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Summer Program to Accelerate Regenerative medicine Knowledge

Blogs from CIRM HigH School Trainees

2018

Alex Ahilon-Jeronimo

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.


Sakina Bambot

“What do you want to be?” As I approach my senior year of high school, I am asked this question often, but never have an answer. I have always loved science, but science is an overarching tree that endlessly branches into different careers. This summer, I wanted to explore my passion for science and dive deeper into this vast field.

My project is related to alpha-thalassemia, a blood disorder which affects the production of hemoglobin, a protein found in red blood cells. Researchers at UCSF recently performed an in-utero bone marrow transplant on a fetus with the disease, where they transplanted a mother’s stem cells into her fetus, resulting in a live birth. This was the first trial of its kind, and in order to ensure future success, a sensitive and reliable method is needed to determine the extent to which the transplant was successful. The Calloway Lab at CHORI recently developed a new method to detect maternal stem cells in the baby’s blood after birth, and my project aims to help test the sensitivity of this method.

My experience this summer showed me firsthand how science is a slow and meticulous process. I often see articles announcing the latest breakthrough in science as if each discovery is like the completion of a jigsaw puzzle. My time at CHORI made me realize that science is an elaborate and difficult puzzle with infinite room to add more pieces. You won’t ever see the last jigsaw piece being clicked into place, but you might be able to put together a small part of the never-ending puzzle and see it grow as your piece interlocks with the discoveries of others. I was lucky enough to be surrounded by scientists passionate about their portion of the puzzle and was constantly challenged and encouraged these past weeks.

Beyond research, I learned how to read scientific papers, write research abstracts and proposals, and present my findings. I wrote to my pen pal, a bone marrow transplant patient, and listened to engaging speakers as part of the lecture series. I initially expected the lectures to solely focus on the latest advances in research and medicine, however it proved to be much more expansive, and I learned about a wide variety of topics ranging from pathways in science to how social factors impact health.

Over the past couple of months, I have gained confidence in myself and in my abilities. I now have a much clearer picture of where I see myself in 10 years, and am incredibly grateful to CHORI and CIRM for this invaluable experience. Thank you to my amazing mentors at the Calloway Lab for guiding me and teaching me a new skill set this summer—I am positive that I will use these skills in college and beyond.


Catherine Campusano

Note the bright red text appears whenever a mistake in the code is made, to reinforce that the program is not happy.

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.


Chima Ezeh

When I applied to this program, I didn’t envision spending my summer staring at mucus and cilia under a microscope, but my constant exposure to such a highly academic environment has elucidated how rewarding of an experience CHORI’s summer research program has served to my intellectual growth.

This summer, I have probed into the mechanisms by which the bacterium Neisseria meningitidis (Nm) colonizes the human upper respiratory tract. My task in the Moe Lab has involved culturing nasal epithelial cells to be used as a model for Nm colonization, and once our cultures have reached the desired stage of growth and development, we will add two strains of Nm followed by antibodies to observe their effect on Nm colonization. Ultimately, we hope to gain insights into effective vaccines for certain strains of the bacteria. In addition to learning the techniques of replacing media and passaging cells, I gained basic lab skills, like micropipetting, PCR, and gel electrophoresis. I also learned how to perform confocal microscopy, which produced fascinating fluorescent images of our model. As part of this CIRM-funded internship, I will present my research at a UC Davis poster day and the CHORI Symposium at the end of the program.

Outside the lab, I have attended weekly seminars given by speakers in science/health careers, which not only detail speakers’ professions but also their life journeys and ultimately what inspired them to pursue their respective career paths. Seminars also serve as excellent opportunities to network with people from various specialties, such as bone marrow transplant therapy.

During this program, I have been fortunate to integrate myself into such a diverse community of students who share an ever-growing passion to further the field of science and medicine. Through bus rides to UCSF, lunches, and workshops, I have truly enjoyed forming relationships with many people.

My biggest takeaway from this internship is that it is okay to make mistakes. I cannot describe how frustrating some days have been where I had forgotten to change pipet tips or repeatedly could not inject DNA samples into a wells. Despite these failures, I know these experiences will only make me a stronger researcher and prepare me for future roadblocks in my academic journey.

Thank you to my mentors and the program staff for showing unconditional support and for providing the necessary resources to excel in this research project!


Jonathan Luo

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.


Pei Wen Xiao

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.

2017

Emily Beckman
Barbara Fairweather
Amira Harara
Sharad Mahajan
Julia Nguyen
Juan Valentin

 

Emily Beckman

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.

Barbara Fairweather

“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.

Amira Harara

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.

Sharad Mahajan

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).

Julia Nguyen

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!

Juan Valentin

My experience with the CHORI student research program is great. I enjoyed every moment in it. The lab I was stationed in is called the Kaufer lab in UC Berkeley. Everyone welcomed me in the lab, and I made a lot of friends in the CHORI program. I enjoyed the opportunities that this program gave me the most. Being able to work in a professional lab was amazing and I learned a lot of new skills. The most challenging part of a normal lab day, is probably waking up early to get into lab in time. Other than that I really love doing research and might consider a career in research. My family thinks this is a great opportunity to get the mindset of working in a research field.

The Kaufer lab is interested in brain disease, and how to cure them. Some examples of diseases are epilepsy, Alzheimer's and Parkinson's. My project is on how epilepsy affects the brain, specifically the hippocampus and the Blood Brain Barrier. The hippocampus is the part of the brain that controls our memories and how we can learn. The Blood Brain Barrier (BBB), is a tube with a lining of cells that fillters blood to the brain, only allowing certain blood cells with certain proteins inside the brain. We use kainic acid (which causes epilepsy) to disrupt the brain and see how the Blood Brain barrier responds to the infection. With this information, our lab can see how fast epilepsy runs through the brain and which functions does the BBB does. Our lab also noticed that, when the brain is injured, the BBB will be disrupted. The BBB will start letting unfiltered blood in the stop the infection, which will hurt the brain more, causing more illness.

 

2016

Ava Daniel Jingyi Shelly Deng Jacqueline Diaz
Maria Carrillo Hernandez Raymundo Sanchez Anna Victoria Serbin

Ava Daniel

Ava 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.

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Jingyi "Shelly" Deng

Shelly

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!

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Jacqueline Diaz

Jacqueline
Hi there! My summer CIRM/SPARK internship at Childrenís Hospital Oakland Research Institute has been an incredibly valuable experience! My project is to use deep RNA sequencing to study hemoglobinopathies, specifically thalassemia.

Hemoglobinopathies are genetic disorders that result in abnormality or deficiency of hemoglobin, the protein contained in red blood cells (erythrocytes) and responsible for transporting oxygen throughout the body. Hemoglobin is made up of four globin subunits; in adult hemoglobin two of the globins are β and two are α. β-thalassemia occurs when there is a deficiency of β-globin, resulting in the formation of toxic α-globin tetramers that cause cell death. Deep RNA sequencing (RNA-Seq) potentially allows determination of the type and amount of all globins present in an individual’s erythrocytes in a single assay. In a patient with β-thalassemia, the relative amounts of α, β, ?, and ? globin are particularly important because a larger disparity between the amount of β-globin and α-globin indicates to greater disease severity. It can be difficult to obtain a precise measurement of these ratios, as current methods require multiple assays; RNA-Seq might thus be more efficient. This summer, I proposed to isolate and sequence my own RNA as well as the RNA of an individual with β-thalassemia minor and analyze the results to obtain precise and internally controlled levels of α, β, ?, and ? globin gene expression. I have completed the RNA-Seq library preparation and am awaiting sequencing results!

In addition to my own project, I am attending bi-weekly lectures. Some lectures I have attended so far include: Health Disparities in Chronic Diseases, Bone Marrow Transplantation, Retinitis Pigmentosa, Heterogenity of Diabetes in Asian Americans, Prenatal Diagnosis of Beta Globin Hemoglobinopathies, and the Impact of Weight Extremes in Pediatric Acute Respiratory Distress Syndrome. I was also given the opportunity to attend the International Society for Stem Cell Research annual conference! With some of my fellow interns, I attended a morning focus session on the ethical implications of genome editing which was fascinating and a seemingly vital discussion as I enter the field of stem cell research.

I have also been participating in a weekly Journal Club in which we discuss a scientific journal that an intern chooses each week. We examine possible biases, statistical analysis used, any problems we see in the study's design, and the implications of the study. This is a great opportunity to learn how to get the most out of scientific papers and is educating me on terminology and statistical analysis I did not previously know!

Overall, this has been a great opportunity to explore the medical scientific field as well as grow as a developing scientist. I would love to thank my mentors Dr. Boffelli, Dr. Martin, and Dr. Heo for allowing me to join their lab, teaching me so much and answering my endless questions!

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Maria Sophia Hernandez

Sophia 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.

Raymundo Sanchez

Raymundo 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.

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Anna Victoria Serbin

Anna 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!

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Revised: Tuesday, August 14, 2018 10:06 AM

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