Undergraduate Research Apprentice Program (URAP)

Apprentices Discuss their Experiences

Apprentice with Professor Michael Shapira (Microbial Biology)

student at labWhat motivated you to apply to URAP?

In my first week on campus as a transfer student, a classmate in my biochemistry class said I had to get involved in research. URAP applications were due in one week, so I applied to several projects, as well as to CNR labs. I had two interviews, and I started right away at the Shapira lab. I apprenticed there for three semesters, and even stayed on as a volunteer last summer.

Had you done research before URAP?

Yes. I was a nursing major in community college, but I got hooked on microbiology and lab work after taking a micro course. I struggled with that class a lot, but loved it and ended up doing well. That inspired me to look for research opportunities (during Covid), and I ended up doing an independent project on salinity effects on brown oyster mushrooms (growing them in a closet at home, which my Mom just loved…). The summer before transferring to Cal I did a URE in the Petit lab at CS Fullerton doing computational organic chemistry research on photobases (challenging!), where I had a great mentor and peer advisors. We’ve all stayed in touch.

What was the topic of your URAP apprenticeship?

The project I worked on in the Shapira lab involved studying the gut microbiome of microscopic (invisible!) worms whose entire existence involves eating bacteria and laying eggs. But… what are these nematodes eating? How many eggs are they laying? What is their lifespan? The answers to these questions can tell us a lot about a range of environmental conditions, like pathogens. What if the worms turn out to be protected from pathogens by eating particular kinds of bacteria? Could they provide a micromodel for the human gut and contribute to disease prevention?

Interesting! Could you describe a typical day in the lab?

Sure. First, I check any on-going experiments to see if I need to make more media or culture. I check in on the worms – how many are alive or dead? – and move the living worms onto new food plates. Then comes the tricky part: paralyzing these nearly invisible worms with a bleach solution and arranging them like a picket fence on a microscope slide to get images of how various strains of bacteria are moving through their digestive tracts. To move the worms, we use something called a “worm pick” (like a pencil with a tiny spoon at the end). It was challenging to get the hang of this technique, and I occasionally catapulted the worms into the air! Over time, though, I essentially had the same responsibilities as the graduate students in the lab: prepping the lab, presenting proposals to our P.I., and so on.

What do you appreciate the most about your URAP experience?

As a new transfer student, the people in the Shapira lab were my first community at Berkeley, which was very important to me. Everyone was incredibly kind and funny. We still stay connected through Instagram and texting. It was amazing to meet others who shared my passions and to celebrate our successes together. The skills I’ve learned and experiences I have added to my resume matter, but I appreciate this sense of community most of all.

And now, you’re a URAP peer advisor – what’s your best piece of advice to applicants?

I love being a peer advisor. I encourage students not to discount applying to URAP projects because they’re not already an expert on the subject or trained in all of the necessary skills. The main thing is whether you are genuinely interested in the research. The PI and grad students selecting apprentices will recognize your interest and, based on that, your willingness to learn.

What else are you up to in your last semester at Berkeley?

In addition to classes, I’m wrapping up an Art of Writing fellowship that grew out of a graphic novel I created for a medical anthropology course. I’m also a writer for an upcoming book by the group Graphic Medicine (graphicmedicine.org), a volunteer organization that explores the intersection between the medium of comics and the discourse of healthcare. These creative, visual projects have provided a great balance to my work in the lab and classroom.

Graduation is around the corner! What’s next?

Medical school applications! But, first, some traveling, including a trip with my boyfriend and then a backpacking trip with my Mom.

Thank you for doing this interview!

Apprentice with Professor Marika Landau-Wells (Political Science)

What motivated you to apply to URAP?

I came to Berkeley as an international student from Pakistan because I wanted to get research experience. I wanted to find out what “research” even meant and why people do it! I heard about URAP from a fellow freshman and applied for projects right away in spring semester. 

What was the topic of your URAP apprenticeship?

I’ve actually had two different apprenticeships. In the first one – “Mental Health and Psychosocial Support in Post-Conflict Contexts” – I worked very closely for three semesters with PhD student Biz Herman (now Dr. Herman). I had actually applied to a different URAP project, but after interviewing me, Dr. Herman thought this project was a better fit for me. She was right! I even took Data 8 to develop the skills I needed in the lab. I loved it so much that I decided to minor in Data Science. The project ended when Dr. Herman left Berkeley, but we presented a poster at a conference and are co-authoring a paper on the prioritization of mental health and psychosocial support in international organizations. This publication is based on the research URAP enabled me to be part of!

I applied to new URAP projects in the fall of my junior year and am now working with Prof. Marika Landau-Wells (Political Science) on “Threat Perception through Natural Language Processing.”

Could you describe a typical day in your current research position?

My current project involves text analysis. I am analyzing the UN general debates corpus, and my fellow URAP undergrad is analyzing speeches from the George W. Bush administration. At our weekly meetings, Prof. Landau-Wells gives us a task list involving this corpus of speeches, which involves coding what was said. Then, usually, something goes wrong (because…coding!), and then I figure out what went wrong. The program searches the speeches for select words – terror, weapons of mass destruction, enemies – and creates a data frame that shows these key words in all the contexts in which they appear. This preliminary process of data cleaning will then be used to contribute to the broader project that seeks to understand how threats such as terrorism are perceived amongst these varying parties.

Is there anything about research that surprised you when you started?

Yes! I usually thought of researchers wearing white lab coats in a lab. But, there’s not one look. My research projects don’t really even exist in a physical space. However, many of the same processes are used in different contexts, and researchers are all contributing to society in some way.

What do you appreciate the most about your URAP experience? 

I’ve gained many new skills – such as coding in R – and have had the opportunity to apply knowledge and skills I’ve learned in class to reality. I’ve also appreciated the networking and teamwork aspect of my URAP projects. It has been a real plus to work closely with professors and graduate students to learn about their research and their experiences after graduating from university. This kind of one-on-one mentoring is one of the best things about URAP.

And now, you’re a URAP peer advisor!

Yes – I saw the call for peer advisor and immediately applied! At a huge place like Berkeley, it is important to have resources that offer individual help. I wanted to help other students find their way to research like I did. Being a peer advisor has been a great experience – we answer questions about URAP, give feedback on applications, and give presentations to different units around campus and at special events like Cal Day. 

Is there anything else you would like to add?

Really, URAP has convinced me to go to graduate school to get a PhD in Political Science. I had a tech internship at a software company last year, but because I had my URAP research to compare it to, I was able to see that the tech route was not for me. I look forward to continuing to work at the intersection of Political Science and Data Science, quantifying political phenomena and analyzing political behavior, particularly in the context of South Asia.

Apprentice with Professor Darcy Grimaldo Grigsby (Art History)

Representation of Scale: What is it like to work closely with a faculty mentor on a book-in-progress project?

Let’s talk about the project you are currently working on.

Professor Grigsby is working on a book on representations of scale of four 19th century French structures: the Suez Canal, the Panama Canal, the Eiffel Tower, and the Statue of Liberty. These colossal structures – the Eiffel Tower was the tallest tower, the Panama Canal was the deepest trench- symbolized Western feats of technological prowess. But immediately, and in the case of the Eiffel Tower and the Statue of Liberty before the structures were finished, they were miniaturized in souvenirs. Many people know them through these souvenirs as opposed to the full-scale structures. During the construction of the Panama Canal and Suez Canal, the images of the work that circulated were not so much in hand-held miniatures or models, but in coins and stereoviews. Stereoviews are now obscure tools, but in the 19th century, they were an extremely popular form of entertainment; everyone had hand-held stereoviewers in their living rooms that would turn doubled photographic images (stereoviews) into three-dimensional projections. Some think of them as precursors to cinema. My research doesn’t necessarily go into all of that; I have been concentrating on theories of scale, and theories of model making. I previously studied architecture, so I have some background, a non-academic knowledge of these subjects.

So this perhaps helps you to narrow down where Professor Grigsby wants you to start your search?

Yes, I think it allowed me to structure my research on two very vast topics. Professor Grigsby is also analyzing structural drawings, architecturally technical drawings, and since I used to construct such drawings, I can read her analysis against my readings of the drawings.

What a great match!

Yes, it was. When we were speaking to the students at the CalSO tabling [Erica participated in an information tabling event for CalSO students], a lot of them asked me “How did you find a good project?” I told them that when I was looking at the list of projects, I didn’t look at my department first, I was just looking into the humanities and something that I would really want to work on. That is definitely one piece of advice that I would give to other students – you have to have a strong interest. I do think that this particular project would work poorly for someone who is not really interested in the topic. It is self-structured, and it requires you to have both an interest and a disciplined way of working. And if you do it right, it is so rewarding- if you find the right project, it doesn’t feel like work. I hope that Professor Grigsby was and is able to access some of my background knowledge, and at the same time, she has helped to bridge my previous professional architectural education with a more academic one. This project has offered an incredible education in research methods and the process of producing an idea, an argument, and ultimately a book.

I want us to talk a little bit about a typical day – what does your schedule look like?

At our first meeting Professor Grigsby outlined her materials, her arguments, and what she specifically wanted me to do. Now, at the end of each meeting, Professor Grigsby discusses what I am supposed to continue looking at. For instance, in our last meeting, it was images vs. models. She wanted to know how architects or engineers discuss the image of their work vs. the model of it. So that becomes my primary research trajectory for me. From that point, I go back to the big, big library, and I spend maybe half a day or so just looking for initial sources.

So you basically have the key terms, and you go to the library – it is that open.

Yes, and it’s been amazing, because I didn’t expect that. I have to say that looking back at my initial notes, I can see that I was much more conservative in the beginning in how I was reporting things to Professor Grigsby. I would quote directly more than anything, and try to screen my own ideas as to why it would be pertinent. I was really just trying to be a funnel from the library to her. And now I think she wants me to distill as much as possible, because it saves time for her, but also because I think she trusts that I have some understanding of what it is she is looking for or what is relevant. I didn’t expect to be able to contribute in that kind of way, so it’s been a real reward. After collecting and distilling the most pertinent articles, I usually send an email to Professor Grigsby with an annotated bibliography and some notes as to why think the sources might be interesting. At the next meeting, we usually go over the work that I did, and she decides the next route to take. Professor Grigsby is an incredible professor. She has made this project so accessible to me and, as much as she possibly can, collaborative, and it is really amazing. She has taught me so much about how to rigorously carry out this kind of research.

Is there anything else you would want students to know before they apply?

One thing that I find important is that students should be aware that they won’t communicate with the professor the same way they do in the classroom. You are no longer completing straightforward assignments for them. You have to learn to work without the immediate affirmation and out of your own motivation. And – this is not a task to do if you are already overextended.

Apprentice with Professor Baquedano-Lopez (Education)

Comparing science education in religious vs. public school education

Please tell us about the project you are currently working on.

I should give you some background. When I first started here (in fall 2005), Professor Baquedano-Lopez had me look at tapes of projects that involved religious schools, Sunday Schools in particular. After that I analyzed data from another project, which was about how to make science more “user-friendly” for elementary school kids by providing teachers with more materials and guidance about curriculum planning. It was a pilot program that was trying to make science easier for the students to grasp, more accessible, especially for kids from poorer schools where the science curriculum might be not very strong.

At the moment, I am looking at the connection between these two projects: I am looking at the differences and similarities between the public school education and the religious school education in regards to science. Professor Baquedano-Lopez is also having me look at how the concept of time is socialized within the two settings.

In addition to the Sunday School education, there is also some data on year-round schools, and I am comparing what those two projects address as far as time and knowledge are concerned: where within each setting does knowledge reside? For example, in the religious education it would be the bible.

How was the data collected?

For one, there are the actual tapes from recording the classes in both projects, and I watch the tapes. Then there are tape logs from other researchers who watched the tapes and took notes on specific aspects they were supposed to look for. For example, in the Religion project there are tape logs that only look at prayer, or tape logs that only look at songs.

There are the tape logs, but there are also notes on specific pieces of narratives, and there are field notes – there is a lot of different data – too much data (laughs). When you finally remember a connection, you have to fish through it all again to find the 5-minute segment you vaguely remember seeing. But in any case, that is what I am doing, describing connections. Patricia (Baquedano-Lopez) and her graduate students are working on a theory right now, which is part of a book that will be written later down the road.

What does a typical day in your apprenticeship look like; what do you do?

Usually, I am here Fridays from 9 to noon. When I come in, sometimes grad students will be here doing their own work, sometimes Patricia will be here, sometimes other URAP students. We all float in and out. I usually just head over here to the computer. I already finished looking at the tapes from the public elementary schools, so now I am going through my notes on the tapes that relate to science and knowledge. Right now, I am also looking through the field notes and other materials for the religious schools, trying to find corresponding material. I collect everything in a word document, and then I write my interpretation of how it relates to what Professor Baquedano Lopez is looking for.

How often do you have meetings?

Usually, at the beginning of the semester when we schedule our hours, Professor Baquedano-Lopez picks the days when she is here. She is usually here Fridays, but she is now also working at the Latino Policy Research Center, so she is not here as often. But I see her at least every other week, not necessarily to meet about something specific, but if I have issues, and if something comes up I just tell her and we meet. Otherwise, I’ll just email her, and if it is something we really need to discuss, we’ll make time.

What do you appreciate the most about this research experience?

I appreciate the most Patricia. I have maybe one other professor I feel comfortable bothering during office hours, and I feel very comfortable around her. And I like that the most.

So it is the connection that you have been able to establish with a faculty member.

Yes, and when she runs into me or the other URAP students, she says things like “Hey, I got some other students who are applying to grad school, do you need a letter of recommendation?” She goes out of her way for us, and I like that; it makes me feel comfortable.

You have been doing this for quite some time – this is your fourth semester. I hope this means that you are having a good experience! Is there anything that surprised you about doing research? Is there anything that was different from what you had expected?

I liked it, and that was surprising. My previous research experience was working in a lab, in Nutritional Sciences and Toxicology, and I just processed mouse colons and put them on slides and looked at them. It was interesting at first, but after a while it got boring. I felt that I was dealing with too much mouse colon for one lifetime…(laughs).

How did you find that research position?

That was before I transferred – it was through the Biology Scholars Program, which works with Transfer Students to get them internship positions for the summer on campus. It was interesting, and I was learning something very valuable, which is that I don’t want to go into that kind of research; I don’t want to work in a bio lab, period.

That is a valuable thing to discover!

And I feel like research in the field of education seems more applicable to real life than in the sciences, because if we’ve discovered something now then maybe we can apply what relates to mice to humans in ten years from now. And I feel that research in the social sciences is more directly about and based on people, so it is more directly applicable to them.

What kind of advice would you like to give to prospective apprentices?

Find a subject that you are interested in as opposed to “I want to be in Medical School, so I need to be in a science lab”. I know that a part of me really wanted to do that even though I don’t really like working with microscopes and mice and tissue samples, because I want to go to Med School, but I was thinking that in the long run it will be more beneficial for me if I do research that I actually enjoy so that when they ask me why I did this for four semesters, I can give a good reason, as opposed to “Well, I didn’t really like it, but I want to go to Med School, so that is the only thing to do”.

And if you realize after a semester or more that it is really not your passion, find something else, keep searching. Is there anything else you would like to comment on?

That some professors are nicer than others. I have a friend who applied to URAP and he said that during the interview it was really scary when he went to meet with the professor he applied to, and he ended up not getting any of the apprenticeships. For me is was different. Professor Baquedano-Lopez was the only one who responded, and she was very friendly during the interview. This was my first semester here, and I felt reassured. I know my friend was a little traumatized and said “No, I don’t want to apply again because I’m not going to get the position anyway”. But I think a part of it is that sometimes people don’t read the description that well and they think “I’m a psychology major, I just apply for the psychology projects”. When you read the description carefully you realize “Hmm, I don’t think this will actually be a good fit for me because of what they are asking for and what they will have me do”. That might have been part of it.

I do think that faculty pick that up in the initial conversation. They probably realize how closely a student has read the description, and if they have gone beyond what is in the description, maybe to the faculty mentor’s homepage or lab page to gather as much information as possible, so there are different elements that come together.

Thank you for doing this interview!

Apprentice in the Harland Lab (Molecular & Cell Biology)

When I was in high school, I had no idea of what research actually meant beyond lab coats and safety goggles; I didn’t know what pipetting or other lab techniques were. After my first semester here I decided to try URAP and was invited for the initial interview with Professor Harland, along with one other student. Doctor Harland asked us about our previous experience, and the student next to me started to talk about all his research experience. He had done some research including stints at UCSF and Stanford. I remember thinking “Darn, I don’t even know what pipetting is”. I told Dr. Harland that I had never done research, and didn’t know if I wanted to go to grad school or med school. I was applying to find out. It turned out that I got the position. That was great. That is the advice I would like to give to anyone who reads this: If you wonder “Should I say this or that about myself” I would say just be honest, and try to show them who you are more than what you have accomplished by making a long list. Be honest, and it will work out better for you.

That is very good advice. Let’s talk a little bit about what is it that you are currently working on.

We were assigned individual projects from the very beginning. There are ten chromosomes in the frog Xenopus tropicalis and each of us was assigned one to two chromosomes. We needed to find the centromere, which is the point where the sister chromatids attach in meiosis. This got us used to PCR (polymerase chain reaction), gel running, and all the other lab procedures. Once we did that, each of us chose one mutation for mapping, and I chose ‘Grinch’. This is an early developmental defect which results in a huge bulge in the chest. From the work of a past undergraduate we suspect it is a defect in the circulatory system or the lymphatic system. The object is to find where this mutation occurs in the genome – to map it. It could be anywhere on anyone of the ten chromosomes.

The first step involves me doing what other postdocs do, which is gynogenesis (Harland Xenopus tropicalis Site). Then I screen the tadpoles for the mutation and extract their DNA. I use these DNA to find where the mutation occurs by doing PCRs and analyzing them through gel electrophoresis. We are zoning in on the actual location of the mutation.

Can you describe a typical day in the lab?

I have collected about 200 embryos that need to be tested. To do all of them at once is a little hard, so I choose anywhere from 15 – 100 and do PCRs- we amplify the DNA. Then I take the amplified DNA and run gels to get the results. Once you know what the results are, you decide what to do next. It is an entirely different story for the rare days when I need more embryos. Then, I first need to figure out which two frogs I need to mate to get mutant embryos

So you are starting at the very beginning.

Yes, at that stage, I have to plan a week ahead, because it takes a while for the eggs to grow.

How often do you meet with your faculty mentor, Professor Harland?

Wednesday mornings is the general lab meeting, where usually two of the lab members present their research. The undergraduates usually don’t present at that meeting (although we are encouraged to), but we usually attend. In fact later in July, another undergraduate and myself will present at this meeting. This will be my first time presenting my project to the entire lab.

After having witnessed a lot of presentations before by the other lab members, do you feel confident about this?

Yes, I’ll be ok. It will be very good practice, and the questions that they’ll ask will make me think more deeply about the project. In addition to the Wednesday meetings, every Friday the undergrads (the trop team) also meet with Dr. Harland and Mustafa Khokha (who started the tropicalis team and is now at Yale University). Mustafa attends the meetings via video chat

Was there anything that surprised you about doing research when you started?

What surprised me the most is how often Dr. Harland is actually there – he is almost always in the lab. In fact it is very rare that he is not. I can talk to him anytime I get results and I talk to him almost everyday. That really surprised me – how accessible and nice he was. It also surprised me how Mustafa is still very involved and I can always ask him for help. Also, the next International Xenopus Conference will be held in Germany this September and Mustafa and Dr. Harland are both going to attend. Mustafa asked me to write an abstract for our project and so I sent it to him and he submitted it. What surprised me the most was that he put me as the first author on it. Mustafa will be presenting for us and I am very excited.

We talked about some advice you would give to prospective applicants a little earlier – is there anything else you would like to share based on your experience?

Don’t choose a project or apply to a lab because you think it is something that will look good on a resume. You are not going to like it as much. Choose something that really interests you and can keep you engaged. Choose something you can enjoy even if it is not related to your major. If URAP doesn’t work, go and talk to the professors on your own; take that initiative. URAP can be pretty competitive. You get your three choices, but if that doesn’t work out, don’t give up.

Thank you very much!