Exposures to Omnipresent Science

We were all probably told in one of our intro courses that science is all around us. As I’m studying here right now, this is observably true: the light illuminating my desk is produced from excited electrons returning back to the ground state; molecules vibrating together at very high speeds make my wooden desk solid; and actin-myosin interactions in my fingers allow me to type quickly and in an agile manner. Biology, chemistry and physics are omnipotent in nature because they create matter and sustain life. But they also form the basis for non-natural, man made technologies, cosmetics and appliances. Thus, as a senior now, involved in research, and getting more exposure to applications of learned concepts, I am beginning to see how science is not only around us, but is a powerful application and solution can be applied to society progressively.

Dr. Chalfie and me at my poster

My most recent exposure to a wide range of scientific hot-topics was last month at the “SACNAS” National Conference. I had the opportunity to travel to San Antonio, TX for a four exciting, stimulating, and deeply memorable days! Our group of Gauchos attending really made the most of this experience by networking, seeking mentorship, engaging with other students and researchers, and presenting award-winning posters. The workshops involved many different topics in science – I really enjoyed learning about heart vessel angiogenesis as a potential therapy for Coronary Heart Disease at a developmental biology session, and an interesting round table discussion mediated by an SDSU faculty. But we learned many other interesting ideas ranging from materials science to drug development to applying to Grad schools too. I had the great opportunity of meeting with one of the pioneers of Green Fluorescent Protein (GFP), Dr. Marty Chalfie, also a Nobel Laureate, and as my project involved C. elegans (the model organism in his lab), and GFP, it was even more exciting to meet him! Though the days were filled 8AM-10PM with workshops, lectures, and presentations, we still managed to peruse the nice surrounding area at the Alamo and Riverwalk, as shown in the pictures on the other blog posts. Presenting for the first time at this National conference with nearly 4,000 attendees was an amazing experience from which I learned so much!

Prof Goldstein giving a MCDB Departmental Seminar

Another recent memorable experience that showed me the power of science occurred last week. I had the honor of hosting Professor Larry Goldstein of UCSD Department of Cellular and Molecular Medicine, as part of the Beckman Seminar course. We invited Dr. Goldstein, a well-respected neurobiologist studying the causes of Alzheimer’s disease using stem cells, as a guest speaker for our “Science for the Common Good” course. Dr. Goldstein was a strong advocate for stem cell research during the ban years, and often was consulted by the government for his opinions. Given his experience with basic science and initiative for its application to society and the common good, he was not only a very interesting speaker for our class, but also a welcomed presenter in the MCDB departmental seminar series. Arranging the departmental and course seminars and various faculty meetings took organization, time and many email messages, but everything came about smoothly. I also had great guidance and help from Dr. Foltz and Dr. Lubin, who are seasoned at organizing such events. For two days, our small group of undergraduates in the class, was able to have in depth, stimulating and thought-provoking conversations with Dr. Goldstein about topics including stem cell controversy, academia vs. industry, university science education thoughts, and healthcare. It was another amazing opportunity allowing me to appreciate the intricacies within academia (collaborations with other labs, busy faculty schedules) and the importance of undergraduate research.

As I continue to work in the lab, I am energized by these exposures and interactions. Science has the potential to change the world progressively by its application to society. And this potential begins to see its fruition through basic research in labs similar to the Rothman lab I am in, and many others around UCSB. The skills I’ve gained in creatively thinking, presenting confidently, and understanding results have exceeded my expectations about research experiences, and I am excited to keep experimenting throughout the year.


In 1963, Sydney Brenner discovered that the tiny, soil roundworm, Caenorhabditis elegans could be a powerful model system in the scientific community. The “worm”, as affectionately called in our lab, has a constant 959 cells in its body after exactly 131 of the 1090 cells die during development. In addition, its genome shares 40% homology to humans and a fast lifecycle with a high brood size facilitates short-time scale studies that have implications toward mammals and humans. These properties allowed developmental cell death pathways and neural development to be extensively studied.

Since then, the c. elegans’ complete cell lineage of all differentiated cells has been mapped making it possible to know exactly how any cell was derived. A comprehensive pathway of programmed cell death, or apoptosis was identified and applied to humans. Interestingly the results from development and apoptosis research using c. elegans allowed new understandings of various proteins and mechanisms in cells, arguably setting the course of developmental biology for the next five decades.

Our lab is dedicated to researching these classic worm studies like apoptosis related effects, and developmental cues and gradients on a molecular and genetic level. Certain projects involve identifying the genes regulating cell determination and differentiation, while others aim to inspect cell fate and reprogramming of a fully developed cell type (a unique and exciting stem-cell biology spin off). The project I have the opportunity to work on nicely blends apoptosis and development to understand the molecular mechanisms ensuring inheritance of healthy mitochondrial DNA.

At the core of the project lies the immortality of genetic information. We, living bodies, are simply messengers or information carriers, alive for enough time to pass on genetic information by egg and sperm through our germline. This tissue producing egg and sperm, the germline, then is an immortal lineage and the only thing connecting us to our ancestors and our ancestors to the future little ones to come. I am investigating how the germline is sustained throughout so many generational transitions, and over such long a time scale, with a focus on mitochondrial DNA (mtDNA) inheritance. We hypothesize germline apoptosis is a crucial step in ensuring preferential passage of healthy mtDNA molecules. In order to understand mtDNA transmission through the germline, I am working on developing a preliminary selection condition, crossing various strains to produce a unique desired genotype, and constructing a visualization method for mitochondria in early embryos. The results of these projects will offer the scientific community a better understanding of mtDNA selection pressures during inheritance, but have offered me both more knowledge of biological techniques and concepts, as well as an appreciation for the patience, persistence, critical thinking and analysis skills required as an effective researcher.

A short term goal reached over this summer was doing a genetic cross to create a double mutant strain. I crossed a strain of C. elegans that had a point mutation on the nuclear gene, ced-3, with a mtDNA mutant containing a 3.1 kbp deletion in the mitochondrial DNA. Since mtDNA is inherited maternally, whereas nuclear DNA is inherited from mother and father, we utilized two different inheritance modes and systematically planned out crossing these two strains to obtain a desired genotype. To confirm the presence of both mutations after the cross, we conducted PCR (polymerase chain reaction, which amplifies a specific area of DNA), and visualized the presence of the deletion and ced-3 gene using another common lab technique, gel electrophoresis.

In addition, I began the exciting yet tedious journey of molecular cloning to create a GFP fusion construct. Ideally, we aim to visualize mitochondria through a fluorescent protein in the germline and during the early embryo stage using an introduced genetically engineered plasmid construct. And although the project is still in its preliminary stages, I’ve isolated the insert containing DNA of interest, and ligated that to a vector backbone containing a unique promoter to drive the genes. I learned how to conduct restriction digests to isolate a specific sequence of DNA. I also became familiar with transformations, which introduce DNA into E. coli bacteria for amplification. And I also refined my skills in running gels, visualizing and extracting bands for sequencing and further digests.

Contrasting from our “macroscopic” world, where, for example, the amount of raisins added in oatmeal raisin cookie recipes can vary, but the final product is the same delicious dessert, the “microscopic” world of DNA is very tightly regulated. During PCR, measurements a few microliters off could potentially yield no product – no amplified DNA. Or, during transformations, if a water bath is not calibrated to the exact 42 degree temperature, in just 30 seconds, the cells will not be fit to uptake DNA and the entire transformation could potentially be void. I’ve learned to be careful in my calculations, and frugal in my volumes used. Many times I’ve seen unexpected results and bands of surprising fragments lengths, which lead me to backtrack and analyze possible areas of technical error, or alternate biological explanations. Each erroneous result, though at times painful, reminds me how blindfolded we are to the polymerases, nucleotides, and protein interactions that compose living systems, but also how refining my experiments is possible for future successes.

This summer, with lab work, writing workshops, skills seminars and GRIT lecture series, has been a inspiring, exciting and stimulating one! I’m grateful to my mentor and faculty advisor for guidance and encouragement, and thankful to CSEP coordinators and The Arnold and Mabel Beckman Foundation for the Beckman Award, which has allowed me to participate in this tremendous opportunity. I’m excited to apply what I’ve learned and observed from the presentations and workshops and to continue researching and growing intellectually as I spend time in the lab.

Wrapping up the summer

As the summer draws to a close, I decided to look back on my research experience here at UCSB as a Beckman scholar.  Over the course of the summer, I learned a lot about what it takes to actually do research, from designing the experiments (Who would have thought there are so many little details you have to worry about for each experiment?!) to interpreting the data to presenting my results.  But, not all the educational value of this summer lies in the area of lab work.  Instead, I found that I learned a huge amount from the research and writing classes offered over the summer.  In particular, the powerpoint presentations we had to give at various points in the summer were probably one of the most helpful parts of the internship, even if they were incredibly difficult to put together.  There’s nothing like trying to fit your research topic (which you can probably talk ad nauseam  about) into 3 minutes and 4 slides, while still having your audience understand fully.  Another summer highlight was the Beckman Scholars Symposium, held at the Beckman Center in Irvine.  During this 3 day event, all the interns in the program travelled to the symposium to listen to the guest speakers and present their research (if it was their second year).  Getting exposed to so many different undergraduate researchers engaged a wide breadth of fields was truly a unique experience, I even got a few ideas for my own project from talking to the other undergraduates there.


Even though the summer may be coming to a close, my term as a Beckman scholar is only just beginning.  I feel that this intensive summer has served as a great preparation for continuing research during the school year and next summer, but there is still a long way to go.  I look forward to getting back to work in the fall, starting up the year with all my summer experience, which will hopefully make research a little more straightforward this time round!

Hitting my stride

After almost two years of working in the same lab, one might think that nothing would surprise me anymore. This is not entirely untrue–The day-to-day routine, the issues that arise, and the overall pace of a research project is no longer a shock to me. What I have found interesting about this summer is not so much the research itself, but the ease with which I have become accustomed to the routine of coming into lab full-time every day. In the previous summers that I did research, the days in the lab felt very long at first, and it wasn’t until the summer was almost over that it felt somewhat normal. This summer, however, I got into the routine very quickly, and have little to no problem spending my entire day working. It feels easy and natural.

Perhaps this is partly due to the fact that I have a much higher degree of ownership over this project than I have had over any of my previous projects. After putting in a large amount of work on a project that was formulated first by someone else, I finally have gained enough knowledge to really propose a new project of my own. This is something else that I have found very exciting about this summer. To have finally reached a point in my research career where I can make legitimate suggestions to my faculty advisors and plan out specific projects is supremely rewarding, and reinforces my choice to go to graduate school.

Smart Materials, DNA, and Kryptonite: Life in a biochemistry lab

Smart materials?  What the heck are those?

Smart materials are more common than you’d think – a lot of people actually make use of them in their daily lives.  If you’ve ever taken a liquid gel capsule (for example an omega 3 dietary supplement) you’re one of those people.  The reasons those capsules are smart is they react and change in response to their environment.  Specifically, in the case of the capsules, they will stay intact in your mouth, but when they hit the your stomach acid they will readily dissolve in response to the pH change.  But a change in pH is a pretty drastic effector for making the capsules dissolve.  What if we could find a way to make them release their contents in response to a more particular cue, like the presence of a particular molecule?

The good news is that such technology exists, right now.  Surprisingly, the basis of this technology is DNA.  Similar to RNA, DNA can also form secondary structures.  DNA strands that form secondary structures as a result of binding a particular molecule, unique to the sequence of the DNA strand, are called aptamers.  Using these aptamers and DNA’s base pairing, it is possible to make a type of chain, one where the links of the chain alternate between aptamer links and normal DNA links.  If the aptamer link binds its unique molecule, it will destroy the chain.  Essentially, this means that every other link in the chain has its own type of “kryptonite”, and the chain will break when exposed to it’s kryptonite molecule.

Now here’s the cool part:  if you take those a bunch of those chains and criss-cross them over a hole in a membrane, you can effectively block transport through that hole, until the chains are exposed to their kryptonite molecule and break apart.  If you put a bunch of these tiny holes in a membrane, block them all with these criss-crossed chains, and place some drugs on one side of the membrane then BAM! you’ve got yourself a smart drug that is only delivered in the presence of a particular “kryptonite” molecule (which, thanks to aptamers, could theoretically be anything!).

Schematic of DNA chain's blocking a nanopore, then reacting to the presence of their target molecule and unblocking the nanopore.

Schematic of DNA chain’s blocking a nanopore, then reacting to the presence of their target molecule and unblocking the nanopore.

But, there’s a problem with this system.  There’s a trade off between how strong we can make those chains and how fast they break apart.  That’s where I come in.  My research project is to optimise this tradeoff, and in doing so figure out design parameters so that the system can also be tuned to fit a wide variety of applications.

Life in a Biochemistry Lab:

My research is conducted in the Plaxco lab through the Beckman Scholars program here at UCSB.  Working full time in a lab is very different form taking normal classes – there isn’t  much in the way of homework or the other usual classroom concerns like midterms.  Instead you find that you have a lot of freedom to take your project in the direction you want (with approval from your mentor/PI of course).  For example, at the beginning of my project I had the opportunity to choose how to monitor the system.  After considering and testing out several different methods, I decided to use fluorescence resonance energy transfer (FRET) as the main signalling method.  With the support of my mentor, I pitched the idea to my PI who approved it, and soon enough I received my first sample.

Labelled Aptamer

Fluorescently labelled aptamer

And in order to actually observe this system, I decided to use a stop-flow fluorimeter (which doesn’t look like much in the picture, but actually has this pretty awesome pneumatic ram as part of the system, which makes it fun to use).

Stopped-Flow Fluorimeter

Stopped-Flow Fluorimeter

Now it was time to begin researching.  The start of the project was the hardest part: I had many new methods to learn and theories to understand. It’s slow going at first, but the learning curve is steep when it comes to research, and in a few weeks I was able to design my own series of experiments that actually worked and resulted in good, useful data.  After running more experiments than I’d like to admit that resulted in either no data or bad data, this was a pretty big milestone.

Overall, I’ve come to understand that working in a research lab really just boils down to a very long series of questions.  Answering those questions takes a lot of time and effort, and the answers you get often just point to many, many more questions.  But even though it might not bring you too much closer to the goal of your research project, there is an incredible feeling of accomplishment that comes from answering these questions, even if its just measuring the simplest of binding curves or finding a melting point, because you’ve done something that might not have been done by anyone else before.  It’s that sense of discovery, and that’s what makes research awesome.