Author Archives: Laura Scarpelli

This past semester I had the honor to be taught by Dr. Gustavo Silva in his Bio201 class – hands down my favorite class last semester. However, in a lecture hall of 300 students, we never heard about Dr. Silva’s past or work. Interesting enough, big topics that we learned in class such as ubitiquination and degradation process are the focus of his research at his lab. A proteasome is made up of a complex of proteins and is known as the “machine of degradation”. Proteasomes degrade about 80% of all molecules in a cell; they know what material to degrade based on a tag that is placed on the molecule to indicate to the proteasome that it must be destroyed. This tag is known as a ubitiquin chain that is placed due to a cascade of enzymes. The researchers in Silva Lab are studying to answer the questions on how what molecules open the proteasomes along with the structure of these proteasomes. An interesting idea for the researchers as well revolves around the function of the ubitiquin chains architecture. The relationship between the proteasome and the ubitiquin chain is interesting to Dr. Silva and its effects on neighboring organelles, for instance, ribosomes. As Dr. Silva spoke of his research, I was fascinated that I understood so much of his talk due to my learnings from his past class. Back in eighth grade when I sat in my first biology class, I had dreams to be a civil engineer or an architect, but after studying the chapter on the cell and learning all its various yet important functions, I knew I wanted to study biology somehow and seeing that Dr. Silva’s work is mainly on a process that occurs only in cells reminded me of my early passion that stemmed from my biology class six years ago. Putting aside his research, Dr. Silva was also one of my favorite speakers this summer as he is a fellow Brazilian that talked about having determination and desire in every central aspect of your life; from soccer to proteasomes he puts in the work to achieve what he desires and the most vital part is that he enjoys what he does – it is admiring.

Everyone this summer is working on interesting and important research areas, however, the one that caught my attention the most is Piper’s research: the gut microbiome. Every day we all consume different types of foods from pizza to fruits to vegetables; each of these are composed of their respective macromolecules and nutrients. From proteins to sugars, our microbiomes are all made up of different bacteria that break down our consumption.

In Piper’s lab, research has already been done on how the gut microbiome changes when consuming food traditionally – through the mouth; however, she is doing research on how it changes when nutrients are delivered via the bloodstream, a procedure known as total parenteral nutrition (TPN). Her patients are hematopoietic stem cell transplant (HSCT) patients who have their cancer treated through bone marrow transplants, thus they receive their daily nutrients through tubes – possibly affecting their microbiome differently. Piper’s main focus is dietary fibers. When long chains of polysaccharides are digested, the bacteria in the microbiome produce enzymes to break them down resulting in short-chain fatty acids(SCFA) (very good for gut health). Thus, she is looking at the ability of these bacteria to break down these insoluble fibers and produce SCFA’s. Her hypothesis for her research is that TPN decreases fiber fermentation levels.

I found her research very interesting because nutrition is an area everyone should be familiar with as well as attentive to as different foods are introduced into our gut microbiomes. Additionally, I am working with stem cell differentiation and her research introduces questions on how the two can relate. Do certain ways of consuming foods affect the nutritional levels of different cells in the gut? If so, would regeneration of cells be important after a certain period? What is the relationship between the microbiome bacteria and nearby cells? Aside from my own research, it caught my attention because I am heavily interested in keeping my body healthy and consuming the correct nutrients for my gut, thus knowing how the bacteria break down my food allows me to understand which foods would keep me healthy. Also, this will aid doctors treating HSCT patients to focus on providing certain nutrients that may or may not be depleted when fed through TPN. Overall, this project is very cool Piper and I absolutely loved hearing your chalk talk!

Kim Petras and Taylor Swift sing to me as my morning commences with my 1.3-mile walk from Swift to Wilkinson’s 3^rd floor. A peaceful walk, not that tormenting hot midday weather, reminding me of home. At 10 am I arrive at the lab where the door is already propped open for my welcome. I peek into the culture room and usually see my mentor, YingYu, already at work; I wave to her with a smile and walk to my cubicle. I lay everything out: computer, protocols, my notebook, and my pencil. I’m ready!

First things first, figure out what the plan for the day is. Due to my project, each day varies a lot. Usually, it consists of changing the media of my plates, passaging the cells, and making vitronectin plates for the upcoming cycles. Other days can consist of learning skills or going with my mentor to perform flow cytometry for her project. On Tuesdays from 10 – 12 pm, we have our lab meetings where we each go around presenting what we have done in the last week and what we plan to do the rest of the week. My most important days are our Electroporation Days (or as we like to call it D-Day). On electroporation day, the protocol is a lot longer than the other days. This procedure takes me about two hours and is the most stressful because our cells keep dying after 24hrs 🙁 so we must troubleshoot the day after on why this keeps occurring (the fun in science and repetition!). On this day we prepare our cells to be electroporated, which means shocking them, to open their cell membranes to engulf the modRNA. Once electroporated, we plate them on their respective media and wait for them to differentiate into endothelial cells (unachieved thus far). I usually have lunch with Amelia around 12 – 12:30 pm for about 30 minutes until we both return to our labs to continue working. The rest of my time at the lab consists of either continuing the electroporation part 2 procedure, checking on my plates, or creating my PowerPoint presentation for lab meetings. Around 3 pm I am pretty much done for the day and like to fill the rest of my daylight hours with an hour at the gym and a hot, less bearable walk back to Swift Apartments.

The endless opportunities in the USA have drawn numerous international students to its realm of scientific research, one of them being my mentor YingYu Lin.

YingYu was born in Taiwan; her older sister and she would love to walk around Taiwan and eat in multiple restaurants. YingYu’s favorite meal is Stinky Tofu (doesn’t sound appetizing but she lovesss it). When the time came for undergraduate school, she attended Taipei Medical University where college was very different than here in the US. She says that during her undergrad it was very chill and not super intense like how some of our classes can get. YingYu would hang out with her friends, watch movies (a proud Ravenclaw member in the magical world), and of course, eat Stinky Tofu. She discovered she truly wanted to be in the medical field when she entered her senior year of undergraduate and had to take a course where for six months she treated patients at the nearby hospital. She joined a cancer lab for about a year after where she went in knowing nothing but loved how everyone was open to teaching her everything. She loved the science, the chemistry, so to the US her next journey began: graduate school. At the University of Pittsburgh, she earned her master’s in Pharmaceutical Science but did not want to stop there; she yearned to learn more about the engineering of chemistry. Paving the path for a Ph.D., she entered Gerecht Lab at Johns Hopkins University where she currently is researching endothelial cells and pericytes. Her project revolves around the broken blood vessels caused by reactive oxygen species due to Diabetic Retinopathy. YingYu wants to provide a method to treat DR by reconstructing these vessels using stem cell differentiation to replace the dead endothelial cells with healthy ones. Seeing their relationship with pericytes, cells that lie right on top of endothelial cells, she works to discover how to build the functioning blood vessels to treat DR. After, hopefully, finding the solution and receiving her Ph.D. in Chemical and Biomolecular Engineering she aims to join the industry and use her skills to improve medicine either in the US for some time or back in Taiwan to be near her family (and Stinky Tofu). Additionally, visiting Finland and learning how to surf are top bucket list items that she would love to check off!

YingYu has been an amazing and inspiring mentor thus far and I have learned immensely from her not just about biomedical engineering but also about what my future could look like. I am delighted and happy to be working with her for at least 5 more weeks!

Most people do not know they have Diabetic Retinopathy until they go blind or have gotten tested (scary right?). Now don’t get your hopes up, I am not finding a cure for Diabetic Retinopathy, instead, I am aiding my fellow Ph.D. scientists on a faster, more efficient way to achieve more data on the cells that cause it. Let me explain:

Diabetic Retinopathy (DR) is caused by an accumulation of glucose in the bloodstream activating the proliferation of reactive oxidative stress (ROS) in endothelial cells. Endothelial cells make up the inner walls of blood vessels, in this case the blood vessels in our retinas. When ROS builds up in the endothelial cells, the cell dies causing the blood vessel to break and no blood to reach the retinas. Now, what if we could rebuild these blood vessels once they have broken? How would we even do that? The answer is Pluripotent Stem Cells (h-iPSCs)! These stem cells have the ability to be cultured and differentiated into any cell we “program” them to transform into. Currently, in the scientific world of stem cells, scientists have a protocol known as S1-S2 to differentiate the h-iPSCs into endothelial cells (h-iECs), but this method takes too long and is not as efficient in differentiating. Two years ago, scientists created another protocol known as S1-modETV2 to achieve the same result and it worked! In just 4 days! Since Gerecht Lab is still using the old protocol, my research, alongside my mentor YingYu Lin, is to replicate the S1-modETV2 with the slightly different materials in the lab (lab ingredients are expensive!).

The difference between the old protocol and the new one revolves around one major addition: modified RNA. This modRNA aids the synthetic RNA to transfer into cells and express protein function as well as encoding for the ETV2 transcription factor. For h-iPSCs to differentiate into h-iECs, they must first transform into mesodermal cells (h-iMPCs), then with the products of ETV2, they will differentiate into h-iECs. Now you may wonder how this connects to DR? Well, once we accomplish this faster method of differentiation, my mentor will continue her project in discovering a way to rebuild the blood vessels with the use of h-iECs when the ROS, caused by DR, breaks them. With future developments, this project can be founding research for cures/treatments of DR and my research can help out Gerecht Lab in discovering these successful results faster and more efficiently!