Speaking of Pathways!

Here I was content with my KEGG. (Yeah that's Kyoto Encyclopedia of Genes and Genomes. Here's the link to their website: http://www.genome.jp/kegg/ . )

And here comes my thesis adviser, urging me to get my proposal done by asking me to choose which genes will I be monitoring as part of my thesis. And so I was about to launch on my report about this website I discovered and which I am using so I could easily follow the pathways involved in the pathogenesis of rheumatoid arthritis when he showed a website with really catchy and colorful representations of the pathways that goes on in our cells...and yeah in our bodies.

And so I saved myself from being bothered with comments like "Ohhh. You're using that one? That is so yesterday." from my adviser and let him describe how his new choice of website on pathways works.

Start with this:

http://www5.appliedbiosystems.com/tools/pathway/

And you are faced with a list of pathways you probably haven't heard of in your entire life. Well, if you're a geek then you've heard probably 1/3 of them. If you're a super geek, then you know 2/3 of them. And if you're an omnipotent being, you don't need this list cause you probably know all what's in the list. There are over 350 Interactive Pathway Maps. And my thesis will deal with probably one or two of them.

And so back to Dr. Matias, my well-known thesis adviser. He made things clear to me by explaining that I should first choose one of the pathways listed. And he said it should touch on Inflammation or Pathogenesis of Rheumatoid Arthritis.

I suggested we start by checking the Jak-Stat Pathway.

Here's the link: http://www5.appliedbiosystems.com/tools/pathway/pathway.php?pathway=JAK-STAT%20Pathway

I clicked on it and what do I get?

I get confused...LOL...

Not only is the pathway so convoluted. It's just toooo much for my mind to take all the participating proteins and genes in it. But since I read some articles about Stat1 and Stat3 assays being used in some laboratories to screen naturally-occurring compounds for their anti-inflammatory activities, I asked Dr. Matias to click on Stat1 and what do you know. A window was opened and led to this link:

http://www5.appliedbiosystems.com/tools/pathway/protein_list_grp.php?pathway=JAK-STAT%20Pathway&pname=STAT1

I clicked on the listed available TaqMan Gene Expression Assay. Oh yeah, that's the good thing about this site. They list down the commercially available assays offered by Ambion, Inc.

Some call it being lazy. But I call it Tech-Savvy. Not only does technology make things easier for businesses. It also makes scientific research less of a nightmare.

But of course, I'm not settling down for Stat1 only. I'm taking advantage of their promo. I'm not sure if this is just a promo of our local supplier but you can ask Ambion about it through their website. But you can order a pair of kits for a lower price. Yeah, that's right!

I'm still choosing between MMP-9. Dr. Matias shoved this on me. But I am beginning to warm up to MMP-9 because of it's many roles in the pathogenesis of many diseases. It means that if my extracts from Centella asiatica will work on inhibiting MMP-9 it could help alleviate many of the diseases involving crazy-ass genetic expression of MMP-9.

I'll talk more about Stat1 and MMP-9 once I'm done reading on them. For the meantime, I already have my first picture for my slide shows when I'll be defending my thesis. Talk about pathways, huh?

Over-Prelude

I know right?

I haven't done much on my thesis. And I went through a lot of soul searching and have come to a conclusion that I owe it to PROCRASTINATION that I haven't done much.

So today, my workmate informed me that two of my batch mates in the MSc Molecular Medicine program are staying late to finish their thesis proposals and letters to PCHRD and that the deadline of the submission of those documents is today. That alarmed me since I haven't really revised my proposal to its finest form possible yet and it was already past 7 pm when she told me about it.

I was suddenly racking my mind for excuses I could put up so PCHRD wouldn't mind accepting my proposal at a later date. Of course, there is no good excuse that's why I set that aside and decided to just tell the truth that it is still undergoing revisions. I also decided, I'll just dish out the most apologetic letter ever. So I headed home, anxious to get that letter done.

But what do you know, I got home. Sat in front of TV...and watched Leverage Season 3 instead. That's when my house mate, who's also enrolled in the program arrived. She propped herself in her usual viewing spot and proceeded to watch TV with us.

It was only after some 5 minutes that I remembered about the letter and told her that she didn't inform me that the deadline of the letter is today. To which she replied, "who said today's the deadline"?

Turned out it isn't the deadline but that PCHRD is urging us to pass it as soon as possible. That made me feel dumb for feeling anxious earlier. But of course, it also brought relief.

After that, I felt more comfortable watching Australia's Master Chef Season 2. LOL.

But hey, I got around to doing this BLOG. See, I decided to BLOG about my progress in thesis. I hope this would get me in the mood to doing my thesis as I will need to produce results to post in here...I love science but I love to write too...creatively...so I might as well do them together. Just so I wouldn't be stressed that much.

So here's my plan for the next days to come.

I need to finalize my thesis proposal. Which I means, I really have to decide now which cell lines are the best ones to test my extracts for their anti-inflammatory activities. I need to be original this time. Because, the last criticism about my initial proposal was that in essence I wasn't really bringing anything new to the body of scientific knowledge. That kind of hurt my scientific pride so hey I said...I better be ambitious and work hard to hit the mark.

I need to really find plant specimens. Lots of them. Last time I was able to obtain specimens, I didn't get to process them well since work got too busy for me to process the plant specimens. My cousin at DENR is helping me with it but I think she doesn't feel the urgency so I'm not going to put my confidence on that. I'll just have to contact Mr. Bandong from the Institute of Biology in UP Diliman.

I am wondering if any of you guys have an idea where to obtain specimens of takip kuhol or gotu kola. Its scientific name is Centella asiatica. I'll post a picture for your reference. Ayt? Help me out guys. Thanks in advance. =D

Photo is lifted from the site http://www.herbalbiosolutions.us. I have no intention of copyright infringement. Please do not prosecute me. =D