Transcriptome analysis of parallel-evolved Escherichia coli strains under ethanol stress

T Horinouchi, K Tamaoka, C Furusawa, N Ono… - BMC genomics, 2010 - Springer
Background Understanding ethanol tolerance in microorganisms is important for the
improvement of bioethanol production. Hence, we performed parallel-evolution experiments …

Transition from positive to neutral in mutation fixation along with continuing rising fitness in thermal adaptive evolution

T Kishimoto, L Iijima, M Tatsumi, N Ono, A Oyake… - PLoS …, 2010 - journals.plos.org
It remains to be determined experimentally whether increasing fitness is related to positive
selection, while stationary fitness is related to neutral evolution. Long-term laboratory …

Cooperative adaptation to establishment of a synthetic bacterial mutualism

K Hosoda, S Suzuki, Y Yamauchi, Y Shiroguchi… - PLoS …, 2011 - journals.plos.org
To understand how two organisms that have not previously been in contact can establish
mutualism, it is first necessary to examine temporal changes in their phenotypes during the …

Inference of transcriptome signatures of Escherichia coli in long-term stationary phase

S Takano, H Takahashi, Y Yama, R Miyazaki… - Scientific Reports, 2023 - nature.com
Abstract “Non-growing” is a dominant life form of microorganisms in nature, where available
nutrients and resources are limited. In laboratory culture systems, Escherichia coli can …

[图书][B] Microarray technology in practice

S Russell, LA Meadows, RR Russell - 2008 - books.google.com
Using chips composed of thousands of spots, each with the capability of holding DNA
molecules corresponding to a given gene, DNA microarray technology has enabled …

FederatedCloudSim: a SLA-aware federated cloud simulation framework

A Kohne, M Spohr, L Nagel, O Spinczyk - Proceedings of the 2nd …, 2014 - dl.acm.org
Recent developments show that the standardization of cloud service descriptions and
exchange leads the way for the rise of cloud federations. In these federations CSPs (cloud …

Phenotypic convergence in bacterial adaptive evolution to ethanol stress

T Horinouchi, S Suzuki, T Hirasawa, N Ono… - BMC evolutionary …, 2015 - Springer
Background Bacterial cells have a remarkable ability to adapt to environmental changes, a
phenomenon known as adaptive evolution. During adaptive evolution, phenotype and …

Growth rate-coordinated transcriptome reorganization in bacteria

Y Matsumoto, Y Murakami, S Tsuru, BW Ying, T Yomo - BMC genomics, 2013 - Springer
Background Cell growth rate reflects an organism's physiological state and largely relies on
the ability of gene expression to respond to the environment. The relationship between …

Universal relationship in gene-expression changes for cells in steady-growth state

K Kaneko, C Furusawa, T Yomo - Physical Review X, 2015 - APS
Cells adapt to different conditions by altering a vast number of components, which is
measurable using transcriptome analysis. Given that a cell undergoing steady growth is …

Multilevel comparative analysis of the contributions of genome reduction and heat shock to the Escherichia colitranscriptome

BW Ying, S Seno, F Kaneko, H Matsuda, T Yomo - BMC genomics, 2013 - Springer
Background Both large deletions in genome and heat shock stress would lead to alterations
in the gene expression profile; however, whether there is any potential linkage between …