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 infoàLab 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!