Author Archives: Ruth Melka

Reflections

It is hard to believe that this program is already coming to a close. If you look back at my first blog post, you’ll see my main hopes and expectations for this program were to expand my knowledge of neuroscience, integrate myself into a community of scientists, gain communication skills, and learn what a career in research entails. I would say that all of these hopes have been fulfilled. I have learned so much science in the past eight weeks. Whether I was preparing for my chalk talk, putting together a presentation for my lab, or making my poster, I felt like I was constantly learning. Not to mention, I learned from my peers’ research as well as the faculty talks. As far as communication skills, this lab has definitely taught me how to work in a team. Being part of a pipeline for DNA isolation with four other people required that we all communicate and coordinate our schedules so the procedures would flow smoothly. My experience outside of the lab, from conversations with my P.I. to lab meetings to faculty talks, has given me a more general view of what research is like.

One thing I’ve noticed is the variable nature of research. Science does not always go as planned – research means adjusting to failures and moving forward. Science isn’t always clear-cut, and neither is the path to a career in research. Every faculty member who came to speak to us took their own unique path to their research, often involving some element of serendipity. I was bewildered by how much chance seemed to be involved in their careers. However, it is also evident that passion and hard work always preceded these fortuitous moments. In the words of Dr. Lefkowitz, “You make your own luck.” (And in the words of Edna Mode, “Luck favors the prepared, darling.”)

With that lesson in mind, as I move forward, I will be earnest in pursuing my interests, asking questions at every turn, and immersing myself in research that I am passionate about. Considering how different research experiences can be, I hardly think eight weeks in one lab is enough to say whether I see research as a career, but I do know that I am a scientist at heart. I love to ask questions, investigate problems, and discover information. I may not know the specific research topic that I will end up pursuing, but in general, I want to investigate problems involving memory/dementia. I hope to contribute to society by making an impact in this field, whether it is through research or clinical practice, or some combination of both.

I’d like to extend my thanks to Paul, KP, and Ron for working so hard to make this program possible. Thank you to the faculty for taking the time to come share their valuable insight with us. I am also grateful to my secondary mentor, Carole Parent, and PI, Dr. Jarvis, for all their guidance and support throughout this program.

 

Dr. Willard’s Words of Wisdom

I feel privileged to have the opportunity to learn from so many esteemed scientists, not only about their current research, but also about their personal development as a scientist. Moreover, we have the opportunity to hear them speak to us in such an intimate environment, with a crowd of just 24 people. They say experience is the best teacher; faculty talks are my chance to learn from these researchers’ experiences.

One talk that stood out to me was that of Dr. Willard’s. Although I certainly valued the factual knowledge and insight I gained about X chromosome inactivation, what I enjoyed most about this seminar, and all the seminars in general, was the level of enthusiasm and passion he had for his work. I often wonder how exactly people get interested in their research, and how much of it is based on their own investigation vs. fortunate encounters that pushed them in certain directions. It seems that for Dr. Willard, it was a combination of the two. His interest in X chromosome activation was fostered through engagement in the classroom as well as a serendipitous encounter with an article at the library. Although I have defined my interests in learning and memory, I am curious to find out what article, book, or seminar may trigger a similar push in my development as a scientist.

Interview with my PI

I recently had the pleasure of sitting down with my P.I., Dr. Erich Jarvis, for an interview that gave me several valuable insights into his personal journey as a scientist as well as the life of a researcher in general. Before becoming a scientist, Dr. Jarvis was planning on becoming a dancer. What made him decide to study science was his mother’s advice – “she told me to do something that has a positive impact on society”, he recalls. When he decided on being a scientist, he was attending Hunter College majoring in both Biology and Mathematics. Faced with the choice of going to medical school or graduate school, he stated that he “was more excited by making discoveries than using discoveries that others made to help cure people”. At this point, he knew he wanted to study either the origins of universe or how brain works. He chose the brain because it felt closer to earth and of his background in dance. In graduate school, he narrowed his interests to learning and memory, particularly vocal learning in songbirds. This topic intrigued him because it has a link to language, the ability to speak and communicate abstract ideas. Interestingly enough, Dr. Jarvis found that being an artist as a dancer was quite similar to being a scientist – “both require discipline, self drive, and creativity.” In fact, his lab recently made discoveries that brain pathways that control vocal learning maybe embedded within brain pathways that control dance. Evidently, having diversity of interest is useful because it helps develop transferable skills and knowledge.

One piece of advice he gave me regarding career development is that seeking out mentorship is essential. Dr. Jarvis still seeks mentorship from his undergraduate research advisor at Hunter College, Rivka Rudner, with whom he worked for four years. Under her guidance, he coauthored six papers from his undergraduate research and solidified his decision to become a scientist. Although he now realizes the importance of seeking mentorship, at the time, Dr. Jarvis did not purposely look for a mentor. Rather, he asked questions to learn from other’s successes as well as their mistakes. Even now, Dr. Jarvis seeks out mentorship from his department chairmen for opinions and advice. With this philosophy in mind, he also insisted the importance of using discretion when considering other’s input and making some decisions for yourself.

Another essential factor of being a scientist is learning how to deal with failure. Dr. Jarvis affirmed that failure is an inevitable part of research, whether it is an experiment that isn’t working, a grant being denied, or getting papers reviewed and declined. His advice regarding failure was to “have some thick skin, and be flexible.” He stressed that the right amount of optimism can overcome failure, and the point of failure is “to change your way of doing things to decreases the probability of failure in the future.”

As a final remark, Dr. Jarvis discussed the issue of what he calls a “social disease”, that leads to the underpresentation of minorities in the sciences. Dr. Jarvis suggested that the best remedy to help resolve the current problem is to lead by example to dispel any evidence that causes others to look down on each other because of gender or race.

Bird’s Eye View

I’ve always been a fan of jigsaw puzzles. There’s something compelling about dumping a huge pile of pieces on the floor, propping up the box lid, and making something coherent out of an assortment of incoherent pieces. Dealing with the details can be frustrating and time consuming, but one glance at the picture on the lid reminds me of how beautiful it will look when it is finished. What I’ve enjoyed about research so far is piecing together several details to make a finished product, whether it is a gel, a set of cut tissue samples, or an excel sheet of information. It was not easy capturing all the details of the procedures, and I’ve made my share of mistakes along the way. In the end, while attending to details can be cumbersome, it is all in the name of good science and a pioneering project. We have established quite the pipeline, and we are diligently working towards our goal of sequencing 10K bird genomes. In my daily experience, what makes each step worth it is the satisfaction of assembling the best product I can make at the end of the day, and eventually at the end of my time here.

“Bridging the Gap”

Finding connections between seemingly disparate concepts is the foundation for innovation; it helps to construct a more comprehensive network of knowledge. In the words of Cambridge neuroscientist Daniel Bor, “The process of combining more primitive pieces of information to create something more meaningful is a crucial aspect both of learning and of consciousness and is one of the defining features of human experience.” In order to fully understand any one concept, we must explore its niche in various other contexts. That is why it excites me to learn about research that connects fields such as neuroscience and music.

Similar to my lab’s investigation of vocal learning, the focus of Wilson’s lab is the neurological basis of music and motor learning, hence his title, “Bridging the Gap.” In his chalk talk, Wilson highlighted two concepts essential to his lab – chunking and anticipatory movement. I understand chunking as a level of learning where several individual impulses are practiced in series to the point where they “chunk” together, and the individual impulses are replaced with a group of impulses firing at once. Anticipatory movement is basically how much earlier the brain fires an impulse before the movement is performed.

Wilson’s project strives to understand how these concepts are involved in music learning. The study subjects are musicians with a range of experience levels from beginner to expert, and he uses an Xbox Kinect sensor to record the movement of subjects as they play piano. Several indicators are used to measure the level of mastery of a song, including the amount of pressure applied to the keys and how quickly the hands move to the next position in anticipation. This is a budding research project, so it is interesting to hear from Wilson about the difficulties of choosing the methodology of such an experiment. For example, any electrical connection to the brain may be impractical because the subjects are playing piano, so the Xbox Kinect sensor can help resolve this problem by tracking motor activity without disrupting the piano playing. 

Memory and music are two topics that have always fascinated me, as they constantly affect my daily life, and this project intrigued me on both fronts. I am eager to see what this lab finds regarding music/motor learning and how the brain can anticipate movements or chunk them into a fluid series of movements. 

 

The Research Life

Life in the lab is progressively falling into a more predictable pattern. Every week we have lab meetings where one person from the lab gives a presentation on a journal article, and we all eat and discuss the paper. These meetings are also opportunities to ask questions and learn more about the lab by hearing from people involved in other projects. As far as my daily experience, I have come a long way since the first week. During the training process, I shadowed a different experiment almost every day. I spent most of the time learning how to avoid cross-contamination of bird DNA samples and helping out with DNA isolation. Now, I have mostly been preparing, running, and analyzing gels. I have also been cutting bird tissue that is to be isolated for the next day. My day to day schedule varies depending on which procedure I’m doing. If I’m running a gel, I prepare the well plate the day before and spend the first part of my day loading the gel. While the gel runs, I make sure all the DNA samples are put away and have my lunch break. Later, I take the gel to the UV box to take the picture and send it to myself and my mentor. The last step is analyzing the gel to asses the state of each DNA sample and decide if it is intact enough to send to BGI. Analyzing the gel is probably my favorite thing to do, because I can take a step back and see the results of our work.

The procedure that I am second most familiar with (next to running gels) is DNA isolation. During DNA isolation, there are a lot of opportunities to make mistakes, from pipetting to mislabeling to cross-contamination. I’ve learned that mistakes happen, but the important thing is to identify them so that we can find a way to fix the problem. Other days, I take tissue samples from the freezer and cut a small piece to send to BGI and a larger piece for us to extract DNA. Cutting the samples requires a great deal of dexterity and hand-eye coordination, because the tissue samples are small and frozen. I can’t say that this is my strong suit, but I have gotten much better. So, overall I am absorbing new information every day and becoming more accustomed to the research life.

Understanding Bird Song

One of the things I love about working in my lab is being able to contribute to one of the many pieces of the puzzle that is the Jarvis lab. The scope of the lab includes everything from evolutionary genetics to electrophysiology to bioinformatics in an effort to understand the brain structures and mechanisms involved in vocal learning of song birds. The hypothesis is that vocal learners have a fundamental genetic difference that accounts for certain neural pathways that allow those species to imitate sounds. I am involved in the part of the lab that is working towards sequence the genomes of vocal learning and non-learning avian species, as well as many other species, in what is called the B10K Project – a project to sequence the genomes of all 10, 000 bird species. This is quite a tall order, but thanks to reduced costs and advancements in genomic technology, sequencing genomes has become much more feasible in recent years. Here is my mentor, Carole Parent, presenting at the Society for Neuroscience convention.

The B10K project is an international effort involving investigators at BGI (Beijing Genomics Institute, the world’s largest genomics institution), Copenhagen University, the Smithsonian, the Chinese Academy of Sciences, and Duke University. Several institutions send us tissue from which we isolate DNA, and we send the isolated DNA to BGI for sequencing. I’m excited by the collaborative nature of this project, not just within the Jarvis lab, but within labs at an international level. Apart from adding to the growing database of genomes and providing a resource for future scientists investigating genomic evolution, the B10K project plays a significant role in advancing genetics of understanding traits. Namely, sequencing bird genomes will help pinpoint the genetic discrepancies between vocal learners and vocal non-learners and allow us to better discern the specific neural mechanisms of vocal learning in songbirds. With this understanding, we could even manipulate the genes of vocal non-learners and make them into vocal learners or vice versa (essentially, we could make chickens sing). This is particularly interesting, because it could potentially lead to greater insight into the neuroscience of language and learned speech. As a last note, it is only fitting that I introduce Alex the parrot, the most famous example of the incredible capacity of some birds to engage in vocal learning.

Connecting the Dots

I remember leaving my high school science fair experience with a sense of fulfillment. The hardships only magnified the reward of finding the answers to my questions, and I am eager to continue gaining knowledge and solving problems through research. In the next two months, I hope to channel this passion into expanding my knowledge of neuroscience, integrating myself into a community of like-minded scientists, and discovering the intricacies of a career in research by observing and participating in a cutting-edge lab firsthand.

I feel privileged to have the opportunity to be a part of Dr. Erich Jarvis’ lab for the next couple of months. The objective of this lab is to understand the genetic differences that account for certain neural pathways that allow vocal learning in songbirds. As a neuroscience major and a musician, I am incredibly excited to see what this lab discovers. The collaboration between the constituent projects of this lab is absolutely fascinating, and I am constantly adding to my knowledge of neuroscience in the context of genetics and evolution in order to translate the jargon and truly grasp the underpinnings of this lab’s investigation. I trust that by the end of this program, absorbing new information through scientific literature will become less of a struggle, and that the skills and knowledge I attain will serve as building blocks for my own investigations.

Collaboration between different fields of knowledge naturally entails collaboration between the experts of these fields. I quickly learned during my first lab meeting that teamwork is not an option, but a requirement, and that science must be collaborative. Science would mean nothing without communication. If knowledge is found but not shared, what is it good for? I hope to learn not only how to absorb knowledge, but also how to communicate. I will have the pleasure of interacting with and getting to know the inspiring people I work with, including people from my own lab, other labs within the Jarvis project, neighboring labs, and my fellow fellows.

Just as I have already gotten to know the collaborative nature of research, I aspire to further develop my knowledge of the lifestyle of a researcher. My goal is to take in as much as I can, observe and ask questions, and ultimately obtain a better understanding of who I might become if I were to become a researcher and how I might integrate that vision with my hopes of making an impact in the advancement of treatment for neurodegenerative diseases. I may not connect all the dots, but I hope to at least collect and arrange them into a more intelligible pattern.