Scuba diving in Okinawa Part 1
Ever since my childhood, I’ve harbored a deep love for the sea and its myriad marine creatures. However, living far from the coast meant that my experiences ...
My research projects
Hi, haven't updated my blog in a very very long time but here I am lol. Happy new year to everyone! How was 2018? 2018 was a rather productive year for me, I started 2 new research projects and probably more to come!So both projects are in different labs in Osaka University, the first one is in Ishihara lab which is one of the newest or probably the newest lab in the School of Sciences where they are doing mitochondrial research, and the other is in the Mechanical Engineering department where I did the university's BIOMOD project a while back.
Firstly, my research at Ishihara lab all started when I had this honor seminar class with regular 1st year students and was just basically going around labs. I visited this lab and I found them really nice and welcoming and they also told us that if we wanted to do some research they might be able to accommodate and so it sparked my interest.
A couple of weeks (or was it months) later, I decided to contact the professor and asked them if I could do some experiments and probably start on a research project at their lab. They were really nice and offered me to do some cell culture and possibly to start on a project that they never did: quantification of mitochondrial morphology.
Going to my research, I had to learn something I had never done before: cell culture. At first, they seemed complex but it was pretty much straightforward. I started with literally measuring pretty much everything until I realized that different from molecular biology, "about" saves time and didn't seem to affect the outcome in any way.
 |
| My work space in a clean bench |
Then, I pretty much just observed knock-down or knock-out cells with different mitochondrial morphology after staining the mitochondria with a special stain that could stain mitochondria due to their different membrane potential, they look like this:
 |
| Just normal wild type HeLa cells with stained mitochondria |
If you're wondering what microscope did I use to observe, I used confocal microscope. Yes, they're letting a 3rd year undergrad student use their most expensive microscope.
 |
| The microscope setup I get to use |
The analysis part is the hardest part as the condition changes every observation and sometimes varies between cells. If I know how to make scientific programs (which I'm sure might take years to master), this would be a piece of cake, but me being me I just read some papers of people doing random stuff using random plugins and I'm just testing which one is best for my samples. <-- pretty much what I'm still doing til now.
Sucks for me, I also have to keep up with classes as I don't have enough credits. Meaning I can't spend everyday in labs doing actual research, but I have to listen to boring lectures and take exams just for the sake of credits. Honestly, I think Japanese universities should setup a thing where we could get credits from doing independent research... And that's basically how I got to start on my first research project.
My second research project (not really my research project) was after the professor who was looking after Osaka University's BIOMOD team suddenly asked for help on his assistant professor's project. Long story short, they are engineers and not used to biological experiments and I get paid for helping them out because I have background in bio. The research project itself is to use FRET to measure tension upon physical stress on actin filaments of mouse cells.
 |
| My work space in the other lab, a bit cramped but I'm not doing a lot of stuff so can't complain |
So when I first started to look into their experiments, they seem to have failed the experiment on multiple occasions after trying to transfect (introduce genetic materials into cells) by using electroporation. They told me that the yield was too low and most the cells have died, furthermore it costs quite a lot, the cuvette costs quite a bit and they had to buy the electroporation machine which costed them around 800k Japanese yen. I asked them if they tried lipofection (lipid based transfection), but they were like "the plasmid was too big" "other researchers did electroporation" "the guy (who sold the machine) told us so", and so I thought they just got ripped off LOL.
The following day, we tried to check the quality of both negative and positive control plasmids and we got two similar bands, turned out that both plasmids were the same length (my bad for not reading into the whole paper on the plasmid). In the end, we couldn't conclude if both the plasmids were contaminated with each other or not and we couldn't confirm it in the experiments as they both express fluorescence. But anyway, we proceeded with lipofection trial using some of the trial reagents that they got.
So we woke up the cells on day one, replated on day two, and transfected on day three before observing on day four. I just made up the protocols for the transfection based on the manual lol. Voila! The results looked like this:
 |
| Succesful transfection using lipofection on 3T3 cells |
So in one week, we managed to perform gene transfer onto the mouse cells with a rather high percentage efficiency, (around 30%-ish?) while saving some of the research money. (They already spent a bit on the electroporation machine... I could've used that!)
The research is still preliminary stages though... I hope I will get my first publication through this research!
Sorry for the technical terms all over this post. Let me know if you have questions and I might just be able to help out on how to start your research early on.
2023
EMBL single-cell workshop in Heidelberg, Germany
Being at OIST, I have 2 yearly trips funded by the graduate school. One of which I used it for a workshop travel in Germany. This was an EMBO practical cours...
2022
Publishing my first research paper
After a year long review, my first paper finally got published: Link. The paper went through 3 rounds of revision, where I believe that the 3rd round was not...
Landing a PhD position
Hi there, I haven’t updated this blog for so long! I have been busy with research and the whole pandemic did not help with the current situation. But, to rec...
2021
What happened to my research?
So COVID struck while it’s been like about a year since my last post. A lot of things happened this year, I learnt new experimental techniques, got an award ...
2020
Getting into Japanese graduate school and getting a “full” scholarship
Hi there, so finally I have almost graduated from my undergraduate program which was in the G30 program. Now I am continuing to grad school in the same unive...
2019
Laboratory assignment, current research, and my first international conference presentation
<div class="MsoNormal">It’s getting really busy lately, so I haven’t had time to update my blog in a veeeeery long time. To sum up: I am currently a 4t...
My research projects
Hi, haven’t updated my blog in a very very long time but here I am lol. Happy new year to everyone! How was 2018? 2018 was a rather productive year for me, I...
2017
Shirahama Marine Biology Field Trip 2017
At the end of the first year, we have an optional (used to be compulsory) trip to Shirahama. If you don’t know what Shirahama is, it is basically a beach in ...
2nd Semester: Labs
Hello there, different from 1st semester, we have labs on our 2nd semester. A rather good thing knowing that we almost never had any lab experience during th...
2nd Semester in CBCMP: Circles and Clubs
I haven’t updated this blog in a while lol… A lot of stuff happened in the 2nd semester honestly. Firstly I joined circles. For those of you who don’t know...
First Semester in the CBCMP
Haven't posted in a while, first sem was really hectic... Let me sum up my first sem in the CBCMP then.. First time I came for the orientation I wasn’t real...
Reaching Osaka University
Usually it takes about some 7-8 hours to get from Indonesia to Japan. However, MEXT somehow managed to book a ticket with a layover at Denpasar (Bali) and so...
2016
About Month After Announcement Of
About a month after the announcement of passing into the university, I was asked to choose among 4 departments: Department of Biological sciences (School of ...
The Next Step to 阪大
So, I’m gonna save the language school post for later and the Osaka University post for today.<div></div><div>Some of you might think that ...
Why Japan?
Out of the countries that I could have chosen to go to, why Japan?The answer is simple: the people.So what’s with the people? How are they different?Well let...
How I managed to get into Japan
So I went to this University fair about 2 years ago and got some info regarding this Osaka University Global 30 program, however I didn’t really look further...
Why this blog and who am I
Maybe a little too late to make a blog, but maybe not too late to share stories.<div></div><div>So let me introduce myself, my name is Joha...