolites, while it downregulated purine biosynthesis intermediates and nucleotide derivatives. Rapamycin alleviated abnormalities in cell growth and cell division caused by sty1 mutants (Δsty1) of SAPK. Notably, in Δsty1, rapamycin reduced greater than 75% of overproduced metabolites (greater than 2× WT), like purine biosynthesis intermediates and nucleotide derivatives, to WT levels. This suggests that these compounds may be the points at which the SAPK/TOR balance regulates continuous cell proliferation. Rapamycin might be therapeutically useful for specific defects of these gene functions

Integrative analysis of multimodal mass spectrometry data in MZmine 3

3 Pág.We thank Christopher Jensen and Gauthier Boaglio for their contributions to the MZmine codebase. We thank Jianbo Zhang and Zachary Russ for their donations to MZmine development. The MZmine 3 logo was designed by the Bioinformatics & Research Computing group at the Whitehead Institute for Biomedical Research. T.P. is supported by Czech Science Foundation (GA CR) grant 21-11563M and by the European Union’s Horizon 2020 research and innovation programme under Marie Skłodowska-Curie grant agreement 891397. Support for P.C.D. was from US NIH U19 AG063744, P50HD106463, 1U24DK133658 and BBSRC-NSF award 2152526. T.S. acknowledges funding by Deutsche Forschungsgemeinschaft (441958208). M. Wang acknowledges the US Department of Energy Joint Genome Institute ( https://ror.org/04xm1d337 , a DOE Office of Science User Facility) and is supported by the Office of Science of the US Department of Energy operated under subcontract No. 7601660. E.R. and H.H. thank Wen Jiang (HILICON AB) for providing the iHILIC Fusion(+) column for HILIC measurements. M.F., K.D. and S.B. are supported by Deutsche Forschungsgemeinschaft (BO 1910/20). L.-F.N. is supported by the Swiss National Science Foundation (project 189921). D.P. was supported through the Deutsche Forschungsgemeinschaft (German Research Foundation) through the CMFI Cluster of Excellence (EXC-2124 — 390838134 project-ID 1-03.006_0) and the Collaborative Research Center CellMap (TRR 261 - 398967434). J.-K.W. acknowledges the US National Science Foundation (MCB-1818132), the US Department of Agriculture, and the Chan Zuckerberg Initiative. MZmine developers have received support from the European COST Action CA19105 — Pan-European Network in Lipidomics and EpiLipidomics (EpiLipidNET). We acknowledge the support of the Google Summer of Code (GSoC) program, which has funded the development of several MZmine modules through student projects. We thank Adam Tenderholt for introducing MZmine to the GSoC program.Peer reviewe

Solution of flow and formation of vortex structures behind a free-standing pillar

The instability of the flow and the formation of vortices when surrounding free-standing pillars is a problem that has been solved for a long time. In most engineering applications we try to minimize their influence. However, some newer applications require them to be maximized. This deals with the study of these effects on the public street lamp using computer modelling in the Ansys Fluent and their use for the production of electricity. The information obtained in this way is then used for the design of a vibration generator, which is then used to transform the energy from mechanical vibrations to electricity

Long-term predictive modelling of nonlinear dynamical systems using recurrent neural networks

Tato bakalářská práce se zabývá zkoumáním rekurentních neuronových sítí za účelem dlouhodobé predikce nelineárních dynamických systémů pomocí rekurentních neuronových sítí. Cílem je návrh a otestování softwarového řešení neuronové sítě na reálných datech pocházejících z měření teplot obráběcího stroje.This bachelor thesis investigates recurrent neural networks for long-term prediction of nonlinear dynamic systems using recurrent neural networks. The aim is to design and test a neural network software solution on real data coming from machine tool temperature measurements.