FGL Community
Newsletter
AUTUMN 2023

It’s that time of the year again when the leaves are red andcrunchy, the pumpkins smiling and scary, and the semester new
and fresh!
In this edition of the FGL Community Newsletter (Autumn 2023), you would
have a chance to read about the Imoni parties, which a lot of us participate
in whether with our FGL friends, our labmates, or our club friends! Our
talks of traditions continue with the article on Wafuku, which you haveprobably seen before but never got the chance to actually learn about. We
also prepared an article for you on how to save money while living here in
Japan, a must-need for every student! This edition, the Ask Senpai andResearch Article were both from FGL seniors that are also FGL
Community members, take a look on what they work on and the tips they
have for all of us! Lastly, we have an Ask Sensei article on Dr. Eriko
Nango, who combines two traditionally very distinct fields: physicalchemistry and structural biology! Please do enjoy the rest of the season
before the crunchy leaves are covered with white powdery snow.

Contents
02 4th­year Research Article
05 Imonikai
06 ASK SENSEI
08 Find the Difference!
09 Saving Money in Japan
11 ASK SENPAI
13 Story about Wafuku

In front of Tohoku University's Main
Library in Kawauchi Campus

4th-year Research Article
Hi! I’m Ryan, an Indonesian 4th year AMB student and the previous
leader of the FGL Community. Unlike the previous 4th year research articles, I
would like to share about the research I did that started in my first year. Why?
Because of the five research projects I’ve been involved in during myundergrad, this one turned out to be the most productive, resulting in a paper
whose first author is me!
As a background, this research was done when I was working for the Frontier Research Institute forInterdisciplinary Sciences (FRIS), the university’s research institute that engages in research from a vast
selection of fields, including but not limited to molecular biology, quantum materials, artificial life, andeven black holes! I was able to get the position because I independently reached out to a researcher who
was in FRIS and, long story short, I was working in the research institute and was leading my own project.
This experience ended up becoming the kindling for my research journey throughout my undergrad andhas impacted me more than anything else despite having absolutely no correlation to my major anddepartmental studies.

Expression Regulation of Shared Subunits Reveals Mutagenic Replication Dynamics
of DNA Polymerase ζ and δ in Fission Yeast
DNA polymerase ζ (Polζ) is responsible for introducing bothspontaneous and damage­induced mutations during replication througherror­prone translesion synthesis, causing it to be significant in causing
spontaneous cancers. Previously, Polζ has been shown to bind with
subunits of the replicative polymerase Polδ in ensuring functionality.
However, how this interaction regulates the extent of mutagenic DNA
synthesis is not known. To elucidate the functional dynamics of Polζ andhow it relates to the activity of the main replicative polymerases, weemploy a functional mutagenic study using fission yeast as a model.
Herein, we show that the ratio of the intracellular abundance between
the catalytic subunit of Polδ (Cdc6) and the shared subunit (Cdc1 andCdc27) is crucial in determining the involvement of each polymerase
during replication. Upregulation of the shared subunit dramaticallyincreases Polζ­dependent mutations while downregulation decreases
them. Downregulation also rescues cellular viability when Polζ isabsent. Additionally, structural disruption of the shared subunit’s
binding site in Polδ increases Polζ activity.

2

Behind the Paper
Interviewed by Max and Suryo
What does the beginning of a research project look like? How do you propose
something and get it approved?
One unfortunate thing is that you really must, in some degree, stick to the host lab’s resourcesand expertise. I would say that most, if not all, people before their postdocs probably performed
research that got to have something to do with the lab’s expertise. However, personally I havealways been able to find a way to bridge my true interest and the lab’s capabilities, also owing
to a tremendously helpful and providing mentor.
So how to do that? Well, in proposing your own research, you really have to know what you
want to know. It does not have to be a very specific hypothesis, as in my case, the DNApolymerase zeta complex was very unexplored so it’s even hard to predict stuff and come up
with a strict hypothesis, but it is clear that the interaction it has with the other polymerases
holds some crucial information, so I just focused my research there.
Once you know what you want to know, you can start planning out the experimental design. Of
course, creating a scientifically rigorous experimental design needs background knowledge on
what methods are typically used and the degree of validity of the methods, not to mention
whether such methods can be done in your specific lab. However, do not let this fact deter you
as I’m sure that most PIs (Principal investigators) are happy to just discuss with you and let you
know of possible experimental designs. In my case, I already had a solid experimental design
in my mind (including time and budget constraints for each experiment), causing my proposal
to be quickly accepted and it allowed me to immediately start experiments.
How did you come to choose this topic to research? Did you get the idea yourself?
I have always been interested in cancer research. Interestingly, I have absolutely no personal
experience with cancer—I have never seen a cancer patient with my own eyes. My fascination
with cancer comes because cancer itself is an interesting intellectual challenge for me, i.e., it’svery hard to cure and I want to try my hand at it. So, after getting accepted at the position, I
browsed through the lab’s current and previous projects to see if there is anything that relates
to cancer. I ended up finding the DNA polymerase zeta topic which, after reading throughreview papers on it, I found out has an interesting yet unexplored relation to oncogenesis.
Because I like my approach to be specific and detailed (so­called ‘reverse genetics’), I thenbrowsed the known complexes that it forms and finished choosing my target genes for myexperiments.

3

If it was your idea, would you say it came naturally to you, or did you have to findinspiration for the topic?
Of course, for the topic in broad, like I said, I have to somewhat align to the host lab’s
capabilities, so in a way my inspiration comes from the lab’s previous project. However, after
finding that out and aligning it with my true interest, how I choose my targets and how I
construct the experimental design came naturally. But personally, I don’t think that whether aresearch topic comes naturally or not necessarily plays a role in how hard you’d work for the
research. Some people may find the ideas that come naturally as a product of their own
curiosity, resulting in them striving harder to prove it. On the other hand, some people may get
so inspired, maybe from other researchers, that they end up getting so involved in the topic thatit starts to feel like their own original one. But one thing’s for sure, you will definitely regret it if
you perform research on a topic that you genuinely have no interest in.
I think a fair share of our readers are high school students planning to enter Tohoku
University. Can you tell us a bit about what your personal experience is with doing
research in Tohoku University?
Although I have faced a good number of barriers when trying to get research experience, I
would say that things are definitely getting better and I have personally proved that, yes, there
is a plethora of research opportunities here if you are willing to actively look for them. Like I
mentioned, I personally have been involved in five different projects that each dealt in very
different fields of biology and on very different scales. As an undergraduate, experiences likethat are extremely rare and beneficial and I have never regretted my choice to participate inthem (and I hope that they can give me a strong edge in graduate school applications, wish me
luck!).
Once I got in an actual position, I would say that the research environment is generally good,
especially because all of the supervisors I have worked with are truly amazing researchers
themselves and really good mentors. In research institutes, I would say that the environment isvery much like a group work, where everyone treats each other as equals and expects eachother to work towards the same goal. On the other hand, in the faculties and graduate schools,
the environment is more education­focused, where professors and senior students would pay
more attention to assist the junior members and help them get a strong grip on what the labdoes and how the lab works. Again, I don’t think that one is better than the other, both still
resulted in a healthy research environment. Not only the actual research, I like that they have aseminar system here that seems to extend to every lab which allows you to not only be morefamiliar with what your peers do, but also helps you to expand your knowledge passively.

4Imoni parties
By Sumaya and Dylan

How do you know winter is around the corner in Tohoku, Japan, without telling? Exactly, you
guessed it right! It is when you gather by a riverside with an outstanding Autumn view to cook a
traditional dish called Imoni. Imoni is a type of nabe (hotpot) meal containing meat and taro
soup, and is usually eaten as part of a tradition in the Tohoku area in the autumn. It is believedto originate in the mid 1600s when a boat filled with cargo reached the Nakayama­machi
Nagasaki area and they had to wait for the consignee to show up. In the meantime, they would
party by the riverside around a pot cooking taro (from the surrounding village) and cod (fromtheir boat) to pass the time.
Imoni has various ingredients in modern times which vary depending on the prefectures.
However, multiple key ingredients are almost always present in Imoni: taro root (里 芋) , thinly
sliced meat (beef or pork) , konnyaku, as well as soy sauce. Additional ingredients could also
include Chinese cabbage (hakusai) , burdock root, daikon, carrot, mirin, and many more.
Yamagata prefecture is heaven for holding an imoni party because of its sacred Mt. Gassan
and ski slopes of Zao Onsen. Every September, a festival is held where a six­meter cauldron
full of Imoni, enough to serve 30,000 guests, is placed. They even have their own excavators to
help mix the stew and the whole cooking process takes around 4 hours!

Image source = https://www.tohokukanko.jp/en/attractions/detail_10064.html

In other prefectures in the Tohoku area, people celebrate Imoni parties by cooking themoutdoors, usually by preparing a fire near a river. Many of the Tohoku University labs alsocelebrate the imoni party with all of its members in the autumn season. This celebration is notjust about the delicious food but also an excuse to bring people together amidst their busy lives
in autumn, and also to welcome the season itself. The convenience stores around the rivers
are brimming with imoni ingredients around this time of the year and that’s when you know you
gotta party soon.

5

ASK SENSEI
Professor Eriko Nango
Interviewed by Aroob and Jojo
The interview transcript between Professor Eriko Nango and ourinterviewers
To start off the interview, could you tell us a bit about yourself?
I was born and lived in Sendai until I was 2 years old, and then spent my childhood in Akita andChiba. I proceeded to the Department of Chemistry, Tokyo Institute of Technology, andcontinued on to the graduate school of the same institute. My favorite pastime is playing the
piano. I wanted to be a pianist when I was a child.
What first inspired or pushed you to study structural biology?
The laboratory that I belonged to in the institute was focusing on “natural product chemistry,”
which is different from structural biology. My research target was the enzyme involved inbiosynthesis of antibiotics. I synthesized substrate analogues and analyzed its enzymatic
reaction with the substrate analogues by NMR and MS spectrometers. I became interested in
the three­dimensional structure of the enzyme, and began studying protein X­ray
crystallography at a collaborator’s laboratory in 2000. Although I became an assistant professor
in the natural product chemistry laboratory, I wanted to engage in development research on
protein X­ray crystallography. Therefore, I resigned from the assistant professor position andmoved to SPring­8 in 2010, changing my research field to structural biology.
Could you tell us a little bit about your work on the use of quantum beams to record
protein conformational changes and chemical reactions?
In 2013, I started to work on the development of protein X­ray crystallography at SACLA, which
was established next to SPring­8, providing a new type of light called X­ray free electron lasers(XFEL). XFEL allows us to observe protein structures before the onset of radiation damage andto capture changes during reactions with a high temporal resolution of several tens offemtoseconds at the atomic level. However, we need to perform the measurement in a different
way from conventional X­ray crystallography due to the nature of XFEL. We challenged time­
resolved experiments to visualize movements in proteins while developing devices for themeasurements. In 2016, we successfully captured conformational changes of the proteinbacteriorhodopsin, a light­driven proton pump during proton transfer after light illumination
using our developed devices as a three­dimensional movie. Bacteriorhodopsin is a membraneprotein with seven helices, and its proton transport mechanism has been of interest for a longtime. Although many photo­intermediates have been determined by conventional X­ray
crystallography, the debate for the mechanism was not concluded. We elucidated how theprotein transports protons in one direction without back­flow from the obtained XFEL data.

6

How has your research and professional journey been for you so far? Has there been
any significant failures or successes that you could share with us?
I became an assistant professor which is a permanent job after completing the doctoral
program, but I resigned from this position to become a postdoctoral researcher which was acontract worker in order to change a research field from natural product chemistry to structural
biology. I also wanted to balance my life and work by changing my position at that time. In
Japan, such a decision would have resulted in almost giving up on a future career as a
researcher. I did not think that I could become a principal investigator to lead my own
laboratory. However, surprisingly, this decision led me to begin the new research using XFEL,
yielding many successful results in protein dynamics studies. The research fields that I
previously studied contributed greatly to protein structure analysis using XFEL. What seems to
be a failure may never be a failure. I believe it is necessary to work on things in the long term.
If you could turn back the time, do you think you would do anything differently in yourcareer?
To be honest, I do not want to go back in time because I had a tough time when I was young. Iftime could be turned back, I would take the same path. Basically, I have no regrets about mycareer to date and am proud to have continued my research while raising two children.
What about your plans for the future? In what direction would you like your research to
go in the next five years?
Visualizing structural changes in a protein is not so trivial because it requires protein molecules
in a crystal to react simultaneously. In the first time­resolved experiment, a light sensitive
protein was used. However, such proteins account for less than 1% of all proteins. Most
proteins bind to small­molecular compounds and initiate reactions. Therefore, I will continue todevelop devices for the measurements using XFEL so that such movements can be observed.
In addition, I would like to extend the technology to rational protein design based on theobtained dynamic structures.
Lastly, do you have anything to say to the students who may be interested in structural
biology?
As the saying goes, “seeing is believing”. In structural biology, we observe an object andunderstand it deeply. So far, powerful methods including X­ray crystallography and cryo­
electron microscopy have been developed to elucidate a target protein. In the future, it isexpected that we will not only analyze proteins but also design a new protein and explore
research using these proteins. If you are interested in structural biology, please feel free to visit
my laboratory!

Find the Difference!
Find the 10 differences between the two images below!

Art by Steven

Go to the ﬁnal page for the answer!

8

Practical Ways to Save Money in Japan
Written by Kamila

The breeze of autumn is coming and so is the new batch of FGL students. Despite having asky­rocketing excitement of starting school, whether they like it or not, one of the mostchallenging things for newcomers starts to show up: adapting to the new environment, new life,and undeniable financial reality ­ the living cost difference.
It’s indeed true that the living cost in Japan could be significantly more expensive compared toother countries. This could be a shock to some people, in which their dreams and plans to go
on trips throughout Japan can be shattered. Here, we are going to discuss a few possible ways
to save money throughout the school year and make it still possible to afford a holiday trip.
Transportation
Depending on which mode of transportation you’re choosing, the transportation costs could
vary. For instance, the cost of subway tickets varies between 210 to 250 yen dependingon the distance between stations. Frequent commuting between adjacent stations,like from Aobayama to Kawauchi, can add up quickly. Other options, such as taxis, can beeven more expensive.
Fortunately, there are some ways to prevent the rise of the transportation cost. The Sendai
transportation bureau offers a city bus and subway free pass for students, allowing them to use
these services throughout Sendai. Picture this: suppose that you do round­trip travels 5 days aweek for 1 month (4 weeks), and the cost of each trip is 210 yen. Based on this calculation,
your total expenditure would be around 8,400 yen. However, by opting for a subway pass,depending on which lines you're choosing, you can spend as little as 6,990 yen for either the
Namboku Line or Tozai Line, or 8,390 yen for both.
Furthermore, if you’re using the buses instead, the cost of the city bus pass will be 5,970 yen
per month. You can get further information regarding this on the following website: Sendai City
Transportation Bureau Gakuto Sendai City bus/subway free pass (www­kotsu­city­sendai­
jp.translate.goog)
Some students also prefer to use bicycles, which can be a cost­effective option in the long run
and could also reach the places that can’t be reached easily by subway or buses alone. As areference, one of the most famous bicycle stores is Hayasaka Cycle where the bike could
typically cost around 10,000 yen or above for non­electric bikes and around 100,000 yen or
above for electric­assisted bicycles. You can also consider purchasing a second­hand bikefrom stores like Hard­Off or online platforms such as Mercari for a more budget­friendly option.

9

Budgeting and PlanningTo effectively save money while studying in Japan, it's crucial to create a well­structured budget
for both your income and expenses. One way to do it is to use an app to help you track yourspending and split your money into smaller amounts. Start by making an outline of how you
want to spend your money and why. For instance, you can allocate 50% to food and 20% tosavings. Subsequently, you can start picturing your financial goals ­ how you want to spend themoney you have saved so far. This way, you can easily track your spending and work towards
exciting goals, like a trip to Hokkaido or buying that electric guitar you've always wanted.
Although there are many budget planning apps available in AppStore and Google Play Store,
you can simply use tools like Microsoft Excel or the Notes app on your mobile device.
Additionally, some individuals prefer to allocate their money for different purposes into separate
accounts or even different wallets.
Cooking
After living in Japan for a while, you might start to notice that your food expenses might bepretty expensive. Preparing your meals is a practical way to press down your spending. There
are many sources of cooking materials on the internet if you just started learning how to cook
for the first time. Furthermore, by cooking your own meals, you gain a clearer estimation of how
much you’ll actually spend in a week whenever you go out shopping.
Talking about shopping, if you go to the grocery store at night, there might be some ingredientsthat are sold at a relatively cheaper price as indicated by a yellow sticker on top of the
packaging. This is a smart strategy to trim your grocery bill.
On the other hand, there are of course some downsides to cooking your own food. As astudent, your main responsibility is to study, do homework, and do other things. Althoughcooking your own food might be cheaper to some extent, it could be time­consuming since not
only do you have to prepare the ingredients and cook them, but you also have to think about
the menus you’ll be cooking. For that purpose, to simplify your food planning process, you canalso surf the internet to find some recipe ideas or even ask ChatGPT to prepare a one­weekmeal plan.

10

ASK SENPAI

Tonklar Khaimuk (TK), 4th year IMAC-U student
Interviewed by Avin

Can you please introduce yourself and tell us a bit about your academic journey inengineering? What inspired you to pursue this field of study?
My name is Tonklar Khaimuk, you can call me TK. I am a 4th year student of the IMAC­U
program. My journey in engineering is quite wild, to be honest. It started as an interest in
robotics from high­school, and then in university, I started to pursue the material side while alsoself­learning the software­engineering side. I want to pursue what I am interested in:engineering as a whole. I am the kind of person who is always having fun while using logic andcreativity to solve real world problems. I explore multiple fields and kinds of engineering to beable to fulfill my goal.

In your fourth year of engineering, can you share some details about your current
research or projects you're involved in? What motivated you to delve into this particulararea of engineering or research?
I am now involved in a project about contacts involving graphene with a metal electrode. By
observing the properties of the contact, especially its electrical properties, it can be made into a
new mechanism of creating an electron pathway for solar cells with very high efficiency.
Graphene has very unique properties which allows electrons to travel through it at very fast
speeds with ease of manipulation. I think this research area has a very good perspective forthe future, especially in terms of solar energy. Moreover, most of the mechanisms andproperties are still unknown, which makes it look fun and interesting.
As a student in Japan, what do you find most fascinating about the country and its
culture? Are there any cultural experiences that have left a strong impression on you?
I think Japan is a very easy place to live with safety. The traffic system along with the town
management impress me so much. From a cultural point of view, I think that temple
architecture and construction are related, and they inspire me. I love going to Japanese
temples, and I love how they are always surrounded by a very beautiful nature. While I haven't
had one single cultural experience that left an indelible mark, I eagerly look forward to
exploring more temples, especially in Nara and Kyoto!

11

Juggling the demands of engineering studies and research can be challenging. How doyou maintain a healthy work­life balance? What hobbies or interests do you have thatprovide a break from your academic and research commitments?
Firsty, I will try to adjust my schedule so that I will also have time for my hobby and to be able
to rest enough. However, it’s very hard to find this balance in practice, since things can get a bit
chaotic when you do not know what will happen tomorrow. When that happens, I experimentwith different schedules for about a week or two to find the most comfortable balance both
physically and mentally. For example, I may shuffle things around a bit so that I can get betterat coping with more various situations, and from that I will be able to maintain the balance in avery chaotic real­world situation. Another point is that I will also keep in mind the importance offree­time to let me have the time to process things. I think these two methods combine to be agood approach to maintain time balance. I have always had an interest in chess, PC games,
and music. These help me to relax, have fun and to reduce stress from academics.

What advice would you give to junior students who are aspiring to follow a similar pathin engineering and research?
I think the best advice I could give is that you need to always have fun with what you do. The
fun in solving things or the fun in curiosity will drive you forward in any thing you do, even forresearch or other things in life. Yes, in a real situation, you will not be able to be happy or havefun all the time, but I think if you always keep this in mind it will always bring you back to theright track ;).
Is there anything else you'd like to share with our readers, perhaps a memorable
experience or an important life lesson you've learned during your time at Tohoku
University
I usually don't say this because I hate telling other people what to do, but one important point I
realized from stressing too much over learning back then is that it feels like your teenager life isruined because you didn’t remember anything other than the time you've spent studying.
University life should be about more than just academics. It is also about making memories
and cherishing them. It is true that you need to concentrate on your learning, but I request
everyone to go out sometimes. You will learn something that sometimes you won’t expect. Youmight end up doing some extra­curricular things and talking with different people. Lastly, don’t
forget the people who are beside you in the darkest time, and be grateful for what life presents
you with.

12

Story about Wafuku:
Japanese traditional style clothing
Article and Illustration by Mimie (Chanisa P.)

What are the things that come to your mind when you think of ‘Japan’? It may be the beautiful
scenery, delicious food, or great anime, and for some, it might be the image of people inbeautiful traditional clothes that pops into our mind. You might have heard about the Kimono, themost well­known Japanese clothing. Actually, other than the various kinds of Japanese clothingthat can be worn on many different occasions and seasons, there are more accessories andinteresting items to learn about too! In this topic, I will mention some of the main Japaneseclothings, accessories, their usage, and maybe some more interesting facts too!

I ­ Clothes
Kimono (着物)Kimono is probably one of the most well­known
Japanese clothes. ‘Kimono’ actually means‘things to wear’, so it is a very broad term todescribe the traditional costume. There are various
styles and types of Kimono, almost all of theclothes mentioned below are a part of kimono too.

Yukata (浴衣)Some people may confuse yukata with traditional
kimono, because both are very often seen on
movies or anime. Its name means ‘bathing cloth’. It
is one of the informal kimonos with less complex
styles originally used for bathing cloth, now it isworn widely in the summertime, especially in thesummer festival and firework watching.

Hakama (袴)Hakama is the long, pleated trouser that was wornby samurai and those of higher class in the past.
Nowadays it is mainly used in many ceremonies
and martial arts, or by shinto priests and monks.

13

Samue (作務衣)

Fundoshi (褌)Fundoshi is a type of men's undergarment
worn in many occasions, mainly at ‘夏 祭 り’or summer festivals performance.

Samue is the loose and more casual
outfit mostly made from blue cottonand originally worn by monks. Now,
it is worn as a regular indoor outfit.

II ­ Shoes
Geta (下駄)Geta is the wooden sandal for everyday life,
some had the ‘歯’ or teeth under that lift theshoes up for walking on the rain or snow.
Okobo (おこぼ)Okobo is the strappy platform shoes that ismostly worn by ‘Maiko’ , as its color represents
the class of Maiko.

Tabi (足袋)Jika­Tabi (地下足袋)

Tabi is the pair of socks that divides
the big toe apart from others, now
still wearable as the regular socks.

Rubber shoes with toe ­ divided platform thatwas inspired from the Tabi sock. Originallycreated for workers in the early 20th century.

14III ­ Accessories
Kanzashi (簪)Hair ornaments with wide variations from
simple to very elaborate made fromprecious materials like gold or tortoiseshell.

Kinchaku (巾着)Cloth bag with drawstrings forcarrying personal effects. Mainly
seen nowadays with kimono.
Sensu (扇子)A folding fan originally used by the peopleof the imperial court, now used in traditional
performances such as Kabuki and Noh.

Wagasa (和傘)Traditional handmade umbrellas made from oiled
washi paper and bamboo frame, some with adelicate pattern or color. It is quite durable against
water, but still needs special care for longevity.

15

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Newsletter published by the FGL
Community of Tohoku University

Other contributions:Introduction written by Ryan
Article proofreading by Alisa
Background and layout by Steven

Find the difference answer key