Through their lens: Michelle Tran learns programming languages to solve biological problems

This summer we’re sponsoring high school interns in stem cell labs throughout California. We asked those students to contribute to our Instagram photos and YouTube videos about life in the lab, and write about their experiences.

Michelle Tran is an incoming senior at the Mira Costa High School in Manhattan Beach. From a young age, she always had a great fascination for the natural sciences, spending hours out in the neighborhood collecting and analyzing plant and insect specimens out of scientific curiosity. More recently her interest has shifted more towards health and biomedical research and was able to pursue this at City of Hope this summer as an intern in the Department of Information Sciences. Outside of scientific research, she enjoys playing the cello, spending time on the tennis courts with her father, stand-up paddle boarding with her mother, traveling, biking with friends, and hiking.

Michelle sent us this video of her experience:

As of now, halfway through my summer internship, I can declare with great certainty that I have already learned much more than I had expected to learn over the entire summer. Before starting my internship at the City of Hope, my experience with computer programming was limited. I had always been interested with working with computers, but had never taken a formal school or online course in programming. On the first day of work, my mentor, a mathematician and scientific programmer, informed me that I would be working extensively with machine learning, Hugin (a software), and R (a statistical programming language) to mathematically model biological processes. Initially I was unsure if I would be able to work with these tools or even understand the technical language everyone in my department spoke, but now, a little over five weeks later, my aforementioned apprehensions are no longer concerns. I am now editing and running several modeling and machine learning programs in R every day.

Every day since my first here at City of Hope has been part of a great, long learning process. Not only have I become more comfortable working with machine learning and computer programming this summer, I have also gained valuable career insight from everyone around me. Although I did not fully realize or appreciate all I have gathered from others, I now look back to my interactions with people here and realized that I have absorbed valuable information and skills that I could have not gotten elsewhere. Over the last few weeks, I have received great exposure to the technical languages that biologists and computer scientists speak and am able to quickly follow their discussions of their thought processes and methodologies. I have also learned much about communicating scientific results efficiently and effectively to others, especially from my fellow summer academy students who did such great jobs presenting at our weekly discussions. Every researcher and practitioner who I have talked to here has given me wonderful life advice about keeping an open mind to learning new things or pursuing other fields.

Working in my lab at the City of Hope this summer has been an experience that I shall always look back on fondly. No matter where I will be ten years from now, the knowledge I have gained from everyone here at City of Hope will still remain with me.

Michelle Tran

Through their lens: Steven Wang learns about stem cells at the heart of cancer

This summer we’re sponsoring high school interns in stem cell labs throughout California. We asked those students to contribute to our Instagram photos and YouTube videos about life in the lab, and write about their experiences.

Steven Wang attends Harker School in San Jose, California. This summer he has interned in the lab of Dr. Peter Lee at City of Hope Medical Center. As an extracurricular, he enjoys playing basketball and baseball.

Steven Wang working in the lab. He submitted this photo to our #CIRMStemCellLab Instagram feed.

When I first applied to this internship, my mind was narrowly focused on cancer and therapies used to treat this disease. I was thrilled at the possibility of working at a comprehensive cancer center over the summer and began to look into labs that had anything to do with cancer research. However, my perspective started to change after conversing and discussing research articles with my principal investigator. He offered a new viewpoint by exposing me to a new theory that combines two almost unrelated elements: cancer research and stem cells. The proposed cancer stem cell hypothesis opened me up to a new view of this topic that explained previously unknown mysteries such as the robust resistance of cancer cells.

Now that I have been exposed to stem cells both theoretically and in the lab, I have come to realize that stem cells can be applied literally anywhere. For example, Karen Aboody, a researcher at City of Hope, is evaluating the efficacy of utilizing neural stem cells for a drug delivery device to eliminate glioma. On the other hand, researchers at the National Institute of Health are investigating the potential use of stem cells to aid transplantations of organs. In my own research, I discovered that stem cell associated genes play an integral role in the development of tumors and utilizing therapies to target these markers may have potential therapeutic impact. I am truly fascinated with stem cells after getting hands-on experience with them and recognizing the applications of these cells in medical sciences.

Steven Wang

Steven submitted this video of his experience:

Hanna Mikkola wins prestigious award for work in unlocking the secrets of blood stem cells

Dr. Hanna Mikkola; Photo courtesy UCLA

It’s always nice when someone whose work you have supported is honored for their achievement, so we were naturally delighted to hear that Dr. Hanna Mikkola from UCLA has been named as the winner of the 2013 McCulloch and Till Award.

The prestigious award, from the Society for Hematology and Stem Cells (ISEH), recognizes a junior scientist in the field of experimental hematology and stem cells who is considered an “outstanding early career investigator.”

Mikkola, who is a member of the UCLA Eli & Edythe Broad Center for Regenerative Medicine and Stem Cell Research, has received two grants from CIRM . One of those is a New Faculty award to help her better understand the biology of hematopoietic stem cells (HSCs) – the blood forming cells in the bone marrow – so we can develop better ways of creating those cells outside the body for use in transplantation to treat leukemia. You can read about her CIRM-funded research here.

Mikkola picked up the award this past weekend at the ISEH annual meeting in Vienna, Austria. In a news release from UCLA she said:

“I am extremely honored and humbled to receive this award. It is very gratifying to receive recognition from my fellow scientists that we have advanced stem cell science in the field of experimental hematology. I thank the ISEH membership and will use this recognition as incentive to continue our research with the passion, rigor and focus that has brought us this far.”

Congratulations to Dr. Mikkola, and her entire team, on the award.

Kevin Mccormack

Through their lens: Vanessa Yu is driven by the possibility of improving lives through research

This summer we’re sponsoring high school interns in stem cell labs throughout California. We asked those students to contribute to our Instagram photos and YouTube videos about life in the lab, and write about their experiences.

Vanessa Yu is a rising senior at Arcadia High School. This summer, she worked in the Department of Molecular Pharmacology at the City of Hope under Dr. David Ann, with day-to-day guidance from her mentor, Dr. Yong Fu. She assisted her mentor in his project to develop a comprehensive molecular and cellular characterization of the functions, identities, and mechanisms of tumor initiating cells using our genetically engineered mouse model that contains a temporally and spatially inducible K-RasG12V transgene. When she is not in the lab, she enjoys baking, swimming, practicing American Sign Language, and watching entertaining K-dramas!

Vanessa sent us this video of her experience:

When I first heard about the internship opportunity through the Eugene and Ruth Roberts Summer Academy at City of Hope, I was ecstatic. The thought of having the chance to apply my knowledge of science outside the confinements of a classroom was and has been a dream come true. It’s hard to describe my exact reaction when I first received the ding! Email notification of my acceptance email. By my side was my ever supporting family who celebrated in the coming night with cheers and a feast to an exciting summer. My parents, both of whom work in the sciences, expressed their excitement in entering the ‘adult world’ with this opportunity that would bring me into contact with real chemicals, real protocols, and real experiment. Still to this moment, when I glance at the badge draped around my neck, I am awed and forever humbled to be a student in the program. They have given me the confidence that I, a mere high school student, will one day have the ability to someday make my own impact on the medical world.

This summer has been an amazing and eye-opening experience. I’ve never done research in a wet lab before and being able to actually perform experiments that I’ve only ever read in my AP Biology book is simply mind-blowing. It’s not just performing these experiments that I revel in, but the fact that I’m learning so much more than I ever imagined whether it be in reading up on animal cell cultures or researching the contents discussed in a lab meeting. This is what fun really is—getting paid to learn and advance myself, to mature and better the knowledge I have in order to help others. What an opportunity to be in as amazing a place as City of Hope where I am surrounded by peers and experienced mentors who are driven by the same passions I hold dear. It is here where conversations at lunch consist around scientific jargon with the same enthusiasm as if it we were talking about celebrities. The energy and optimism is truly inspirational to see and in the future, I hope to be working fulltime in such an environment that nurtures and stimulates my appetite for science.

The challenges of research are so large and emotionally draining at times that they cloud the bigger, overarching goal. Yes, it’s depressing when I don’t get the desired results from a gel. It’s frustrating when my experiments fail from a careless mistake. However, the hopeful prospect of changing others’ lives for the better and the fact that I do have the power to do that in research is what drives me, and I’m sure others, to keep going despite these obstacles. Furthermore, this summer through the much appreciated support from CIRM, has brought me into contact with the growing research world of stem cells of which the therapeutic potential is immense and exciting beyond words. It is this aspect of science where we are always discovering and finding new opportunities to cure the world of its ailments that ignites my curiosity for learning. And this internship has really shown me in a wonderful journey what I love doing the best—conducting research in the lab!

Vanessa Yu

Scar-forming cells in the heart converted directly into beating heart muscle

Last year, our grantees at Gladstone Institutes worked a neat trick: they converted the scar-forming cells of the heart directly into beating heart cells in living mice. (We wrote about that work here.)

The cells they converted, also called fibroblasts, are the ones that create scar tissue in the heart after a heart attack. Their work created the possibility of directly replacing scar tissue with healthy heart muscle following a heart attack.

But that work was in mice. The real test was to work the same conversion in human tissue, which they just published in the journal Stem Cell Reports. The group, which includes senior author Deepak Srivastava and Benoit Bruneau, coerced human fibroblasts in the lab dish to convert directly to beating heart tissue.

A press release from the Gladstone Institutes quotes Srivastava:

“With more than five million heart attack survivors in the United States and climbing each year, our findings come at a critical time. We’ve now laid a solid foundation for developing a way to reverse the damage—something previously thought impossible—and changing the way that doctors may treat heart attacks in the future.”

The group did run into hurdles along the way. They’d originally used a group of three factors to convert the mice fibroblasts to heart muscle. Those same three factors weren’t effective in human cells. Instead, they had to start over, testing a large pool of different factors before narrowing down the group of factors needed to work the conversion. They still have some work to do, too. Only about 20% of the cells converted. Gladstone quotes the lead author Ji-dong Fu talking about this effect:

“Clearly, there are some yet-to-be-determined barriers preventing a more complete transformation for many of the cells. For example, success rates might be improved by transforming the fibroblasts within living hearts rather than in a dish—something we also observed during our initial experiments in mice.”

Gladstone produced this cool 3-D animation about the work:

3D reconstruction of a cardiomyocyte (heart muscle cell), derived from a fibroblast via direct reprogramming. Direct reprogramming allows scientists to transform one cell type into another without first reverting back to the pluripotent, stem-cell state. [Animation: Scott Metzler]

CIRM funding: Deepak Srivastava (RB3-05174); Benoit Bruneau (RN2-00903); Paul Delgado-Olguin (TG2-01160)

Amy Adams

Through their lens: Alexander Seutin learns how computer technology can help unlock secrets of blood cancers

This summer we’re sponsoring high school interns in stem cell labs throughout California. We asked those students to contribute to our Instagram photos and YouTube videos about life in the lab, and write about their experiences.

Alexander Seutin did a stem cell research internship this summer in the laboratory of Ravi Majeti at Stanford University.

This summer I worked at the Stanford school of medicine, conducting research in a lab run by principal investigator, Ravi Majeti in the stem cell department. We focus on a group of hematopoietic clonal disorders called myeloproliferative neoplasms. These blood disorders are characterized by their unregulated trilineage proliferation in myeloid cells, resulting in irregular hematopoiesis, often leading to many other complications down the line.

This category of diseases was first discovered in 1951 by William Dameshek who called attention to the morphologic similarities between chronic myeloid leukemia, polycythemia vera, essential thrombocythemia and primary myelofibrosis. In the years to follow, stem cells would emerge at the forefront of science and people would realize that these diseases produce cells that share a similar hierarchy to the healthy hematopoietic stem cell. It was then that people began to think about a leukemia or cancer stem cell.

In my project I analyzed gene expression data from microarrays run on these types of stem cells taken from individuals who have obtained one of these disorders. I then had to figure out how to interpret this immense quantity of data that had been given to me and it was then that I began to gain a real appreciation for what we are doing. I learned how to use many bioinformatics tools such as DAVID, gene expression commons, gene set enrichment analysis, hierarchical clustering, and many others all while gaining a deeper insight as to what I was actually doing. This insight not only allowed me to utilize these skills within my own project but also permitted me to gain a more universal understanding of modern science.

I slowly began to become more comfortable with my field through reading scientific papers, attending lab meetings, and by doing research on my own. This then allowed me to absorb more and more information about what people are presently doing which would not only show me how amazing the things we are doing are but more importantly teaching me that there is a giant window of opportunity in research, opened by modern technology, computer programming and the whole of bioinformatics. It is one that my generation will have to learn to exploit, hopefully allowing us to discover something great.

Alexander Seutin

Through their lens: Anne McDermott works on better ways of culturing embryonic stem cells

This summer we’re sponsoring high school interns in stem cell labs throughout California. We asked those students to contribute to our Instagram photos and YouTube videos about life in the lab, and write about their experiences.

Anne McDermott did a stem cell research internship this summer in the laboratory of Jan Nolta at the University of California, Davis.

My name is Anna McDermott, and at the beginning of this summer I was offered the opportunity of a lifetime. Chosen as one of ten creativity students for the UC Davis Institute for Regenerative Cures, I spent my summer working at the Institute for Regenerative Medicine at the UC Davis Medical Center. During these eight weeks I have learned about cell culture, attended a class on stem cells, and gained invaluable experience in the lab.

My focus during this internship was my project, in which I compared various feeder free substrates for possible future ways of culturing human embryonic stem cells. I cultured human embryonic stem cells on four different feeder-free substrates. Embryonic stem cells offer great potential to regenerative medicine. Because of their pluripotency, or ability to differentiate in any cell type in the body, they offer enormous potential to medicine. Embryonic stem cells may one day be able to treat spinal cord injuries, or improve eyesight in patients with macular degeneration. However, before embryonic stem cells can be used to save and improve life, several difficulties must be overcome.

One of the challenges facing the use of embryonic stem cells is the risk of contamination and the variation that results from using animal component containing mediums. Embryonic stem cells are typically grown on live animal cells, mouse embryonic fibroblasts, and are fed with serum containing media. By using feeder-free substrates and xeno-free mediums the risk of contamination with animal virus or prion material can be eliminated. Variability in results from lab to lab will be reduced, and greater expansion of cell lines will be possible.

Although I had researched stem cells while creating my website focused on the current and potential therapies stem cell promise, working in the lab with researchers changed my perspective about stem cell research. Reading information through research provided me with information. However, observing, and working with stem cells provided me with a greater understanding about the science behind stem cells.

During my time at the lab I also witnesses the research being conducted in the lab for various stem cell therapies, from Huntingtons disease to ALS to wound repair. The dedication and passion of these scientists was inspiring. From a young age my father, an opthamologist, instilled an interest in science and medicine. Although I was at first unsure which path I should take to pursue both my passion for both medicine and research, this internship has shown me that through stem cell research I can work to research and develop treatments and cures for diseases, diseases that were before untreatable or incurable. This summer has been an unforgettable and life changing experience.

I would like to thank Whitney Cary, for teaching and inspiring me, Jan Nolta, Nolta lab, Gerhard Bauer, CIRM, and the UC Davis Stem Cell Program. Thanks for an amazing summer!

Anne McDermott

Through their lens: Ami Thakrar finds a career path in the lab

This summer we’re sponsoring high school interns in stem cell labs throughout California. We asked those students to contribute to our Instagram photos and YouTube videos about life in the lab, and write about their experiences.

Ami Thakrar did a stem cell research internship this summer in the laboratory of Joel Rothman at the  University of California, Santa Barbara.

Thakrar working in the lab. She submitted this photo to our #CIRMStemCellLab Instagram feed.

Today was officially last day of my summer internship. It feels like the time has gone by too quickly! I’m fairly certain that I’ll be experiencing “lab withdrawals” soon; I’ve honestly spent more time in the lab these past few weeks than I have at home. But I’ve liked it. No, I’ve loved it!

I was lucky enough to get the opportunity to work in the Rothman lab at UCSB (University of California, Santa Barbara) studying embryogenesis in the nematode C. elegans. Before I began this summer internship, I did not have much knowledge about working in a research laboratory. When I first started working in the lab, my mentor supervised my lab partner and I very closely (for good reason), often having to interject with a “don’t forget to sanitize the tip of your pipet!” or a “make sure your samples are in the correct incubator!” However, I would say that by my second or third week in the lab, I had reached a high level of proficiency in the procedures of my experiment, which was quite exciting for me. I do not know very many other high school students, besides my fellow CIRM-intern peers, of course, that can say that they’ve worked in, let alone have become comfortable in, a real laboratory environment.

Additionally, it was amazing for me to actually get to have the chance to actually apply all of the knowledge that I had learned in my biology classes. In high school, it often feels like answers are spoon-fed to students, who then regurgitate the information for a test, and proceed to forget it immediately after setting foot outside of the classroom. In research, however, this is definitely not the case. We had to utilize critical thinking skills to analyze data and arrive at our own conclusions. It was scary, but at the same time exciting, knowing that there was no answer-key with which to check our work like there would be in a typical high school setting.

Overall, my experience in the lab over these past five weeks has made it clear that a career in science, specifically biological research, is the path for me. I think it would be safe to say that spending my summer as a CIRM-funded intern was one of, if not the most, enriching high school experiences I have ever had, and it opened my eyes to all of the different possibilities that exist in scientific research.

Ami Thakrar

Ami sent us these videos of her experience

Through their lens: Christina Bui tries to understand how a protein guides new neural stem cells

This summer we’re sponsoring high school interns in stem cell labs throughout California. We asked those students to contribute to our Instagram photos and YouTube videos about life in the lab, and write about their experiences.

Christina Bui did a stem cell research internship this summer in the laboratory of Theo Palmer at Stanford University.

Christina Bui submitted this photo showing data produced during her internship to our #CIRMStemCellLab Instagram feed.

Hi everyone!

My name is Christina Bui, and I am a rising senior at Piedmont Hills High School in San Jose. This summer, I am doing a research internship at Stanford through the SIMR (Stanford Institutes of Medicine Summer Research) Program, and I’m working in the Theo Palmer Lab (Department of Neurosurgery).

The project that I am working on with my mentor and two other lab members this summer focuses on a candidate protein called MFG-E8. We are studying MFG-E8 because it is very important in many physiological functions, like alleviating inflammation and maintaining healthy tissue. Since MFG-E8 is limited only to the area where new neurons are born during adulthood, we decided to see if MFG-E8 plays a role in regulating what cell types that neural stem cells differentiate into. We hypothesized that MFG-E8 affects the differentiation of neural stem cells and that MFG-E8 helps neuronal development.

To test the hypothesis, we extracted neural stem cells from the hippocampi (where neurogenesis occurs) of wild type (has MFG-E8) and knockout (does not have MFG-E8) mice, and did immunohistochemistry on the cells. We stained for certain antibodies to identify whether the stem cells differentiated into neurons. To analyze, we looked at the cells under a fluorescence microscope, and gathered our data from there. In the end, we discovered that our hypothesis was supported.
These past seven weeks, I have learned so much about stem cells and neurology. That’s what I’ve enjoyed the most throughout this internship—just learning about a particular field of science that a normal high school course wouldn’t focus on. Attending lectures, working with my mentor and other lab members, and talking to my fellow Stem Cell Institute members about our times in lab have been some of the best parts of my time at Stanford.

Although my summer internship is coming to an end, I may continue working on a second project on weekends during the school year in the Palmer Lab. I will always look back at this internship as one of the best summers I’ve ever had, and I hope to continue research in the stem cell field.

Christina Bui

Christina sent us these videos of her experience:

Through their lens: Gloria del Rosario Castaneda learns that research is research because there are still unanswered questions

This summer we’re sponsoring high school interns in stem cell labs throughout California. We asked those students to contribute to our Instagram photos and YouTube videos about life in the lab, and write about their experiences.

Gloria del Rosario Castaneda did a stem cell research internship this summer in the laboratory of Fan Yang at Stanford University.

Gloria del Rosario Castaneda with her mentor and other students in the Fan Yang lab. She submitted this photo to our #CIRMStemCellLab Instagram feed.

You know you’ve had too much biology when you unconsciously type “genes” instead of “jeans.” Some may say I’ve had too much biology during my CIRM internship this past summer, but I would disagree.

My past summer has been filled with bittersweet realizations, startling discoveries, and gigabytes worth of new knowledge. I have found a new passion: biomedical research. My specific project focuses on the rapid synthesis of monodisperse, biodegradable polymeric microspheres using droplet microfluidics, then studying their potential to encapsulate important therapeutic factors by manipulating the characteristics of the microspheres to achieve different coordinated release profiles that could demonstrate as useful to advance regenerative medicine. I had the opportunity to learn how to culture multipotent human adipose tissue-derived mesenchymal stem cells, which were used to determine the bioactivity of released growth factors from the microspheres. The most confusing thing to me about my project is that I actually understand it.

But that is not why I am fascinated by stem cell research nor biomedical research. The more I listened to my mentor and teachers discuss stem cells, regenerative medicine, and the specific impact my project would have, the more I realized that people don’t fully comprehend any of it. That is why it’s called “research,” but even after research becomes bio dogma, we will only get close to completely understanding it, just like a simple logarithm will never reach zero yet go beyond infinity. It’s this desire to touch zero as I my research nears infinite that makes me want to pursue research.
My findings reflect my passion. Some of my findings suggest that I can engineer microspheres of different polymer concentrations to create different release characteristics and accomplish temporal release at variable rates. However, my data for spheres of variable size are inconclusive. In other words, the data doesn’t make sense or demonstrate a clear trend. Although I have worked intimately with my project and it makes sense, I realize I don’t nor will ever understand everything there is to know about the concepts involved in my project.

Now that I am rereading this blog, I am starting to think that I might have had too much biology. I don’t comprehend all of it, but I am getting closer to zero as I near infinity.

Gloria del Rosario Castaneda