Student Blogs

This summer, I learned many new skills. But among pipetting, passaging, preparing media, programming cell culture robots, and PCR, one more covert skill that I had to master was problem solving. I was working in the Mattis Lab at UCSF Parnassus, studying iPSC and iHepatocyte behavior when introduced to fatty acids, and whether their lipid accumulation was faster when they were derived from patients with nonalcoholic steatohepatitis, a fatty liver disease. I began my experience shadowing the everyday lab work and performing the simpler, lower-stake tasks. Culturing cells takes great caution and precision; one simple slip-up could cause contamination or differentiation or apoptosis.

Naturally, then, I managed to mess up. Many times. One time, I was preparing media for passaging cells. I was pipetting out 45mL of media, and absent mindedly added 50mL to the solution instead, messing up the ratio of reagents. Thankfully, this was an easy fix. I changed my total volume of solution and increased the amount for all the other reagents. Or another time, one of the lab’s more important cell lines– some of which another student and I had handled– became contaminated. Out of guilt and curiosity, we tried to salvage those cells by culturing them in media with extra antibiotic solutions which would hopefully eliminate the contaminants. And even though we were unfortunately unsuccessful in this mini experiment, it showed me that there can be ways to recover from mistakes, and that it’s valuable to try.

Sometimes, too, problems will arise that aren’t your fault. For instance, for my research project, another student in my lab and I were tasked with learning how to use the robot that our lab had to culture, add solutions to, and image our cells. Although incredible, this machine became the bane of our existence. Every time we tried to run an experiment with it, it would present us with a new roadblock. It was almost comical how many we encountered. Take some particularly frustrating ones: “Error: Focus Z calibrations needed,” “Error: Code 550E,” “Warning: O₂ levels too high,” or, one of its favorites: “Error: The reader is not communicating.” We tried everything to fix this problem, but we couldn’t figure out what was causing it or what exactly would solve it. It took us several hours of combing through user’s manuals, unplugging and replugging, and long phone calls with IT to finally figure out this error. (As it turns out, the solution to this problem is simply to restart the computer). But eventually, once all the possible issues had been cleared, the machine worked and I had practiced the crucial skill of problem solving.

Ultimately, that’s what science is: a series of trials and (lots of) errors. Working through these human and other inevitable errors not only makes the experiment possible, but also makes it that much more rewarding to finally see that “SUCCESS” message on the computer, or spot those beautifully crisp, uncontaminated iPSC colonies under the microscope. I am endlessly grateful for the opportunity that the CIRM and UCSF CHORI internship has given me, and for all of the lessons and skills that I took away from it.

Everybody loves to have their dreams come true. Unfortunately, wet-lab research seemed like more of a nightmare– in my mind, pipetting for hours on end was a sure way to get back issues.

When it came to my first day working with cells (HepG2 cells treated with antibiotics to prevent contamination), my nerves joined the witty encouragement from one of the undergrad volunteers and caused me to spill my media out of my cell plate. The next morning, I unearthed my cells from the SSRP student incubator, Cogsworth, only to find three massive blobs of mold covering my plate. Despite me making 70% ethanol my best friend that day, my cells were ruined.

My experience in the Medina Lab has been a glimpse into reality. Here, there are dreams of successful differentiations ruined by nightmares of contamination. Despite the uncertainties in research, one thing remains true: the individuals in the Medina Lab truly want you to succeed.

Our All-Woman Lab Team

Huh7 hepatocytes, my second attempt at culturing cells. With advice from Dr. Yuanyuan Qin in hand, I was ready; by meticulously following each step of the protocol with my ethanol in hand, I was able to successfully passage my cells.

Passaging in the Biosafety Hood

My next challenge? Understanding the project I was tasked with: Establishing a FACS-based method to detect cell-type specific markers during the differentiation process of iPSCs into iPSC-Heps. Through the patience of mentors Dr. Yuanyuan Qin and Dr. Marisa Medina, who so thoughtfully answered every question I had, I was able to comprehend my project and its scope.  The Medina Lab focuses on non-alcoholic fatty liver disease (NAFLD), and in liver diseases associated with hepatocyte dysfunction (like NAFLD), and iPSC-Heps are key to researching disease mechanisms and modeling individual-level disease risk. My project would be to confirm that iPSCs have differentiated correctly by assessing the presence of markers of different cell stages (pluripotency, endoderm, progenitor, and mature hepatocyte markers)

iPSCs Under a Bright Field Microscope

After weeks of mycoplasma treatment, the iPSCs were finally ready to be differentiated– only three weeks before the program ended. As deadlines for CIRM abstracts and the cumulative poster approached, I began to stress. I had no real results yet; compared to the other individuals, I was behind. Taking advantage of the small groups SSRP’s program leaders Ellen, David, Lisa, and Roi set up, I heard my groupmates’ similar concerns. The other CIRM-funded students also acted as support for me– we were all in similar boats. With determination, assistance from my mentors, and no shortage of procrastination, I have been able to articulate the full extent of my summer experience through presentations, research proposals/abstracts, and posters.

My experience at the Medina Lab has been truly eye-opening. Without bold ideas or unique perspectives, our forefront of science would remain stagnant. I have learned that research is so much more than mixing chemicals or running gels; it is about the process of observing, questioning, and most of all, trying passionately. Moreover, I thank the SSRP community– the team that has made this experience possible and my fellow researchers, whose questions during lectures inspired my own. From the endless supply of chocolate in my lab’s mouse-proof snack box to the lively gas tank changes we made, this summer has been nothing short of a dream.

When I applied to CHORI, I had little idea of what to expect, as it marked my first venture into the world of STEM jobs. However, my school courses in biotech and biology had equipped me with some scientific and professional knowledge for working in a lab. Although the prospect of stepping into   the unknown made me nervous, I was also filled with excitement to finally address the questions I had pondered for years: "What part of STEM do I want to do in the long run?" and "Is this field still my interest?" On my first day at the Medina Lab, I was introduced to iPSCs (Induced Pluripotent Stem Cells) and their significance. Soon after, I learned and got into my primary research focus, which revolved around Non-alcoholic Fatty Liver Disease. The subject captivated me right from the beginning. My journey began with hands-on tasks, like the pipette test, where Sheila Teker, my lab member, guided me throughout the initial two weeks. Cell passaging became my daily task to do research about, and though my early attempts were less than perfect, my lab colleagues and mentor displayed incredible patience as they assisted me. Through their support and my persistent practice, I eventually reached a point where I can confidently perform cell passaging my first Huh7 cells independently.

My experience in the lab has been a valuable life lessons with patience, active listening, and the importance of asking questions. Overcoming obstacles such as cell contamination and obtaining undesirable data has taught me to think swiftly and adapt to unforeseen circumstances, especially when time is limited for data collection. Being part of an all-woman lab environment has been nothing but inspiring, as it has encouraged me to embrace confidence in pursuing my passions. The amazing support from everyone around me has been truly motivating, as they genuinely want me to succeed and reach my full potential this summer.

Mastering my summer project proved to be a challenge that required maximum effort and numerous trials. The techniques I had to use for my summer project being cell culture, cell staining, and FACS analysis. Observing my lab member, Grace, and my mentor, Dr. Qin, allowed me to grasp the idea of iPSC cell culturing and discern their distinctions from Huh7 cells or HEPG2. Dealing with nile red presented its own set of difficulties due to its sensitivity to various factors, particularly light. The FACS machine played a crucial role in measuring lipid accumulation, which contributed highly to the final data for my project. The main objective was to learn whether healthy patients exhibited higher lipid accumulation than those afflicted with Non-alcoholic Fatty Liver Disease.

I am immensely grateful to the Medina lab for providing me with this life-changing summer experience and for the incredible amount of support I received throughout this. This summer will forever be special as it has helped my passion for this field and help me believe that I belong here. I will also like to appreciate CIRM for offering such an informative program, and I cannot thank Ellen and David enough for granting me this amazing opportunity to grow and learn. As my summer journey draws to a close, I look forward to carrying the valuable lessons and memories with me on my continued path in the world of STEM. Thank you.

Over two months ago, I would have never imagined I would be saying “I wouldn’t want to stress out my cells” so casually. Too long outside of the incubator and I’d be afraid that the not-so-optimal temperature and humidity would damage the cells. UCSF’s Summer Student Research Program (SSRP), where I was chosen to be a CIRM SPARK student, has given me more hands-on experience than all my high school classes combined.

One of the trickiest parts of starting off the summer was the scientific articles. The jargon was intimidating, and it felt like I was missing out on years of experience to fully grasp the meaning of the paper. Nevertheless, I pored over all the articles on the spread of alpha-synuclein in Parkinson’s Disease. While the words “uptake” and “pathogenesis” felt foreign in the beginning, now I can wield them as if I have been saying them my whole life. I spent hours upon hours highlighting vocabulary. Never before had I been so invested in truly understanding what an academic article had to say. My tabs were a combination of words followed by “meaning”, “simple definition”, and “explained.” In high school, we were taught to browse through and only choose what felt relevant. But through SSRP, I learned that the failures and mistakes are just as vital as the successes.

Even though I have already graduated high school and gone through the basics of biology, taking on research at UC Berkeley’s Schekman Lab felt daunting. The nerves that come with entering a new setting and the gaps in knowledge I realized I had after reviewing cell biology made it so my first few visits to the lab were spent hyper-focusing on the smallest detail of the lab protocols. Even something as small as what angle to hold the pipette felt like pertinent information.

Now, in the last few weeks of the program, I still feel it necessary to question every color, shape, curve, and angle to my experiment. Whether it's fluorescence microscopy or changing the media for my cells, I want to absorb every detail; I’ve jam-packed my brain with facts on phosphorylation, kinases, and lewy bodies. I’ve spent hours going over this particular niche of molecular biology and it has only made me more enthused to continue into higher education.

I’ll be heading into Stanford University this fall, and it is hard to imagine what it’d feel like to go in not having had this experience. Thanks to CIRM and SSRP, I feel excited to continue exploring biological research. Even if my cells did clump–a sign of cell death–being able to put on a lab coat and working in a tissue culture hood has given me the confidence I needed to start college off strong.

If my life was an equation, then my love for science would be a constant. For as long as I can remember, I had always wanted to be a scientist “when I grew up.” So, I decided to apply for an internship at UCSF, to see if the career lived up to my expectations.

Something I learned during my time at UC Berkeley’s Zoncu Lab is that research definitely is not a 9 to 5 job. There were days where I needed to stay at the lab for 12 hours or weekends where I needed to come in to set up for experiments I wanted to do later that week. If you’re curious, here’s what an average day in my life looks like:

6:00 AM — This is when I’ll get up and get ready for the day.

7:00 AM — I’ll get onto the BART, which is a public transportation system in the San Francisco Bay Area. The journey from my place to UC Berkeley would take about an hour and a half.

8:00-9:00 AM — I arrive at the lab somewhere between 8:00 and 9:00, ready to get started. Usually, my mentor Dr. Rose Citron and I would sit down at the beginning of the day and plan out my experiments or go over the results of yesterday’s work. Then I would get started on whatever the plan for that day is: developing a western blot, passaging cells, etc.

12:30-1:30 PM — Usually, I’ll take a break for lunch around 12:30; however, the exact time varies depending on my experiments for the day. I’ll meet up with another CIRM student who works in my building, and we’ll go out to a restaurant nearby. There’s so many options in downtown Berkeley!

2:00-5:00 PM — Every Tuesday and Thursday, as part of the UCSF program, I have the opportunity to attend lectures given by various medical and research professionals. These are very fun and informative, and they give me exposure to all the possible career paths I have before me.

6:00-7:00 PM — After the meeting, I’ll finish up the rest of my work and head home. I’ll chat with my mentor at the end of the day and fill her in on my plan for tomorrow. At the beginning of the program, I relied on my mentor to tell me what to do and plan out my day for me. But later, my mentor “cut me loose” and pushed me to design my own experiments. I began to gain confidence in my own skills and knowledge, and it made me feel more like a scientist.

8:00 PM — I’ll arrive home around 8:00 and relax before doing it all again tomorrow!

Of course, this is not what every single day looks like. One thing I’ve learned during this program is that it is pretty much impossible to maintain a strict schedule while in research. Sometimes, my cells don’t grow on schedule and they’re too sparse for the procedure I planned, or I need to redo the experiment because the results don’t look very clean. This means I’ll need to postpone my other procedures, or stay longer at the lab to finish. And that unpredictability is what makes research exciting!

Before I joined the summer student research program, a lipoprotein didn’t mean much to me. When I first heard the word, I had just envisioned them as being simple particles found in your body that stored or transported fat. I would have never imagined how much could be learned by isolating and analyzing the composition of a person’s lipoproteins or how significant the different densities and sizes of these tiny particles could be to a person’s health.

I’ve learned that lipoproteins are particles composed of lipids and proteins that transport triglycerides and cholesterol through the bloodstream. They’re characterized by size and there is an associated risk between concentrations of different types of lipoproteins and cardiovascular disease. Having a high concentration of HDL which is high density lipoprotein is generally thought to be good while LDLs which are just low density lipoproteins are associated with cardiovascular disease. Advanced lipoprotein testing has helped characterize known size regions of lipoproteins but has also uncovered an uncharacterized region which is being called the midzone. Particle diameters fall between HDL and LDL. This summer I’ve been working in the Krauss lab which is doing work to better understand the midzone to determine if certain particles can be associated with elevated or reduced risk of cardiovascular disease. The lab has a machine that does ion mobility which allows them to take plasma and separate lipoprotein particles within it by size which produces a graph that shows concentrations of the different particles. How the machine works is very complex and something I’m still in the process of learning but it is crucial to the work done in the lab as it can uncover the cardiovascular risk of a person based on patterns in their results.

For my project this summer, I’ve been utilizing tools such as ion mobility while trying to better understand some particles thought to be found in the midzone. More specifically, I’ve been looking at two proteins, complement C3 and haptoglobin trying to understand their role in the context of cardiovascular disease and mortality. I’ve had the opportunity to take two different approaches to my project; we’ve done many western blots where we look for the proteins in actual patient plasma samples as well as immunofluorescence with primary liver cells.

It’s been an amazing experience being able to work in all the different labs I’ve been in and hope to continue applying the skills and knowledge I’ve gained from this project in any future research opportunities I come across.

Epigenetics. When I first heard the word, I was reminded of biology class in my freshman year of high school. Although my class was unable to fully explore epigenetics, my main takeaway was that our DNA is affected by our lifestyles and environments. What we eat, the pollution we breathe in, where we live -- that all affects our DNA in some way.  

However, through my CIRM program experience, I have uncovered a whole new side to epigenetics. Instead of focusing on factors outside the human body, I am now studying chemical changes that affect DNA from inside the human body. 

This summer, I have been working in the Nuñez lab, which studies epigenetics. For my project, I am studying Methyl-Cpg-Binding-Domain Protein 3, also known as MBD3. This protein is part of the MBD nuclear protein family (proteins found within the nucleus). MBD3 is the smallest protein in the family, making it an attractive choice for epigenetic editing. 

When it comes to engineering new technologies to modify the genome, the primary issue is size. Cells are small, so whatever is being used to edit DNA needs to be even smaller. Our goal is to modify the epigenome with MBD3, so we are forming five DNA fragments that contain varying MBD3 regions. We want to determine where exactly in the MBD3 region does transcriptional repression occur.  

Before this summer, I was nervous about working in a wet lab for the first time. But with the support of the Nuñez lab, I have learned so much in terms of new material and techniques. From DNA methylation (adding a methyl group  to DNA in the form of a “tag”) to the centrifuge (a machine that utilizes centrifugal force to separate different parts of a liquid), this experience has continued to increase my love for science. Furthermore, I have discovered that science is not linear. When conducting experiments, I may not always get the result that I want. But, I know that I have to keep trying. 

I have always loved science, specifically biology, but I have never been given an opportunity to delve deep into it before CIRM. The program includes weekly lectures that touch upon new scientific breakthroughs, daily lives of various individuals in medicine and science, and more. CHORI SSRP and CIRM have allowed me to venture beyond the boundaries of what I previously thought was possible with science. 

For any other high school students who are nervous for their first laboratory research experience, I have some advice to offer. First, don’t be afraid to ask questions. Everyone around you wants to support you! Second, label everything. Always make sure to label all of your tubes, plates, etc. so you know what you’re working with. Third, never stop writing notes, either in your lab notebook or somewhere else. For some of the experiments you will do, such as PCR amplification, you will most likely need to do them again in the future. My lab notebook contains all the procedures for the experiments I have conducted and I constantly refer back to those pages. Fourth, read, read, read! Look up scientific papers that go into detail about what topic you’re studying. Fifth, take some time to soak it all in. This is a special opportunity, but it may be overwhelming at times. You should take a moment to relax and to realize how lucky you are to work in a professional lab!

Being part of the CHORI SSRP and CIRM program has allowed me to explore the wonderful world of cells. I am excited to see where this research takes me!

As an alumni applying to the SSRP, I wanted to experience something new this summer and to challenge myself. Last year, the programming was online and I learned the ways of research all through my computer. This year, I was fortunately able to experience what it is like to be in an actual lab!

My research project is centered around neural stem cells. Before this, I had no idea what stem cells were. After attending a workshop, I was fascinated to find that stem cells have the ability to either renew themselves or become specialized cells that have specific functions. This unique ability is a promising area of research because of the potential of stem cells to replace damaged cells in order to treat many diseases that we don’t have cures for today.

In the adult central nervous system, neural stem cells are found in different locations (or niches) in the brain. My project is part of a bigger research project which seeks to figure out how cell-to-cell communication in aging neurogenic niches affects neural stem cell fate decisions. As we age, there’s a decrease in neurogenesis which is the production of neurons. This leads to a decline in cognitive abilities such as learning and memory, as well as weakened repair of damaged tissue. Two causes for reduced neural stem cell neurogenesis with age are the decrease of the neural stem cell pool from cells increasing their asymmetric divisions, and the transition of neural stem cells into an inactive state. To see how neural stem cells’ function and behavior change as the niche ages, I will recreate the subventricular zone niche in vitro. Results of this project will aid in the research of the niche's control of neurogenesis in the adult brain, and why cells go dormant and how to induce proliferation. Overall, this has the potential to help in the development of therapies for neurodegenerative diseases in the future.

As we all know, the mitochondria are powerhouses of the cell, providing energy in the form of ATP. But what happens when the instructions, or DNA, in the powerhouse are disrupted, and subsequently, proteins are not able to function correctly? Mutations in mitochondrial DNA (mtDNA) can cause mitochondrial disease and each year about 1 in 4,000 children in the United States are born with a mitochondrial disease caused by mtDNA mutations. Not only can mtDNA mutations cause mitochondrial disease, but they are also linked to cancer, cardiovascular diseases, and neurodegenerative disorders. Mitochondrial DNA (mtDNA) research is a relatively new field of study, and for the first time in 1963 researchers Marget and Sylvan Nass discovered DNA fibers outside of the nucleus and in mitochondria. 

At the Lewis Lab at the University of California Berkeley, we are working with the nematode Caenrohabditis elegans in order to unlock the mysteries of mitochondrial DNA. Specifically we are looking at C. elegans with a deletion in the mtss-1 gene, that codes for the mtss-1 protein. This protein is involved in keeping single stranded DNA separated and preparing the DNA for adding the new complementary strand during replication, and is preserved in humans as the SSBP1 gene and protein. C. elegans are a great model organism for this mutation accumulation experiment because it is able to reproduce in about 3 days enabling us to rapidly observe the different generations. 

For our project, we are specifically comparing C. elegans with a perturbed mtss-1 gene in order to determine if more random mutations arise in the mutant C. elegans compared to non-mutated, also known as wild type C. elegans. We will observe both groups over 10 generations, and transfer C. elegans onto new seeded plates in order to keep all lines in parallel, and allow for spontaneous mutations to accumulate with minimal natural selection. After 10 generations, we will perform PCR on both the control and mutant worms, observe the deletions during gel electrophoresis, and send the information for sequencing to determine the specific deletions. In addition, we will also be comparing the C. elegans brood size or number of offspring they produce in both the control and mutant worms, as well as image the C. elegans to observe if the location of mitochondria, and shape of mitochondria changed in the mutant types. 

Understanding the mitochondrial DNA mutations that arise in C. elegans is extremely important because it will help us understand how mitochondrial diseases arise in humans with the same deletions. With further research on mtDNA mutations, we can develop a refined list of targets for the development of mitochondrial disease therapeutics, and drugs that target the protein product of the mtss-1 gene and its human homolog SSBP1.

When I was 14 I had a recurring question asked to me. “what do you plan to pursue in a few years?” they spoke as if i should have it all figured out by the prime age of 14. Visible terror shines through my rosy pink cheeks as I tell whomever asking that I don’t know quit yet , then the expected response of “you’re still young you will figure it out eventually” comes along with the slightly judgmental smile insinuating that time flies and you need to start figuring it out. Starting then every adult entering a room would make me feel a sense of pressure to have it all figured out. Not until I entered my newly chosen class titled Principles of Biomedical Sciences did I truly discover my passion for science.  I found myself excited to learn, I got a thrill being able to run a small experiment or run a PCR or use a pipette. I vividly remember being able to dissect my first mouse after learning about the digestive system and realizing that the world in STEM will give me endless opportunities.

On the hunt to find hands-on opportunities , I applied to CHORI SSRP in hopes to gain experience. As a highschool student I was prepared to be told I was too young to do anything but watch. I was immediately proved wrong when I was introduced to my mentors Dr. Medina and Dylan Chhetri. They had me put to work immediately , I started off practicing my pipette techniques and shadowing Dylan with his cell cultures. For 3 weeks I watched , read, and learned how to culture iPCS.

“Are you ready?” Dylan asked , I shook my head in response as I persuaded myself that I've studied these techniques and I've got it all under control. Not to my surprise, my once seemingly stable hand went shaky , and the procedure that I swore I could repeat backwards had drawn blank in my mind. But as we all know practice makes progress , with Dylan’s patience and continuous practice I was able to get comfortable with Hepg2 cells and move on to iPSC. My research this year was based on nonalcoholic fatty liver disease (NAFLD) which is characterized as the accumulation of fat within the liver. Thanks to CIRM we have the privilege of using iPSCs from patients with and without NAFLD to test our hypothesis that iPSCs from NAFLD patients will have greater oleate induced intracellular lipid accumulation than iPSCs from healthy patients.

Mistakes are inevitable and are a part of the learning curve. Words will never be able to describe my gratitude towards this program and the amazing people I've met along the way. Because of the resources CIRM has provided I have had the honors of working and getting comfortable in a lab setting. As well has built a foundation of basic lab research , which will help me tremendously in my future laboratory work.

As my time at the lab comes to an end, I am beyond grateful that the once daunting question of what I want to pursue is not as daunting anymore. Having the honors of coming into labs everyday and being surrounded by highly intelligent and motivated individuals have given me the motivation to one day conduct some of my own research and explore a hypothesis of my own. Huge thanks to Dylan Chhetri , Dr. Medina Marisa , and CIRM for creating an unforgettable experience. My journey begins here.

On my first day at the Medina lab located in the UCSF MLK Research Building, I learned that I would be working with Induced Pluripotent Stem Cells (iPSCs): stem cells that are derived from somatic (or nonreproductive) cells acquired through blood samples and then transfected with 4 Yamanaka transcription factors to encourage pluripotency, or the ability to differentiate into almost any type of specialized cell. Here I was, a curious and bright-eyed intern learning about this incredible scientific innovation, and yet, all I could think about was a sheep – Dolly the sheep to be exact. For context, Dolly the sheep was the first mammal to be cloned from an adult cell, equipping scientists with the necessary knowledge to develop personalized stem cells (iPS cells) – the exact type of cells I would be working with. I guess my AP Biology class reading finally paid off.

This summer, my research project involved studying how the Transmembrane Protein 55B (TMEM55B) gene affects intracellular lipid accumulation in an iPS cell line by using CRISPR to knock out the gene and observing the subsequent effect in cells. In a broader context, my research will help better understand the genetic dispositions and causes of Non-alcoholic Fatty Liver Disease (NAFLD) which is a disease characterized by excess lipid accumulation in liver cells. NAFLD can progress from simple steatosis to nonalcoholic steatohepatitis (NASH), cirrhosis, and ultimately liver cancer or liver failure. Furthermore, NAFLD is estimated to be the most common cause of chronic liver disease, affecting 80-100 million individuals in the US, and approximately 1 billion individuals worldwide. Unfortunately, there are no targeted therapeutics for the treatment of NAFLD at this time.

Although Dolly the Sheep got my foot in the door of stem cell research, it was ultimately up to me to explore the fascinating realm of scientific knowledge present within. Soon enough, I became a frequent visitor of the magical portal of PubMed, a royal squire in the town of Ted-Ed, and an enthusiastic explorer of the biosafety hood within my lab. I came to realize the vast utility of stem cells and the unbound potential of CRISPR (knockouts, insertions, working as a transcription factor, and more!); I was enchanted.

As I centrifuged, pipetted, and cultured my way through the summer, I came to realize how much I have truly learned and gained from this experience. Many describe their internship-self as a “sponge”, soaking up the extensive knowledge of their plentiful experiences, taking the expert advice of their mentors, and being fulfilled by the plentiful relationships gained and lessons learned. While I very much do echo this sentiment, if I had to quantify my CIRM UCSF Benioff Oakland internship experience and self as an object, I would choose something that I have been working with all summer: a stem cell. Ever since I was young, I have always known that I wanted to pursue medicine, that much was for certain, but all the other aspects of my aspirations were, as they say, undifferentiated. Through culturing stem cells, I myself began to grow as well. Working with stem cells, CRISPR, and a variety of laboratory machines/processes including flow cytometry, qPCR, and fluorescence microscopy, exposed me to a whole new world of translational research, inspiring me to one day start a lab of my own while working clinically as a Pediatric Oncologist. Although I certainly hope that my plate of stem cells won’t accidentally differentiate, my UCSF lab experiences have acted as growth factors, prompting my own differentiation into a more persistent, curious, and ambitious scientist and individual.

Whenever people ask me about how I got into research, I tell the same story. The story starts with how I didn’t want to do research at all. I imagined myself alone in a depressing lab doing mind-nunbing “research”. Eventually my mind changed when I did a program that brought in speakers from all sides of the science/healthcare spectrum to talk about their experiences doing research. The first speaker described research as discovering what no one else has discovered before. He proceeded by talking about his own research where he blasted cells with a laser and stuffed them with mitochondria as a potential way to treat mitochondrial diseases. That’s a gross oversimplificaiton of his research, but that was enough to make me fall in love with research. So simple right?

What wasn’t simple was actually doing the research. But after a year, I got my first research opportunity in stem cell research for UCSF’s Summer Student Research Program. I was overjoyed when I was accepted, I could finally help discover what has never been discovered before. But what special about stem cell research, was that it also helped cure the uncurable.

I was stationed at the Li Ka Shing Center at UC Berkeley, under the mentorship of Dr. Miriam Hernandez-Morales. The lab’s research focused on enhancing the current regenerative therapy for Parkinson’s Disease, which involves replacing the dopaminergic neurons lost due to the disease. I loved every part of my time in the lab. I loved it when my hands cramped from pipetting. I loved going down to the basement of Barker Hall to buy new supplies for the lab. I was even happy when we ran into problems- such as our cells dying. I knew that in research I would run into many problems and dead ends- and that’s okay. Failure is a normal part of research and if I’m going to love research, I’ll love the moments of failure too.

What was so unexpected was how flexible and kind the lab members were. When I had to take two weeks off to recover from surgery, no one was mad. My mentor was even kind enough to tell me not to rush to respond to her emails and focus on recovering. I was overwhelmed by the patience of the lab staff when it came to teaching me how to pipette, I received lots of praise as my shaky hands sucked up droplets of water. I didn’t realize how supportive and wonderful a lab group could be.

I don’t know what comes next in my story, but I know that I want to keep discovering what hasn’t been discovered before and I want to keep curing the incurable through stem cell research.

Although my poster presentation was on Sunday, I choose to attend the first day of DDW (Saturday) beginning my day early. My mentor, Dr. Jennifer Price was giving a lecture on HCV screening in pregnant women at 8 AM. This was part of a panel made up of women researchers on women’s health in liver disease. The second lecture was on sex disparities in liver transplants. It brought up many problems in the match system which I had never considered. Dr. Lauren Nephew also discussed the revised guidelines which did nothing to address the systemic issue rooted in height-based disparities. When controlled for height, data reflected that taller women had match rates in line with those of men. Next was Dr. Carla Brady on guideline updates for the management of pregnant women with liver disease. I found this extremely interesting as the topic and data aligned with similar readings I had done in my Reproductive Justice/Health/Politics course this quarter. Lastly, was a lecture on the rising rates of alcohol- associated liver disease and its implications for the care of women patients. The widespread marketing campaign targeting women consumers was extremely thought-provoking and something I subsequently brought up with the women in my life. Next was a panel on advances in hepatology, which I found a bit less engaging because of the level of prior knowledge required to understand the data being presented. What was most surprising was a train-based model used by Dr. Marc Sherman which was the first time I truly understand the practical application of 1st order kinetics. This was a talk about mathematical modeling predicting the resolution and persistence of liver injury independent of absolute serum transaminase levels for real-time estimation of active liver injury.

Saturday evening into Sunday morning I was very nervous about my poster session and read over my speech script many times. I worried over possible questions I could be asked that I may not know the answer to. Saturday night I finished rereading the Viral Hepatitis National Strategic Plan for the United States: A Roadmap to Elimination (2021–2025). While waiting for my poster session to begin at 12:30 PM I was rereading the AASLD guidelines for chronic hepatitis B, Dr. Price contacted me. It was amazing that Dr. Price took the time out of her busy schedule, having completed her conference responsibilities that morning to meet with me. She answered last-minute questions I had. Additionally, a UCSF GI fellow took the time out of their schedule to drop by my poster. They posed great questions that have helped Dr. Price and me as we continue edits on our CID manuscript.

Overall, my DDW experience was an amazing education experience. As my first medical conference where many attendees were M1 students or higher in education levels, I was intimidated. But I felt so welcomed by the GI community and was reminded of the amazing mentorship that Dr. Price continues to provide even after SSRP 2021.

When the CHORI security guard implied that “kids aren’t allowed” on my first day -- likely assuming I was a 10-year-old smuggling myself into a highly professional laboratory – I’d also personally doubted my presence there. Being 16, I wasn’t sure I’d fit in with others in such an intimidating environment; and never did I think, applying for this program, that I could be working with stem cells.

I’d heard about stem cells in the news, science classes, and the like, but even doing any cell culturing at all seemed inaccessible to me. At my age, I’d become accustomed to and discouraged by rejection since I was perceived as “too young” for anything.

Now in the Medina lab, and working with induced pluripotent stem cells (iPSCs), I’ve shifted my perception regarding my abilities as a high school student: working with incredible mentors and doing what’d prior seemed a fantasy, I’m more confident in advocating for myself. Because I’ve been able to break traditional boundaries of the “proper age” for conducting more advanced scientific research, I’ve come to disregard comments concerning my abilities; knowing I can assimilate to any environment and demonstrate my proficiency (to be quite honest, I think security will now have a hard time getting me out of the lab!).

Moreover, I’d initially expected to be mentoring in a hospital – aware of my sensitive, compassionate personality, thought it logical for me to work alongside patients, observing their diagnoses -- it was a shock to instead be examining a very disease’s mechanisms instead!

Approximately 40% of adults worldwide are afflicted by nonalcoholic fatty liver disease (NAFLD), and it pains me to know I’d been completely unaware of such a prevalent illness -- though now I'm eager to study it. And if this initially seemed scary, I believe one can imagine my panic upon learning about transmembrane protein 55B (TMEM55B), a newly identified regulator of cellular cholesterol metabolism (it’d taken me at least 2 weeks to say it’s a “phosphatidylinolsitol-[4,5]-biophosphate phosphatase” after frantically asking equally confused others what pronounciation they thought was correct).

Knowing TMEM55B influenced intracellular lipid accumulation in previous studies, I was tasked with using iPSC lines to test whether varying levels of TMEM55B transcription levels influenced this lipid accumulation, and if so, what the correlation was between these two variables.

I think at this point in the blog, it’s quite obvious that the pattern of demolishing expectations persisted. Writing my research proposal, saying we’d be using differentiated iPSCS, my P.I. had corrected, “No, no, no, Sheila, the significance of this research is that we’re using undifferentiated iPSCs!”

I’d been bewildered; how could we study a liver disease but not utilize stem cell derived hepatocytes? My mentor had emphasized that iPSCs and iHeps both accumulated lipids to a similar extent, and undifferentiated iPSCs were simply better for timing -- though I ultimately made my own conclusions to accompany those rationales for our choice of cells. Knowing that diseases ultimately impact the entire body; we could utilize the basic stem cells that all other specialized cells originate from to understand the basic mechanisms and behaviors of bodily cells in the pathogenesis of various diseases.

Participating in this CIRM program has gone beyond what I’d ever hoped for, and I’ve absolutely fallen in love with working with cells, much so that I’m planning to choose an undergraduate major which will allow me continue working in a lab like CHORI.

I guess you could say that it’s this summer experience from which all the various opportunities, life lessons, and the like that I’ve been surprised by “stem” from!

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Entry 2:

For other students working with stem cells, I’d like to impart some crucial advice to know before entering the lab (and what I wish I’d known). In the spirit of stem cells (in my case, iPSCs), let’s talk about the 4 Yamanaka transcription factors transfected into iPSCs to make them pluripotent (able to differentiate into all nonreproductive bodily cells) while discussing four tips that can all-around enlighten and make more positive your research experience!

KLF4: Yamanaka transcription factor involved in a wide range of cellular processes

Tip One: ethanol is your best friend – it should be involved in everything you do at the lab

You might doubt at first the power of ethanol, but surely after having HepG2 cells get twice contaminated, Huh7 cells contaminated, and mold in your iPSC well plates (these are all just from observation, luckily not personal mistakes), I’ve found that the only way to sleep soundly at night without concern that your cells are dying is by appreciating your soon-to-be best friend.

c-Myc: Yamanaka transcription factor that’s important in cell growth, proliferation, and differentiation

Tip Two: Cato the Elder wasn’t lying when he said “patience is a virtue” -- important quality that may need some development to be successful in the lab

Oftentimes, there's no explosions or anything imminently gratifying as so in the lab (and that excitement sizzles out quickly), but rather lots and lots of waiting; though I can promise that getting results and being able to analyze them -- after waiting weeks for cells to grow, hours for the PCR, cDNA synthesis, or incubation to finish -- provides for much greater contentment and self-praise. Take your time with procedures as well to maintain precision, accuracy, and prevent possible contamination.

SOX2: Yamanaka transcription factor with an important role in maintaining pluripotency; low levels induce differentiation

Tip Three: ignorance is not bliss; studying is key, as low extent of knowledge brings on confusion

Especially when you feel intimated by the entirely new lab environment, it’s essential to make sure you do the research your mentor asks you to, do some studying on your own in free time, and read all the protocols. When you don’t understand something, don’t shy away from asking what it means, how you do it, where it’s located, etc. -- they’ve signed up to be mentors for a reason :) And you definitely see the results in presentations/flash talks, when you clearly convey to the audience an exceptionally nuanced understanding of your research!  

OCT4: Yamanaka transcription factor that is a key regulator of stem cell pluripotency; it is very highly expressed in early embryonic development, when many cells are pluripotent

Tip Four: be open-minded about stem cell research; this is the most important to know, because it should be fun!

Although one may perceive working with stem cells as challenging, frustrating, or simply not what they were interested in, give it a chance and allow yourself to explore cell culturing! Feeding, passaging, running various tests that you’ve never done before is much more exhilarating than one might imagine, and the experience exposes you to a possibly new field that you may just fall in love with!

You know the first day of school when your teachers do icebreakers and don’t give you any homework? Well that was not SSRP. First day in, they threw six different research guideline trainings at us that took me five hours. Two mandatory videos for half an hour. A one hour lab safety simulation. And a four hour diversity, equity, and inclusion training. Despite half of these assignments having over a two week deadline, I felt overwhelmed. At the time, my favorite thing to do when I was overwhelmed would be to ignore my problems. So that’s exactly what I did. After our first orientation meeting ended, I went outside on a run. I ate dinner with my family. I washed the dishes. And I slept. The next day was basically the same thing. I’d finish all my OTHER work, eat food, help my mom clean the house, send my siblings to camp, and sleep. In the general program, I learned worlds upon worlds of knowledge about every field of science. From my research mentors I learned everything from the origins of sickle cell anemia in stem cells to the symptoms and real life consequences of what seemed to be such a simple problem. Yet after two weeks in the program, I hadn’t finished half my assignments. Everything I learned made me feel like I was a whole new person living in a whole new world, but with the same old problems.

Fast forward a few weeks into the program. It was July 1, one day before what seemed like 15 different deadlines were due. I worked for hours upon hours focused in my work, only to fall asleep on my desk at the end of the night. The next day, I woke up in a panic. So of course, the first things I did was to go out on a run, eat brunch with my family, wash the dishes, and finish my WORK. As if I was taking the SAT, I turned my mind on overdrive for the next six hours and finished the work… with a whole extra two hours before the deadline. I felt relieved, satisfied, EXHAUSTED. So of course, I slept. But after the entire experience, what I learned was that although procrastination may help me focus and work efficiently, the anxiety of 15 different assignments in the back of my mind was more important. This whole program taught me worlds of knowledge, but the most important skill that I learned with the help of this program was the motivation to keep on working and keep on learning.

Ever heard that the common chimpanzee are close relatives to humans? It might catch someone by surprise to learn that mice and humans are biologically similar. This means that body systems like the reproductive system in mice and how they develop sperm and eggs are quite comparable to that of humans.

This summer, I focused on a ribosomal protein called Rpl41 and its role in reproduction and fertility. Ribosomal proteins serve an important role in the cellular process of translation responsible for protein synthesis. For the majority of my project, I spent days zooming in and out of stained images of ovaries of female mice in efforts of counting and classifying oocytes which are immature egg cells that will eventually continue growing until they reach a mature stage where they can be fertilized. I was often concerned if I double counted or missclassified an oocyte, but regardless of whether it was imperfect, I learned the importance of remaining consistent.

Although I didn’t get the chance to process ovaries or embryos in a lab setting, I still enjoyed learning about indirect immunofluorescence and digitally quantifying images of ovaries and embryos. I learned to be meticulous and detail-oriented when counting cells to minimize error.

Aside from writing and assembling research proposals, abstracts, and posters, I attended weekly lectures and heard from professionals in various fields and occupations. I got an inside look of a dermatologist and nurse’s day in the life and heard from a sickle cell patient. Through learning about possible career paths, I was able to identify aspects that are interesting to me and initiate further exploration. It was truly inspiring and motivating to listen to speakers from disadvantaged backgrounds who were able to overcome their obstacles and pursue their passions.

Despite the absence of in-person lab experience, I was still able to learn basic lab skills through Labster modules. Each module begins with reminding me to put on a lab coat and gloves before getting started on experiments and I have ingrained in my mind to replace pipet tips to avoid cross contamination. These modules allow me to experience a breadth of fields of study, engage in stimulating problem solving exercises, and test my newly acquired knowledge through quiz questions. I look forward to completing these modules each week and learning something new. 

After completing this internship, I am more confident in my ability to digest scientific information and to pursue a career in science. I have grown an immense appreciation for research scientists who dedicate themselves to the advancement of knowledge. I am beyond grateful for CHORI and my mentor for being so welcoming and providing me an invaluable experience.

           When I first saw this research program offered at my school at the end my senior year in high school, I didn't even think I would get accepted or even apply because I felt like I was not capable of managing it and was a little worried of being ignorant about a lot of things. But luckily I got very supportive family members and not to forget my high school teachers who encouraged me to sign up. But CHORI turned out to be beyond my expectations. It is one of the safest learning environment I have ever been. Since the day I started till this day, all the students, mentors are extremely supportive,kind and very patient in helping you expand your knowledge which honestly boosted my confidence.

        This summer, I had a pleasure to work with my mentor from UC Berkeley,  Professor Samantha C Lewis about an organelle called mitochondria. Organelle is a structure within a cell that has a specific function and mitochondria is often referred to as the powerhouse of a cell. It turns the sugars and fats that we take from food into a chemical form that the cell can use in the form of a molecule called adenosine triphosphate (ATP).Different cells need different amount of energy in order to function well and the function of a cell affects the shape and internal structure. We used Caenorhabditis elegans as our model in this project. We chose C.elegans because it is one of the simplest organism with the whole nervous system, easy into grow in bulk population and its a multicellular(more than one cell) organism with a whole genome sequenced (complete set of genes).We took images of different cells using a microscope. After that I used FIJI software to data quantify and see the amount of mitochondria found in each cell type to help find the shape of mitochondria.

        The purpose of this research in the long term is to be helpful in developing drugs that could treat diseases where mitochondria aren’t functioning optimally due to defects in their morphology(the branch of biology that deals with the form of living organisms, and with relationships between their structures.)

       Personally I believe that lack of motivation and role models is one the reasons for failing to achieve the set goals that we gave but in this program, I learned and was encouraged by the weekly lectures from varies talented, intelligent people and their journeys. Although I did my research mostly remotely but the ‘Labster’ activities made me feel familiar with the laboratory and the equipment. Secondly seeing my mentors trying their best to pass on their knowledge to the students and lastly the support and connection that you make in this program is something that I found super helpful in career journey.

Before the CHORI program began, my expectations of the amount of involvement throughout the summer would be that of an observer due to my inexperience. However, my doubts were quickly proven wrong when my mentor, Dr. Ashley Frakes, welcomed me to the Dillin Lab with open arms and introduced me to the brand new world of medical research. 

I started off meeting with my mentor virtually where she taught me all the background information necessary for me to start the project. I learned about the unfolded protein response (UPR), which is responsible for countering stress the endoplasmic reticulum (an organelle that maintains protein homeostasis) undergoes, and that increasing expression of a transcription factor associated with the UPR called Xbp1s in C. elegans would cause the worms to be more resistant to ER stress and longer-lived. When Xbp1s was overexpressed in mice (GFAP-XBP1s mice) and given a high fat diet (HFD) to initiate ER stress, it gained less weight than mice on a HFD that did not have Xbp1s overexpressed, even though both groups had the same amount of food. 

Slowly, overtime, I was able to transition to in-person meetings and began working on my project, which will aim to identify whether GFAP-XBP1s mice have increased energy expenditure that causes the reduced weight gain on a HFD. This research could potentially allow us to identify a therapeutic target for metabolic disease and aging. Throughout the project, I learned a wide range of lab techniques, from micropipetting and handling worms on petri dishes, to homogenizing tissues and RNA isolation. 

My experience at the Dillin Lab has not been limited to strictly research. I have had the opportunity to meet multiple other research staff and associates and learn their backgrounds and the paths they took to reach where they are today. I also had the chance to attend the weekly meetings at the lab where guest speakers discuss the project they are working on or learning new lab techniques for various applications. 

Spending time with CHORI and the Dillin Lab for the past few months has given me lots of valuable insight about the medical scientific field and what it’s like to be a developing scientist. I would like to thank CHORI, my mentor, and the CIRM SPARK program for making this summer of discovery a reality for me.

As I applied to CHORI SSRP, I had no idea what to expect. In high school, the closest thing I have done relating to doing anything research based was looking using a microscope. All I knew at the time was that medical research was something I was interested in, and this looked like the perfect opportunity for me to test the waters before committing to this profession. It was then that I realized that this was going to be the hardest challenge I’ve faced yet.

Personally, learning how to pipette, the big vocab words and understanding the fundamentals of my experiments were some of the hardest aspects of research. I once believed that I had a steady hand and that I could become a surgeon one day. That was until I had to pipette water into a conical tube. My hands shook so much, that at some point my pipette tip dipped into the water. If I were using expensive chemicals, I could’ve contaminated the entire substance. As with most things in this world, I was able to improve my pipetting through practice and I am more confident in them. Yet when it comes to understanding the experiment and the large vocab words, I don’t think I will ever have them memorized. But as time progressed, I am finally able to understand what my mentor, Tony, is saying to me. This challenge was one of the best aspects of the internship. Not knowing anything about what I’m doing reminded me that I have a lot left to learn, and knowing that I survived this internship makes me feel excited and ready to enter other spaces.

While these skills were hard to grasp, it was nothing compared to how intimidated I was in entering such an academic and professional environment. I felt that my ability to code switch wasn’t where it should have been prior to the program, which made it harder to feel comfortable in the lab. If it weren’t for Tony, I think I would’ve never grown comfortable with the environment. Tony’s personality was really relaxed and easy going. He was incredibly friendly and talked in a way that made me forget that I was participating in a research internship. Seeing him succeed in such an environment reminded me that I too can participate in research without completely changing how I talk and act around others. After this experience, I am taking medical research as a career path that I may pursue. I found it to be very enjoyable, and something that I look forward to doing again in college.

Van Dinh

Dillin Lab, UC Berkeley

Mentor: Ryo Sanabria-Higuchi, PhD

After the last bell of the school year had rung, nearly every one of my classmates were dashing out the door ready for summer beach parties, tours of European countries, cruises in Hawaii, camping trips (basically anything they could fit into the only ten weeks we are free from the anchoring thought of having to maintain a good GPA). I, on the other hand, was preparing for my summer research project at the University of California, Berkeley through the Children’s Hospital Oakland Research Institute, funded by the California Institute for Regenerative Medicine (this is me bragging). But in all honesty, I was extremely excited to engage in new challenges and expand my knowledge in the science field.

Along with the feeling of excitement was nervousness. I was assigned to work in the esteemed Dillin Laboratory in the tightly secured Li Ka Shing Center at UC Berkeley. This would be my first time working in a professional lab. I felt like a beginning swimmer, about to be thrown into the ocean without a life jacket. Was this too big of a jump for me? Will the researchers in the lab laugh at my lack of knowledge and experience? These daunting thoughts filled my head as the start of my internship was approaching.

Much to my surprise, the Dillin Lab, filled with intellectuals holding great knowledge about science, is a welcoming and relaxed working environment. (My name and photo was even posted on their website on my first day!) My mentor and labmates were very understanding didn’t expect me to have a great comprehension of science. Getting to know the people in the research field is an experience I will likely never forget.

My project involved working with C. elegans, a type of microscopic worms. I was to identify genes that are required for survival under mitochondrial stress. I measured the stress response by observing the worms under a fluorescent microscope. Although many would find these worms repulsive, I couldn’t help but be in awe of the green light they exhibit through the fluorescent microscope. It started to become a repetitive task after observing a couple hundred plates of worms, but it was nevertheless rewarding.

Before I knew it, the end of my summer internship was approaching. This was a great learning experience that helped branch out my knowledge in the science field. I had a lot of fun these past two months working with people in the Dillin lab and gained valuable laboratory techniques that will be of great advantage in the near future. I would choose this experience over a trip to Hawaii any summer!

Sofia Espinoza

Moe Lab

Mentor: Greg Moe, PhD

Before this program, I never thought much of science research, or about science in general. I have never been particularly fond of science in school, and never felt the need to learn much more than the basics in any given science class; that cells are in your body, and the mitochondria are the powerhouses of the cell. When deciding to apply for this program, I thought it was unlikely that I would get accepted – I thought that I didn’t know enough science to be considered for such a great program.

When I got the email saying “congratulations” and that I’ve been selected for the 2019 CHORI Summer Student Research Program funded by CIRM, I was shocked. After the initial few minutes of awe following the email, I decided that this was the opportunity I had unknowingly been waiting for – the opportunity to learn science, and to utilize the knowledge I had once thought I’d never use outside of school.

The first few weeks of the program were undoubtedly challenging, to say the least. My project, being the conditional reprogramming of primary human nasal epithelial cells for investigating the effects of vaccine-elicited antibodies on colonization by Neisseria meningitidis, I was easily lost in the sea of scientific words. When the time came to work in the lab, I struggled to understand the medical jargon used daily, and the academic language written in scientific papers. I had days to catch up on research that had been going on for years. Thankfully, my mentor, Dr. Greg Moe, and his lab technician Vianca Vianzon took the time to slow everything down and explain to me what was going on, and I was finally able to get a grasp on what my project was, and what was needed to complete it.

The following weeks were filled with changing media of cells, spending whole days in a small, dark room to take pictures of cells (I like to refer to them as “cellfies”), and writing various papers. Though tedious, it was worth doing the work because it allowed me to understand what I was doing in a different way than having someone explain it to me. In class, I would always leaf through the biology textbook to see the vivid pictures of cells, and the complex diagrams of what is inside of them in hopes of distracting myself from the lecture of the day. Never did I think that I would have the opportunity to be looking at real cells under a microscope, or that I would have my own group of cells to culture. It was because of the hands-on experience that this program gave me that my opinion began to change about science. When I applied to the program, I was just testing the waters to see if I could change my perspective about science; little did I know that coming out of the program I would want my major in college to be biology.

Overall, this summer has taught me many things; how to write formal papers, how the human immune system works, what human nasal cells look like, how to take cellfies, and much more. But most importantly, what I learned this summer was how to act, think, and speak like a scientist, and that is something I hope to keep with me as I go to college as a human biology major.

Chima Ezeh

Bissell Lab, Lawrence Berkeley National Laboratory

Mentor: Mam Mboge, PhD

I have experienced a tremendous amount of personal and intellectual growth during my past four years of high school. I attribute part of this growth to my striving to make the most out of my summers. And now heading into college, I look to pursue activities that will further such growth. The CHORI summer student research program has undoubtedly helped me achieve this goal.
 

This summer, I have had the incredible opportunity to work under Dr. Mam Mboge in the Bissell Lab at Lawrence Berkeley National Laboratory. My research focuses on exploring the role of stemness-related markers in metastatic breast cancer. There are currently publicly-available databases that provide various markers’ expression levels, and the goal of my project is to extract patient data for specific stemness-related markers and to validate their expression in cell culture. It has been truly rewarding to hone former skills, such as proper pipetting technique, and learn new ones, such as fluorescence microscopy. Inevitably though, this learning process has included countless mistakes; forgetting to change pipette tips among other errors has made my research project a humbling experience and reminded me that frustration, trial, and perseverance precede success.  

While lab skills will prove useful in future research opportunities, my biggest takeaway from this internship is that collaboration is the key to success in any field. Attending lab meetings, engaging in discussions with senior researchers, and receiving constant constructive feedback from peers and mentors has showed me that science, when cultivated by a community of the brightest, most persistent minds dedicated to a common cause, can reap innumerable benefits for humanity.

Outside the lab, I have attended numerous social events, from enlightening seminars detailing speakers’ (health/science and even non-science professionals) circuitous career paths, to sobering talks at Be-the-Match workshops providing patient perspectives on bone marrow stem cell transplant therapy. These get-togethers serve as excellent opportunities to network, bond with fellow interns, and hopefully form long-lasting relationships. Through bus-rides to and from social events, I am glad to have met the science’s community’s up-and-coming intellectuals who are diverse in endless ways but connected by their like-minded curiosity and insatiable desire to improve the lives of others around them.
 

I am extremely grateful for the CHORI’s summer student research program’s invaluable opportunity for science education. Thank you to Dr. Mboge, the CHORI program staff, and CIRM for your unconditional support and for providing me with the necessary resources to succeed during this research project. Best wishes to future students!

Kerry Lin

He Lab, UC Berkeley

Mentor: Andrew Modzelewski, PhD

Interning at the He Lab is one of the most enjoyable internships I had ever experienced. During the first week, I recall being extremely anxious because I believed my mentor and his colleagues would have high expectations for me. As the days passed, I relaxed into this new environment with tightly-knit undergraduates and postdocs. The work people did in this lab however, were no joke.

I was trained from start to finish when I created tissue slides for my project. I got to see first-hand how the organs were collected from sacrificed mice which would be fixed in a formalin solution. Then, I followed the two-day protocol of tissue processing and occasionally panic as I struggled to not drop the miniscule ovaries into the waste bucket.

Sectioning wax blocks of tissue was a painful process on the first day as I was only able to produce 20 successful slides in three hours. It did not come easy, but I am proud to say that I can now create almost 40 slides in three hours. With determination and perseverance, I had accumulated a mixture of over 200 slides of ovaries, skulls and testes in six weeks. Finally, I imaged my slides using a light microscope. I sat in a dark room for hours staring at the computer screen as I adjusted and focused the slide to take the most flattering snapshot of the ovaries. Every day the work was relentless and tedious, but all the effort I poured into each step showed gratifying results. I received praise for my histology slides which was said to be comparable to textbooks. It was overwhelming and exhilarating to hear such a compliment because I thought that my work was average compared to published pictures by other researchers. I knew I truly enjoyed my time at the lab when I missed working at my internship while I was attending an orientation at UC Davis.

I am beyond grateful to have worked with Dr. Andrew Modzelewski this summer. He provided an innumerable amount of insight and assistance to help me understand what I was getting myself into. When I had a question, he had an answer or he redirected me to someone who knew about the topic in question. I would love to stay longer in this lab to help bring this budding research into completion, but I will be moving on to next chapter of my life. Thank you to my mentor, the members of the He Lab, CHORI, CIRM, and my fellow interns for this unique and unforgettable experience.

Lessons from the Laboratory: How I Made the Most of My Summer Research Internship

By: Sarah McCarthy

Ngai Lab, UC Berkeley

Mentor: Rebecca Chance, PhD

This summer I was granted the wonderful opportunity to be a researcher for 9-weeks through the CHORI Summer Research Internship. I had the honor to work in the Ngai lab at UC Berkeley studying stem cell activation in the mouse olfactory epithelium. Entering into the internship, I knew that there would be a steep learning curve. Over the course of the summer, I learned several lessons that made my summer experience easier.

1.) Read Papers Related to Your Project 

When I first started reading scientific articles, I did not know where to begin. The paper felt like it was written in a foreign language because of all of the abbreviations, techniques alluded to, and unfamiliar science. I was overwhelmed to say the least. But, after I read the paper several times, googled numerous unfamiliar terms, and asked several questions, I felt like I had a grasp of the paper. 

When my internship started, the benefits of pushing through my struggle became apparent. First, I had exposure to the scientific vocabulary in my lab. I remember a conversation with my mentor during my first week where we were discussing our project and I was able to (mostly) follow what we were talking about. I still had a lot of learning to do but the curve was more shallow. Second, I was able to ask my mentor useful questions. Personally, when I am completely lost, I have trouble asking questions to clear up my confusion. However, from reading the papers, I was able to pinpoint a few areas where I needed clarification. 

2.) Do Not Be Afraid to Make Mistakes + Accept Failures 

I made countless errors this summer. For example, I forgot to write important experimental details down, pipetted incorrect volumes, poorly conducted procedures (skinning a mouse head is hard!), and used incorrect reagents. Despite always striving to do my best, accidents still did happen. During these frustrating moments, I reminded myself that mistakes are a natural part of the learning process, and I needed to be patient with myself. Another type of failure in a laboratory is when an experiment fails despite the execution being flawless. During both of my research experiences, the majority of my time was spent optimizing a research protocol. At first, I felt frustrated when my results were unclear after the third or fourth attempt, but now I know that optimization is an important part of research (maybe this is why optimization word problems are included in Calculus 1). 

3.) Ask questions

I know this is so cliché, but there are no stupid questions. During my first lab experience, I was shy about asking questions. This summer, I tried to ask “stupid” questions such as why a procedure is done a certain way, what the purpose of a step is, or how this relates to the bigger picture. I also learned that the opportunity to ask questions is not limited to the laboratory setting. For example, after seminars, I utilized the opportunity to approach the speakers to ask a question or two. Additionally, if I found myself at a table with my lab mates, my fellow interns, or my mentor, I asked about their career path, goals, or research experiences. Asking questions gave me insight into new ideas and career paths.

4.) Research is Not Exclusively Bench Work

One of my biggest takeaways from this internship is that there is so much more to research than pipetting. Research includes networking with other scientists, reading research papers, analyzing data, evaluating research protocols, planning experiments, attending seminars, and communicating findings among many other activities. Some days I would run long experiments that took all day, and I would feel accomplished because I went through dozens of pipette tips and numerous pairs of gloves. Other days I would spend my time attending seminars or doing computer work. Both types of days are equally important to successfully conduct research. 

This summer has reinforced my love for research. I am so happy that I had the opportunity to learn new research techniques, attend fascinating seminars, and meet interesting people. As the CHORI program comes to an end, I am excited to utilize the skills that I developed this summer when I start my undergraduate studies in the fall. 

Alp Sozat

Medina Lab, CHORI

Mentor: Marisa Medina, PhD & Antonio Munoz

In the Medina lab, I have worked on a research project about how certain gene variants can lead to non-alcoholic fatty liver disease (NAFLD), which is a spectrum of liver disorders characterized by excess liver fat in the absence of alcohol consumption. NAFLD can progress to cirrhosis, in which scar tissue replaces liver cells, and may lead to liver cancer and liver failure. Approximately 90 million people in the U.S are affected by NAFLD and its downstream effects are currently the leading cause of liver transplant in the U.S. Obesity and type 2 diabetes -- which are both very prevalent -- contribute to NAFLD risk. 

Additionally, two gene variants (PNPLA3 rs738409 and TM6SF2 rs58542926) have been strongly associated with the development of NAFLD. PNPLA3 is involved in cutting up triglycerides in fat cells, while TM6SF2 modulates the secretion of triglyceride-rich lipoproteins. Both gene variants result in loss of function mutations, leading to fat accumulation in the liver cell. My lab generated a panel of subject-derived induced pluripotent stem cells (iPSCs) -- stem cells derived from adult blood cells -- from carriers and noncarriers of the PNPLA3 and/or TM6SF2 gene variants. These cell lines retain the genetic information of the donors, and thus can be used as a model system to evaluate the effect of specific gene variants on cellular characteristics. 

Since I wanted to test whether iPSC lines that carry the TM6SF2 and/or PNPLA3 gene variants have increased cellular fat compared to lines without either variant, I incubated cells with or without oleate (a type of fatty acid used to create fats) and stained them with Nile Red dye to label lipids (i.e. fats) and Hoechst dye to label nuclei.

One of my mentors -- Tony Munoz -- taught me that one of the most important aspects of cell culture is sterility, since an experiment will be ruined if any plates with cells become contaminated with other pathogens such as bacteria or fungi. Consequently, I learned to spray everything with ethanol before inserting it into the cell culture hood -- a space in which flowing air keeps out pathogens -- to preserve my experiment. 

After imaging the cells with a fluorescent microscope, I was surprised to see a noticeable difference in cellular lipids among cell lines exposed to oleate. To quantify lipids, I used three methods. First, I used an image processing program -- ImageJ -- to estimate the number of cells (based on the number of nuclei) and lipids for each sample. Second, the intensities of the Nile Red and Hoechst dyes were quantified by a fluorescence plate reader as relative fluorescence units (RFU) to determine the average amount of lipid per cell in each sample. Third, I used fluorescence activated cell sorting (FACS) to measure the cellular lipids on a per cell basis. I compared the differences in lipid content and morphology of iPSCs with oleate, BSA (a negative treatment control), and the difference between the oleate and BSA treated cells.

I have felt thrilled to learn many techniques through the study including feeding cells, passaging cells, visualizing cells under a microscope, staining cells with certain dyes, analyzing stained cells, aspirating media from cell plates, general aseptic technique, image analysis, and how to use a fluorescence microscope and plate reader. 

I expect that cells with TM6SF2 and/or PNPLA3 gene variants will accumulate more lipids than cells with neither gene variant only when exposed to oleate. If successful, these studies may demonstrate that iPSCs can be used as a cellular model system to evaluate genetic contributors to NAFLD. 

Every summer, I set out to find something that will help me grow as an individual and challenge my way of thinking in a constructive way. This summer, which was my last prior to beginning my college experience, I did my best to look for an opportunity that would fulfill my goal. The CHORI summer research program has far exceeded my expectation.

 I have had the honor to work in the Dillan lab at UC Berkeley, as a student researcher, for the past 6 weeks. The majority of my work has involved working with near microscopic worms, called C. elegans. I’ve been conducting experiments on C. elegans, inducing a stress response and measuring it by using fluorescent microscopy. While the experiment may have seemed straightforward from the beginning, I learned really quick it would not be as easy as I thought. What I believed would take days or two to perfect, would end up being me pianistically practicing every week to inch closer and closer to get it down. While many may not understand the joy of being able to pick up 10+ worms in one swing, just know it's as satisfying as cashing in your first check. My experience has reinforced critical habits, such as persistence and the value of hard work.

What I’ve come to learn and value the most, of my time over the summer, has been getting to know the people and setting that make up the field of research. What I thought to be a strict, no room for error type setting turned out the opposite. I saw how even while maintaining a high level of quality and professionalism, the setting stayed relaxed. This was due to the fact that the people who made up the lab were kind and collaborative with each other. There was no one person who claimed to know all the answers and each and every one of them were open to asking a question and happy to help each other out.

My time in the Dillan lab, as part of the CHORI summer research program, has opened my eyes to a career, which a month ago, I would have never really considered. But through my experience, I’ve learned the field shares some of the same core values I hold dearly. In addition, I’ve learned that research could, in fact, help me fulfill one of my lasting goals in life: to have a lasting impact on the world and community around me.

As a digital native, I have always empathized but never truly understood the plights of older generations’ efforts to adapt to today's rapidly advancing technologies. When my mentor, in the weeks leading up to the beginning of the summer research program, proposed a project involving programming/informatics I eagerly agreed, trusting in my technological codependence.

My project focused on utilizing data previously obtained and running it through various programs, most often RStudio, in the effort to better understand the erythroid differentiation pathway. The data sets that I worked with spanned 12,000 genes over thousands of cells which would be loaded into the statistical software. The resulting matrices would then have to go through transformations, essentially mashing them together to make an even larger matrix than the previously existing three. A majority of the R packages that the data was then run through required manual coding by yours truly. Keep in mind that at the start of the summer I had no coding experience what so ever. It was a simple reality to those in my life that I was completely inept when it came to technology. My mother, a tech guru, had always told me that coding was important but I simply never got around to learning it. Fast-forward to the start of this summer and I was completely out of my element. There would be days where I would spend hours on a few lines of code (10-20) and keep getting error messages. Sometimes the problem would be 5 lines up, but the code kept running and would ruin the rest of the data that was produced. In these cases, I was so grateful to those in my lab, specifically, Fiona Hennig and Dr. Boffelli who would notice the simple mistake in the coding (a missing quote = false or sep=’’ ) and patiently walk me through what went wrong. However, after a few weeks, I began to better understand where the code was coming from. The first time I was able to upload data into the GOrilla RNA-seq program and got my first output for enriched GO terms I was ecstatic. The lists of thousands of genes became colorful pages, which were not only resembled rainbows but also explained how these genes were responsible for minute processes in the life of an erythroid cell.

I am also extremely grateful to Dr. Boffelli for also allowing me to see how current research can have a meaningful real-world effect. With the lab's approval, I have been able to shadow in the BCHO sickle cell clinic and see the physical manifestation of the disease that up until then I only had a conceptual understanding of. Shadowing in the clinic allowed me the very rare opportunity to see both the laboratory research around it and the patients it may one day help. I express my gratitude to both Dr. Boffelli and Dr. Neumayr who have accommodated my research schedule to allow me that amazing opportunity this summer.

As the CHORI summer research program comes to an end, I am so happy to have had the opportunity to see and participate in the research that is currently being done in the scientific field. Seeing how new technologies and methods could one day have a real-world impact is inspiring and has only fueled my excitement and interest in research.

It is often said that baking is a science, but you rarely hear anyone saying science is like baking.

Here’s a little taste of what a normal day at the lab for me is like:
Pipetting. Lots and lots of pipetting. That’s the gist of what running a quantitative polymerase chain reaction—a.k.a. qPCR—is like. Although tedious, it is one of the most important and widely used techniques by molecular biologists to determine gene expression in a specific sample of DNA. And in the lab, running a plate a day has become a fundamental part of my daily routine.

To me, performing qPCR can be likened to the process of baking a very simple four ingredient cupcake, except you almost never bake few, but rather in the likes of 75 per well plate. Each well, or “cupcake” has the same recipe, requiring:
1) 10-μL Real-Time PCR Master Mix
2) 1-μL Hydrolysis Probe (made for the specific gene/ protein you are analyzing)
3) 2-μL cDNA (c for complementary, as the DNA used for qPCR are synthesized from single stranded RNA)
4) 7-μL water (nuclease-free or distilled).

As I had 24 cDNA samples, done in triplicates to ensure precision, plus an extra three wells as H2O controls, that meant that I had 24*3+3 or 75 wells I needed to fill, and you guessed it, a whole bunch of pipetting to do—I mean just look at the tired, pained expression of the poor pipetter in the bottom right image.

Day after day, I labored to pipette drop after drop into their appropriate wells, bent over and fatigued. It was repetitive; it was boring; but, the opposite was true as well: It also compelled me to be focused and determined, making every drop perfect and consistent with the last. My mentor, Pete Zushin, informed me of how ridiculously expensive lab materials were, and knowing that, I wanted to make every drop count. But, my drive could only go so far, as 150-200 reps in, the strain of pipetting started to set in, reminding me that my right thumb was still getting a pretty hardcore workout.

Thus, finishing the pipetting process is undoubtedly the most satisfying moment of qPCR. After sealing a completed well plate and spinning it down in a centrifuge much like the one shown in the bottom left image, few things are more gratifying than seeing consistently pipetted wells of liquid ready for analysis.
Just as one would need to bake their cupcakes, a qPCR plate is “baked” in its own “oven.” The only differences are that the plate is analyzed throughout the process, and that the “oven” is a qPCR Thermal Cycler. After a one and a half hour analysis period, an amplification plot can be generated such as the one shown in the top right image, as well as a variety of other graphs and results. In fact, the now fully analyzed plate actually comes out of the machine warm and toasty, so the process really isn’t that different compared to baking.

After performing qPCR day after day, and observing my mentor perform complex laboratory techniques such as Adipose-derived Mesenchymal Stem Cell Isolation and cDNA Synthesis, it would be an understatement just to say that I’ve learned a lot. As much as I have learned throughout my time in the lab, I have also enjoyed and grown from it. I’ve learned countless new skills, gained a great amount of knowledge in the field of molecular biology, and of course, had lots of fun. Back at CHORI, the weekly seminars have given me invaluable insight into the process of pursuing a career in STEM, something that I certainly intend to do. Words cannot describe how grateful I am for CHORI, CIRM, UC Berkeley’s Stahl Lab, and my mentor Mr. Zushin for granting me the opportunity to participate in this wonderful program, and making my experience truly unforgettable.

But perhaps most importantly, I will leave this experience with extreme respect for laboratory scientists all over the world, who inarguably have the strongest thumbs on the planet.

Stem cells are sensitive things, and it takes a great deal of effort to keep them happy. Within the first few days in the lab, I was conditioned to handle them with the utmost care. When passaging them, forceful bubbles from the pipette are a disgrace. When changing their media, a gentle stream down the side of the plate is necessary. So, when the time came to wash them for approximately twenty times, I thought, yikes. My hands are going to hurt and my cells are going to die. After subjecting our neural stem cells to conditions that could potentially affect their proliferating behaviors, we planned to collect the data using immunocytochemistry, a technique that allows us to detect the presence of Ki-67, a marker for proliferation. Every step must be executed with care, being mindful to not disturb the cells excessively such that they detach. If detachment occurs, it would yield absolutely nothing left for us to image. Granted, I didn’t need to keep the cells alive anymore, but surely, won’t I wash them all away?

The morning of the destined day, I transported the plate of cells from their cozy incubator to the fume hood to begin the protocol. I aspirated the media and replaced it with phosphate-buffer saline (PBS). After a few moments, I removed it, and as the final drop joined the waste container, my lips curved into a tiny smile. First wash done and a lot more to go. Next, I became a cell murderer. I pipetted a layer of 4% paraformaldehyde onto my cells that essentially kills them while preserving their cellular structure. Goodbye, dear little cells; it was nice knowing you. After ten minutes, the cells received the next three washes. Slowly and steadily, I pipetted the PBS so that it glides smoothly across the surface. Typically, “washing” cells doesn’t require the use of actual cleaning products, but in this case, “washing” became quite literal. The cells were then treated with Triton X-100, a detergent that permeabilizes the membrane so that intracellular proteins such as Ki-67 can be detected. How did we remove the detergent? More washes. By this point, it was no longer morning. My hands were sore and my patience was dwindling with each press of the pipette. Fortunately, I was almost done. I added the primary antibodies to the last wash and stored the plate in the cold room to block overnight. A whole night was plenty of time for me to fret over all the possible things that could go wrong.

Alas, my cell washing days weren’t over, for more washes awaited me the next morning. What wash are we on? I’ve lost count. Imagine my relief when the fluorescent stains were finally added, marking the end of the treacherous washes and the beginning of microscopy adventures. As my mentor prepared the microscope, I waited anxiously. Did I complete the protocol successfully? Were there still cells left for us to see? When I finally mustered enough courage to look through the eyepiece, a giddy feeling erupted in me. They were beautiful. Given, I fully realize that they’re cell corpses, but they fluoresced like twinkling stars in the night sky. At that moment, I realized that even seemingly mundane tasks also have a purpose and greater implications; the process was essential to obtain data for our project. Even though this assay wasn’t a direct solution to the problem we were exploring, it provided useful information and taught me the importance of understanding the reasons behind everything we do. Thus, I am extremely grateful the exceptional mentorship I’ve experienced this summer.

What is the longest time you have spent staring at worms in a single day? Is it 1, 2 hours? Maybe even 3? For me it was 8 hours. 8 hours staring at almost microscopic worms, C elegans. Worm after worm, plate after plate, looking desperately for a dead worm. I was running a lethality screen on my worms. Healthy worms were useless. I needed the sick ones, the dead ones, the short ones, the skinny ones, the males. (Quick side note, C elegans are typically hermaphroditic, but sometimes they are known to turn into males when a population is under stress to increase genetic diversity. How cool is that?) It was mundane, almost mind numbing, but for some reason it was also incredibly intriguing. I would get into this zone and the world would melt away. The only thing that existed my microscope and my worms (and occasionally my lab note book to record results).

Sometimes I would go plate after plate after plate without finding a single hit. My anticipation for the next hit would grow and grow and grow and when I found a hit I felt almost giddy. There is no real reason as to why I found this so interesting and the truth is that I was simultaneously bored out of my mind (who wouldn’t be less than an hour in?) and obsessed with my work. I was obsessed with the idea of finding a hit. My eyes were tired, my neck hurt, my feet were numb, and let’s not even talk about my back (I have some hereditary back issues that make it so my back starts hurting if I sit down for too long without any breaks). Even so, I wanted to finish. I needed to finish. So I finished. It was one of the most satisfying things I have ever done.

“What is your availability this week?” Asked my neighbors, who I babysit for sometimes
“I work from 9-5 Monday through Friday” “Oh that’s great that you got a job! Where are you working and what are you doing?” “I am working at the Children’s Hospital Oakland Research Institute through the California Institute for Regenerative Medicine. I am an intern on a project that is researching genetic therapies for Sickle Cell Disease.”
“Wait…That's your 9-5 job? I thought you were in high school!”

That is the reaction I have experienced from most people when I tell them about my summer job. I feel not only fortunate to live in an area that is rich with scientific opportunities for the youth, but I also feel honored to have been selected to be a CHORI intern, as well as a CIRM intern.

My project has been amazing. It is a project where everyday, I am learning something new, developing additional skills, and working towards a treatment for a lethal disease. Sickle cell anemia in the most common monogenic disorder, and affects 100,000 people in the United States. Of the newborns in Africa that are diagnosed with Sickle Cell Disease (SCD) at birth, 90% of them are dead by the age of 5. The current treatment for SCD, like Bone Marrow Transplants (BMT) and blood transfusions, do help to manage the many symptoms of SCD, but they do not offer a long term solution, and come with many risks. The project I am working on would eliminate the need for blood transfusions and BMT in sickle cell patients, as well as eliminate the risk of rejection and graft versus host disease, which is one of the biggest risk factors of BMT.

Being a part of this project, I have built on my skillset in so many ways. Simple things that I thought I knew, I have improved upon. I have also learned so many new techniques that are specific to this project. I can now confidently harvest a femur from a mouse. I have learned how to handle lab animals, how to pellet cells, as well as aspirate supernatant. I learned about SPLiT-Sequencing, its many parts, the purpose of each of those parts, and how to perform each part. Flow Cytometry? I learned about that too this summer! In addition to being a part of this amazing research, I have also been introduced to so many new technologies and developments in the scientific world, and it has been amazing.

As I approach the end of my internship I leave remembering all of the people that have helped me along the way, the things I have learned, and the experience I have gained. I want to thank everyone who makes the Summer Student Research Program possible at CHORI, as well as the people who make the CIRM SPARK program available for all of the students like me, who want to further their interest in science, and make a difference in the scientific world.

It was a day like any other. I walked into the room, just two minutes past 10:30am, ready for another adventurous day in the lab. Just as I settle down, I am greeted by my mentor with the most terrifying task I have ever been asked to perform, “Will you passage the cells for me...alone?” Sweat begins to pour down my cemented face as I consider what is at stake.

The procedure was possibly thirty steps long and I have only executed it twice, with the supervision of my mentor of course. To be asked to do the task without the accompaniment of an experienced individual was unthought-of. I feel my breath begin to shorten as I mutter the word “Ok”. Yet it wasn't just the procedure that left me shaking like a featherless bird, it was the location of my expedition as well. The dreaded tissue culture room. If even a speck of dirt enters the circulating air of the biosafety cabinet, your cells are at risk of death...death! I’ll be a cell murderer. “Alright”, she said, “I’ll just take a look at the cells then you’ll be on your way.” As we walk down the hallway, my eyes began to twitch as I try to recall the first steps of the procedure. I remember freezing our plates with Poly-ornithine and laminin, which essentially simulates the extracellular environment and allows adhesion between the cell and the plate itself. I must first add antibiotics to rid the frozen plate of potential bacteria. Then I should remove my cells from the incubator, and replace the old solution with accutase and new media, to nourish the cells, as well as unbind them from the plate before. Passaging is necessary when the cell density gets too high, as the cells must be relocated to a roomier environment to better promote survival. As we approach the tissue culture room, my jaw unclenches, as I realize the whirlwind of ideas meant I know more than I thought. My mentor retrieves our cells, views them under the microscope, and deems them ‘ready for passaging’.

“Good luck Amira” she says to me with a reassuring smile. I enter the room ready for battle. Placing first my gloves and coat, I then spray my hands and all things placed in the cabinet with 70% ethanol, to insure a sterile work environment. Back to the procedure, I’ll place the cellular solution of accutase and media into a covalent tube. After, I’ll centrifuge it for two minutes until a cellular pellet forms at the bottom, then dissolve the cells in fresh media, check its density using a cell counter, and calculate the volume of cellular solution needed to add to my once frozen plates. Wait, once I do that, I'll be all done.

I eagerly execute all the steps, ensuring both accuracy and sterility in my work. Pride swells within me as I pipette my last milliliter of solution into my plate. The next day, my mentor and I stop by to check on how our sensitive neural stem cells are doing. “Wow Amira, I am impressed, your cells seem very confluent in their new home, great job!” I smile slyly and begin to nod my head. I now walk these hallways, with a puffed chest, brightened smile, and eagerness to learn. My stem cells did not die, and having the amazing opportunity to master their treatment and procedures, is something I can never forget.

This summer I have had the pleasure of doing a research project at the wonderful Stahl Lab in Berkeley. Being in a lab has not been exactly what I thought it would be like. In my head, I pictured scientists hard at work, isolated from their peers. However, upon entering the lab, I find that there is a lot of collaboration, and you can always find an interesting conversation including topics of pop culture, rap music, great food, and of course, science. My mentor, Dr. Kevin Tharp, is one of the most technical people I have ever seen, and his knowledge in science seems unlimited. Throughout the day, other scientists are constantly asking him for his opinion on their data and how to do certain methods. Two of the most challenging facets of working in lab for me have been understanding the methods you use, and how to present your data in an effective fashion. Whenever I run any method, my mentor wants me to understand how the results are created on a molecular level to see potential caveats. For example, one of the first methods I learned was how to run a Bicinchoninic Acid Assay (BCA). This assay quantifies the amount of protein in a given sample by measuring the amount of reduction of Cu2+ to Cu1+ by the protein. The Cu1+, after reduced, then binds to Bicinchoninic Acid and produces a purple color. The darker the purple is, the more protein. The assay creates a beautiful purple gradient across the well (pictured below).

With the results from the BCA protein assay, I was able to normalize the amount of fat per sample to protein. I have found that it is very important to normalize data to decrease variance and ensure accuracy. In addition to running quantitative tests, we also sectioned tissue to run immunohistochemistry (IHC) and Trichrome staining. IHC uses antibodies to target specific parts of a tissue. Under a specific microscope, immunofluorescence highlights the antibodies (pictured below).

The green is actin and the blue are nuclei. We took this picture above as a control comparison for my project. IHC captures the magnificent heterogeneous structure of tissue, and using imaging software, we can create three dimensional images. Using my quantitative and qualitative data, I created a presentation for our lab meeting. While understanding and executing the methods were challenging, organizing my data to present to my lab was equally as nerve wracking. I tried multiple formats with my mentor’s help until I felt comfortable relaying my progress so far. I then presented in our principal investigator’s, Dr. Andreas Stahl, office (pictured below).

It’s not often that you hear a high school student coming home one summer day saying, “Hey Mom, guess what? I got to play with a whole lotta blood today.” But for CIRM students, coming home late in the summer afternoon telling stories of their mad-scientist shenanigans in the laboratory is pretty much guaranteed. Of course, this internship is about more than just lab work. It is about joining a community of curious, intelligent, and like-minded individuals. It is about making new, valuable connections with my fellow CIRM friends, my mentors, and other students and scientists involved in the program. It is about getting inspired by the talks given by prominent scientific figures and the touching stories of bone marrow transplant pen pals. And it is about learning the true ways of science and getting the opportunity to contribute to humanity’s growing pool of knowledge.
My contribution was investigating the effects of the storage time and temperature of plasma on the stability/yield of cell-free DNA, providing details that would ultimately help improve accesss to non-invasive prenatal testing, a relatively new but promising method of screening fetuses for genetic disease. In the process, I learned that the journey of a scientific experiment is not a smooth one; rather, it is a roller coaster, with its own ups and downs, twists and turns, rewards and frustrations. Under the patient mentorship of Drs Katie Carlberg and Sandy Calloway, I learned to navigate the challenges of this roller coaster, whether that be extracting and quantifying cfDNA in the lab, interpreting and making sense of data, or finding solutions to problems and mistakes along the way. I would like to express my deepest thanks to my mentors, who have taught me so much about science, from the technical and ethical aspects to the arts of patience and perseverance.
Not long ago, I was watching a promotional clip given as a teaser for a 2012 sci fi movie called Prometheus, and while I did not watch the actual movie, I was captivated by this clip. The clip itself was not really trailer; in fact, it wasn’t even footage from the film. Rather, it was a fictional TED Talk from the year 2023, given by a fictional character in order to frame the events for this fictional film. But part of the speaker’s talk alluded to the scientific and technological advancements of human society since the beginning of ancient times. The speaker listed many of humanity’s most notable inventions and breakthroughs in chronological order, and then finally noted that the 21st centruy had been the birth of revolutionary biotechnology and stem cell therapies. Though the scene itself was completely fictional, I could imagine it being real. It illuminated to me the amazing speed at which science, specifically biomedical and stem-cell science, is progressing in my current day, and given that at the time I was preparing to begin my internship at CHORI, courtesy of CIRM, I could not have been more excited and moved by his words. I realized that we are in the midst of another huge scientific milestone, and I envisioned how cool it would be if, many years from now, people would be giving TED Talks similar to the one presented in the clip, speaking proudly this biomedical revolution. I am immensely proud and honored to say that I am a part of this scientific endeavour, even if it is just a small part, and I look forward to being able to reflect back years from now and say that I contributed to something that changed human society for the better.

I’d like to share my experience as a follow-up to one of my posts on #cirmsparklab.
So if you don’t get to spend the ideal summer on the beach, what do you get as a CIRM student working with scientists all summer?
You get hours of hard work in the lab, many times on boring procedures, panic when you mess up a step, and frustration when the result is “out of range.”  Really? Really, but that’s not all. 
 
When I applied to the CIRM-SPARK program at CHORI, I set the goals for myself: first to learn all - well, most - about stem cell research and secondly to experience the life of the people who do it (aka scientists) and decide if I want to follow in their footsteps in college.  I don’t know if I’m even anywhere close to accomplishing the first goal, but half way through the program, I think I have already discovered the second part.
 
I am lucky enough to have two mentors that I can reflect upon, my principal investigator, Dr. Sandy Calloway, and a pediatric hematologist/oncologist, Dr. Katie Carlberg.  Dr. Calloway is super busy overseeing numerous research projects at once, while Dr. Carlberg splits her time between treating patients at Benioff Children’s Hospital and conducting research in our lab.  When I started working in the lab, I asked myself, “Isn’t it enough for Katie to see sick children at the hospital all day already? Why would she want to double her workload by working in the lab?  I was even more surprised when Katie told me she didn’t get enough sleep the night before, staying up until 2-3am finishing up a lab report for a meeting that morning.  I told myself, “No, this is not for me!”  Then, during my second week at CHORI, I performed an arduous procedure, a complicated one with no less than 20 convoluted steps to separate plasma from whole blood and extract its cfDNA.  It was 6:50pm and I hadn’t had lunch yet; I was almost done when I realized that I’d forgotten to turn on the heat block from step 5, and therefore I had botched the whole extraction! In panic I texted my mentor.  Katie told me what to do and tried to comfort me, but I was furious at myself for making such a ridiculous mistake.  “This is definitely not for me!” I told myself.
 
In the third week at CHORI, I received a letter from my pen pal.  Lena is 4, but she has already gone through 2 bone marrow transplants.  Instead of playing at the park, Lena spends her childhood in bed, waiting for matches or fighting off GVHD.  At Stanford Be the Match day, I listened to the touching stories of both bone marrow donors and recipients alike, and was profoundly moved by their memoirs.  I have made it a personal mission to spread the news and encourage all prospective bone marrow donors.  We all can give a hand – to be exact, a little marrow – to help bring these children back to the life they deserve.  I want to thank Lena and the Stanford speakers for helping me experience a very powerful feeling.  Now I can really understand and feel what motivates many scientists to work relentlessly in the lab.  If I were a doctor who sees firsthand the hardships that these patients experience, I wouldn’t mind working another shift in the lab in hopes that one day a cure or better solution would be found for them.  With that then, I say, “Hooray to scientists!” especially, of course, to stem cell scientists!

Many people love science, but many often do not have access to opportunities that allow complete self-immersion in the wonders of scientific research and discovery. I am honored that as a part of the CIRM SPARK Award Internship and CHORI Summer Student Research program, I was able to have this exact opportunity.

Graduating high school and awaiting my departure for college, I have been excited yet apprehensive because I struggle with what exactly I want to pursue as a career. I've always pictured myself going into science, but the problem is that the broad goal of "going into science" yields endless possibilities. After having exposure to and working within a regenerative medicine laboratory last year, I was determined to gain even more experience in the research field and gain a more comprehensive idea of what a career in research could be for a person like me.

Walking into the Tjian lab at UC Berkeley, I was definitely intimidated by the unmistakable prestige and high caliber of intelligence that surrounded me in every direction; but simultaneously, and to my surprise, I felt comfortable. I was excited to have the chance to thrive in a place like thisówith daunting high stakes, but incredibly rewarding potential outcomes-and I'm very happy and fortunate that I have. Under the amazing mentorship of Dr. Claudia Cattoglio, a senior researcher in the lab, I was able to watch, learn, and do things that I never thought I would, and especially at the age of eighteen. The project I am working on is centered around studying TAF9B, a paralogue of the TATA box binding protein TBP-associated factor TAF9, and evaluating its role in oligodendrogenesis (formation of oligodendrocytes). Along with this project, I have been able to extract tissues, RNA, and protein from mice, for the purpose of qRT-PCR and Western Blot analysis. These procedures are just a handful of the things I've been able to do during my time at the Tjian lab, in addition to meeting and listening to numerous post doctorates from all over the world as they give presentations of their groundbreaking research.

In a nutshell, I am just amazed. Entering college with the experience and knowledge I have gained from this internship will undoubtedly prepare me for my coursework and allow me to earn even more prestigious opportunities. I feel extremely well equipped for the future in science and medicine that I want to pursue. My experience as a CIRM SPARK Award intern has given me the confidence that I could not only do research like this, but excel in research like this. From here, I see no other direction for me to go but up.

I love cakes. One may wonder what do cakes have to do with the CIRM SPARK Summer Student Research Program. Well, this CIRM SPARK Award Internship has been a wonderful experience, and I see fit to compare it to a cake and its components.

The Cake: My Research Project, Lab Techniques, Tools, and Instruments
The center of this research program is my research project. Our goal is to develop a non-invasive prenatal testing method for thalassemia and other autosomal recessive diseases using next generation sequencing and target-probe capture to analyze cell-free fetal DNA in maternal plasma. My project aims to evaluate the sensitivity and specificity of the probe in quantitatively identifying the genotypes of the major and minor contributors in contrived DNA mixtures of blood from thalassemia patients. In lab, I fragmented the DNA using the Covaris, prepared DNA libraries, performed probe capture enrichment, and finally sequenced the mixtures using the Illumina MiSeq. I also learned about PCR, quantification of DNA using PicoGreen, and checking the quality of the DNA libraries using Bioanalyzer. During this entire process, I have learned so much about research, from writing a research proposal, planning and running experiments, and analyzing the results, to reading and citing scientific journals. All of these invaluable experiences will help me make a more informed decision to whether or not to continue with my pursuit in research.

The Frosting: The Mentorship and Guidance
Besides teaching me the process of research and helping me with my research project, my mentors, Dr. Katie Carlberg and Dr. Sandy Calloway, have offered me guidance with respect to my growing passion and desire to continue with medicine and research. As a Clinical Hematology/Oncology Fellow, Dr. Carlberg tells me about her experiences in Children's Hospital Oakland (CHO), such as what is it like to be on call or see patients and what consult weeks are like. I have attended one of her fellow's talk in which she gave an in-depth presentation on platelets-related conditions, and I am thrilled to have the opportunity to shadow her as she sees patients. Dr. Calloway, on the other hand, has given me her perspective as a researcher, informing me about her job and her path to being a scientist. Knowing that I have been contemplating which graduate degree to pursue, Dr. Calloway has spoken to me in that regards and given me reading materials to help me decide tentatively what fits best for me.

The Decorations: The Talks and Conferences for Exposure and Exploration
The different talks and presentations have provided great exposure and an opportunity for my own exploration. With other CHORI students, I attended informatic talks given by doctors and medical professionals every Thursday. Some were very scientific-based, such as the seminar on bioinformatics, but others helped us grow and develop as a person, such as the seminars on stress relief. However, my favorite part of the Thursday lectures is the student presentations, in which we hear each other give elevator pitches about their research projects. After their presentations, I often find myself researching about the diseases or conditions that they spoke about. In addition to the Thursday lectures, the grand rounds at CHO, the faculty lecture series at CHORI, the casting clinic (where we learned to cast a wrist), and the International Society for Stem Cell Research (ISSCR) Annual Meeting were all amazing learning experiences. Just as the cake, the frosting, and decorations are essential parts of a delicious cake, my research project, the mentorship, and the various exposures all played a role in making this summer research program an amazing, worthwhile, and valuable one!

I stood still staring straight at my solution, swirling it to make sure that my eyes did not fool me. The solution was clear! "My actual solution was clear", I recalled repeating over and over again. Quickly, I motioned my mentor to come and together we stood staring in silence.

"My turbid solution should not have turned clear without apolipoprotein A-I" I said to mentor worried. "Sophia," my mentor said while smiling,"you either did something amazing or made a simple mistake." For about two days, my mentor and I retraced each step both verbally and physically. We wanted to get to the bottom of what might have gone wrong. I did everything exactly the same way I did the first time I got my solution to be clear and by the end of the day I reproduced the results three times. Eventually, we figured that the solution I was using actually contained a fluorescent that allowed the solution to become soluble. This discovery was a surprise, but more importantly to our disadvantage. All the data collected before that day was scratched because the fluorescent altered my results. That day was hard to accept that all my hard work was not compatible with my research. The idea that I had to start from new five weeks into my internship with only four more weeks left worried me.

I chose to blog about this experience because I learned a huge lesson and gained a valuable experience. In research, nothing will go as plan and if something goes right it is reasonable to assume that it's, in fact, wrong. Whether one might think of this experience as a burden or not, I realized that regardless if my results were wrong I gained valuable skills and knowledge. If I had not done what I did, then I would have never discovered the flaw in my work. I also know that my research will not go perfectly from this point on because mistakes come when one least expects it, but I think you learn more from your mistakes than your success. We thought that the solution will only become soluble with apolipoprotein A-I, but a fluorescent works too. Why? We do not know, but thatís the beauty of science. In research, there will never be a day where there is nothing new to learn. From this experience, I realized that I absolutely enjoy discovering the unknown and research has become my way of exploring my passion.

It is already week six of my internship this summer and as I reflect back on what I have learned, I am amazed. I am a researcher in the Dillin Lab at UC Berkeley this summer working with microscopic worms, C.elegans. Bleaching worms, picking worms, and performing fluorescent microscopy have all become a part of my daily routine. However, the actual lab techniques I have learned are not what is most important about my experience. The environment I have been surrounded by and the setbacks I have faced are what have made this opportunity most rewarding.

Working next to highly educated scientists who are passionate about their research has allowed me to imagine myself in their shoes. It has led me to ask myself questions like "Can I do this in the future?", "Would I enjoy waking up every day to know I will be working in a lab?", "Can I imagine myself eventually publishing a scientific paper?", "How rewarding will it actually be to pursue a PhD?", and "What kind of research would I enjoy doing?" I come to the lab every day hoping to find the answers to these questions, but I have come to realize that it's not that simple. I am not going to wake up one day and suddenly find the answer. It is the accumulation of my experiences and thoughts that will lead me to an answer. Once I have discovered my answers, then I will grow even more passionate about what I plan to pursue in my future.

Another aspect of my experience that has made this summer rewarding is the challenges I have faced. Whether it was because I didn't follow the protocol correctly or I simply couldn't figure out what went wrong, I learned something important. I learned persistence is essential. Without persistence science wouldn't progress. Nobody writes a hypothesis, performs an experiment, and gets it right the first time. I realized failure is not a waste of time. Failure tells what not to do or helps determine how to adjust your experiment. Once you adjust your experiment you may even discover something new. You may discover something you haven't ever come across before. This may lead to another question you may want to answer or something else that you want to research. This is what makes science unending.

Now I don't mean to disparage the techniques I have learned and make it seem like they are unimportant. They are all completely necessary and without them, no work would get done. However, they are simply a minor piece of what makes a successful scientist. I realized that the skills one has can take them far, but it is persistence, patience, and passion that will take somebody else farther.

This time around, I am constantly asked, "what have you done in your past month or so of summer?" The least I can say is that the trip my brain has been taking since June 13th to now is mind-boggling! Dr. Frans Kuypers and Sandra Larkin have been my experienced guides in my journey as a summer intern at the Children's Hospital of Oakland Research Institute (CHORI).

I am studying Sickle Cell Disease (SCD), which can be cured only by a stem cell treatment using bone marrow. SCD is a hereditary disease of the red blood cells (RBCs) caused by a single amino acid substitution, leading to the expression of Hemoglobin S. Due to the abnormal beta subunits, hemoglobin polymerizes in lower partial pressures of oxygen, causing the RBCs to change shape (sickling). Only one official drug currently curbs sickling, but this medication may have harmful long-term effects. Such a limited scope of effective anti-sickling agents has led to my research project this summer.

At the Kuypers Lab, I have been testing a potential anti-sickling agent to observe if it increases oxygen affinity without damaging the RBCs. To do this, I learned how to operate the Hemox Analyzer, which is used to observe oxygen affinity shifts, and the Advia 120, which identifies many aspects of the RBCs (cellular volume, hemoglobin, etc). Working in the lab has been life changing, and has given me a sweet taste of what it is like to work in research. Outside of the lab, I have had multiple chances to learn about research that is being currently done. I have attended various lectures in CHORI and conferences hosted by CIRM. The International Society of Stem Cell Research (ISSCR) 2016 Annual Meeting was the first professional seminar that I ever attended! It was inspiring to see so many researchers gathered at one place to share unpublished discoveries with each other. I also had the opportunity to attend one day of the CIRM Bridges Conference. The CIRM Bridges interns were happy to explain their projects to me, and seemed immersed in what they were studying. Several expert researchers spoke after the poster session, specifically about the paths that they took to their research.

As my time at CHORI ends, I am happy to say that this summer full of discovery has been of large growth to me, and has brought to light unforgettable opportunities I thought were once far from my grasp. May this be the beginning of many adventures to come!