いきもんタイムズをwebで読む▶

RIKEN Center for
Biosystems Dynamics Research

Unraveling what it means to be alive

2024 SUMMER

16vol.

16vol.

2024 SUMMER「 生きている」仕 組みをひも解く。

生命機能科学研究センター
理化学研究所
Read more onthe web▶

ネホリ
Dive intoハホリ

BDRʼs intriguing
research
A graduate of Nara KOSEN!
Yakushiji(Y)▶ Let me cut to the chase. What kindof research are you doing?
Shibai (S)▶ The research projects in the Furusawa
lab, which I currently work in, can be largely
divided into two directions; experiments involving
making bacteria evolve in the laboratory andworking to automate those experiments. My
research focuses more on the side of automation.
Y▶ So, your background is not in biology butautomation?
S▶ I was actually studying robotics during mytime at Nara KOSEN. The regular course at KOSEN
is a 5-year curriculum, but I spent another twoyears after that enrolled in a specialized advanced
course, meaning that I was at Nara KOSEN until I
finished the equivalent of fourth year university
education. I started working on bacteria research
for my masters degree and I came to RIKEN after I
received my PhD. All that led me to my current
main work of automating experimental bacterial
evolution using robotics.

What is experimental
bacterial evolution?
Y▶ What kind of experiments are you doing forexperimental evolution of bacteria?
S▶ Have you heard of drug-resistant bacteria?
"Drug resistant" means bacteria become moreresistant to antibiotics. From the human perspective, this type of bacteria is troublesome because
they cannot be killed with antibiotics, but from an

What’s Important for
Experimental Automation?

after that. This seemingly roundabout evolutionary
pathway is in fact the most efficient way for bacteria to evolve and reach the targeted resistance.

Automation is impressive

This time I talked to Dr. Atsushi Shibai, who works in a laboratory that
researches experimental evolution and experimental automation. I previously
talked to Dr. Uchida from the same laboratory about her research using medakaﬁsh, but I heard that Dr. Shibai is more of an engineer-minded person So, I
went to delve deeper into who he is.

experimental point of view, it is important tounderstand how these bacteria have evolved toadapt to its environment in order to survive.
In my experiments, I decide in advance the target
level of resistance of the bacteria to each of thedifferent drugs to be used, and then test whether I
can steer evolution of the bacteria in a targeted
direction by administering multiple drugs simultaneously. Recently, there are super drug-resistantbacteria that have emerged, where antibiotics ofall kinds are proving to be ineffective. If we canreveal how they evolved into such bacteria, wemay be able to find ways to use antibiotics so thatbacteria are less likely to develop drug-resistance.
Y▶ How do you control evolution?
S▶ When you administer antibiotics to bacteria,
most of course will die, but there will be somebacteria that will survive that are slightly resistantto the drug administered. You then select thebacteria that survived, administer the drug again,
select the surviving bacteria, and then repeat thisprocess over and over. Gradually the bacteria will
evolve into a drug-resistant strain.
If you are looking at drug resistance to one drug
substance, you can start by culturing the bacteriawith low concentrations of the said drug andgradually increase its concentration. But if there
are three drugs, there is an infinite number of
combinations of the concentration balances ofeach drug. We need to determine experimentallywhich out of the infinite number of combinations
can efficiently drive evolution of the bacteria. You
would think that the most efficient evolutionary
pathway would be for the bacteria to develop
resistance to all three drugs at the same pace.
However, if you run experiments, you find that thebacteria will first acquire resistance to one drug,
and then will acquire resistance to the other twoY▶ How long does it take to complete evolution?
S▶ It takes about 20 years for humans to generate
one generation, while bacteria can divide in about
20 minutes, so thatʼs about 2,000 generations in
one month. During that time, they divide every
hour of every day, so regardless of whether its
Saturday or Sunday, they need to be passaged. As I
mentioned earlier, in an experimental system forbacterial evolution, we select multiple conditions
from among the infinite number of drug concentration combinations, so we are always maintaining about 300 different strains. This means anenormous amount of work needs to be carried out
at the same time. Furthermore, the amount ofsolution administered varies between strains andfrom day to day, meaning we need to change thepipette settings each time.
Y▶ That means that you have to rotate the dial on
the micropipette about 1,000 times to complete
one operation! There is no way you want to dothat by handS▶ This is why automation is necessary. We alsoneed to calculate what concentration is needed in
the next step based on what was used in theprevious round. These calculations are needed forall strains and for all drugs.
Y▶ Humans are bound to make mistakes if they
were to do all of this.
S▶ I noticed that the software that came with thedispensing robot I was using for my experimentsallowed users to write a program script, so I wrote
a really long program that can calculate theconcentration and the amount to be dispensed.
Once I did that, the rest was easy and now thesetting process is much less labor intensive, and I
am free from having to rotate the dial 1,000 times.
Y▶ Automation and robots are impressive indeed.

Atsushi ShibaiSpecial Postdoctoral Researcher in the Laboratory for Multiscale Biosystem Dynamics. After
studying robotic engineering at the National
Institute of Technology (KOSEN), Nara College(NITNC or Nara KOSEN), he went on to enroll in
the graduate school program at Osaka University to pursue his doctorate. He is skilled at building devices and writing control programs, but
his ultimate dream is to create a device that
where you just put what you need in a tank andthen it will produce the desired cells or organs
̶something like you would see in a science
fiction movie.

Automation can be more
ﬂexible if we use ingenuity

×S▶ To be honest, I sometimes wonder whether
automation research commonly done in biology
can actually be called automation research. It is
hard work to learn how to hook up the equipment
you bought and then run it as laid out by themanufacturer. But, because I went to a technicalcollege, I am more keen to work on building anddeveloping different things.
My research topic in graduate school was looking
at the relationship between bacteria and spontaneous mutations. So my work consisted of endlessly exposing bacteria to ultraviolet (UV) light. It wasa perpetual repeat of feeding the bacteria, changing the medium, passaging the bacteria, andexposing them to UV light. The first year, I figured
this was part of the experience, so I spent countlesshours doing that. I was making 500 plates a week,
and spent 12 to 13 hours a day, including weekends, doing experiments. That was my life.
However, these tasks were very simple. So, I
thought I could probably automate this process,and in my second year I built a device that could
do just that. All I needed was a UV lamp, and avisible LED and photodetector pair to measure theia t octearnce toabwant resists yoaucquiregurD

Hideki YakushijiFirst generation

Tens ofthousands ofgenerations

Succession of drug-resistant lines

Business developer based in Kobe, and a
RIKEN alumni. He has a broad background inareas such as analytical chemistry, optics,biotechnology and IT. He is involved in a wide
range of activities to assist in commercializing
technologies and ideas born from academia,
including setting up opportunities for idea
sharing, finding investors, and strategicplanning.

01

い きも んTIMES

02

turbidity of the culture medium. The UV light cost
about 10,000 to 20,000 yen, but the visible LED andphotodetector pair only cost about 300 yen. For
my first prototype, the case to hold the test tube
was an empty gluestick casing. It was the perfectsize. In the end, I made one using a 3D printer. For
the controls, I used an open source single-board
microcontroller. This device, something I built fromparts that I bought out-of-pocket, was actuallymore accurate in measuring turbidity thancompared to commercially available spectrophotometers.
Itʼs not uncommon for the automated robots anddevices that are used in biological experiments tocost tens of millions of yen per unit. On top of that,
there are some challenges with them as well. For
example, biological shakers must continuously bemoving. When there are a lot of moving parts, they
can wear and break. The purpose of automatingtasks is to allow handling of large numbers ofsamples at once, so if you have a device that can
shake 100 plates at one time and that breaks
down, then 100 plates of your experiments will beruined at once. There will also be a large number ofexperiments that you cannot do while you wait for
the equipment to be repaired.
So when I automate tasks, I also build small devices. Like one where a small robot handles only a few
plates. Basically, something too simple for it tobreak. And if you have a lot the same small devices
lined up, you can handle the same large numbersof samples. I think itʼs interesting to come up withthese kinds of devices on your own.

first-place team commented that they had tried
using image processing to count the dice, butwere unable to beat the performance by humans.
The team that wrote the report describe thereason for their own defeat was because they
were working on their program up until the lastminute to improve the accuracy of one method
and they didnʼt have time to compare it to othermethods. They admit that they should have triedcounting by hand as long as the rules permit it.
And itʼs true that nowhere in the rules did it say“Counting by hand is not allowed.”
How you interpret this problem will affect yourview on automation. As long as its not somethingthat should not be done, we should try out allpossibilities. And sometimes if we think about itvery carefully, there are cases where it may not beworth automating. So I hope to maintain a flexible
mindset by not going overboard with the notionthat automation and robots are great, and leave
open the option of humans doing some tasks.

We can do moreby using our owningenuity.
We should takeon variouschallenges.

Donʼt rule out all options
Y▶ What is it that motivates you to work in the life
science field as a graduate of a technical college?
S▶ I would really like to promote the connection
between biology and robots. But I also want tostay aware of human performance.
There is a national KOSEN programming contest
held every year, and at a contest held about ten
years ago, the participants were given a task tocount the number of dice in an picture with diceof all different sizes stacked in a pile. Since it is a
programming contest you would expect that theprogram would involve some sort of image
processing. However, the first- and third-placewinners had counted the dice by hand.
Y▶ Isnʼt that cheating?
S▶ When you read the report reviewing thiscontest, what was interesting was that thePostscript

We touched on a wide range of topics that I had
not previously heard much about during myother interviews for this series, such as stories
about KOSEN and robotic competitions. We
probably covered enough topics for a manuscript three times longer than this one. Our talkmade me realize how different things can seem
when you come from different backgrounds.

Peek-a-LABooBDR Photo Tour

Introducing interesting research equipment and devices as well as favorite
spots at BDR campuses in Kobe, Osaka, and Yokohama.

4K 1 GHz NMR Spectrometer(West NMR Complex, Yokohama Campus)

This time we hear from RIKEN Hakubi Team Leader Masaya Hagiwara, who leads the Human Biomimetic System
RIKEN Hakubi Research Team that joined the RIKEN BDR in April 2023, about his laboratory.

Human Biomimetic System RIKEN Hakubi Research Team

Observing proteins in ultra-high magnetic fields

On thecover!

Q

Before establishing your laboratory at RIKEN, where and what kind of research were you doing?

AI always preferred tinkering with mechanical things over biology. With my background in mechanical engineering,I have worked for an automotive company making transmissions and during my doctoral studies, I was working on
developing microrobots. Even during my postdoc at UCLA where I was developing microfluidic chips based on newprinciples, my research was more often dealing with man-made objects. Later, I realized there were many interesting
things that could be discovered by applying such manufacturing techniques to cell culture, and I established anindependent laboratory at the Osaka Prefectural University (now Osaka Metropolitan University). There, I carried out
research to try clarifying fundamental cellular principles by using microfabrication techniques to build a spatial
platform that allows cells to recapitulate their behavior in a highly reproducible manner.

A car navigation screen?

・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・

Q

What kind of research are you aiming to conduct at RIKEN?

AI am aiming to establish technologies for generating organs from cells in vitro. Within the actual body, cells andorgans always develop into the same shape despite the complex interplay of various factors in their surroundings. My
major goal is to establish technology that can recapitulate the complex developmental environment needed fororganogenesis and control the process of organ formation from cells. I would like to establish a spatial platform
adapted to designing and generating each organ, which will be able to successfully guide cells to take on theirintended form and function within the organ.

The nuclear magnetic resonance (NMR) spectrometer uses nuclear magnetic resonance phenomenon to study the structure ofmolecules. A strong static magnetic field of 23.5 Tesla (equal to proton resonance frequency of 1.0 GHz) is applied to the center ofthe cylinder by a superconducting magnet cooled to -269℃ (4K*). To avoid disturbing this magnetic field, the structures andbuilding surrounding the instrument are made of wood and other non-magnetic materials.

*K: kelvin; SI unit of thermodynamic temperature

Researcher setting a sample tube to be analyzed in the 1 GHz NMR・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・

spectrometer. The tube is then carried to the top of the instrument by aQWhat is the composition of your lab members like?

pneumatic transport tube and automatically loaded inside theAMany of the members who have joined my lab are from Southeast Asian countries such as Malaysia, Thailand,
Vietnam and Myanmar. In the lab, we all generally communicate in English and at lunch, you will spot a variety ofdifferent lunch boxes that each person has made. We have people with backgrounds in engineering and those withbackgrounds in biology in the lab, and we work together to advance our research by covering each otherʼs shortcomings.

magnet.
The wooden scaffolding around the 900 MHz NMR spectrometeruses the techniques of the(shrine and temple carpen-

tour the facility were intrigued to see the traditional craftsmanshipcombined with cutting-edge instruments.

Please tell us something unique to your laboratory.

AOne of our major strengths is that we can propose new approaches for cell culturing experiments based on manufacturing ideas unique to engineering without being bound by conventional thinking. For experiments, we can create
what we donʼt have, which allows us to be flexible to try out and give shape to new ideas. However, we donʼt want tocreate what may be an amazing engineering technology, but that is in fact difficult to use or apply. So we try to keep
in mind what is ultimately being sought when creating something new.

Credit: Lab for Biologically
Inspired Computingters) and does not use nails. High school students who came to・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・

Q

This is a simulation modelof the network of chemical
reactions (metabolic pathways) occurring within thecell visualized in a virtual
reality platform. The
metaverse platform allows
multiple researchers toanalyze and build models
collaboratively within avirtual space.

BDR TIMES vol.16
2024 SUMMER
Issued July 01, 2024
Published by RIKEN
Center for Biosystems
Dynamics Research (BDR)
E-mail: bdr-riken@ml.riken.jp
https://www.bdr.riken.jp/en/

・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・

Q

What type of people do you want joining your lab?

ASomeone with a lot of passion. Before finding out whether or not someone is good at what they are doing, I think thatpeople who believe what they are doing is interesting are more enjoyable to talk to and their enthusiasm for what
they are doing will become contagious. Perhaps itʼs my experience of diving into different fields that I knew little
about that leads me to be more interested in learning about why someone wants to do something rather than how
well they can do something.

RIKEN 2024-033

03

BD RTIMES04