Author Archives: Yilin Yang

The morning seminars have all been absolutely amazing. It’s great to hear about how all the speakers got to where they are, and most importantly, the science that they are doing. From fruit flies to lemurs, from evolution to medicine, it has never occurred to me that there are so many distinct yet interrelated branches under the huge umbrella of biological science, and every single one of them deserves being delved into.

As someone who is extremely fascinated by genes, I found Dr. Charles Gersbach’s talk on his life path and his research particularly fascinating. Dr. Gersbach focuses on cellular and molecular engineering. Specifically, one of the major aspects of his research is using genome editing technology to correct mutations that cause genetic diseases. For example, he and colleagues have successfully corrected dystrophin mutations in vivo in mouse models with CRISPR/Ca9 system, and this technology can potentially be translated to bedside, curing Duchenne Muscular Dystrophy in human patients. I found gene/cell therapy very promising because it can get deep down to the fundamental level of genetic diseases and correct the mistakes at that level. In contrast, most of the therapies currently are only able to ameliorate the symptoms at the surface level rather than actually cure the disease. There is a fundamental difference between drugs targeting bad proteins produced by bad genes, and drugs that directly target and fix those bad genes. I believe that once the gene editing technology becomes mature enough, it will have wide-ranging effects on healthcare.

Also from Dr. Gersbach’s talk, I learned that being a biomedical engineer does not mean dealing with brain signals / machines all the time, as how biomedical engineers are stereotypically pictured. Editing genomes and regenerating tissues are also part of problem-solving, therefore also part of engineering. The use of the CRIPR/Cas9 system for genome modification is an excellent example. The technology is adapted from bacterial adaptive immune system, and therefore part of basic science. On the other hand, it is utilized to solve problems on actual human patients, and therefore part of engineering. Dr. Gersbach’s research is really at the intersection between basic science and engineering, and for me personally, working at the interface between these two would be a very enjoyable and rewarding experience.

Of course, Dr. Gersbach’s life path is very inspiring too. Started off as a chemical engineer, he didn’t follow the majority and went into chemical industry. Instead, he tried to figure out what he wanted and followed it. This let me know that, as an aspiring scientist, there are really thousands of different roads ahead. No matter it’s the main street or it’s the road less taken, it’s important to always find my passion and follow my heart, alway do things I truly enjoy. As the program is almost coming to conclusion, I want to thank all the faculty members who shared about their life paths and research with us. All the seminars so far have been really fun and inspiring, and I can’t wait to hear about the life and research of the last two scientists next week!

My project seemed very simple in the beginning: no difficult biochemistry, no complicated experimental procedures, and honestly, the fanciest machine ever involved in my experiments is probably the thermal cycler, aka the PCR machine. But in reality, as I’ve slowly found out, problems never stop, frustrations never stop. They come and go one after another, and I not only have to solve them scientifically, but also have to deal with them mentally.

The first real problem occurred as early as I was testing the primers I designed to amplify the gene of interest. I designed 4 different primer sets to amplify 4 different portions on the gene. Despite that theoretically, they should all work perfectly, oftentimes the case was, either the PCR reaction didn’t work at all and I didn’t see my target on the gel, or multiple nonspecific amplifications occurred and lots of bands of the wrong size showed up on the gel. I spent almost the entire first half of the program perfecting PCR — redesigning primers, playing with the annealing temperature of each primer, adjusting the amount of reagents in the reaction, etc. Everyday just involved an enormous amount of PCR and gel electrophoresis and attention to details: keeping detailed notes of what changed and what remained unchanged, while making sure I didn’t use up too much of a patient’s DNA for testing and troubleshooting.

When I got my PCRs working after almost 4 weeks of troubleshooting, I could finally send the products to sequencing. My hopes were high: after the sequences are back, I could start searching for mutations! But again, the sequencing reactions didn’t go smoothly. For mutation-searching, the quality of the signals is very important. Any contamination could bias the result, but the sequences were seldom free of contamination/noise. As a result, I had to start troubleshooting the sequencing reaction: designing new primers for sequencing, adjusting the concentration of the template, etc. As of today, there are still a few samples of which I haven’t got perfect sequences, and I’m still working hard on perfecting the results.

For the samples whose sequences were clean enough, I started to actually search for mutations. Mutations are, however, really, really, rare. So far, I’ve only spotted three, among which two are synonymous (they don’t cause a change in amino acid) and therefore clinically irrelevant. The most exciting one showed up just two days ago because it actually caused an amino acid change from tyrosine to cysteine. My mentor and I spent the entire afternoon almost frantically looking up this mutation, trying to figure out the details of it such as its functional relevance. Disappointingly however, it turned out that it was just a common variant across human population: it has an allele frequency of 1.8%, which is way too high to be considered rare or pathogenic.

In summary, I’ve not gotten any real “results” in my project. But in retrospect, I actually enjoyed this whole troubleshooting->working->failing process rather than got beaten by it. What’s exciting about scientific research is not entirely the groundbreaking discoveries, but all the different paths that lead to that destination as well as the views along them. I will continue working hard on my project and try my best to search for mutations, even if they are not there.