Visitor of the Week: Mahlon Collins

Meet Mahlon Collins of the University of Minnesota. Mahlon is a member of Dr. Frank Albert’s laboratory in the Department of Genetics, Cell Biology, and Development. In 2018, Mahlon made his maiden voyage to CSHL to present a poster during The Biology of Genomes meeting. He returned this spring for the Ubiquitins, Autophagy, & Disease meeting, and again this month for the Computational Genomics course. This is his first course at CSHL and he wishes he “had taken one sooner!” However, we have a feeling we’ll once again be welcoming Mahlon at one of our future Biology of Genomes or Ubiquitins, Autophagy & Disease meetings!

What are your research interests? What are you working on?
I study how genetic variation affects cellular physiology. My current work focuses on how individual genetic differences influence protein degradation, an essential biological process implicated in a variety of diseases, including neurodegenerative diseases, cancers, and immune disorders.

How did you decide to make this the focus of your research?
I enrolled in the neuroscience program at the University of Pittsburgh for my graduate training. My thesis focused on molecular mechanisms of the neurodegenerative disease amyotrophic lateral sclerosis (ALS). While completing my PhD, I was surprised to learn how little we know about the genetic basis of this and related diseases. Near the end of my PhD, a series of papers were published that creatively used the yeast Saccharomyces cerevisiae to provide new insights into the genetics of ALS. I read more papers about the power of yeast genetics and decided to become a yeast geneticist myself for my postdoctoral training. I joined the Frank Albert laboratory in late 2016 and have been busy since that time developing new tools and methods to map genetic influences on protein degradation.

How did your scientific journey begin?
Like many scientists, as a child, I enjoyed figuring out how things work by taking them apart and putting them back together. Unlike many scientists, however, I grew up in a town of less than 500 people in Michigan's Upper Peninsula. Coming from a small town, I was unsure of what career paths were available or of interest to me as a freshman undergraduate student. Fortunately for me, a faculty member, Dr. Deb Poole, saw my natural curiosity and encouraged me to try scientific research. I thoroughly enjoyed the process of research and enrolled in graduate school after completing my bachelor's degree. Since then, I've become interested in genomic and proteomic technologies and have worked with these in both my graduate and postdoctoral research.

Was there something specific about the Computational Genomics course that drew you to apply?
My research identifies regions of the genome that influence protein degradation. These regions are often large and contain many genes. A major challenge is predicting and identifying which genes in these regions are truly influencing a phenotype of interest. I wanted to develop a computational approach to predict candidate causal genes in these regions. To do so, I used methods we learned in the course for variant detection, annotation, and functional interpretation.

What and/or how will you apply what you’ve learned from the course to your work?
I developed several approaches for identifying, annotating, and analyzing genetic sequence variant data while at CSHL. One of the best aspects of the course is that these workflows are saved and I can access them when I return to my home institution. Because many of my labmates perform similar experiments, I'm looking forward to sharing my methods and results with them and working together to make them even better. The course also gave us access to great resources for further training in computational genomics methods and I'm looking forward to building on what I've already learned in the future.

What is your key takeaway from the Course?
They weren't kidding when they said 12-15 hour days!

More seriously, a key concept from the course is the central role of probability distributions in making statistical inferences in genomics. It's neat to see how the same mathematical frameworks can be used to solve problems across multiple domains of genomics, from detecting sequence homology to identifying differentially expressed genes.

If someone curious in attending this course asked you for feedback or advice on it, what would you tell him/her?
First, if you're thinking about taking the course, do it. It's both excellent training in the foundations of computational methods used in genomics and a survey of the latest developments in the field. The faculty are incredibly generous with their time and expertise and you can even bring and analyze your own data.

Second, "Computational Genomics", is more than a course, it's an experience. Beyond the lectures and laboratory exercises, you'll spend a week with a group of talented graduate students and postdocs learning, working together, and getting to know each other. On top of that, you'll get to do so in a beautiful place filled with history. It's a completely unique, incredibly memorable experience and I can't speak highly enough of it.

Lastly, one pro tip: You'll be sitting a lot, so take time to exercise in the morning. There are lots of great places to run in the area and the gym in Dolan Hall is nicely equipped and not crowded if you can make it there before 7:30 a.m.

What do you like most about your time at CSHL?
Life at CSHL is like attending summer camp and my favorite aspect is the sense of community and camaraderie. This starts with living together in cabins and builds through the unique experiences you have while at CSHL. I have fond memories of long, early-morning runs led by Randy Hampton at the Ubiquitins, Autophagy, and Disease meeting from earlier this year and, now, of James Taylor introducing our group to Little Vincent's 'Long Island cold cheese pizza' while we worked late into the night on our course projects. That you can have these experiences while interacting with leaders in your field and hearing about great science is truly remarkable and unlike any other meeting or course I've attended.

Thank you to Mahlon for being this week's featured visitor. To meet other featured scientists - and discover the wide range of science that takes part in a CSHL meeting or course - go here.

Visitor of the Week: Burcu Alptekin

Meet Burcu Alptekin of Montana State University. The Ph.D. Candidate has her eyes on a Spring 2020 graduation date. Burcu is a member in Dr. Andreas Fischer lab which focuses on studying the cereal senescence processes, and is currently with us for her first meeting at CSHL: Plant Genomes, Systems Biology and Engineering. She may have set foot on our North Shore campus with little knowledge of it but she quickly picked up on the “friendly and cozy environment” our meetings embody and exude.

What are your research interests? What are you working on?
I am generally interested in plant molecular biology from a basic science point of view. Currently, I am working with malt barley to improve the quality of barley seeds for malt production with molecular genetics.

How did you decide to make it the focus of your research?
I was always interested in molecular biology. It is fascinating to me that there are these tiny molecules in every cell determining the way of life. After my undergraduate education in molecular biology, I decided to focus on genetics and got into the plant genetics field by working with wheat and barley.

How did your scientific journey begin?
I always wanted to be a scientist. Starting from my first introduction to biology via science classes at the primary school, I was already fascinated with cell, genes in general, and everything related to molecular biology. I decided to study molecular biology when I was like 14 and have been working on that goal since that day. I got my undergraduate degree in Molecular Biology and Genetics from Istanbul Technical University (Turkey) where I got opportunity to be exposed to many different research fields. During my undergraduate, I had several internships in cancer biology and neuroscience but during a molecular physiology lecture, when we had to dissect the sciatic nerve from a frog, realized that human genetics was very much not for me because I was afraid to perform experiments on animals. Meanwhile, I discovered that plant genetics is much more complex than humans, because you have a bunch of polyploid organisms with multiple genomes. I was fascinated by this and decided to work in plant molecular biology and genetics.

Was there something specific about the Plant Genomes, Systems Biology and Engineering meeting that drew you to attend?
CSHL is known for its good courses and seminars, and its great science. I decided to attend this meeting because there were a lot of experts in the field attending and as a Ph.D. candidate, I thought it would be great to learn from experts in the field as well as my peers in a historic place of biology. Also, I am particularly interested in plant synthetic and systems biology, this was one of the limited meetings in the field where you can get exposed to these subjects.

What is your key takeaway from the Meeting?
With all of the technological advances, it is great to be a plant molecular biologist in today’s world. We can advance agriculture and our society in such a way where everyone will able to access food and I believe we will able to achieve this in a sustainable way thanks to the developing new technologies. This meeting also reminded me that this is one of the most exciting times in history to be a biologist.

What and/or how will you apply what you’ve learned from this meeting to your work?
I learned a lot of new things and techniques. I realized how epigenetics is becoming more and more accessible in plants and how it can advance our knowledge of plant biology. I also made some great contacts that I plan to maintain as I continue into my postdoctoral studies.

If someone curious in attending this meeting asked you for feedback or advice on it, what would you tell him/her?
I would highly recommend coming to this meeting. They will find a chance to learn cutting edge science from experts in the field. Plus compared to some big conferences, it is a smaller sized meeting  where you get a lot more chances to network with others.

What do you like most about your time at CSHL?
I really like the environment in CSHL, all the trees around and historical buildings. I also really like the biological sculptures around such as the polypeptide sculpture. It is a dream place for a biologist.

Thank you to Burcu for being this week's featured visitor. To meet other featured scientists - and discover the wide range of science that takes part in a CSHL meeting or course - go here.

Visitor of the Week: Emma Spikol

Meet Emma Spikol of Johns Hopkins University School of Medicine. The graduate student in the Neuroscience Training Program is doing her thesis work in the lab of Dr. Marnie Halpern at the Carnegie Institution Department of Embryology, and serves as the co-president of Project Bridge a student-run outreach organization at Johns Hopkins Medicine. Emma travelled north to Long Island to take part in her first meeting at CSHL, Zebrafish Neural Circuit and Behavior where she presented a talk on “Identifying targets of the asymmetric dHb-IPN neural pathway” that was met with “interesting questions that got [her] thinking about future experiments.”   

What are your research interests? What are you working on?
The Halpern lab uses the zebrafish model to study a region of the brain which exhibits prominent left-right differences both neuroanatomically, and in neural responses to negative stimuli. I’m working on understanding how these responses might be propagated through connected neural pathways to influence fear behaviors.

How did you decide to make this to focus of your research?
I became fascinated by neuroscience and the zebrafish model while studying regulation of neurohormone gene expression for my undergraduate research project in the lab of Dr. Eric Glasgow at Georgetown University. Zebrafish are exceptional breeders, making them highly amenable to genetic manipulations. Their embryos are also transparent, which provides easy access to manipulate and observe the nervous system in live animals. I was inspired to use zebrafish to study conserved vertebrate neural pathways, while taking advantage of the genetic tractability of this model to manipulate specific neuronal subpopulations.

How did your scientific journey begin?
After becoming fascinated by genetics during my high school biology class, I worked in a Drosophila lab led by Dr. Julie Williams at the University of Pennsylvania. While maintaining the fly stocks and learning other laboratory tasks, I joined in conversations with students and postdocs and attended seminars—I was excited to realize that a career in science would involve both imagination and lively discourse. The lab focused on the genetic underpinnings that regulate immunity and sleep, which got me interested in the relationship between genes, neural circuits, and behavior.

Was there something specific about the Zebrafish Neural Circuit and Behavior meeting that drew you to attend?
I was drawn to this meeting because of its specialized nature—I was excited to engage in conversations with other researchers in the growing field of neural circuits and behavior. Also, as a graduate student, the chance to present my work was important—a great opportunity to get feedback and improve my communication skills. 

What is your key takeaway from the Meeting?
Sophisticated genetic tools and imaging technologies are being applied in creative ways to understand how neural circuits influence many different behavioral outputs in zebrafish.

What and/or how will you apply what you’ve learned from this meeting to your work?
I think there were a lot of interesting presentations about circuits that control motor behavior. I’ve been thinking about how the neurons I’m studying might influence these circuits, which could lead to some interesting research questions in the future.  

If someone curious in attending this meeting asked you for feedback or advice on it, what would you tell him/her?
I would say it’s a great opportunity to meet and talk to others in your field. The small size of this meeting allows you to take advantage of the opportunity to sit with others outside of your own lab at meals and other events.

I knew this would be a great opportunity to hear about the latest work in my field and get critical feedback on my own project, but I wasn’t expecting to meet so many new colleagues. It has been really fun to meet other researchers and discover that we already have mutual friends or are connected in some way!

What do you like most about your time at CSHL?
Sitting outside and taking in the gorgeous views and natural setting!

Thank you to Emma for being this week's featured visitor. To meet other featured scientists - and discover the wide range of science that takes part in a CSHL meeting or course - go here.

Visitor of the Week: Rio Sugimura

Meet Rio Sugimura of the Center for iPS Cell Research and Application (CiRA) in Kyoto University (Japan). After a six year hiatus, the Japanese national returns to CSHL for his first-ever course: the Scientific Writing Retreat. Rio is a research scientist at CiRA (which he describes to be similar to a senior postdoc running a team) was first here for the 2013 meeting in Stem Cell Biology and has plans to return for its 2021 iteration.  

What are your research interests? What are you working on?
I am interested in stem cells and bioengineering, and am working to understand the fundamental mechanism of human blood development.

How did you know you wanted to study this/make it the focus of your research?
My MD background drove me towards a medicine-relevant field. I chose hematopoiesis as a model to understand stem cells and regeneration for my PhD study and my research has since been around hematology and stem cell biology. At CiRA, a world-renowned institute for induced Pluripotent Stem Cells (iPSC) study, I acquired the latest on iPSC technology which has helped with establishing my research program over the past year. With great collaborators, I employ bioengineering approaches to better understand the fundamental mechanisms of human developmental hematopoiesis.

How did your scientific journey begin?
I was a medical student who was always interested in the power of science. When current medical practices could not save my parents from cancer, I decided to pursue research to push out the limits of medicine.

Was there something specific about the Scientific Writing Retreat that drew you to apply?
I found this workshop via Twitter. I aim to share what I learn at the course with my students in Japan where traditionally, and when compared to the US, the importance of science writing is not emphasized enough.

What and/or how will you apply what you’ve picked up from the Workshop to your work?
Science writing is an algorithm. For example, an abstract conveys the clear structure with background, hypothesis, methods, results and conclusion/significance.

What is your key takeaway from the Workshop?
In the beginning of the workshop, we went through 10 tips for a stronger written piece. My favorite tip is “Know your writing kryptonite.” My kryptonite is the tendency to write run-on sentences. Being now aware of this, I can properly adjust how I revise my written work.

If someone curious in attending this workshop asked you for feedback or advice on it, what would you tell him/her?
You cannot miss such a wonderful opportunity to learn with and get to know great attendees and lecturers.

What do you like most about your time at CSHL?
Food and accommodation. Also interacting with rising scientists at a career stage similar to mine.

Rio received a scholarship from the National Institute of General Medical Sciences (NIGMS) to cover a portion of his course tuition. On behalf of Rio, thank you to NIGMS for supporting and enabling our young scientists to attend a CSHL course where they expand their skills, knowledge, and network.

Thank you to Rio for being this week's featured visitor. To meet other featured scientists - and discover the wide range of science that takes part in a CSHL meeting or course - go here.

Visitor of the Week: Deeptiman "Deep" Chatterjee

Meet Deeptiman “Deep” Chatterjee of Tulane University School of Medicine. Deep is a fifth-year Ph.D. candidate in Dr. Wu-Min Deng’s lab taking part in Single Cell Analyses. This is his first meeting at CSHL and he came into it with a bang: Deep presented a flash talk introducing his poster entitled “Constructing a Comprehensive Transcriptomic Atlas of Developing Adult Drosophila Ovary and Oogenesis”. His approach from a biological perspective without much computational made his poster different than that of the other presenters. But as they “all are working towards the same goal, [Deep was still able to have] a great experience to learn from others and get fresh feedback and good comments!”

What are your research interests? What are you working on?
My research interests lie in bridging developmental biology with that of tumor biology. I generally use classical genetics, confocal microscopy and single cell sequencing techniques in the fruit fly model system to address specific questions. In my current research, I’m trying to understand what makes specific groups of cells to consistently be more susceptible to tumor formation than their neighbors in the ovarian epithelial tissue.

How did you decide to make this the focus of your research?
My mother was a cancer survivor, and she died from cancer-related complications 11 years later. Experiencing this debilitating disease from such proximity made me appreciate this disease and I wanted to study its fundamentals at its earliest stages. Fruit flies have been extensively used to study some of these basic steps, and so when I got the opportunity to work in Dr. Wu-Min Deng’s lab, I knew I had to take it.

How did your scientific journey begin?
We had a retired biology teacher in middle school back in India, who would still teach us because he simply loved teaching. He told us to break down every complex concept into its simplest parts. I still use that logic. I also was inspired by my biology teacher in high school, who singlehandedly had set up a simple biotechnology lab for only 6 students, teaching us to standardize some of the most common protocols used in biological labs. That hands-on experience set me up for an early career in science. I went on to do an MS in yeast genetics, and I switched fields for my Ph.D.

Was there something specific about the Single Cell Analyses meeting that drew you to attend?
The methodologies used in our lab have always been wet-lab benchwork. But we have never shied away pursuing new approaches. We have recently been involved in a lot of single cell transcriptomic data generation to answer relevant questions raised in many projects in the lab. I have learnt to process and analyze these datasets in the last year by myself but was limited by my limited knowledge of the field. This being my first single cell analysis meeting of any kind, I wanted to gauge the current state of the field, to learn from it and to apply my biologically-relevant perspective to it. The opportunity to present my work as a poster allowed me better participation in a field that I’m not so familiar with.

What is your key takeaway from the Meeting?
Single cell analysis is a rapidly evolving field, and to come to meetings such as these, even for participants out of this field, is a massive learning opportunity. It also makes one appreciate the importance of interdisciplinary sciences, connecting distant fields.

What and/or how will you apply what you’ve picked up from the Meeting to your work?
I particularly liked the entire session on spatial transcriptomics, which seems most relevant to my field of research and is also really cool! I also really enjoyed the talks on RNA velocity and vector fields and would love to integrate them into my research if it applies.

If someone curious in attending this meeting asked you for feedback or advice on it, what would you tell him/her?
Definitely attend! Even if it seems irrelevant to your field, it showcases really cool science and due to the structural and functional nature of the applications of single cell techniques, it can always be applied somewhere. It’s also a great learning opportunity from some of the pioneers in the field!

Also, definitely go to the bar at the end of the day. Some of the best scientific discussions transpired there.

What do you like most about your time at CSHL?
CSHL definitely loves to feed you. Thanks for having me!

Thank you to Deep for being this week's featured visitor. To meet other featured scientists - and discover the wide range of science that takes part in a CSHL meeting or course - go here.