National Institute ofInformation and Communications Technology

2 018

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No.

Vol. 470

ICT Frontier Exploring with
Bio-inspired Strategy

2018 No.4 Vol.470
National Institute ofInformation and Communications Technology

CONTENTSFEATURE		 ICT Frontier Exploring with Bio-inspired Strategy

1

INTERVIEW		What is the "BioICT" that will open up the future
		 of information and communications?
		
Kazuhiro OIWA

4 Designing a Real Artificial Intelligence through Imitating

		 Memory of a Fruit Fly, Drosophila		Motojiro YOSHIHARA

6 Development of a Chemical Substance Identification

		 Device Using Microorganisms
				Understanding the "meaning" of chemical substances to living creatures whileconstructing and using bio-devices

		
Hiroto TANAKA

8 Analysis of the Recognition Mechanism of Exogenous

		 Materials in Living Cells
		

Toward an understanding, mimicking, and regulating the cellular ICT		Shouhei KOBAYASHI

10 Super-resolution Microscopy to Observe "Intellect in Nature"		Clarifying the nanostructures of organisms

		Atsushi MATSUDATOPICS

12 Recent Initiatives by NICT for Realization of 5G– From an NICT Press Release –		
13 Awards

Cover photo: "Observation of microtubule motion utilizing a total reflection
fluorescence excitation system"
This photo is a total reflection fluorescence excitation system superimposed withan observed image of microtubule motion. Microtubules execute a sliding motion
on a glass substrate surface that has adsorbed a protein motor. If we use the exuding of light that occurs in total reflection (evanescent light) to excite a fluorescent
substance marking a microtubule, we can see the movements of each individual
microtubule.
Upper left photo: "Observed image of a collective motion of microtubule motion"
Furthermore, we learned that when microtubules engage in collective motion witha high density, a millimeter-sized vortex is created.

ICT Frontier Exploring with Bio-inspired Strategy

Interview

What is the "BioICT" that will open up the futureof information and communications?

Kazuhiro OIWA

The progress of technology has ups anddowns. There are times when it grows rapidly and there are times when it stagnates.
We can perhaps conclude that currently information and communications technology
is stagnating somewhat. Moore's law stating that the components per chip will double every 18 months is also breaking down.
There are no longer sufficient resources forprocessing the volume of information which
continues to increase dramatically.
What has the potential to drive thewedge of a major breakthrough here are
the mechanisms of living things. I asked
Kazuhiro OIWA, Distinguished Researcher,
Advanced ICT Research Institute and NICT
Fellow, about the current state of theresearch and future prospects.

Distinguished Researcher
Advanced ICT Research Institute
After gaining a Ph.D, Kazuhiro Oiwa worked
as an associate professor at the Teikyo University. In 1993, he joined the National Institute of Information and Communications
Technology (NICT, former Communications
Research Laboratory) in Kobe. Since then,as a staff scientist and as a group leader,
he applied his knowledge and techniques
to understanding the properties of protein
motors as nanometer-scale machines. After serving as the Director General of theAdvanced ICT Research Institute, he is theDistinguished Researcher and the Fellow of
NICT. He was awarded the 23rd Osaka Science Prize in 2005.

— I often hear the initialism "ICT" which
stands for Information and Communications
Technology, but what kinds of things does
"BioICT" indicate?
OIWA: BioICT is the approach of knowing
living things, learning from living things, using
the characteristics of living things, and applying
them directly or indirectly to ICT (informationand communications technology).
Living things have repeated a process oftrial-and-error during a history of nearly fourbillion years of evolution and adapted to theirenvironment and have survived. During theprocess, living things have gained outstanding
characteristics.
Areas in which these kinds of characteristics
of living things can be applied technologicallyare called biomimetics. These are ideas thatare often used as breakthroughs when there aretechnological dead-ends in a variety of areas,
and this means that "we should learn fromliving things when we are in trouble."
For example, the nose cone which is thetip of the Nozomi 500-series bullet train wasmade with reference to the shape of the beakof the common kingfisher. This is because it
optimized air resistance when entering a tunnel.
Furthermore, resistance in water is being
reduced by making the surface of swimsuits forcompetitive swimmers like the skin of sharks.

Long ago, the details of the structure of
the skin of sharks were not well understood.
However, as biology progressed, details of
the structure of the skin of sharks (small
protuberances lined up regularly) became wellunderstood. However, this alone would notlead to a breakthrough. This is because thetechnology to make the tiny protuberancesis necessary. When technology progresses,
development advances suddenly. It became
possible to mimic the structure of the skin of
sharks technologically.
— What is your image of biomimetics
in information and communications
technology?
OIWA: For example, a porifera or sponge called
Euplectella (Venus's flower basket) with askeleton that uses fibrous glass for a mesh lives
in the deep sea. The structure of this glass fiber
is the same structure as the optical fiber madeby humans.
How were living things able to make thiskind of outstanding optical fiber? When we
make quartz optical fiber, we add heat to melt
the quartz and then draw out the optical fiberfrom it. However, these living things are notdoing anything like this. They are synthesizing
optical fiber under the ordinary temperaturesand pressures in which they live.
If we utilize this finding, we can achievethings that were thought to be difficult until
now. For example, suppose we try to add metal
ions such as sodium, etc. in order to improve theproperties of the optical fiber. It is difficult to add
metal ions under high temperature conditions,but if we use the mechanism possessed bythis porifera or sponge, that becomes possible.
Furthermore, it is reported that it contains
organic materials such as proteins, etc. so it ispossible to make optical fiber that is pliable anddifficult to break.

■ Learning from "Intellect in nature"— What BioICT research are you attempting
to do?
OIWA: NICT is a national research institution
for ICT, so of course we should engage in

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ICT Frontier Exploring with Bio-inspired Strategy

Interview

What is the "BioICT" that will open up the futureof information and communications?

"Intellect in nature."— What is "Intellect in nature" specifically?
OIWA: For example, there is the collective
motion of schools of fish and flocks of birds.
They move around as if the overall grouppossesses one intelligence. A group of whitecheeked starlings is not run by centralized
control but somehow they fly in a beautiful
formation. The birds are not looking at theoverall situation. They are only observing
what the bird next to them is doing. A model
stating that kind of collective behavior emerges
when the birds maintain position, distance, andvelocity with the bird next to them has been
proposed. Similar collective movements to thisare found in simple and small biomolecules
such as protein filaments, etc. It is conceivablethat the findings obtained here could be applied
to control technology in self-driving cars, toensure that they do not crash into other cars or
objects.
research in cutting-edge areas of informationand communications, but I believe we mustalso conduct high-risk research that companies
would hesitate to do. One kind of research
like this is bio research for ICT. As I statedabove, there are many examples of researchers
gaining hints from living things. However, thequestion of how to apply this to information andcommunications technology is the issue going
forward.
Firstly, it is important to come into contact
with the functions of organisms and realize that
"this could be used as a new idea." I intend
to combine these kinds of organism-derived
technological concepts under the term "Intellectin nature."
Now technology of artificial intelligence isdeveloping rapidly. On the other hand, a large
number of phenomena can be found in thenatural world which also seem to behave witha high level of intelligence. What is behind
the intelligence possessed by nature? We canconclude that it is the information possessedby nature and the information processing of"Intellect in nature." In the same way as analgorithm (computational procedure) in theinformation processing of computers, someform of algorithm is also functioning inside

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— The information science of living things is
simple, isn't it?

OIWA: Living things use their own uniqueinformation devices such as information
systems and sensors, etc. in order to survive.
These correspond to the IC chips and sensors
used in general computer systems.
The digital devices we use were developed
based on the idea of using a lot of energy to
reduce noise. In contrast to that, the information
systems of living things are in the middle ofnoise. Despite that they work properly, it seems
that living things do not use much energy to
reduce noise. If we learn from this technique,perhaps we will be able to efficiently drawout significant information from information
containing a lot of noise, and the huge amountof electricity for reducing noise will probably
become unnecessary.
There is still another way in which thesystems of living things are superior. I mean
their sensitivity with respect to a particular
substance, or in other words their specificity,
is extremely high. Furthermore, we canconclude that even if each individual device
is small and moves in a different way, they
have the robustness (stability with respect to a
disturbance) of functioning stably because they

Figure 1 “Intellect in nature” — the “intelligence” that is discovered in all structure hierarchies of organisms

We exhibit in exhibitions, etc. too. I think theimportant thing is to learn about what kindsof needs there are in society by deepening
collaboration with outside organizations. Basic
research that pursues truth is also important,but I believe that it is also important for us as anational research institution to conduct researchthat meets the needs of society.
— How do you think you would like todevelop this Research Institute?

Figure 2 Overview of bacteria chemical sensing that combines chemotaxis mechanism of bacteria withmachine learning based on Bayesian inferencefunction as a group.

■ The role of BioICT— In what kinds of areas can the information
systems of living things be applied?

— At the Advanced ICT Research Institute,
how do you proceed with human resources
development and collaboration with outsideorganizations?

OIWA: One is application as chemical sensors.
We humans have used the characteristics ofliving things for the sensing of chemicals forsome time. For example, it is reported that in theold days coal miners took canaries with themwhen they entered the mine shaft. A canarydetects poisonous gas and lack of oxygen andreliably reacts sooner than a human being, so
if the canary stopped chirping the miners knew
they were in a dangerous situation.
Chemical sensors using Escherichia coli
were developed by obtaining hints from thiskind of sensing of chemicals by living things.
We can conclude that the modern canary was
made using Escherichia coli. This technology
can be used in the quality control of food, etc.,
so collaboration with companies is proceeding.

OIWA: This Research Institute also offers
graduate school education through partner
graduate school agreements with universities,
so many students come here. The advantage
for the students is that this Research Instituteoffers a wide range of research areas. They
can have an interdisciplinary perspective.
There is nanotechnology, device engineering,and biology; moreover, within biology there
is biology using individual organisms like the
Drosophila fruit fly and research targeting cells
and protein molecules. There are researchers
specializing in information science and in
neuroscience too.
We are also actively advancing technology
development in partnership with companies.

OIWA: There is an institute that I imagine tobe the model. That is the Woods Hole Marine
Biological Laboratory in Massachusetts, theUnited States. That is the workplace of Osamu
SHIMOMURA, who was awarded the Nobel
Prize in Chemistry in 2008. This Laboratory
is in a summer retreat area, and in the summer
it runs a summer school in an environment
in which researchers and students gathered
together from many places can all hold openminded discussions. Researchers in different
areas can conduct information exchanges there,
and as a result academic exchanges progress
further, leading to new discoveries.
I believe that we should learn from Woods
Hole and invite many researchers and students
who are the future of our institute to create aforum enabling discussions and informationexchanges.
Living things are a treasure house ofknowledge. I intend to further increaseknowledge regarding living things and at thesame time I intend to introduce to many people
about the research activities at this ResearchInstitute to make it a place which spreads
knowledge further. In addition, I intend to go
beyond the world of biology and, with the helpof researchers in a wide range of areas, utilize
the rich world of living things in informationand communications technology.

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ICT Frontier Exploring with Bio-inspired Strategy

Designing a Real Artificial Intelligence through Imitating Memoryof a Fruit Fly, Drosophilae frequently observe the misunder-

Motojiro YOSHIHARA
Chief Senior Researcher
Frontier Research Laboratory
Advanced ICT Research InstituteHe received a Human Frontiers Science Program fellowship to do postdoctoral work at
the City of Hope, California. After working as
a visiting scientist at MIT, he joined the Department of Neurobiology at the Universityof Massachusetts Medical School as a faculty member in 2006. In 2013, he left University of Massachusetts Medical School towork as a visiting professor at MIT. In 2014,
he moved back to Japan, and joined NICT.
Ph.D. (Science).

References＊1 Yoshihara et al., (2005) Science
310, 858-863.
＊2 Flood, Iguchi, Gorczyca, White,
Ito, & Yoshihara (2013) Nature,
499:83-87.

W standing that "artificial intelligence"■ New hypothesis about memory

using deep learning, etc., which is extremely popular currently, functions in thesame way as the original "intelligence" produced by the brain, but actually the humanrace still does not know much about how "intelligence" functions in the brains of humanbeings and other animals. This is because
the mechanism of the original "memory" inthe brain is not yet understood, in spite of
the fact that the "memory" (a katakana word
without an accent at the beginning) of computers is used freely. It is this "memory" thatis the foundation of intelligence, and knowing how memory is created and stored is understanding the essence of intelligence.
However, there was no method of knowing how nerve cells, an element of the brain,create memory, so understanding the mechanisms of memory was always impossible
until now. There is no alternative but to create an entirely new, original method to attempt to solve a mystery that no one in theworld has been able to get close to solving.
In this paper, I present the methodology ofmemory research that we developed overmany years in the United States before I
joined NICT, its development at the Advanced ICT Research Institute, the conceptof "real artificial intelligence" which began
to bear fruit when combined with the technology of NICT, and the limitless possibilities of the methodology which started fromnothing.

It is believed that memory is possible dueto the changes in the connections between
nerve cells (neurons). Therefore, firstly, I useda simple experimental system to investigate themechanisms of that synaptic plasticity.
That experimental system consisted of theactivity-dependent changes in the synapses
connecting the motor neurons and muscle cellsof the fruit fly, Drosophila, and I investigatedthat system in detail and proposed in Sciencea hypothesis of memory based on a completely new idea, the "local feedback hypothesis"(Figure 1).*1 I thought that positive feedback
is generated between two cells connected in
the brain being reciprocally strengthened byreleasing transmitters to each other, resultingthat memory is retained in a single synapse,
furthermore causing morphological changes
in the synapse that change it into a persistentmemory. It is a "physiological condition" rather
than molecules that retains short-term memory.
This is a new way of thinking that did not exist
before, and it explained the many experimental results reported until then well, so I expectthat this was the general "micro" mechanismthat forms memory. However, there was no experimental system for connecting this to macro
memory for testing, so this hypothesis was no
more than a desktop theory. If this was reallyoccurring in the brain, then it would be a basic
principle of brain function, so I thought of anexperimental system for testing this any way I
could, and deployed all the resources of the laboratories I was presiding over at the Universityof Massachusetts and MIT to attempt to create
an experimental system for verifying this hypothesis from nothing.

＊3 Yoshihara (2012) JoVE 62: e3625.

＊4 Motojiro Yoshihara (2013) Life
Science First Authors(http://first.lifesciencedb.jp/
archives/7415#more-7415)■ Original experimental system
connecting micro to macro —"Feeding" command neurons＊5 Sakurai, Littleton, Kojima,
Yoshihara, currently being
prepared for publication

Figure 1 "Local feedback hypothesis" (Science, 2005)

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In order to connect the micro-mechanism
between cells postulated in the local feedback
hypothesis to memory, it is necessary to get micro cell changes to correspond to the memorythat is manifested as macro behavior. The newstrategy I thought of for that purpose was to use
the concept of a "command neuron" establishedFigure 2 Witnessing memory being achieved with the feeding neurons in the brain of the fruit fly,Drosophila in real time. (Nature, 2013)① stimulus
Unconditioned

Dog food

by Dr. Kazuo IKEDA, the mentor of this author, in the 1960s as a neuron that commands
behavior. If memory is formed by changes in
micro synapses on this neuron then that should
be manifested as macro behavior changes, anddue to that we can make micro and macro correspond. Therefore, firstly, we started by developing a method for finding command neurons. We
discovered the "Feeding neuron" commanding
eating behavior which is optimal (refer to thenext page) for memory research (Figure 2) andreported this to Nature.*2 Furthermore, I independently developed an experimental system
which we could observe the micro activity ofcells in the brain while at the same time observing macro eating behavior.*3 Due to these technical developments, we completed preparations
for getting micro cell phenomena to correspondto macro behavior.

■ Pavlov's fly
I thought of conducting an experiment similar to the classical conditioning of Pavlov,
which is well known as a model of memory,in order to create memory in the Feeding neurons. It is predicted that the inside of the brainof a dog would change through this "conditioning" as the sound of a bell activates the neural circuits equivalent to the Feeding neurons.
Therefore, if we conduct a similar experiment
to the "Pavlov's dog" experiment using a fly,I expected that we could track the "single celllevel" memory created in the Feeding neurons*4(Figure 3). Together with Dr. Akira SAKURAI,
who had come to study at the laboratory of theauthor in the United States as a post-doc student (currently Senior Researcher at NICT), we
developed an experimental method for classicalconditioning of a fly based on Pavlov's experiment. In the Memory Neurobiology Project of
the Frontier Research Laboratory in the NICT
Advanced ICT Research Institute, it was confirmed that due to conditioning, the reactivityof the Feeding neurons changes; in other words,
new connections are formed in the neural circuits.*5
Currently, we are using a two-photon microscope that can see deep brain parts to attempt
to detect the changes in the connections in the
Feeding neurons when a fly remembers throughFeeding command neurons

Bell onlyBell
Conditioned
stimulus

Training

Saliva of the dog(feeding behavior)

Saliva of the dog(feeding behavior)

Figure 3 Pavlov's classical conditioningclassical conditioning. Using the methodologythat we built up uniquely, we can observe a
scene that the human race has never seen before,"the moment in which memory is achieved," inreal time. We have traveled a roundabout route,but I am excited to say that, as indicated by thesaying "seeing is believing," after this seriesof technical developments, it has finally become possible to verify our original hypothesis(Figure 1), and we are able to reach the principles of memory at last.

■ Future prospects — Designing
real artificial intelligence byimplementing, on a device, thechanges in a single cell whenmemory is formed
This research goes beyond basic research on
the principles of memory to an analysis of thesingle cell level when memory is formed, whichenables us to understand for the first time in history the mechanism by which each and every element of the brain stores memories, or in otherwords the functioning of "memory" in the brain.
These obtained findings, by themselves,
make it possible to directly develop devices
that imitate the functions of nerve cells, so inthis project we are already planning to carry
this out jointly with the group of Advanced
ICT Research Institute Director General
Iwao HOSAKO, which is developing high-performance semiconductor devices. By connect-Figure 4 Many devices imitating the input-output
change of the feeding neurons areconnected in order to artificially recreate
the neural circuits that retain memory.
Blue arrows: input-output of each device(ellipse); red: the circuit that retains thememory.

ing many of these devices together to make a
network (Figure 4), we can create "real artificial
intelligence" for the first time by truly imitating
the functions of the brain.
There is a possibility that this will lead to thedevelopment of computers with much greater
energy efficiency like the brain. In addition, we
can expect that creating silicon circuits modeled on neural circuits will conversely becomea new methodology that gives insights into theinformation processing of the brain and also tooutstanding problems of the brain such as consciousness, etc. Going forward, the dream will
expand even further to new information andcommunications technology / new biology ofthe brain.

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ICT Frontier Exploring with Bio-inspired Strategy

Development of a Chemical Substance Identification Device Using Microorganisms
Understanding the "meaning" of chemical substances to living creatures while constructing and using bio-devices

hemical substances possess a vari-

C ety of effects including taste, aroma,

Hiroto TANAKA

Senior Researcher
Frontier Research Laboratory
Advanced ICT Research Institute
After completing a doctoral course in thegraduate school, became a Research Scientist of JST and then joined NICT in 2009as Senior Researcher. Has been engaging
in research and development of chemical
substance identification technologies. Ph.D.
(Science).

Heading toward theconcentrated areas offavorite substances
Swimming straight ahead
Switching stochasticallyRandomly changing direction

Attractants

Observation

Cells(CW)Clockwise(CCW)Counterclockwise

Glass substrate

Figure 1

6

The chemotaxis response of Escherichia
coli and an example of the observed
imagesa. Chemotaxis response b. Tethered assay
c. Image observed under the microscope(phase difference image, scale bar :5μm)

NICT NEWS 2018 No.4

pharmaceutical benefits, toxicity, etc.
These kinds of effects have "meaning" due tothe "existence of living creatures." One typeof microorganism, the bacteria Escherichia
coli (E. coli), detects chemical substances inorder to live, and cells of E. coli change their
behavior deperding on the properties of
the chemical substance. We use the behavioral changes of cells of E. coli to "visualize"
the chemical substance properties, andconstructed a foundational technology for"identifying chemical substances" from theproperties visualized via behavioral change
by using statistical techniques. In this article,
we present the background to the technology development, the details of our efforts,
and the prospects going forward.

■ Background to the development research
Due to technological progress, there are now
a variety of chemical substances in the environment surrounding us. The chemical substancesthat exist in this kind of environment affect living creatures in a variety of ways.
The effects of chemical substances on living
creatures are wide-ranging, so chemical substance evaluation and identification (categorization) of their bioactivity have become more
and more important in recent years.
We thought, "if living creatures are affected by chemical substances, could we use thefunctions of those living creatures for chemical
substance sensing?" and studied the possibilities for being able to use microorganisms for thesensing of chemical substances. The bacteria
Escherichia coli, one type of microorganism,
detects the chemical substances in its environment and swims in the direction with a highconcentration of substances it likes (attractants)(chemotaxis response, Figure 1a). Escherichia
coli are unicellular organisms with a size of several microns, and we can say they are a chemical substance detection device that engages in"packaging from the chemical substance signal
input to the response output." We worked on thedevelopment of a chemical substance identification device by applying this chemotaxis response of cells of E. coli.

■ "Quantitative measurement of the response of microorganisms" that visualizes the properties of chemical substances
using microorganisms
Using living creatures as chemical substancedetectors consists of the detection of chemical
substances which have interactions with living
creatures (bioactivity). Escherichia coli changes the way it swims depending on the types andconcentration of diverse chemical substances,
so many chemical substances can be detected.
In order to correctly determine what the chemical substances detected from this chemotaxis response are, it is necessary to accurately quantify
subtle differences in the response. With the chemotaxis response, "swimming straight ahead"and "changing direction" switch stochastically.
This swimming switch reflects the rotation direction switch of the flagellar motor (a molecular motor at the base of the roots of flagellum).
What we focused on here was the changes in
the chemotaxis response over time (the adaptation process). Here, we used a tethered assay(Figure 1b, c, one of conventional techniques
for research into the Escherichia coli chemotaxis response) to acquire data by photographing
the rotational motion of the cell body (reflecting the rotation of the flagellar motor) for ten
minutes at a frame rate of 100 Hz. For this dataacquisition, we improved the micro-channels inorder to reduce effects of the speed of flow whena solution containing a chemical substance wasexchanged (Figure 2a, b), and developed an image analysis program to quantify the motion of
the several hundred cell bodies that existed on
the photographic screen and computed the ensemble average in order to reduce fluctuation of
the individuality of the cells (Figure 2c). Due tothe development of this measurement system,
we were able to acquire large amounts of data
related to the chemical substance input and response output and it became possible to use thebehavior of the bacteria Escherichia coli as adetector.

"Blind sake tasting"
Estimationof the sake brand

Taste? Aroma?

Blind sample (blind tasting)Chemical substance detection sensor(using bio-functions)Chemical substance??

Figure 2 Quantitative measurement of the response of
microorganisms
a. Measurement chamber b. Infusion of the test solution
c. Measurement system (mainly comprised of a
microscope, high-speed camera, and computer)■ Extraction of chemical substance information using statistical processing"From detection to identification ofchemical substances"
If the swimming of cells of E. coli changes,
we know that some kind of chemical substanceis present there (detection), but identifyingthat chemical substance is difficult. In orderto overcome this difficulty, we used statistical techniques. Conceptually, like "blind saketesting" carried out by humans, by statistically
speculating (identifying) the type of chemical
substance with "detecting chemical substances"by Escherichia coli and statistical techniques(Figure 3), we can say that we have truly developed a "method (device) for identifying chemical substances using microorganisms" based ona measurement system and statistical analysis
techniques. For basic research, we tested amino acids as a standard sample (training data).
We applied a solution containing one type ofchemical substance from the standard sample tocells of E. coli inside micro-channels, and recorded the changes in the chemotaxis responseover time. In order to test the possibilities forchemical substance identification including the
response fluctuation for each measurement, we
decided to dispose the cells and the micro-channels after each single measurement (response
measurement for ten minutes). We carried out
this measurement repeatedly while changing
the type and concentration of the amino acids,
acquired a large amount of data, and evaluatedidentification performance (Figure 4). Due tothe properties of Escherichia coli, in the caseof the identification of amino acids, the identification rate changed depending on the combination, but with the combination of L-glutamic
acid and L-asparagine, the identification rate of
the blind sample exceeded 90%. The results ofthis test showed that our techniques functioned
well and a solution containing a chemical substance can be identified by combining living
creatures and statistical techniques.

"Detecting chemical
substances"

Estimationof the substance typeTime (s)Figure 3 "Detecting chemical substances" using the bacteria
Escherichia coli

Acquisition of training data(standard sample)
e.g.)Compiling a databaseof response outputs

Figure 4 Compiling a database of standard samples using Escherichia coli

■ Future prospects
As we stated at the beginning, it is conceivable that the technologies presented in this article could be used as sensors for monitoringchemical substances present in the environment, etc. Furthermore, there is the possibility
that they could be used as evaluation devices fordrinks and food by applying their "identification
device" aspects. Regarding identification ofchemical substances from the output responseof the bacteria Escherichia coli (above, "detecting chemical substances"), we skipped thedetailed description here but the important thing
in preparation of the "standard sample" used for
acquisition of the training data (database creation) is that "the standard sample is labelled(amino acid name, drink name, production region, origin, etc.)." It is easy to understand if
one thinks of "blind sake testing," but there areno major restrictions on the object to be identified. Sake, wine, beer, soft drinks, etc., areitems for which living creatures (human beingsand Escherichia coli) can detect differences(the items have bioactivity), and if the brand isclear then they can be objects of identification.
For example, water that has been used to wash
rice, vegetable juice, etc., can also be selected

as objects of identification. In the future, if thesekinds of ingredient inferences and production
region inferences, etc., of samples are achieved,
applications to the safety of food and the quantification (visualization) of branding, etc., areexpected.
In this article, we presented the fact that using living creatures as detection devices enables
identification of chemical substances with bioactivity as the filter. It can be concluded that weare utilizing information that "has meaning forliving creatures" such as the taste, aroma, toxicity, pharmaceutical benefits, etc., possessedby chemical substances. This can be concluded to be a basic technology for quantifying andtransmitting "meaning and value" of chemical
substances produced by interaction with living
creatures, rather than composition or structureof chemical substances. In the future, it may be
evolved to technology for communicating the"aroma" or storing the "taste" associated withmemories. Our approach can be said to be an
instance of utilizing biological features in ICT. I
hope we can make a contribution from the starting point of developing the biomimetics field of
information processing, which involves learning techniques of chemical substance information processing from living creatures.

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ICT Frontier Exploring with Bio-inspired Strategy

Analysis of the Recognition Mechanism of Exogenous Materials in Living Cells
Toward an understanding, mimicking, and regulating the cellular ICT

ur research project aims to create a

O new ICT paradigm using the informa-tion processing and communication
capabilities of the cell, the smallest functional unit of life, by carrying out research anddevelopment into technology for measuring
and controlling cell functions. This article focuses on what has been clarified for the firsttime regarding how cells obtain informationon the outside world, and how they respondflexibly to it, by an original measuring technique using artificial beads.

■ BackgroundShouhei KOBAYASHI
Research Manager
Frontier Research Laboratory
Advanced ICT Research Institute

After completing a doctoral course in thegraduate school, joined NICT in 2005 andhas been engaged in researches on understanding cellular responses against invading artificial materials. Currently, a research
manager (since 2018). Ph.D. (Engineering).

Living cells exchange information with theoutside world through molecular communication. This concept of molecular communication
applies not only to communication within individual cells, but for example, it also applies to,e.g., communication between cells that make up
our immune system, as well as a variety of otherphenomena (Figure 1). Molecular communication is biocompatible, and it is useful because
it can even function in aqueous environments.
Therefore, if it could be mimicked artificially

Figure 1 Molecular communication carried out by living cells, and extensive
related fields

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and controlled, it could be used to complement
existing telecommunications technology, e.g.,
optical telecommunication, or even surpass it
depending on the environment in which it isused. It has the potential to become a new formof telecommunications technology.
It has only been 10 years since the conceptof molecular communication was put forth,making it a new research field, and a lot of theresearch carried out so far has been theoretical.
However, due to advances in bioimaging techniques, measuring techniques using microfluidic devices, etc., in recent years, the groundwork
has been laid down for carrying out research
involving demonstrations through biologicalexperiments. This has resulted in increased attention to molecular communication research.

■ Introducing artificial beads into
living cells and inducing autophagy
As a first step toward gaining a better understanding of how living cells carry out molecularcommunication, and controlling it, we focusedon how cells obtain information on the outside world. Research on this issue had focused
mainly on the signaling pathway via receptors,
but due to, e.g., the small size of observation
targets, little was known about the phenomena
taking place immediately after drugs and otherforeign substances entered cells.
This led us to develop a technique for measuring the cellular response (Figure 2a) thattakes place in the vicinity of non-biodegradable, biomolecule-coated beads introduced into
living cultured cells (HeLa cells). By using thenon-biodegradable beads as markers in microscopy, this method enables detailed observationof the cellular response to the biomolecules attached to the surface of the beads. Moreover,
the observations were carried out using fluorescence live cell imaging technology (Figure 2b)
cultivated over many years by our group, andlive CLEM imaging to examine the same area
observed under a fluorescent microscope using
an electron microscope.
So far, this method has been successfully
used to induce autophagy (autophagy: a typeof protein degradation mechanism in cells. Targeted substances are engulfed by a membrane
structure, then broken down) in a limited area

Figure 3 Image of DNA-coated bead 1 hour after introduction into a cell. The same beadseen in the fluorescence image was observed under an electron microscope.
It can be seen that a membrane structure similar to a nuclear membrane has
been formed around the bead (shown in red in the schematic diagram) to avoid
autophagy (green).

Figure 2 Technique for measuring the cellular response
upon introducing an artificial bead into a living cella. Overview of experiment to introduce a bead
into a living cellb. A high-resolution fluorescence imaging systemused for observing living cells. The microscopeis set up inside a temperature-controlled room
to maintain stable observation conditions.

around the bead introduced into the cell, withall the details successfully monitored. Thismeans that cells make use of the autophagymechanism to deal with foreign substances thatenter them.

■ The discovery of a mechanism
for avoiding the autophagy ofexogenous DNA
So, are all foreign substances captured andbroken down through autophagy? Recent studies have revealed that at least DNA is treateddifferently.
The introduction of DNA into living cells is
a technique that is indispensable to fluorescencelive cell imaging, gene therapy, and a variety ofother fields. Various kinds of techniques haveso far been developed to introduce DNA into
cells, but little was known about when and how
the entry of DNA was actually being detectedby cells. This prompted us to introduce beads
coated with double-stranded DNA into cells,
and analyze the cellular response. As a result,it was revealed that the DNA-binding protein,
BAF (barrier-to-autointegration factor), immediately detects the exogenous DNA, and forms
a membrane structure similar to a nuclear membrane around it within approximately 10 minutes. On the other hand, the membrane typicalin autophagy was unable to engulf the bead andwas finally observed only in areas far away

Figure 4 Mechanism by which exogenous DNA avoids degradation through autophagy

from the bead (Figure 3).
In light of what we know so far, it seems
that in autophagy, it is the invasion of exogenous material (the breakdown of the endosome*membrane) that is being detected rather than theforeign substance itself (upper part of Figure 4).
This is a very good strategy to adopt, because it
allows the handling of all foreign matter regardless of type. On the other hand, it is believedthat the DNA sensor molecule, BAF, directly
detects the introduced exogenous DNA, andforms a membrane structure around the bead
before autophagy begins in order to protect itfrom degradation (lower part of Figure 4). If we
could gain a better understanding of this flexible foreign substance recognition mechanism ofcells, we believe it will lead to the developmentof a technique for introducing substances of our
choice into living cells, and making it function
reliably.

■ Future prospects
The experimental method of using artificial
beads has enabled us to analyze what happens
inside cells when foreign substances are introduced into them with high spatial and tempo-

ral resolution, which we knew little about until
now. In the future, we hope to further improve
this technique of measuring and controlling thefunctions of cells using artificial beads, so that
we may control the timing of the entry of the artificial beads into the cells, create and use beads
with multiple types of biomolecules attachedto them, etc. We believe this will lead to thedevelopment of technology that would enable,
by making use of the capabilities of cells, extraction and utilization of information associated with chemical substances and the like.

＊EndosomeA structure seen during the process of the cellular uptakeof a substance from outside the cell (endocytosis), and it
is formed by the invagination of the cell membrane as it
engulfs the targeted substance. The foreign substance isreleased inside the cell when the endosome membrane disintegrates (= the invasion of a foreign substance).

NICT NEWS 2018 No.4

9

ICT Frontier Exploring with Bio-inspired Strategy

Super-resolution Microscopy to Observe "Intellect in Nature"
Clarifying the nanostructures of organisms

he sophistication achieved by organ-

T isms far outperforms the technolo-

Atsushi MATSUDA
Senior Researcher
Frontier Research Laboratory
Advanced ICT Research Institute

After receiving Ph.D., the author studied
biology at Purdue University (USA), thenchanged subject to microscopy after having moved to University of California, San
Francisco. In 2010, he became a researcher
at NICT and began studying microscopy forbiology.

gies created by mankind. Mosquitoesthat suck human blood, for example, aremerely 2 mg in weight. The reason why thistiny little organism is capable of far outperforming today's robots is because it consists of microscopic molecular complexes
with a variety of functions measuring only
10 – 150 nm (a nanometer is one-millionthof a millimeter), which are capable of functioning as molecular devices. Countless molecular devices like these work as high-sensitivity sensors, motors, memory devices andso on, forming cells and bionts with complex
functions. Organisms harbor unknown principles and materials with the potential torevolutionize current robots and computers.
High resolution measuring technologies forlive organisms are indispensable to understand and make use of these principles. We
are therefore currently developing new microscopy technologies using light.

Cancer cells in humanConventional microscopyY

The cells that make up the bodies of organisms are so small that they are almost invisible,
but it is believed that inside these tiny cells are
particles and fibers that are one-thousandth or
one-ten-thousandth the size of even these cells,
undergoing drastic transformations to form
structures that are elaborate overall. A characteristic of structures formed by organisms
is that they are not static. In other words, they
are constantly changing. These structures canbe observed at extremely high resolution byusing electron microscopes, but their dynamic features cannot be observed. Measuring thetrue nature of biological structures will requirea high resolution imaging technique that uses
light to monitor organisms as they are.
Fluorescence microscope imaging using
visible light has resulted in a variety of breakthroughs in medical and life science research.
One of the founding technologies was the dis-Super-resolution microscopy

5 µm YX
Junctions between homologous
chromosomes in mouse
Conventional microscopy■ A revolution in super-resolution
microscopy using light

Z

Super-resolution microscopy

Chromosomes infission yeast
Conventional
microscopy

2 µm
Super-resolution
microscopy

5 µm
Figure 1 Comparison between conventional fluorescence microscopy and super-resolution
microscopy. In the upper panel, different molecules within the cell have been labeledin three separate colors. To the right of the planar images are three-dimensional
images seen from the side. In the lower panel are images of overlapping fibers thatwere indistinguishable from one another using conventional microscopes, but can
now be seen clearly due to super-resolution microscopy (below left: modificationof image taken from Optical Alliance (March, 2014), pp.31 – 35. Below right:
modification of image taken from Chromosoma (2015) 125: pp.205 – 215).

10NICT NEWS 2018 No.4

Figure 2 A super-resolution microscopy image seen in a frequency space.
The image on the right is a magnification of the area in the image
on the left enclosed in the yellow box. Bright spots due to straylight are indicated by red arrowheads (modification of image takenfrom Nature Protocols (2017), 12: pp.1011 – 1028).

covery and application of a green fluorescentprotein, which was awarded the Nobel Prizein Chemistry in 2008 (Osamu SHIMOMURA
et al.). A protein synthesized through genetic recombination emits a fluorescent light, sothat when an excitation light is illuminated ona living organism, only the targeted protein
shines, enabling its observation against a dark
background. Then the development of a super-resolution microscope, which was awarded
the Nobel Prize in Chemistry in 2014 (StefanHell et al.), realized a method superseding thetheoretical limit of optical resolution. The resolution of a fluorescence microscope is limitedby the diffraction limit of light, which is around
250 nm. However, using super-resolution microscopy realizes a resolution of 15 – 100 nm,
allowing things to be seen that have never beenvisible until now (Figure 1). Research and development in this area has greatly expanded thespace-time of technology for measuring organisms, resulting in the possibility of continuous
monitoring of smaller targets.

■ Technology for realizing extreme
resolution
The principle behind super-resolution microscopy has been experimentally proven, but
it is extremely difficult to take actual measurements using live organisms. It is difficult
enough obtaining normal resolution using liveorganisms, so realizing an extreme resolutionthat is several times higher requires extremecare. We have therefore been developing thetechnology needed to use super-resolution microscopy on actual organisms. For example,
in three-dimensional cells, fluorescent shotnoise from out-of-focus planes increases inintensity, greatly reducing the resolution. In
our super-resolution microscopy, we applied
deconvolution to remove this fluorescent shotnoise from out-of-focus planes, and image processing techniques such as denoising to reduce
this noise, and succeeded in obtaining high resolution even in its presence. Moreover, images
obtained through super-resolution microscopy
faced the problem of interference patterns created by artifacts (errors in the data and warped
signals generated during the processing of signals and images), but identifying their causes

Figure 3 The newly developed chromatic aberration correcting software has
been made available to microscope users throughout the world.

was difficult. In response to this problem, we
proposed a solution for easily identifying problems in optical adjustments such as misalignments in the optical axis and presence of straylight, by carrying out a spatial frequency analysis of the obtained images (Figure 2).
Another thing that we have been working on
is high-precision chromatic aberration correction. In fluorescence microscopy, multiple molecules can be targeted simultaneously for observation by labeling different molecules withdifferent fluorescent colors (blue, green, red,etc.). However, the refractive index for lightdepends on its wavelength, resulting in minor
chromatic shift in microscope images. With theenhancement of resolution through super-resolution microscopy, even the slightest chromatic
shift makes the results difficult to interpret. The
refractive index variation in organisms in particular is unpredictable, so it was extremely difficult until now to correct the chromatic shift in
the observation of organisms. We developed a
new method to acquire microscopic images andto measure the chromatic shift in the images,
and achieved a correction accuracy of around

15 nm when observing three-dimensional samples (Figure 3). This level of accuracy will allow the correct interpretation of multi-coloredsuper-resolution microscopy images. To contribute to the progress of biological research,
we are providing this high resolution chromaticaberration correcting software that we developed for free.
https://github.com/macronucleus/Chromagnon■ Future prospects
If we could elucidate the principles behind
the impressive functions found in organisms,
it would advance human innovation to a newlevel. Super-resolution microscopy has thepotential to revolutionize the field of life sciences, but there are still numerous issues thatneed to be resolved, such as the toxic effects by
exposure to strong excitation light to monitor
living organisms over a long time. In addition
to further enhancing resolution, we will continue our research into new directions to improvethe method to observe living organisms, e.g., by
mitigating its toxic effects.

NICT NEWS 2018 No.4

11

Recent Initiatives by NICT for Realization of 5G– From an NICT Press Release –T

he fifth-generation mobile communication system (5G) hasfeatures that could not be provided by previous mobile communication systems, such as ultra-high speed, ultra-low latency, alarge number of concurrent connections, etc. and is expected toconnect all objects wirelessly and become the "infrastructure" ofsocial life. NICT is advancing the implementation of demonstration
tests toward the realization of 5G.
The NICT Wireless Networks Research Center, aiming to construct intelligent transport infrastructure utilizing the "ultra-low latency" of 5G, developed a system to ascertain the traffic conditions
on the surrounding roads in real time (Figure 1). In this system, thesensors of an electronic roadside mirror (a standard roadside mirror
with a stereo camera and laser range finder (LRF) installed) can carryout automatic identification, and then the information can be compressed and wirelessly send to a server and also integrate multiple
pieces of diverse sensor information to construct a highly reliable
and advanced map database (dynamic map).
Using this system, the Research Center constructed a test environment for an intersection simulated at the Yokosuka Research
Park (YRP) and confirmed that it was able to accurately ascertain thepositions of cars and pedestrians.

Furthermore, the Research Center used the wireless accessmethod called the Grant Free method, the introduction of which is
being considered for 5G, to confirm that "a large number of concurrent connections" of approximately 20,000 terminals were possible
with regards to one base station. If this method is applied, even ina situation where congestion of communications occurs, such as innatural disasters, etc., information can be transmitted from many
terminals within a limited time. This demonstration showed thatthese functions can be utilized effectively in the two use scenariosof a disaster prevention warehouse when there is a disaster, and afuture smart office (Figure 2).*
At Wireless Technology Park 2018 held from May 23 (Wednesday) to May 25 (Friday), 2018 (at Tokyo Big Sight), demonstration exhibits and lectures related to 5G/IoT, including the above outcomes,
were presented (Figure 3). The visitors showed interest in new concepts for wireless system utilization, and there were opportunities
for discussions about technical issues, etc. with people from a variety of industries. Regarding 5G, a variety of issues can be consideredbased on the use scenarios, so the Research Center will continue toadvance research and development while also advancing discussions with people from a variety of industries.

Figure 2

Smart office environment utilizing a variety of 5G
functionsFigure 3

The exhibits at WTP2018

Figure 1 Configuration of the constructed intelligent transport infrastructure＊ Some of the research and development regarding electronic roadside mirrors is the outcomeof an R&D of frequency-effective utilization technology from the Ministry of Internal Affairs andCommunications. Furthermore, the demonstration of many simultaneous connections is theoutcome of a contract for research and examination regarding the technical conditions, etc. for a
fifth-generation mobile communication system from the Ministry of Internal Affairs and Communications, and was implemented through joint research with Itoki Corporation, ABIT Corporation,
Sharp Corporation, and SoftBank Corp.

▪ Related Press Releases• "Confirmation of Simultaneous Connection of 20,000 Terminals in the 5G Demonstration Test" (Dated March 29, 2018)
http://www.nict.go.jp/press/2018/03/29-1.html (only in Japanese)• "For Realizing an Intelligent Transport Infrastructure Utilizing 5G Ultra-low Latency" (Dated June 7, 2018)
http://www.nict.go.jp/en/press/2018/06/07-1.html

12

NICT NEWS 2018 No.4

The Space Development and Utilization Grand Prize gives recognition to outstanding achievements in contributing greatly to the promotion of space development and utilization. The awards aim to contribute to the further promotion of space development and utilization,and cultivate greater awareness and understanding for it among people in Japan. The Maejima Award was established in commemorationof the achievements of Hisoka MAEJIMA, a founder of the telecommunications industry, and to pass on and build on his spirit. The awards
are presented to people with outstanding achievements in the advancement of the information and communications (including postal
services) or broadcasting industries, and two awards were won by people at NICT at the 63rd award-giving ceremony held this fiscal year.

Minister for Internal Affairs and Communications Award 3rd
Cabinet Office
Space Development and Utilization Grand Prize
National Institute of Information and Communications Technology＊
Overview●Description: Contribution to the social activities through the development and operation of
space weather forecast system
We have been monitoring the ionospheresince 1958 to forecast and issue warnings regarding the transmission of radio waves. Since
1988, we have also been involved in ascertaining the status of space weather, which causes
disturbances in the ionosphere, and providing
information on forecasts for 365 days of theyear, in addition to engaging in research anddevelopment aiming to improve the accuracy of
forecasts, for which we were given the award.

＊Awarded to the organization

We won high appraisal, particularly for our major contribution to the development and utilization of space, including the issuing of warnings
in the event of major solar flares to prompt theimplementing of measures by satellite operators,
airline companies, and so on.
●Date: March 20, 2018

Comment from the Recipient
It is honorable to recognize our continuous
effort for space weather research and dissemination for a long period. We would like to contribute to social activities with improving andproviding space weather information.

Mamoru ISHII
Director of Space Environment Laboratory,
Applied Electromagnetic Research Institute

Tsushinbunka Association

63rd Maejima Award
Mizuhiko HOSOKAWA
Vice President

Overview●Description: Research and development ontime and frequency standards and standard time
As a leader of research at a time / frequency standards organization in Japan, he won highappraisal for leading research and development
into high-precision time / frequency standards
technology, a cutting-edge fundamental technology propping up the modern-day ICT society.
In the development of the Cs primary frequency

standard they created a type of equipment that
qualified for participation in the development ofInternational Atomic Time on which the world's
standard time is based. As for the next generation of atomic clocks, the values measured by a
Sr optical lattice clock they developed, said to be
the most promising candidate for "redefining thesecond," has been adopted by an international
committee.
●Date: April 10, 2018

Comment from the Recipient
I believe I was awarded this prize as a repre-

Daisuke INOUE

Yu TSUDA

Director of Cybersecurity Laboratory,
Cybersecurity Research InstituteResearcher, Cybersecurity Laboratory,
Cybersecurity Research InstituteKoei SUZUKI

Yaichiro TAKAGI

Senior Technical Researcher, Cybersecurity
Laboratory, Cybersecurity Research Institute

Overview●Description: Research and development on an
integrated analysis platform against cyberattackand its social application
The researchers won high appraisal for developing NIRVANA-KAI, the world's first "integrated analysis platform against cyberattack"capable of monitoring and analyzing traffic on
the networks of organizations in real time to deal
with targeted cyberattacks. The system enables
the gathering and analyzing of huge volumesof alert information in almost real time, andsentative of all the people involved in R&D in
the field of space-time standards at NICT.
We would like to continue contributing toachieving valuable results in this field. Thankyou very much.

Fixed Term Technical Researcher,
Cybersecurity Laboratory, Cybersecurity
Research Institutethree-dimensional visual displaying to allow the
implementing of speedy measures, prioritization, and automatic protection measures.
The three-dimensional visualization andanalysis technology of NIRVANA-KAI is being
used at SECCON and other cybersecurity competitions as well.
●Date: April 10, 2018

Comment from the Recipients
NIRVANA-KAI is a platform that enables
speedy responses to cyberattacks. The results

At the party after the award ceremony. From left; Koei
SUZUKI, Daisuke INOUE, Vice President Mizuhiko HOSOKAWA, Yu TSUDA, and Yaichiro TAKAGIof research and development, so far, have beenused at universities, companies, government offices, and so on, throughout society. Moving forward, we plan to continue extensive promotionof our results.
We would like to take this opportunity to
express our gratitude to all the people whohave contributed to R&D and the spread of
NIRVANA-KAI throughout society.

NICT NEWS 2018 No.4

13

NICT NEWS 2018 No.4 Vol. 470

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Issue date: July. 2018 (bimonthly)

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