BMES @ UCSD

Maintained by Justin Catalana, BMES

Amy Choi, 2007, Biotechnology, y2choi@ucsd.edu

I have been involved in a discovery research of the tensile properties of the human meniscus at Dr. Robert Sah’s Cartilage Tissue Engineering Lab. A meniscus is a crescent-moon shaped fibrocartilage located between the condyles of the femur and tibia of knee joint. Meniscus has been recently discovered to participate in a number of important biomechanical functions such as load transmission, shock absorption, stability and joint lubrication. My focus has been on the effect of age and degeneration on biomechanical and biochemical properties of the meniscus. Meniscus is a tricky tissue to work with by nature, so while much of my work involved repeating the same experimental procedure found in the published literature, a lot of it also has been trying to find the optimal sample preparation techniques for the most consistent and accurate results. Recently, I have been involved in determining how calcification affects the surface characterization as calcification is suspected to weaken tensile properties of the collagen fibers at the surface of meniscus. My experience at CTE has been truly unique as I was involved in a wide range of activities from writing a proposal to carrying out the experiment to method finding. I’ve realized that research is a plenty of dealing with challenges and coming up with new ideas thus a truly creative and enjoyable experience. Although I am considering careers outside of research in the long run, I am planning on attending grad school for further studies in biotechnology related fields.

Daniel Goodman, 2007, Bioinformatics, dbgoodman@gmail.com

One is a project of my own, mentored by Shankar Subramaniam at the SDSC. It involves creating a homology database primarily using existing gene homology and protein family data from a variety of sources. This summer, an early version of the project was released via Google’s “Summer of Code” program, which encourages student programmers to contribute to the open-source community. I’ve learned a great deal from this project because I’ve been mostly on my own. More than my other projects, its given me a much clearer picture of the sort of ‘nitty-gritty’ work people do in this field, and I now have a better idea of the kind of research I’d like to do in graduate school and beyond.

The second is a project with Lei Xie and Phil Bourne at the Protein Databank. We’re designing and implementing a set of tools relating to ligands and their binding sites on proteins. These tools will deal with binding site homology, prediction, visualization, etc, and will be incorporated into the PDB website. The project has allowed me to finally unite my computer science and biology knowledge. It’s been very technically challenging and the implications for this research are very exciting.

My third project is at UCI, in the BioMINT lab in the Biomedical Engineering department. This project is much more engineering-based: we’re designing a microelectrode array that will be able to sense different types and densities of cells based on electric properties. While most of my involvement has revolved around the software that interprets this electrical data, it’s given me some interesting EE experience and it’s been fun to work on, over all.

The UCI project has already yielded a conference paper, and the other two projects should also yield papers in the future. And of course, I’ve cultivated relationships with a wide range of faculty as a result of the research.

Ed Chuong, 2007, Bioinformatics, echuong@ucsd.edu

I am currently volunteering at Dr. Hoekstra’s evolutionary genetics lab, using comparative genomics to identify rapidly evolving genes related to pregnancy. The premise is that in some promiscuous species such as mice, litters often consist of pups that all share the same mother but have different fathers. Because of this, it is in the developing embryo’s evolutionary interest to selfishly sequester more resources from the mother, effectively competing against its siblings. However, the mother’s evolutionary interest is to distribute her resources equally to the entire litter. The resulting evolutionary “arms race” can often leave traces in the nucleotide sequence of the genes involved in the conflict, which can be detected by comparing genes between closely related species and identifying those that exhibit the highest rate of amino acid change. Understanding these rapidly evolving genes can further our understanding of post-zygotic speciation The buildup of mutations in these genes may have “unintended” pleiotropic effects which can contribute to pregnancy-related problems such as premature abortion.

Though evolutionary biology is not directly related to bioengineering research, I learned a lot about fundamental bioinformatics methods such as gene prediction and alignment, and how to work with available tool sets such as ENSEMBL and BioPerl. I also got to present my work at both UCSD and national research conferences, and publish a paper, which were great experiences that confirmed my interest in research as a career.

My time in the lab also led to other opportunities. I started TAing as a 2^nd year for lower division biology classes for my PI, which actually really fun and you also get a much better understanding of any subject material once you teach it to others.

I plan to apply to graduate school in bioinformatics-related research.

Ian Kerman, 2007, Bioinformatics, neodenium@gmail.com

I’m working in a molecular biology lab studying the development of beta cells in the pancreas. These are the cells that are responsible for secreting insulin into the blood.

Specifically, we’re looking at the activation of a transcription factor, PDX-1, that is known to be responsible for the differentiation of the pancreas in the embryo, but only stays active in the adult beta cells. To do this, we are looking at the methylation patterns upstream of the gene.

Working in an actual research lab has given me a look at the real “scientific method” that we all here about in middle and high school and is very different from what I experienced doing science in a teaching lab. It taught me not to look at a problem and how to solve it, but how to approach the problem and identify other problems that may extend from it being solved. An important aspect of doing research is that it never ends. One project always leads to another and then you just have to decide what the next project should be.

Joyce Luke, 2008, Biotechnology, cluke@ucsd.edu

I am currently volunteering at Dr. Hasty’s biodynamics lab, studying genomic instability in yeast cells. In humans, the incidence of cancer increases exponentially with age, and it is believed that an abnormally high rate of mutations in DNA leads to the development of tumor. A group has used incidence of Loss of Heterozygosity as a measure genomic instability in yeast cells. They inserted a marker gene in one copy of a locus and they could detect LOH when a genetic alteration occurred in which the marker was lost, and cause a colony growing on a plate to turn to a particular color. And in order to detect LOH, they would have to physically separate a new daughter from its mother and wait for it to form a colony. Dr. Hasty’s lab tries to improve this procedure by using genetically modified yeast cells that can produce fluorescent proteins under normal conditions. The absence of fluorescent proteins in a cell would be an indication of LOH. The graduate students have developed a microfluidic device that can detect fluorescence and photograph individual cells. I have learned about various biochemical techniques and computer tools in this lab. I will continue to do research as an undergraduate and I plan to attend graduate school.

Alumni

Ronnie Chen, 2006, Biotechnology, r1chen@ucsd.edu

I have been working in Dr. Xiaohua Huang’s genomics and systems biotechnology laboratory for the past couple of years. While human genome sequencing technology has already been developed, it is still a very expensive task to undertake, costing on the order of tens of millions of dollars. Cost is one of the main factors limiting the practicality of genome sequencing in medical research. One of Dr. Huang’s goals is to develop an extremely low-cost human genome sequencing method that will aid in the studies of human genetic variations and complex human diseases. I am working on the development of a novel method of massively parallel DNA amplification to be used in high throughput genome sequencing.

Through my research I have learned much about current genome sequencing technologies and where the field is going, how to approach various research questions, and basic laboratory techniques. I plan to apply to medical school after I graduate.

John Yamauchi, 2006, Biotechnology, jgyamauc@yahoo.com

For the past two years I have participated in research for the Pharmacology department under the supervision of Palmer Taylor, Ph. D. and Zoran Radic Ph. D. Dr. Taylor’s research interests include the structure, recognition properties and function of receptors, enzymes and adhesion molecules involved in neurotransmission. I have worked closely with Dr. Radic to study the structural and kinetic properties of the protein Acetylcholinesterase (AChE). AChE is involved in the regulation of the neurotransmitter acetylcholine via catalyzing the hydrolysis reaction of acetylcholine to choline and acetic acid. I have studied the induced conformational changes in AChE upon binding of various substrates and ligands by generating mutants of AChE in the active center gorge (20 Angstroms deep) and the Omega loop region. The mutations in the active center were designed to observe and characterize the differences in binding affinities for various substrates and inhibitors. In addition, mutations were made in the exterior Omega loop region to attach a fluorescent label for the observance of fluorescent chromic shifts and intensity changes. These changes indicated movements of the Omega loop in directions either away or towards the surface of the protein at the time of association. The application of covalent inhibitors, especially phenyl-triflurormethyl ketone (TFK⁺), with these mutants provided important information regarding the residues in the active center gorge that were involved in the interactions of inhibition.

Conducting this research has been a rewarding experience. I have been able to learn information that I could have never acquired in a classroom and made important contacts that are priceless. The lab website is new and under development at http://pharmacology.ucsd.edu/faculty_site/taylor/Taylor.htm

Shirley Lee, 2006, Biotechnology, s7lee@ucsd.edu

Previously, I have volunteered in the Chien Lab under the guidance of post-doc Dr. Jason Haga. I learned how to perform several biochemistry procedures including immunoprecipitation, gel electrophoresis, and Western blotting to see how cyclic stretch affected the association between proteins Rac and RhoGDI.

Victor Chiu, 2006, Bioengineering, vichiu@ucsd.edu

I currently work under Dr. McCulloch and Dr. Omens in the cardiac mechanics research group (CMRG) here at UCSD. The lab has many different projects going on all regarding cardiac mechanics, from computer modeling to understanding signal pathways. I entered CMRG through one of my TAs for an upper-division class. I now work with her under a post-doc on a daily basis, assisting with surgeries, computer data acquisition, data analysis, and other projects that might be going on in the lab.

I would highly suggest joining a lab as soon as possible. Any lab will teach you extremely valuable skills and processes that help you define your educational and occupational goals. I’ve found that most of my lab work complements and sometimes parallels my educational experience at UCSD, and understanding the applications has helped me realize the importance of what’s learned in the classroom. I plan to join the workforce immediately after my undergraduate study and eventually pursue an MBA and/or masters in Bioengineering.

 

Alexaner Varond, 2006, Bioengineering Premedical, avarond@gmail.com

Internship at private law firm:

I was a Bioengineering: Premed major and I began thinking that medical school was not right for me. I had heard that premed bioengineers were at a competitive disadvantage for traditional bioengineering jobs and therefore I wanted to extend myself into something more. I was also mildly opposed to doing pure bioengineering. I had always imagined myself going into the business side of a biotech firm? and getting an MBA straight out of undergraduate school. (That was my uninformed, high school dream that no longer looked very good to me anymore).

The work that I accomplished during the internship fit into the organization very simply. I was able to wear almost every hat in the organization. I learned and performed almost all of job functions of a legal assistant/paralegal and some of the functions of a full-fledged lawyer. A lot of my time was spent learning. Interns are probably a zero net gain for their employers as so much time is spent teaching / learning though I produced significant and important work products for the firm.

This internship served to further clarify my career path. I debated with UCSD Speech and Debate for 4 years and I had a strong sense that I wanted to become a lawyer. I was never compelled to become a lawyer by TV shows (e.g. Law and Order, The Practice, etc) so I wasn’t shocked when I learned that the legal practice was incredibly different than the way network TV portrays it. To me, the demystified practice of being a lawyer is mostly about pushing paper, client service, and wise business decisions. I definitely want to become a lawyer; although I’d prefer not to work in personal injury, estate planning, or workers compensation. For anyone even considering going to law school or becoming a lawyer, I absolutely recommend doing a private law firm internship.

Francis Chang, Alumni, Bioengineering: Pre-Med, itsfrancis6@gmail.com

While I was a student at UCSD, my first internship was with in Dr. Schmidt-Schoenbein’s lab under Dr. Ayako Makino. We were analyzing the effects of different levels of shear stress had on the production of certain small GTPases in neutrophils. My responsibilities involved maintaining the HL60 cell cultures, differentiating the cultures using DMSO, and performing the Western Blot. It helped me gain alot of experience regarding details and lab procedures and sterile techniques.

Afterwards I had an internship through the SDSU Foundation with Dr. Michael Latz at SIO. We were analyzing the effects different concentrations of dinoflagellates and flow rates had on the amount of bioluminescence that was produced. My main responsibilities were preparing the growth media, setting up and performing the flow chamber and couvet experiments.

My last job I had before I graduated was as a Research Associate and then a Manufacturing Technician at Beckman Coulter. My project as a Research Associate was to determine the what the optimal pH and concentration were for using an ELISA assay. I also worked with the Manufacturing group for a month and a half creating monomers and folding them into tetramers, concentrating them, and storing them in the -80C freezers and preparing the assay kits that were being shipped to other companies.

For the past year I have been a Clinical Research Assistant at NeurogesX, Inc (www.neurogesx.com), which is a small biotech company located in San Carlos, CA. I was recently promoted to Clinical Research Associate. Clinical Research is a growing field as more and more drugs are being developed and need to be tested in humans for safety and efficacy. Although not all companies are going to be successful, it is fairly easy to network with many people and the industry is constantly growing.