Evaluation of my Goals

Here are my goals:
I want to understand what I am doing in the lab at all times and to further my knowledge on anything that relates to biology and medicine.

I want to remain focused while I am setting up tests so that my data is accurate. 

I want to be able to form basic conclusions with the data that I get. 

I just wanted to go over them quickly:

I feel like I have definitely furthered my knowledge when it comes to medicine because of all of the talks that I've listened to. Whether it be Doctor Willey or the fellows I shadowed in the clinic, I know that I've increased my understanding about medicine. Unlike last year, I knew exactly what I was doing in the lab. I could troubleshoot without going to other people because I understood what went wrong from the data displays.

Based upon Xiaolu glancing at my data, I feel as though it is very comparable to her. In addition, I know that I was focused through the testing while I was at Winterim, and it seems to have paid off.

Because we ran out of chips, I didn't get to generate as much data as I would have liked. However, I do not want to base a large conclusion upon a few data points. I can see that there is a drop off in gene expression because of the siRNA, but I would want to run many more tests before I would form a conclusion.

Last Days at UTMC

Last Friday and Yesterday were kind of emotional days.

On Friday morning, we had to deal with the Inspector from the Department of Agriculture. Basically, I hid in the back setting up tests for two hours so that she wouldn't interrogate me. However, Erin did mention that I was apart of the lab staff, so the inspector demanded that I get high-level lab training. That to do that I needed to get registered in UTMC's database. The only problem is I had been recently deactivated. I needed to wait the weekend for the IT department to reactivate my account. I will do the trainings tomorrow morning.

For the rest of the time, I did the normal setting up tests and chips to get data. Overall, I didn't get nearly as many data points, but there wasn't much I could do about that. In my free time, I talked with Doctor Willey about what I'm doing for Winterim Fair, and I think that I have a pretty good board made up. Hopefully I'll see everyone there.

Also, on Monday morning, I brought in donuts as a thank you for all the members of the Lab. When I said my final goodbye, I got kind of emotional. I had working with a few of the members of the lab for the last two years. I had really gotten to know them and I knew that they had my back whenever I messed up. They all told me to come back and visit sometime. I most definitely will.

Throwback Thursday November 21st

When I mean Throwback Thursday, I mean I threw back to a time when I had chips and I could run them properly. Today I was able to run 2 chips (that's 24 samples) and get 6 data points (I had 5 at at the start of the day). All of my data made sense and seemed to be accurate based on Xiaolu's cursory glances. I felt really proud that I started to produce good data on my own. I can see why some people make research their lives' work. It was almost a sort of high when I saw that I had obtained good results. I can even imagine how ecstatic one must feel when they publish a noteworthy paper.

Speaking of which, I got to listen to Grand Rounds (a large weekly presentation accompanied with free pizza). The Dean of Medicine at UTMC, Dr. Hoover, talked about Renal Stenosis. He had found over the course of the last 15 years that the insertion of a stent into the closed renal artery (a costly and risky procedure) doesn't not have decreased risk of clinical incident (a major health problem like a heart attack or stroke) compared to treatment with new pharmaceuticals. He had even helped find a potential solution that would save kidneys and lives. He recently published his findings in a high level medical journal and praise was coming in. At the end, he cried and was greeted with a large round of applause, which he obviously deserved. But the thing that stuck out most for me was that he had spent 15 years of his life, many of those years away from his family, in order to obtain this conclusion. As amazing as he must of felt, I don't know if I would find it worth it to sacrifice 15 some years of family life in order for an amazing paper or two. Just something for everyone, especially myself, to think about.

I didn't run any tests in the afternoon because the National Institute of Health is coming in tomorrow to inspect Dr. Willey's Lab. Every one in our lab, including Dr. Willey, cleaned up in the lab area. Hopefully tomorrow goes well.

November 20th THAD THE SHADOW

This morning was the typical morning. I ran some PCR and froze the samples. To my extreme pleasure, the electrophoresis chips arrived in the mail. I almost screamed in joy. This means that I can get some data when I have time. However, I had planned to shadow Dr. Willey this afternoon since the chips hadn't arrived yet. All afternoon I followed Dr. Willey and his fellows at the Rupert Center.

Before I went to shadow him, I ate lunch with Dr. Willey. He told me that I wouldn't be seeing Lung Cancer patients today, but merely patients who had problems with their lungs. Doctor Willey is a Pulmonologist at the Critical Care and Sleep Medicine Clinic at the Rupert Center. He told me that they often lump both Critical Care and Sleep Medicine because they both intermingle with the lungs. Lots of the problems that deal with sleep are a result of some problem with the airways and usually with the lungs specifically. In addition, Critical Care usually involves people on ventilators, so they like to have Pulmonologists deal with those patients.

I followed one of his fellows, named Anthony, for the majority of the time. We saw 3 patients during our time and all three had severe lung problems. I noticed that they all shared some similar characteristics: GERD, COPD, Chronic Bronchitis , and Asthma, and nearly all resulted from extended tobacco abuse. Each time, Anthony would go in, get the history of the patient, and then report his findings to Doctor Willey. Doctor Willey would then talk to Anthony for a bit about what they thought was the best course of action. They all three of us would go and talk to the patient for the final time.

What I really enjoyed about shadowing Doctor Willey was seeing how doctors work. For the most part, people were talking the entire time. There was a constant flow of information from the patient to the fellow to the other doctors. It was amazing how fast their mouths were moving and all of the background information that needed to be known. A doctor has to be conversational, be extremely intelligent, know a tremendous amount of background information, and be able to solve problems very quickly. It seems like the perfect fit for me.

But at the same time, the research aspect of medicine requires nearly the same skill set. I could go into either clinical medicine or medical research... or potentially both, only time will tell. I hope to maybe shadow Doctor Willey again before I go to college.

Bigger Picture! IMPORTANT TO READ!

Background information: Currently, roughly 19% of people in America smoke cigarettes on a semi-regular basis. However, only 10% of people that smoke heavily get Lung Cancer. Lung Cancer kills the most people every year out of all cancers, mainly because it present asymptomatically until it is inoperable/untreatable. The reason that Lung Cancer occurs in a higher percent of smokers is that the inhalation of all the chemicals in the cigarettes causes many cells in the airways to die. The surviving cells then have to replicate more then they are supposed to, which leaves them at a higher risk for random mutations to occur in the DNA. Often these mutations are corrected by DNA repair enzymes, outside Macrophages who realize the cell is aberrant, or the death of the cell as a result of a mutation in a vital pathway. But since the amount of replications in the air way has been exponentially increased, the random mutations are more likely to add up to the point where a cell becomes cancerous. Thus, Lung Cancer is a fairly large problem in the smoking community, but not limited to just them.

The government allocates nearly $5 Billion a year for CT scans of smokers so that they can hopefully catch the disease in its incipient stages. Doctor Willey, a researcher of both lungs and cancer, sought a way to proactively test people for Lung Cancer. One of the major papers that Dr. Willey's lab produced in the last few years talked about a pattern seen with the levels of expression with certain antioxidant and DNA repair genes in airway epithelial cells (click here to read the paper). They found that there was a  "safe" zone in the amount of mRNA that would be transcribed from the cDNA that had been harvested from air way epithelial cells.

They concluded that for each of the 14 genes that the person does not fall into the "low prevalence" zone, the risk increases. 

Generally in the above graph the higher the number of genes that are out of the safe zone in the test (RTV) means a much higher chance of cancer. Most of the people with above 8 will develop cancer at sometime as they age.

Knowing the risk can allow for the people who haven't developed cancers to go through pre cancer therapy so that the cancer does not proliferate and kill them. This test was recently approved for usage across the country, and it will likely be used commonly by primary care physicians in the next year or so. Doctor Willey told me if they can cut the amount of CT scans they need for diagnosing cancer by just 20 percent, they've already saved the government $1 billion. This is because the biomarker tests are much cheaper and much more effective than the CT scans, saving lives and money.

In addition, another thing that is being looked at in the Willey Lab is a potentially easier method of extracting cells to test. Currently, they use cells that are harvested from Bronchoscopies, a process that takes a fair amount of time and effort to do. They're trying to find a way to get the same Lung Cancer test readings from different cell types, such as cheek cells or skin cells. This would make the Lung Cancer test even more convient and save even more money. 

So now you're probably wondering why this factors into what I'm doing. Well good question! I'm glad you're interested enough in what I'm doing to ask that. If you look above in the table with the 14 genes, you will see that CEBPG is one of the important genes. It actually has one of the smallest "safe" zones of the 14 genes. Based upon a paper that Dr. Willey's Lab produced in 2005, they know that CEBPG controls main of the important genes in air way cells, including many of the Antioxidants and DNA repair genes. All of the PCR and DNA chip electrophoresis has been centered around CEBPG. I'm helping Xiaolu and Doctor Willey with is seeing how treating cells with siRNA for CEBPG affects the expression of the other important lung genes, many of which are some of the other 13 genes in the Lung Cancer test. Depending on the results, it could be a treatment option or a new mechanism to be documented/researched. Hopefully, this has helped you understand more about the bigger picture around what I am doing this Winterim.

Lunch with Important People

Today was a pretty normal day for the most part. I reviewed the Real Time PCR results with Xiaolu first thing in the morning. I was slightly confused at first, but Xiaolu showed me how to get the number of targets produced per million ACTB by using exponential equations. I still don't understand it completely, but Xiaolu wants me to run a set of RT PCR before I finish Friday, so hopefully I will be able to explain it soon. 

After that, I started another round of PCR for a different cell line. Same old same old. I put the results in the freezer to run when we get chips. 

But then, I went to lunch out. Today, Mr. Boehm was supposed to meet with Dr. Willey and I to discuss how I was doing. However, Dr. Willey got called to listen and comment on a presentation at the last second. So all three of us went to listen to this presentation on Pneumonia and COPD (a lung disease). It was the first time in a while that I did not eat by myself. We ate sandwiches while the person talked over a special type of Pneumonia that results from complications with COPD. I was pretty interested by the topic, but I struggled to completely understand what was going on (mainly because I am still in high school). At the end of the presentation, Dr. Willey got up and answered more complex questions on the subject.

(Pictured is the building we ate lunch in)

After the presentation finished, we all sat and talked. Dr. Willey said I was doing a good job in the lab and at there were no complaints against me (yay). Mr. Boehm wanted to know more about why  research I was helping with mattered. This started a rather long and drawn out discussion about what's going on in his lab and Mr. Boehm eventually understood why what we were doing is important. I agree with him when he told me that he felt that my blog was lacking an explanation of the bigger picture. I will post again soon to clarify and explain why what I'm doing matters.

Also I'm planning on shadowing Dr. Willey in the lab tomorrow, so I will hopefully have a interesting post tomorrow. Stay tuned!

November 18th BUSY DAY

Today was easily the busiest day that I've had.
Even though the chips are still in the mail, I still wanted to do a lot of work. Doctor Willey and Xiaolu want to make an abstract before an upcoming conference, so there was an abundance of work in the lab.

(The list of all the work)

My job for this week is to get the ERCC5 and ERCC4 values for cDNAs from 3 different cells lines. I set up the test and ran the PCR. So that the PCRed samples do not deteriorate, I'm going to put them into the freezer. I currently have 25 samples that are waiting in the freezer for when the chips get back. I still have 24 more samples to make.

BUT I learned a really cool new test today called Real Time PCR. Xiaolu taught me that this test has 2 steps. For the first step, she puts in the different samples in a rack with 8 wells by 12 wells. She puts the same reagents in and for 18 cycles, it goes through PCR. During these cycles, the signals that the cDNA produces get amplified. Then, the samples are diluted to 1/10, 1/100, and 1/1000. I don't know the reasoning, but then  they undergo another 14 cycles of PCR. They then can determine how many molecule of the gene was produced per million ACTB (exactly the same thing I did with electrophoresis) based upon how much fluorescence is produced (it's produced by the probe finding its complementary sequence [check the wikipedia article it's kind of hard to explain]). Anyways, we get the same results, quicker and more accurately. Xiaolu and I are looking at how siCEBPG affects the production of MUC5B (another gene) in the cell lines.

Also, I talked to Xiaolu and the reason that they are looking siCEBPG knocked down cell lines is that they want to see (if there is) a mechanism involved when CEBPG regulates cell functions. I'll try to explain that more tomorrow.