Today was a less exciting day at the Sheikh lab, but a few interesting tidbits of knowledge were imparted!
On a fun trip to collect cell media from the tissue culture facility, Shruti and I talked about the importance of keeping things cold in a lab environment. If the temperature gets too hot, sensitive samples like DNA and RNA can easily denature. Dry ice and regular ice are both used commonly to keep things cold. It’s pretty common to see things being held in a rolling cooler around campus, especially around the areas filled with science labs and research buildings. The cell media that we were bringing back to the lab was going to be used to help grow the colonoid cells, which sadly, I was unable to see. I did have a lot of down time on this day, but I was able to spend more time getting comfortable with the campus and get to know some of the researchers on a more personal level.
Today I got to shadow Dr. Deepak Pasi from North Carolina Heart and Vascular at Wakefield. I had an amazing time overall, but the most interesting thing that I got to learn about was a procedure called angioplasty, which helps remove blockages in the arteries. I got to watch a catheterization (through a monitor) LIVE, as the different movements of the catheter were happening! It was probably the next best thing to being in the cath lab! Dr. Pasi walked me through the technical aspects of the procedure, and how stents are used to clear arteries.
Another really special experience was getting to watch as Dr. Pasi saw patients in the different exam rooms. I got to listen to the lung and heart sounds of different patients, including a patient with a heart murmur (which is when blood flow is extremely turbulent, sometimes indicating valve problems). I also got to hear a patient’s lungs, but instead of hearing the normal air whooshing in and out, I heard a faint crackling noise because the patient’s lungs were filled with fluid.
Without context, a lot of things can be unclear. I’ve found that this principle holds especially true in the world of medical research. The research conducted by the Sheikh lab uses various biological samples, such as tissue, serum, individual cells. However, the one thing that binds all of these types of samples together is where they come from: a sick patient. Understanding the patient’s illness is just as important as understanding the sample that they provide us. So, on Tuesday afternoon, the entire Sheikh lab got together to hear Dr. Sheikh give a clinical talk briefly outlining the two main types of inflammatory bowel disease that the lab’s research is aimed towards.
Both Crohn’s disease and ulcerative colitis have genetic, immunological and microbial factors that contribute to a given patient’s susceptibility; however, it usually takes an environmental factor to trigger a patient into actually contracting the disease. Essentially, there’s currently no way to predict if a person will get either disease because there’s no directly linked cause. Furthermore, it’s hard to pinpoint one of these diseases exactly in a diagnosis because the symptoms that patients have aren’t solely limited to the gastrointestinal tract. The elusive cause and the difficult diagnosis are just a couple of the reasons why the lab’s research on inflammatory bowel disease is so important.
So, you’re watching the season finale of the Bachelor and you’re about to find out who receives the final rose, and just like that the screen cuts to black and an image of blackened lungs fills the screen with bright red letters forming the blaring message “Smoking Kills”. We’ve all been there (more or less). Something really interesting that I learned in Dr. Sheikh’s talk was that for patients with ulcerative colitis, smoking has actually shown to have beneficial effects in fighting the disease. The nicotine in tobacco helps suppress the immune system and reduce inflammation, essentially countering the disease’s effects on the body head on. So for patients with UC, smoking doesn’t kill, it saves!
It’s sort of a given that if you’re working in a medical research lab, you’re going to be surrounded by really smart people. Even if they don’t bear the title of Principal Investigator, everyone I’ve been surrounded by for the past few days has clearly radiated intellectual prowess. On Monday, I witnessed this phenomenon times a hundred, with a visit to the Genetics building for the monthly inter-lab meeting. The point of these monthly meetings, or “journal club”, is for different people to present scientific research that relates to their current field of study. Whether it’s a new technique that could serve as a better alternative to an existing one, or a particularly interesting set of data that reveals a finding that may change the course of their own research, journal clubs are designed to keep the researchers updated and informed.
When we all started learning foreign languages as sixth graders at Cary Academy, we often searched for words that we recognized in a sentence and used context clue to figure out what was being said. As an avid language learner, I was excited to try to use this strategy to get the most out of the lab meeting. However, I quickly realized that the tactic I used to get through those first few Spanish classes was not going to work when trying to understand complicated molecular biology and genetics. Through my exposure to the sciences especially, I’ve recognized the importance of building a solid foundation of knowledge from which to build off of. If your foundation is weak, you won’t be able to grasp more complicated topics. I’ll be very honest: a lot of the advanced concepts that were presented in the meeting flew straight over my head. In fact, there isn’t very much of the presented research that I could specifically reference and clearly describe right now, even just a day after attending the meting. However, what I did appreciate and enjoy was the engagement and discussion from the rest of the audience following the presentations. People weren’t afraid to challenge the claims made through certain charts and figures or to express their genuine interest in learning more about the subject.
While I may not have learned much actual science today, I did learn a lot about how science is communicated in a practical way. For example, graphs and figures need to be understandable and clear in order to deliver the intended message. One of the really interesting figures that we looked at in the meeting was a 3-D online model of the data that could be spun around to view from all angles. I also recognized how much effort scientists around the world put into making sure that their research can be shared, exemplified through the intricate 3-D online model.
Fridays in the Sheikh lab mean lab meeting days, or where technicians meet collectively with Dr. Sheikh to provide progress updates and get feedback on ongoing experiments. I got to sit in on the meeting and listen to a summary of some of the major happenings in the lab over the past week. I was able to learn a bit more about the everyday workings of the lab, or what happens in addition to the cool experiments. While at first I was disheartened to be sitting in on a less-than-thrilling lab meeting after an especially exciting day of experiments on Thursday, I learned that a lot of the work in a lab involves collaboration and discussion and careful research much before experiments can be conducted. I guess this could be considered part of the daily grind, the less exciting but nevertheless necessary tasks that make up part of this profession.
Later that afternoon, Ashley (the lab’s clinical coordinator) and Shruti and I took a walk over to the UNC Children’s Hospital to collect tissue samples from pediatric patients with inflammatory bowel disease. As we trekked through the intricate maze that is the hospital, we talked about the importance of collecting the various tissue samples so that they could be used in experiments at the lab. Although it was a slower day, I still was able to learn a lot!
Day 3 in the Sheikh lab began with a bang, or should I say a splat? In the morning I watched Matt, one of the research technicians, complete a series of protocols to isolate RNA from a human tissue sample. However, on the way from the fume hood to the walk-in fridge, Matt dropped one of the samples and about half of it splattered out across the floor. We had to stop what we were doing and carefully clean up the mess with ethanol to take care of the potential safety hazard. Even though we laughed about the silly mistake, it brought up a good point: accidents happen all the time in the lab, and what’s most important is how you choose to deal with them. Even though Matt lost over half of the treated sample, he decided to continue processing it anyways, because any amount of tissue can provide helpful data. If you decide to throw out the sample after you’ve already done a lot of work with it, you’re just wasting resources. The spill also brought up the necessity of the taking careful notes during your experiment, so that when you get inconsistent or abnormal data, you can come up with an explanation for what might have happened. For example, once the isolation process was completed, the sample that spilled would have significantly less RNA in it, so in order to explain the results, you’d have to look back and remember that you lost half of the sample.
TRIzol, a chemical buffer used in the homogenization processThe human tissue samples being kept cool in an ice bucketCentrifuging the tiny samples in the giant walk-in fridge!A view through a microscope of artificially grown cells called colonoids. I’ve just started learning about what the lab’s doing to grow these cells and do experiments with them, and I’m excited to discover more!
I stepped onto UNC’s campus early this morning, ready for the work experience I had been waiting for, ready to finally begin my time at the Sheikh lab. Contrary to my initial belief, I was actually far from ready to jump into the complex realm of gastrointestinal immunology and genetic research that the lab specializes in. You see, I had spent some time on Day 1 struggling through a scientific review paper that I had been instructed to read, as a means of familiarizing myself with the current research available on the topic of inflammatory bowel disease. However, “struggling through” was not an understatement; the task of reading a scientific paper requires far more than a pen and a comfy place to sit. With my colorful highlighters in one hand, post-it flags in the other, and Dictionary.com at my side, I began to slowly work my way through the extremely technical language and concepts that the paper discussed. As I embarked on my treacherous literary journey, all I could think of was how tiny the font was and how unhelpful the complicated scientific diagrams were. But as I persevered, scary phrases like “nucleotide-binding oligomerization domaincontaining 2” were shortened to simply “NOD2”, and I recognized that with a little patience and courage, I began to actually understand what I was reading, and it turned out to be really interesting!
Some light reading
The paper discussed the pathogenesis, or development in regards to disease, of inflammatory bowel disease, particularly Crohn’s disease and ulcerative colitis. Inflammatory bowel disease is particularly elusive in the medical world because the exact cause is still unknown. We know that there are significant genetic linkages, but environmental, microbial and immunological factors still play an important role in patient susceptibility. Upwards of 160 susceptibility genes have already been identified and scientists are working on piecing together the connections between those genes and the responses they cause and the responses in IBD patients.
Throughout the morning I continued my preliminary research by supplementing the initial paper I read with another one that went deeper into researching the cause of IBD in patients. When Shruti, the lab technician and my mentor for the internship, arrived, we had a short conversation about the lab’s current ongoing projects which led to a discussion on PCR techniques. Later this afternoon, Shruti took me down to the Lineberger building, which is equipped with a special machine able to conduct and monitor digital PCR. She walked me through how the machines were used to further explore gene expression of a certain genetic target through testing the fluorescence of individual droplets. If a single droplet contained the target particle, it would glow and the machine would measure it and store it next to the data for the thousands of other droplets tested. The process was complicated and tedious, but being able to visualize the ratio of positive droplets (with the target particle) to negative ones using the computer program assisted with my understanding.
This is the droplet reader that carries out digital PCR. A needle on the inside of the green hood sucks up individual droplets that are made with a mixture of oils and primer. Some of the droplets contain the rare target particle, and some only contain the more common DNA particle. The droplets with the rare target particle exhibit a special glow, which the machine measures and uses to create groups of positives and negatives. Complicated statistics and programs can be used to backtrack from the data collected; essentially, you can figure out what the starting distribution of the target particle must have been in order to have gotten to the current distribution. The numbers you get tell you how many copies of the target particle were present in any random sample.This is the automated droplet generator, which creates the tiny droplets used in digital PCR. Some of the droplets encase regular DNA particles, while some hold the special target particle. Sometimes, multiple target particles could be found in one single droplet, but that’s okay because the amount of glow measured by the other machine accounts for that possibility.We passed by this cool collection of a BUNCH of different kinds of buffers, which I learned about in AP Chem this year with Mr. Rushin. Buffers regulate the pH of a certain solution so that reaction can take place in the right environment. It was cool to see a connection to something that I had learned at school at the lab!
There was an issue at Dr. Sheikh’s lab that prevented me from going in today, so I spent the day with my dad, Dr. Neeraj Sachdeva, who is a gastroenterologist with Wake Endoscopy Center in Raleigh. Together, we reviewed a few recent studies and cases he had been involved with, including a case report of a woman who presented with what looked like a heart attack, but turned out to be hiatal hernia, along with a study regarding the detection rate of potentially pre-cancerous polyps (called adenomas) based on different conditions possessed by patients.
Through our discussion of the case, which combined work from both the cardiology and gastroenterology realms of medicine, I learned about EKGs and how to read them and what kinds of conditions could be indicated by different patterns of the waves. I also learned about a rare condition called an aortic dissection and even rarer one called a hiatal hernia and how to recognize both on CT scan images. While the case in question ended well with no particularly extreme measures taken to ensure the health of the woman, I learned how it is still important that my dad and his fellow physicians publish this information to other doctors, so that if another patient presents with similar symptoms in another part of the world, the possibility of hiatal hernia should not be immediately ruled out simply because of its rarity.
We also touched on a recent study conducted retrospectively based on data collected from the different colonoscopies done by doctors at the practice. The study addressed correlations between comorbid conditions such as obesity, diabetes and hypertension in relation to the discovery of pre-cancerous growths during colonoscopies. The study found that hypertension or high blood pressure didn’t play that much of a role, diabetes played close to a significant role and obesity played a very critical role in adenoma detection. Since we had a copy of the original raw data, I learned how to make conclusions based off of simply numbers and apply that to find implications for patients everywhere.
