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Dive into the research topics where Reiko Okura is active.

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Featured researches published by Reiko Okura.


Proceedings of the National Academy of Sciences of the United States of America | 2016

Noise-driven growth rate gain in clonal cellular populations

Mikihiro Hashimoto; Takashi Nozoe; Hidenori Nakaoka; Reiko Okura; Sayo Akiyoshi; Kunihiko Kaneko; Edo Kussell; Yuichi Wakamoto

Significance Differences between individuals exist even in the absence of genetic differences, e.g., in identical twins. Over the last decade, experiments have shown that even genetically identical microbes exhibit large cell-to-cell differences. In particular, the timing of cell division events is highly variable between single bacterial cells. The effect of this variability on long-term growth and survival of bacteria, however, remains elusive. Here, we present a striking finding showing that a bacterial population grows faster on average than its constituent cells. To explain this counterintuitive result, we present a mathematical model that precisely predicts our measurements. Furthermore, we show an empirical growth law that constrains the maximal growth rate of Escherichia coli. Cellular populations in both nature and the laboratory are composed of phenotypically heterogeneous individuals that compete with each other resulting in complex population dynamics. Predicting population growth characteristics based on knowledge of heterogeneous single-cell dynamics remains challenging. By observing groups of cells for hundreds of generations at single-cell resolution, we reveal that growth noise causes clonal populations of Escherichia coli to double faster than the mean doubling time of their constituent single cells across a broad set of balanced-growth conditions. We show that the population-level growth rate gain as well as age structures of populations and of cell lineages in competition are predictable. Furthermore, we theoretically reveal that the growth rate gain can be linked with the relative entropy of lineage generation time distributions. Unexpectedly, we find an empirical linear relation between the means and the variances of generation times across conditions, which provides a general constraint on maximal growth rates. Together, these results demonstrate a fundamental benefit of noise for population growth, and identify a growth law that sets a “speed limit” for proliferation.


Current Biology | 2016

Bacterial Autoimmunity Due to a Restriction-Modification System

Maroš Pleška; Long Qian; Reiko Okura; Tobias Bergmiller; Yuichi Wakamoto; Edo Kussell; Călin C. Guet

Restriction-modification (RM) systems represent a minimal and ubiquitous biological system of self/non-self discrimination in prokaryotes [1], which protects hosts from exogenous DNA [2]. The mechanism is based on the balance between methyltransferase (M) and cognate restriction endonuclease (R). M tags endogenous DNA as self by methylating short specific DNA sequences called restriction sites, whereas R recognizes unmethylated restriction sites as non-self and introduces a double-stranded DNA break [3]. Restriction sites are significantly underrepresented in prokaryotic genomes [4-7], suggesting that the discrimination mechanism is imperfect and occasionally leads to autoimmunity due to self-DNA cleavage (self-restriction) [8]. Furthermore, RM systems can promote DNA recombination [9] and contribute to genetic variation in microbial populations, thus facilitating adaptive evolution [10]. However, cleavage of self-DNA by RM systems as elements shaping prokaryotic genomes has not been directly detected, and its cause, frequency, and outcome are unknown. We quantify self-restriction caused by two RM systems of Escherichia coli and find that, in agreement with levels of restriction site avoidance, EcoRI, but not EcoRV, cleaves self-DNA at a measurable rate. Self-restriction is a stochastic process, which temporarily induces the SOS response, and is followed by DNA repair, maintaining cell viability. We find that RM systems with higher restriction efficiency against bacteriophage infections exhibit a higher rate of self-restriction, and that this rate can be further increased by stochastic imbalance between R and M. Our results identify molecular noise in RM systems as a factor shaping prokaryotic genomes.


生物物理 | 2013

1P137 幹細胞ミニマルモデルのin vivo実装(09.発生・分化,ポスター,日本生物物理学会年会第51回(2013年度))

Sumire Ono; Reiko Okura; Yuichi Wakamoto


Seibutsu Butsuri | 2013

1P137 In vivo realization of the minimal stem cell model in Escherichia coli(09.Development & Differentation,Poster,The 51st Annual Meeting of the Biophysical Society of Japan)

Sumire Ono; Reiko Okura; Yuichi Wakamoto


Seibutsu Butsuri | 2013

3P258 On phenotypic drug tolerance based on expression noise of antibiotic resistant gene(20. Origin of life & Evolution,Poster)

Takashi Nozoe; Reiko Okura; Yuichi Wakamoto


生物物理 | 2012

1PT215 幹細胞様のふるまいを示す人工遺伝子ネットワークの構築(日本生物物理学会第50回年会(2012年度))

Sumire Ono; Reiko Okura; Yuichi Wakamoto


Seibutsu Butsuri | 2012

2C1610 Characterization of Death and Division Process in Synthetic Bacterial Population with Antibiotic Treatment(Mathematical Biology,Oral Presentation,The 50th Annual Meeting of the Biophysical Society of Japan)

Takashi Nozoe; Reiko Okura; Yuichi Wakamoto


Seibutsu Butsuri | 2012

1PT215 Synthetic biology of stem cells : creating artificial gene network of "differentiation"(The 50th Annual Meeting of the Biophysical Society of Japan)

Sumire Ono; Reiko Okura; Yuichi Wakamoto


Biophysical Journal | 2012

Single-Cell Level Verification of Relation Between Gene Expression Noise and Phenotypic Adaptation to Antibiotic in Escherichia Coli

Takashi Nozoe; Reiko Okura; Yuichi Wakamoto


生物物理 | 2011

2J1524 細胞の成長と遺伝子発現ゆらぎの関係(計測、その他,第49回日本生物物理学会年会)

Mikihiro Hashimoto; Reiko Okura; Yuichi Wakamoto

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Călin C. Guet

Institute of Science and Technology Austria

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