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.


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