Profile

In some bacteria, when they are exposed to environment with alcohol (for example, ethanol and propanediol), they produce an icosahedral (a polygon with 20 faces) organelles.  The covering of this icosahedral organelle (think of an egg shell) is made of thousands of seven types of proteins (imagine you smash the egg shell into pieces and you will have thousands of egg shell pieces). Inside this organelle, a number of enzymes convert this alcohol into something more useful for the bacteria like food (now, imagine again – egg – inside you have egg yolk and egg white, where some sort of reaction is happening).  In our lab, what we want to know is, how are these proteins assemble together (or how do we piece together a jigsaw puzzle of cracked egg shell pieces) and more importantly, how do these proteins function such that it allows entry of alcohol but also preventing the enzymes inside to get out (or how does egg allow air to go in so the chick will survive but also don’t allow the food to leak out of the egg).

To do this, what I do is take the gene of the protein (DNA sequence) and places it in a “special” bacteria that is able to produce this protein in bulk.  Then I get the protein out of the bacterial cell, purify such that I got only my protein of interest, and then use the technique called protein crystallography, where I turn this protein solution into solid microscopic crystal. Next step is to hit this crystal with X-ray beam to produce a pattern of black spots. This will be my data and using complicated mathematics, which mostly the computer does nowadays, I can extra information where each atoms of the protein is situated in a three-dimensional plane, which therefore, could give me information how this protein look like.

Everyday is a unique day for me.  Although, I do have a research routine, they usually span 3-4 days, rather than a single day. That is why if it did not work on day 1, I can’t proceed to day 2 of experiment.

What I usually deal with:

– Planning of experiment. This includes thinking about what solution should I used, what kind of changes should I do in my method to achieve a better result, what should I continue doing and what I should not.

– Carrying out of experiment. Stuck in the lab. Moving flasks. Watching columns. Using various solutions in the experiment. (See more on me and my work)

– Analysing data and results. This involves identifying amino acid and fitting it into a map; checking if the data makes any sense.

– Publish results. Once I got my data and if it is of reasonable amount to create a story, I make a scientific narrative and send it to publishers.

– I also have to deal with other involvements such as teaching undergraduates, making reports and writing up my thesis.