Keita ASHIDA Web Site

I’m Keita ASHIDA.
I was a postdoctoral researcher at Ito Lab at Universal Biology Institute, Graduate School of Science, The University of Tokyo, Japan. I was investigating stochastic thermodynamics in biological systems. I have a background in neuroscience with a quantitative biological approach, especially for fluorescence imaging and Caenorhabditis elegans.

Interests

Understanding neuronal information processing using quantification and physical and mathematical analysis

Fluorescence imaging
Compartments in a single neuron (dendrite, axon, organelles, and so on)
Thermodynamics
Information theory
Dynamical systems
Control engineering

Skills

Fluorescence Imaging (Ca²⁺, Membrane potential, Synaptic vesicle release, Neurotransmitter, and so on.)
Programing for data analysis and computer simulation (C++, Python, MATLAB, and so on. ODE, PDE, SDE)
DIY Bio (Microfluidics devices, Arduino, Electronics Kits)
Cloning

Publication List (Google Scholar)

Preprint

K Ashida, K Aoki, S Ito. “Experimental evaluation of thermodynamic cost and speed limit in living cells via information geometry”.

In this article, We evaluated the thermodynamic cost of the extracellular signal-regulated kinase (ERK) phosphorylation from the time series of the fluorescence imaging data by introducing information geometry. We investigated a thermodynamic efficiency based on the thermodynamic speed limit. The thermodynamic speed limit is the trade-off relation between thermodynamic cost and transition speed, and is now a hot topic in physics. I performed mainly data analysis.

2020

K Ashida, H Shidara, K Hotta, K Oka. “Optical dissection of synaptic plasticity for early adaptation in Caenorhabditis elegans” Neuroscience, 2020 Jan 21; 428: 112-121 (preprint).

In this article, dissect the modulation of the pre- and postsynaptic relationship in vivo based on optical methods in C. elegans. We showed that Ca²⁺ response of AIY interneurons is modulated by 5-min odor pre-exposure, but not one of AWC sensory neurons. Furthermore, both synaptic release from AWC and synaptic inputs to AIY are also modulated. These results showed that AWC sensory neurons modulate synaptic release without Ca²⁺ modulation. I performed all of the experiments and analysis.
K Ashida, H Shidara, K Oka. “Food Deprivation Changes Chemotaxis Behavior of Caenorhabditis elegans” Seibutsu Butsuri 2020 Nov 28;60（6）: 346-348 (in Japanese, Review paper).

2019

H Mori, K Ashida, H Shidara, T Nikai, K Hotta, K Oka. “Serotonin modulates behavior-related neural activity of RID interneuron in Caenorhabditis elegans” PLoS One, 2019 Dec 4;14(12): e0226044.

This article revealed that Serotonin modulates RID interneuronal activity when worms change their direction. To reveal this, we developed a custom-made tracking and imaging system, and imaged the RID activity of freely moving worm. I mainly supervised and planned the experimental scheme.
K Shimizu*, K Ashida*, K Hotta, K Oka. “Food deprivation changes chemotaxis behavior in Caenorhabditis elegans” Biophysics and Physicobiology, 2019, 16: 167-172 (*both authors contributed equally). Biophysics and Physicobiology Editors’ Choice Award

This article revealed that food deprivation changes worms chemotactic strategy depending on the duration of food-deprivation. While 1-h food-deprivation changes the weathervane strategy, 6-h food-deprivation changes the pirouette strategy. I mainly performed data analysis.
K Ashida, K Hotta, K Oka. “The input–output relationship of AIY interneurons in Caenorhabditis elegans in noisy environment” iScience, 2019 Jul 23;19:191-203.

In this article, we revealed that the fluctuations of glutamate inputs to an interneuron evoke Ca²⁺ responses without explicit stimulation change in C. elegans using various simultaneous imaging. Our results suggest that the fluctuation of sensory inputs induces behavioral variability under a natural condition. I performed all of the experiments and analysis.
K Ashida, T Kato, K Hotta, K Oka. “Multiple tracking and machine learning reveal dopamine modulation for area-restricted foraging behaviors via velocity change in Caenorhabditis elegans” Neuroscience Letters, 2019 Jul 27;706:68-74 (preprint).　

This article revealed that velocity change is important for food searching behavior in C. elegans using inverse reinforcement learning. I mainly performed data analysis including inverse reinforcement learning.
K Ashida, K Oka. “Stochastic thermodynamic limit on E. coli adaptation by information geometric approach” Biochemical and Biophysical Research Communications, 2019 Jan 15;508(3):690-694 (preprint).

This article revealed that the efficiency of E. coli adaptation using both stochastic thermodynamics and information geometry. We suggest that there is an appropriate noise level for achieving the adaptation efficiently. I formulated and simulated the efficiency in this paper.

2018

T Yoshimizu, H Shidara, K Ashida, K Hotta, K Oka. “Effect of interactions among individuals on the chemotaxis behaviours of Caenorhabditis elegans” Journal of Experimental Biology, 2018 Jun 12;221(Pt 11).

This article revealed that the chemotactic behavior of a nematode is affected by around worms. The worms modulated turning behavior against odor decrease by their pheromone. I mainly performed a computer simulation of odor diffusion in this paper.

Emplyoment

2019 Oct. - 2021 Aug. Universal Biology Institute, Graduate School of Science, The University of Tokyo.

Education

2016 Sep. - 2019 Sep. Ph. D at Keio University
Thesis: The input-output relationship under environmental noise in cellular and sub-cellular system
Advisor: Dr. Kotaro Oka

2015 Apr. - 2016 Aug. Master of Science at Keio University
Thesis: The Modulation of Neuronal Activity in Compartmentalized Subcellular Units of Sensory and Interneuron in Caenorhabditis elegans
Advisor: Dr. Kotaro Oka

2011 Apr. - 2015 Mar. Bachelor of Science at Keio University
Thesis: Input-output Characteristics of Sensory Neuron in Caenorhabditis elegans
Advisor: Dr. Kotaro Oka

Awards and Scholarships

2020 Mar. Fujiwara Award (Fujiwara Scholarship Fund, Keio University)
2016 Nov. Student Presentation Award at The 54th Annual Meeting of the Biophysical Society Japan
2016 Sep. - 2019 Aug. Yoshida Doctor 21 (Yoshida Scholarship Foundation)
2015 Apr. - 2016 Sep. Japan Student Services Organization Student Loan Repayment Exemption

Research Grants and Fellowships

2020 Apr. - 2022 Mr. Grant-in-Aid for Research Activity Start-up
2019 Mar. - 2019 Sep. KLL Ph.D. Program Research Grant
2018 Apr. - 2019 Mar. KLL Ph.D. Program Research Grant
2017 Apr. - 2018 Mar. Graduate School Doctoral Student Aid Program, Keio University
2017 Apr. - 2018 Mar. KLL Ph.D. Program Research Grant
2016 Oct. (Declined) Research Fellowships for Young Scientists DC1
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Contact: keita.ashida _ at _ ubi.s.u-tokyo.ac.jp