Post about The Lab

In this post I am going to talk about lab stuff, and try to explain some of it. So here it goes. During the first three weeks or so, I spent my time isolating RNA from xenograft tumor and normal samples. The xenografts were tricky but do-able, however the normal samples were a huge pain in my... I managed to succeed finally after many tries. Only then, to take the samples out of the freezer a couple of days later to find that they were all degraded. So I was very thankful when another fellow in the lab, Andy, (thank you Andy) was able to successfully isolate normal RNA and give some to me. From there I was able to proceed in doing many RT-PCRs. That is a Reverse Transcription - Polymerase Chain Reaction, which is converting the isolated RNA into cDNA and then amplifying certain sequences of it to eventually compare expression levels between normal and tumor samples. So that's what I have been doing for the past 3 weeks now. Here is a picture from my lab meeting presentation of the hippo pathway that I will explain below.
Click for hippo size
The Hippo Pathway is a growth regulation pathway, first discovered in flies, but also present in mammals, which when activated stops the growth of certain organs. Animals who lack this pathway have large overgrown body parts, and look like hippos, which is where the name came from. The picture shows the known components. The five that I circled are the genes that I have been looking at. Next picture.
Click for make bigger here
This picture shows the results after running the PCR product on an agarose gel. Each gene has its own row, and each sample its own column. GAPDH was used as a control, but it didn't work out so well because all the bands were supposed to be the same strength. Pay attention to the difference between the average normal sample, OD Mix, and the rest. Especially for Yap-1, which the tumor samples are over expressing by far. More pictures.
Engorgio (harry potter joke)
This picture has the other two genes, and GAPDH as well. Same story as before although the first ones were better. Because the here the no template control started acting up again and I have no idea where that band came from, it's supposed to be empty. And sample 552 just disappeared in some places, which hasn't been helping things. So that's where I am right now in the lab. My next thing to do is to use a new control other than GAPDH, in order to try to get more equal expression levels. I hope I did a good job of explaining. You can ask questions in the comments section below. I turned it on it should work. This is my last week in the lab so there might only be one more post after this one ;(

Post about The Lab (Coming soon)

This is just a teaser since I don't have time for the full post I want to do right now because I'm studying for my final in Psychology. Each picture is a different gene in the Hippo pathway. GAPDH is a control (which is supposed to have the same level for all samples...). Notice the difference between the OD Mix and the rest. For the most part the tumors are over expressing these pathway components, which is good for me. More info later I promise, monday night or tuesday.

Post about surgery

Last thursday I was in the OR again for the entire day. This time it was much more fun for me, since I didn't get lost or locked out. Also I was able to pop in and out of different surgeries this time since I knew the drill. I got to see a Liver transplant, which was very interesting. It took the entire day. The anesthesiologists started at 9 AM and the actual surgery started at 11 AM and they finished at around 4:30 PM. With no breaks or resting. And they were standing up the entire time. During the middle one of the nurses pointed out to me the difference between the liver that was going in and the liver that was coming out. But I didn't need her to show me anyone could easily tell the difference and which one was the healthy one and which one was not. The patient needed a new liver because he is an alcoholic, and his was no longer functioning properly. The surgery went well and I wish him a speedy recovery. I got a free lunch again, which is the best kind of lunch there is. And I saw a bunch of people who I met the week before, even though I was following a different doctor. It was a good day, hopefully I'll have time to do a second post today about the lab since some very interesting things are happing there now.

Two Tales of Irony

Alright. It's been over a week since my last post so I am definitely not keeping up with the twice a week goal I mentioned before. So I thought I'd tell two stories to make up for it. Last Thursday I spent the day in the Surgical Intensive Care Unit (SICU). It was a much more depressing experience than being in the OR. Mostly because the people there are the ones who need the most care, many of them are on multiple forms of life support. In particular, there was one patient who had been recently admitted after being hit in the head by a car. He had suffered serious brain damage, and had emergency surgery to remove half of his skull to relieve the pressure. His family showed up by midday to see him and to talk to the doctors. Around the time I left I heard they had decided to take him off of life support. This was a very different experience for me and I send my sympathies to the family. Boston Globe article of the story: http://www.boston.com/news/local/massachusetts/articles/2009/07/17/man_still_in_mgh_following_car_crash/?page=1 Now that wasn't supposed to be one of the stories but I guess it is now. Now the real story, with irony. After observing rounds in the morning I went to the conference room to grab some pizza and listen to a speaker. Turns out she had come to talk about nausea and vomiting. So I ate my food I listened to all the different reasons someone might feel sick. And which medications help with which kinds. I wanted to ask her what I should take for pizza plus all this talk about vomit. But I didn't. I was concentrating on preventing things from leaving my mouth, words included. The second story, with less irony, is also somewhat of a lab update. So far I have isolated enough RNA to outweigh a dollar bill. No seriously it's a ton. (more like 0.9832 grams, but this is RNA) When it comes to RNA degradation is the enemy! I managed to isolate some RNA from pancreatic tumor samples and stored it in the freezer. Then I moved on to normal pancreatic samples. Just a little background here, the pancreas has the most RNases of any organ in the body. A RNase is something that degrades RNA. RNase=Bad! So as you might be able to tell, I have had a fun time isolating RNA from normal samples. So last week when I finally managed to get two samples one day and three the next, you can know how excited I was. Then after I presented this at Lab meeting I got a complement but also a, "we'll see how long they last in the freezer" I had assumed that they would last a long time since some of the samples were already from '05 or something. So low and behold, last week I took the samples out of the freezer to test them and they were all degraded. And that wasn't even the worst part. The worst part the "I told you so" I got from Dr. Thayer. OK I just re-read that and it sounds worse that it really is, but I said it would be ironic so I was just being dramatic. The truth is that is what science is all about. It is never perfect, especially the first time. I hope that post was good enough, becase its about to be over. I have to get back to work. Actually not really, Its almost 3 and I havent done anything at all important today

A little bit of MGH history for you. I'll try to take some more pictures since I have a nice 3 mega pixel camera (iphone) now.

Surgery Day

I had my first clinical day on thursday. I got to follow two anesthesiologists around all day and watched a bunch of surgeries. It was tons of fun. I was right in the OR with all the surgeons, nurses, and scrub techs. Not up in some booth like you see on TV. I don't even know if OR's like that exist in real life. I got to see a neck biopsy, a gall bladder removal, and two others. And I managed to take a picture of myself with scrubs on. Normally I don't like people who take pictures with the camera in them, but I only had few options. So thank me blog readers for doing this for you. Also, notice the stethoscope, very key while trying to look like a doctor. And even better when one of the nurses mistakes you for the anesthesiologist and almost hands you some full syringes... This was probably because I looked the same age as the real anesthesiologist, who must have only been 3 years older than me. All in all that was a great day, and I can't wait for next week, so stay tuned for all the Highlights. Hi Sam, if you want you can call me and I can tell you more about surgery and stuff I cant post publicly online...

This is me at the statue of John Harvard, in the center of Harvard Yard. I decided to play tourist and take a picture of me touching his foot, which is good luck. Even though I knew that some seniors pee on his foot every year. I used "anti-swine" (Purell) afterwards. If you look closely you can see my MGH ID. I'll try to get a camera to take some pictures of the lab and post them here.