Laboratory assignment, current research, and my first international conference presentation

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 4thyear student, and I am currently doing my undergraduate thesis research.

I have joined a lab for my undergraduate thesis research. My lab is the Laboratory of Cell Systems of the Institute for Protein Research check it out for more info à Lab website (I made the website lol). Our lab’s focus is about quantification cell signaling pathway. To be specific, we try to incorporate mathematical models to describe dynamic cell signaling system by using experimental data (Next generation sequencing analysis and other wet experiments).

For my undergraduate research thesis, I am researching on NF-kB nuclear dynamics. This protein pathway has been reported to control cell fate and determination. The final protein in this pathway regulates gene expression needed for survival/death/differentiation by acting as a transcription factor and binding to enhancer and promoter sites of genes.
To simplify again, this protein regulates the production of other proteins by binding to DNA. In my research, I am trying to understand the molecular mechanism of NF-kB regulated gene expression in immune cells (B-cells).

For my current work, my approach is rather unconventional, in which I try to combine both imaging and next-generation sequencing (omics) analysis to get an overview on NF-kB driven transcription. For imaging, I have a confocal microscope which I am using by myself (at least for now) to get image data before using ImageJ (open-source image analysis platform) to perform automated image analysis.

Left: my current microscope setup: Olympus + Yokogawa confocal microscope
Right: my current (still messy) desk

For the omics analysis side, I am using different tools and programming languages (R and unix) to understand the opening and closing of chromatin and its relationship with subsequent gene expression. At first, programming was a bit hard as I never had any background on this, however after several months, I was able to write scripts and codes to simplify many of my analysis.
I was also assigned a side project regarding T-cell differentiation. For this work, I was doing analysis on RNA-seq data (total mRNA level) of a new T-cell subset. The paper has been submitted for review and hopefully can be published ASAP.

Currently, I just got back from Okinawa for my first academic conference presentation. The academic conference is called ICSB (International Conference on Systems Biology). It was held at OIST (Okinawa Institute of Science and Technology) which has a really nice campus.

Garden in the middle of OIST.

I did a poster presentation of my current work. It was also a really good opportunity as I got new connections and planned future collaborations. Unfortunately, I did not see a lot of participants with similar research field, so I was only able to discuss deeply about my research with several people.

Me and my poster.

After the conference, we had some free time so the students from our lab went to Churaumi aquarium which is quite famous in Japan. After that, of course we had Okinawa Soba, which was really good but I forgot to take pics lol.

Whale shark, the main display at Churaumi aquarium.

Alright, I'll leave it here as I still have so much things to do. As usual, let me know if you have any questions or comments!


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 ...

Back to top ↑


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...

Back to top ↑


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 ...

Back to top ↑


Back to top ↑


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...

Back to top ↑


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...

Back to top ↑


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...

Back to top ↑