The University of Osaka · Biochemistry, Genetics and Molecular Biology
Professor Hiroshi Shimizu's research lab specializes in advanced environmental sensing and bioprocess engineering, focusing on innovative lidar techniques for atmospheric monitoring and the development of sustainable energy systems. The lab pioneers cutting-edge methods in metabolic flux analysis using stable isotope labeling to understand microbial physiology, particularly in extremophile and industrially relevant microorganisms. Research also extends to bio-inspired vehicle design and microbial co-culture systems for biotechnological applications, such as pH control in antimicrobial peptide production. The lab integrates physics, microbiology, and engineering to address challenges in environmental monitoring, energy efficiency, and industrial biotechnology.
Figures are computed from collected data and may differ slightly.
A new lidar technique for measuring the profiles of backscatter ratio, atmospheric visibility, and atmospheric temperature is proposed. Based on the theory of high resolution Rayleigh/Mie scattering, the feasibility and advantages of using atomic vapor cells as blocking filters for measuring atmospheric parameters are demonstrated with a numerical example worked out in detail. Ten percent accuracy in determining backscatter ratio and visibility can be achieved easily. With a SNR of 300, temperat
In 1994, the Eco-Vehicle Project was begun to develop an electric vehicle (EV) using a ground-up design approach that incorporates unique designs specific to an EV. The Eco-Vehicle will be a high-performance, but ultrasmall, battery-powered vehicle. New designs for the Eco-Vehicle include an in-wheel motor drive system, a hollow load floor which will house the batteries, and a new battery management system. The Eco-Vehicle may also utilize other advanced concepts suitable especially for EVs, inc
Our results suggest that activity of cell growth defined by specific growth rate of the yeast cells adapted to stepwise increase in ethanol concentration did not decrease during repetitive cultivation in high-ethanol-concentration medium. Moreover, fatty acid content of cell membrane and the size of ethanol-adapted yeast cells were changed during adaptation process. Those might be the typical phenotypes of yeast cells adapted to high ethanol concentration. In addition, the difference in sizes of
The in vivo measurement of metabolic flux by (13)C-based metabolic flux analysis ((13)C-MFA) provides valuable information regarding cell physiology. Bioinformatics tools have been developed to estimate metabolic flux distributions from the results of tracer isotopic labeling experiments using a (13)C-labeled carbon source. Metabolic flux is determined by nonlinear fitting of a metabolic model to the isotopic labeling enrichment of intracellular metabolites measured by mass spectrometry. Whereas
Cyanobacteria have flexible metabolic capability that enables them to adapt to various environments. To investigate their underlying metabolic regulation mechanisms, we performed an integrated analysis of metabolic flux using transcriptomic and metabolomic data of a cyanobacterium Synechocystis sp. PCC 6803, under mixotrophic and photoheterotrophic conditions. The integrated analysis indicated drastic metabolic flux changes, with much smaller changes in gene expression levels and metabolite conc
To control the pH during antimicrobial peptide (nisin) production by a lactic acid bacterium, Lactococcus lactis subsp. lactis (ATCC11454), a novel method involving neither addition of alkali nor a separation system such as a ceramic membrane filter and electrodialyzer was developed. A mixed culture of L. lactis and Kluyveromyces marxianus, which was isolated from kefir grains, was utilized in the developed system. The interaction between lactate production by L. lactis and its assimilation by K
To examine the effect of trehalose accumulation on response to saline stress in Saccharomyces cerevisiae, we constructed deletion strains of all combinations of the trehalase genes ATH1, NTH1 and NTH2 and examined their growth behaviour and intracellular trehalose accumulation under non-stress and saline-stress conditions. Saline stress was induced in yeast cells by NaCl addition at the exponential growth phase. All deletion strains showed similar specific growth rates and trehalose accumulation
The objective of this article is to propose an algorithm for the on-line estimation of the specific growth rate in a batch or a fed-batch fermentation process. The algorithm shows the practical procedure for the estimation method utilizing the macroscopic balance and the extended Kalman filter. A number of studies of the on line estimation have been presented. However, there are few studies discussing about the selection of the observed variables and for the tuning of some parameters of the exte
Cyanobacteria have received considerable attention as a sustainable energy resource because of their organic material production capacity using light energy and CO2 as a carbon source. Therefore, it is important to understand the cellular metabolism of cyanobacteria for metabolic engineering. In this study, to shed light on the central metabolism of cyanobacteria, we performed transcriptomic and metabolomic analyses of a glucose-tolerant strain of the cyanobacterium Synechocystis sp. PCC 6803, w
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