Author Archives: Emre Kiziltug


BSURF has been a great summer experience for me.  Prior to this program, I didn’t really have a substantial research experience and didn’t know exactly what it was like to go to lab every day and do experiments to answer scientific questions. I knew I wanted to become a scientist, but I didn’t know what was expecting me. Thanks to BSURF, I have a much better understanding of what the life of a researcher is like.

At the beginning, Dr. Grunwald told us that there are 4 fundamental components of science: Asking thought-provoking questions regarding the direction of research, doing craftwork (techniques, designing experiments) , communicating the work (poster presentations, chalk talks) and lastly doing all this under the frame of work ethics. After 8 weeks of being involved with all of these components, I can easily say that I have progressed significantly in these areas. I asked a lot of questions to my mentor about our project, I learned many great basic craftworks such as doing PCRs, running western blots, doing transfections and so on. I communicated my work by giving a chalk talk to my fellow BSURFers and presenting my poster. Lastly, I learned more about scientific integrity and research misconduct to make sure that I was doing everything in the right way.

Overall, I had a great time with all the enjoyable and informing seminars, daily lab work, and sharing my experiences with my peers. I thank the Trinity College for funding, Dr. Ron Grunwald and Jason for planning this great program, Dr. Chay Kuo and Dr. Khadar Abdi for their mentorship with my research, the faculty members who all gave great talks and my peers for the great time we spent together. I wish you all a great summer and hope we keep in touch in the future.

A Great Talk by Dr. Robert Lefkowitz

Throughout the BSURF, many distinguished faculty members from a variety of biological fields talked about their career paths as scientists and what kind of research they did. These talks helped me grasp the different aspects of different areas and what type of opportunities or problems I would encounter if I decided to become a scientist. Although each seminar was interesting in its own way, I think Dr. Robert Lefkowitz’s talk was quite fascinating.

Dr. Lefkowitz is a cardiologist and Professor of Medicine at Duke University. He won the Nobel Prize in Chemistry in 2012 for his groundbreaking discoveries about G protein-coupled receptors. He decided to become a physician when he was 8. He went to the Bronx High School of Science in New York City, a high school that has 8 Nobel Laureate alumni. He emphasized that only 11 countries in the world have more than 8 Nobel Laureates. After high school, he went to Columbia University where he majored in Chemistry and then got his medical degree. He told us that he loved doing clinical work but he wasn’t interested in doing research at all. During the Vietnam War, he was drafted by National Institute of Health (NIH) and did research for 2 years mandatorily. After that experience, he realized that he really liked working in a lab and delved into research more and more as the years went by. Now, he said to us that he hasn’t seen a patient in 15 years. When asked whether he regretted his medical training and sees it as a waste of time, Dr. Lefkowitz stated that the medical training helped him correlate his basic scientific research to applicable drugs that could treat diseases.

Dr. Lefkowitz told us that we could never foresee the future even though we plan it and go in a direction we decided. If it weren’t for the Vietnam War, he would have become a physician, not a scientist. He also said that most of the experiments, researches in science fail and the important thing is not the give up. As Churchill said, he quoted, “Success is the ability to move from one failure to another without loss of enthusiasm.”. He added that for an average scientist, one percent of his/her experiments succeed; for a world class scientist, that ratio could be as high as two percent!

I was inspired by Dr. Lefkowitz’s great story. I hope that one day, I could also have such an amazing story to share with young scientists.


Unexpected Outcomes

When I first saw my research project for the summer and what I would need to do to accomplish it, I thought my tasks were pretty straightforward and I would be done in two weeks with clear results. Well, turns out I was somewhat naïve and uninformed about this whole doing science because that didn’t turn out to be the case at all. I was unaware of unexpected outcomes. We finished the sixth week now and I just hope that I’ll be able to get my results by the poster presentation session which is in two weeks.

My project involves mutation of a particular gene using PCR and running Western Blots on human cells after transfecting them with these mutated genes as I mentioned multiple times in my previous blogs. I need to go through this process multiple times for different regions targeted for mutations and compare the results. So far, I have been able to get my mutant genes but it took 5 weeks for me to do it which would normally take one if everything went smoothly. Of course, nothing went smoothly. I encountered problems and made mistakes at every step of the way. Sometimes, PCR didn’t work, sometimes transformation and sometimes the transformed plasmids didn’t have the desired plasmids. I had to optimize the method by adjusting the temperature, tweaking protocols and adding some different chemicals to make the experiments work. Eventually, I was able to get the mutations I wanted, and the feeling of overcoming problems and reaching my goal was quite pleasing.

Now that I finally have my mutations, I will proceed to the next steps which should take about four days –again— if everything goes smoothly. I hope that I can troubleshoot my way into the results before two weeks. Although the problems I had to cope with and the mistakes I made were occasionally frustrating, they taught me one valuable lesson about research as Thomas Edison said: “Our greatest weakness lies in giving up. The most certain way to succeed is always to try just one more time.”

May I Present to You, The One and Only Ricardo Matias!

This week, I had the opportunity to learn more about the research projects of my fellow BSURFers. Every one of them was very unique and interesting. I really enjoyed my peers’ presentations and thank them for such a great experience. Among all, I found Ricardo’s project about brain machine interface (BMI) to be the most intriguing, so I will be reflecting about it in more detail.

A brain-machine interface is a direct communication pathway between an enhanced or wired brain and an external device. Ricardo’s lab is seeing this interface as a possibility to restore mobility in the limbs of people who have paraplegia.  He particularly analyzes the lag times between neural firing rates and velocity in monkeys. He uses the data from the previous experiments where monkeys are given a joystick that controls a cursor on a screen and asked to move it to a specific target. He compares the lag times of bimanual tasks (monkeys use two joysticks to move two different cursors to two different targets) to those of unimanual tasks (monkeys use one joystick to move one cursor to one target) performed by monkeys and uses MATLAB to produce graphs that could help him understand the relationship between these two different type of tasks.

I think, in the future, the brain-machine interface could be a solution to people with different type of disabilities. Ricardo did a great job by presenting his very interesting project. I will be excitedly waiting to hear more about the developments in this project from Ricardo.


A week in The Kuo Lab

I don’t have a typical day but I do have a typical week in Kuo Lab. I conduct a thorough mutagenesis experiment where I complete multiple different steps and ultimately mutate the desired sites of the gene.

I start with preparing agar plates (plates that have the necessary conditions for bacteria to breed) and store them in the cold room (4 °C) for later use. Then I prepare my PCR samples by aliquoting the necessary reagents and template DNA plasmid. I add primers – specifically designed to mutate the desired codons of the amino acids – and run the PCR samples in a thermocycler where they get amplified. After that, I run a gel electrophoresis to check whether the reaction actually worked. Having confirmed that PCRs worked just fine, I use kinase, ligase and Dpn1 enzymes to convert the linear DNA product to circular (because bacteria would chop up the newly transformed DNA if it were linear) and get rid of the original non-mutated  templates. Now our products are ready for transformation. I start transforming the mutated DNA plasmid into bacteria to further increase the number of the plasmids. I thaw the frozen bacteria and aliquot the PCR products into the bacteria tubes. I incubate the bacteria in ice for 30 minutes and then do a heat shock by placing the tubes into the heat block at 42 °C for 30 seconds. This helps transformation since the pores in bacteria enlarge and take up the plasmid DNA more easily. After this step, I place the bacteria to agar plates and do an overnight culture to grow bacteria colonies.

Next day, I look at my plates first thing in the morning. If some of the plates don’t have any colonies, I start over for them and redo the previous steps (I know, kind of frustrating). For the ones that worked, I pick three colonies from each plate and prepare them for plasmid DNA purification by doing an overnight liquid culture. The next day I do a miniprep to purify the mutated plasmid DNA. I add buffers and centrifuge the cells multiple times in order to digest them and precipitate the unwanted biomolecules (fats, carbohydrates, proteins, RNA and bacterial DNA). After that I use a spectrophotometer to measure the concentration of the DNA. To make sure that my plasmid DNAs have the mutated gene insert, I use restriction enzymes and run another gel electrophoresis. After confirming, I send my samples for sequencing and get the results the next day.

Of course, none of this process goes smoothly. When I started my project the first week, I thought I would be done with this part of the project (generating mutated plasmid DNA) in two weeks. I can now see how naive I was. During these steps, we had to readjust the temperatures for thermocyclers multiple times to get a better yield from PCR and ensure transformation. We had to add new chemicals to PCRs because some of our primers had rich G-C nucleotide contents which made them bind to the other strand very strongly and disrupted the PCR. Sometimes everything seemed to work and we sent the plasmids for sequencing, only to find out that the original template DNA was transformed not the mutated ones. So, we had to restart everything and wait for Dpn1 enzyme to operate much longer to thoroughly get rid of the original template DNA. I will start my fifth week tomorrow and I still need two more mutations to proceed to the final part of my project. Although there were times I got really frustrated about my experiments, these experiences have taught me that troubleshooting is very important in scientific process and we have to be very resilient to reach success. I am pretty sure that my Western Blots won’t go as planned either and I’ll have to perform a lot of them. But I believe I will be able to overcome the hardships I encounter by trying new adjustments and not giving up until I succeed.

Differentiation of Ependymal Cells

Hello everyone! This week I wrote about the overall research project in Kuo Lab and describe my particular role in it. I hope you enjoy it!

Ependymal cells located in the walls of brain ventricles play an important role in neurogenesis (the growth and development of nervous tissue) and maintenance of brain homeostasis through regulation of cerebrospinal fluid. They are derived from radial glial cells which also give rise to the neural stem cells responsible for adult neurogenesis.  The neural stem cells located in the subventricular zone of the brain are surrounded by ependymal cells and need these cells to differentiate into new neurons, astrocytes and other type of neural cells. Although some studies have claimed to show that ependymal cells may also give rise to new neurons under certain conditions such as concussions or brain injuries, this subject is fairly controversial and need to be studied further to provide a clear answer. Recently, my lab discovered a gene that is critical for maintaining ependymal cell stability. I am conducting mutagenesis experiments to identify functional residues of this protein to make it non-degradable and further investigate the role of it in ependymal cells.

Hopefully, I will be able to find some answer to my questions by the end of the summer and continue to develop this project in the foreseeable future.

The Adventurous Journey of a Great Scientist: Dr. Chay Kuo

This week, I had the opportunity to interview my Principal Investigator, Dr. Chay Kuo. He went through a very unique path which eventually led him to become a successful medical scientist in the Department of Cell Biology at Duke University. The more I learned about Dr. Kuo’s academic career and his passion for science, the more I was fascinated by his marvelous journey.

Dr. Kuo was born in Taiwan and moved to California at the age of 10. During high school, everyone thought he was going to be a mathematician because he was great at Math and studied for Math Olympiads. After high school, he went to MIT where he majored in Architecture (Yes you didn’t read it wrong, Architecture). MIT had a very liberal grading policy for first-year students where classes were graded either Pass or No Credit. This means that if a student fails a class, it wouldn’t even show up on his/her transcript. Because of this lenient grading policy, Dr. Kuo took the most hardcore and interesting science classes during his first year. He stated that his first year in MIT is why he became a scientist because he didn’t worry about his grades, instead, he devoted his time to learn about subjects he was curious about. He said “In life, what you learn in school can only take you so far. Everything else after that, is what you do with that knowledge. In school exams, I could answer any questions if I had access to the textbooks. Right now I can look up any information I want, but I still don’t know the answers to many of my questions. So, you should worry more about learning than your grades in order to become a true scientist.” He took architecture classes for the same reason and decided to become an architect major afterwards.

After graduating from MIT at 1993, Dr. Kuo worked as a lab technician for several months in the Department of Cardiology at Harvard. Then, he went to the School of Medicine at the University of Chicago and completed his MD-PhD there. He actually wanted to go to an architecture graduate school. But his father told him that he would cover his cost of attendance only if he went to a medical school. Dr. Kuo realized that he hated medical school but he liked to do research as he explained: “There are two different ways to solve problems. One is the medical type of time-dependent probability problems where you have a time constraint and you need to figure out three most probable diagnoses with 90% confidence. This requires a broad but shallow knowledge in a wide range of areas.  Every test in medical school is based on this understanding. The other type of problems is scientific type of time-independent problems where you need to discover the least probable answers. If you try the most obvious solutions, you are going to be wrong. Because someone else tried that path and failed. You need to find a novel way; you need to look at the 10% nobody has researched before. I sucked at the first type of questions but I was really good at the second type. So I did a PhD in Dr. Jeffrey Leiden’s lab and enjoyed every second of it. Then I chose being a medical scientist over being a physician.” He finished his MD-PhD in 2002 and started his post-doctoral fellowship at University of California, San Francisco.

Having completed his post-doctoral fellowship, Dr. Kuo continued his research projects in Duke where he focused on neurogenesis and neural stem cells. When I asked about his goals as a scientist, he told: “I have a two dimensional diagram of where I want to be as a scientist. The x-axis has ‘significant’ on one end and ‘obscure’ on the other. The y-axis has ‘the red ocean’ and ‘the blue ocean’ on its ends. The red ocean is where all the boats, i.e. scientists, are. The blue ocean is where there are no boats. If you want to find funds easily, you should be at the significant end of the red ocean. Because that’s where everybody works and it’s more likely to discover something significant in an area if a lot of people are contributing collectively. However, breakthroughs do not occur in red oceans. They occur in the significant end of the blue ocean. They need to be not only significant but also something totally novel. I like to be in the blue ocean, I’m an adventurous scientist. I want to take an area that’s in the blue ocean where no one works on, and turn it into a red ocean area by making great discoveries and drawing attention of other people. When asked about where the new breakthrough will occur in medicine, David Baltimore, a Nobel Laurate, answers ’If I knew, it would not be a breakthrough.’ Personally, I found his metaphor very interesting and I plan to use his diagram throughout my career.

Lastly, I asked Dr. Kuo whether he had any advice for undergraduate students who want to become medical scientists. He replied: “You need to figure out what type of problems you are good at solving and whether you actually want to do research. To know that, you need to expose yourself to basic science labs and see your capabilities and feasibility of your goals. Also, don’t worry about your grades to an extent that will prevent you from pursuing your true academic interest. In the long term, you will see the benefits.”

Overall. This interview had profound effects on how I view science and research. I quite enjoyed Dr. Kuo’s inspiring story and great advice for students like us who want to have an academic career in medical field. I hope I could be as adventurous as he is when I conduct my own research projects.

Baby Steps of an Inexperienced Researcher

When I started my first week at BSURF, I felt very excited and eager to finally take part in a research project where I could explore and learn the different aspects of doing science. My only experience with biological research has been the lab component of Bio201 class, so I was a little nervous and worried about whether I could pull this off. First week in Kuo lab, I learned a lot more than I expected. I started with attending the lab meeting where lab members were presenting their data and analyzing it with Dr. Chay Kuo, my principal investigator. I would like to share something Dr. Kuo said during the meeting (as far as I remember) and I really liked: “Don’t be frustrated when you get a result you didn’t anticipate. Be excited, because you will learn new things with your unexpected results, not the expected ones.” I think this accurately demonstrates the paths scientists go through when they make breakthroughs and I set this as my first guideline when doing research.

In this summer, I will be conducting a mutagenesis project where I will try to determine which site of a protein is accountable for degradation of that protein in ependymal cells of the brain. I will mutate the protein multiple times and hopefully find the right site by the end of the program. During the first week, Khadar, my supervisor, taught me how to prepare agar plates, do bacterial transformation and some other basic lab techniques which will be very important when I start my mutagenesis project next week.

Besides those techniques, essentially I did a lot of reading regarding the literature related to our research and at first it seemed somewhat boring. But then I realized how important it is to understand what really is going on. In order to understand my role in the project and contribute to it, to find solutions to the problems we encounter, I should have a very good grasp of the experiments conducted, the techniques used , why, where and when they are used and which results could they provide to answer our questions. Sure, learning to follow protocols, pipetting, doing PCRs flawlessly are all very important since they will lead to correct results, but I think I can learn doing those things over time, as I do them repetitively and learn from my mistakes each time I make one. What I really want to learn this summer, besides perfecting my basic lab skills, is to think like a scientist. In the long term, I want to be able to ask the right questions and make the right decisions to control the direction of the research. So far, I found everything I looked for and I hope to continue in Kuo lab  not for just 2 months but for years.

On a side note, I  took some Turkish Delights to the lab and especially Dr. Kuo loved it. So, as long as I keep offering him more Turkish delights, I think I’ll have a secure spot in this lab.