Visitor of the Week: Kelsey Scott

Meet Kelsey Scott of The Ohio State University! A member of Jason Slot’s lab within the Department of Plant Pathology, the PhD student is about halfway through her training at the annual course on Programming for Biology. This is her first course at CSHL and she “had no idea what to expect, besides prior attendees calling it “coding boot camp”.” The course, as usual, delivers and “has turned out to be a lovely opportunity to work closely and learn alongside a great group of people.” So much so that if Kelsey has the chance to return for another course, she “will definitely take it.” 

What are your research interests? What are you working on?
I’m interested in identifying the genomic attributes of fungi associated with particular lifestyles, focusing on secondary metabolite-related gene clusters. For example, what’s genetically different about soil-dwelling fungi compared to fungi that eat other fungi, or non-pathogenic fungi that live inside a plant?

How did you decide to make this the focus of your research?
This project is interesting to me because of the technology I use to generate my data, both the continually-developing sequencing technology as well as the software used to process the data. I love how there are constant technological improvements and we can achieve goals previously thought to be impossible. 

How did your scientific journey begin?
Ever since I was a kid I knew I wanted to become a scientist, but I always assumed that I would only ever work with plants. Dr. Cynthia Briggs, one of my favorite professors in undergrad, encouraged me to check out the field of plant pathology so I could work with both plants and my other love, fungi. Fast forward a few years and now I’m in a mycology lab in a plant pathology department, a perfect fit! 

Was there something specific about the Programming for Biology course that drew you to apply?
My research depends on using a long and involved pipeline to obtain genome annotations from raw genome sequence data; I wanted to learn how to automate this pipeline and other routine processes so I have more time to focus on my research questions. I was especially interested in the workshop seminars on genome sequencing wet lab methods and genome assembly software, so I could learn how to improve my own techniques.

What is your key takeaway from the Course?
My key takeaway from this course is that just about any data manipulation can be made faster and more efficient with a Python script.

What and/or how will you apply what you’ve picked up from the Course to your work?
I’ve tried to learn Python coding using online modules and classes, but nothing ever stuck until I attended this course. I’ve been at CSHL just over a week and I already feel so much more confident in my skills--I’m excited to write scripts that can process my large datasets automatically.

If someone curious in attending this course asked you for feedback or advice on it, what would you tell him/her?
I highly recommend this workshop for anyone that has little to no experience in Python coding and wants to apply these skills to biology-related research, especially if they need to handle large amounts of data. This workshop is a fast-paced and immersive experience, and the instructors and TAs work tirelessly to provide their students with a great learning opportunity.

What do you like most about your time at CSHL?
I love how close the beach is! Whenever I have the chance, I walk to the beach to take pictures and search for horseshoe crabs.

Kelsey received financial support from National Human Genome Research Institute (NHGRI) to cover a portion of her course tuition. On behalf of Kelsey, thank you to NHGRI for supporting and enabling our young scientists to participate in training courses where they expand their skills, knowledge, and network.

Thank you to Kelsey 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: Xavier Le Guezennec

Meet Xavier Le Guezennec of the Institute of Molecular and Cell Biology in Singapore, where he holds a dual role in the Regulation of Membrane Traffic Laboratory as a senior research fellow and core manager of the Institute’s siRNA screening facility. The French national just finished training at Antibody Engineering, Phage Display & Immune Repertoire Analysis, which also happens to be his first course at CSHL.

What are your research interests? What are you working on?
Our lab has observed fundamental mislocalisation of enzymes involved in early O-glycosylation pathway which leads to specific changes in cell surface proteins. We work currently on multiple strategies to target these cell surface proteins in liver cancer.

In addition, we study many fundamental cell membrane traffic regulators using siRNA genome wide screens with high content imaging.

How did you decide to make this the focus of your research?
As compared to proteomics or genomics, glycosylation is a field well underappreciated. There is good opportunity in this field to discover new findings but the set of tools available to study glycosylation are still highly limiting.

How did your scientific journey begin?
Initially French-educated, I moved to the Netherlands for a PhD in transcriptional regulation then to Singapore where I expanded my skillset learning mouse in vivo techniques. A second postdoc gave me the chance to learn some basis in making microfluidic chips  which led to a position in Singapore Biotech for a couple of years With this biotech company we developed applications and tested them in the field to various biopharma customers worldwide. It was fun but then became too commercial for my taste so I decided to return to academia and apply my acquired and valuable pharma high content screening skillset to the IMCB core facility.

Was there something specific about the Antibody Engineering, Phage Display & Immune Repertoire Analysis course that drew you to apply?
Our lab has a fundamental need for antibodies used in mouse liver cancer studies. Antibody phage display allows one to obtain human antibodies in a fast manner which is very valuable for our goals. The course program covers all practical basis from real experts and also some aspect in converting antibody design to CAR-T, which is very exciting. 

What and/or how will you apply what you’ve learned from the course to your work?
At the lab, we already started to screen human antibody libraries but I surely feel more confident to screen more targets after attending this course. Building an immune antibody library is complex and the course surely gives all the tips and tools for us to build antibody libraries back home with confidence. This could certainly expand the capabilities in our institute beyond monoclonal antibody generation with hybridomas.

What is your key takeaway from the Course?
Phage displays allows one to fish for a needle in a haystack in a very fast manner. Harvesting antibody repertoire from any species is accomplished with basic molecular biology tools/skillset.

If someone curious in attending this course asked you for feedback or advice on it, what would you tell him/her?
Hurry up, go for it.

What do you like most about your time at CSHL?
The wonderful natural settings of CSHL provide high serenity almost to a point where I could compare it to a scientific monastery.

Thank you to Xavier 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: Sunil Kumar Kenchanmane Raju

Meet Sunil Kumar Kenchanmane Raju of Michigan State University! A research associate in Chad Niederhuth’s lab within the Department of Plant Biology, Sunil returns to CSHL for another plant science-centric course. In 2015, Sunil trained at the annual summer course on Frontiers & Techniques in Plant Science. This year, he is back for the week-long Workshop on Cereal Genomics where he is picking up techniques he’ll use to help analyze his ATAC-seq data. Sunil has also been a CSHL course ambassador of sorts, informing his fellow workshop trainees that the course goes beyond the lecture room: Speak with everyone in the course and build your network – including the instructors and lecturers. 

What are your research interests? What are you working on?
My research focuses on how plants adapt to changing climates and how genomic interactions with the environment shape complex trait evolution. Currently, I’m working on utilizing comparative epigenomics to understand variations in low temperature tolerance in maize and its close relative, temperate-adapted Tripsacum dactyloides.

How did you decide to make this the focus of your research?
Temperatures in my native South India typically range between 70 and 90 degrees Fahrenheit. When I first arrived to Lincoln, Nebraska for my grad school, it was a cold December night. I was immediately cold stressed and that frigid experience became the motivation behind my want to study cold stress. <Fun emoji> Jokes aside, the changing climate is threatening our ability to produce enough food for the growing population. Food security depends on the ability of plant scientists to develop climate-resilient crops that withstand the challenges of the changing climates. We don’t have to re-invent the wheel: some crop-wild relatives are naturally adept to stressful environments. My motivation is to understand stress adaptation of crop-wild relatives at the genomic and epigenomic levels, and translate stress-resilience into major crops.

How did your scientific journey begin?
When I was a kid, my pediatrician used to tell my parents that I will grow up to be a politician or a scientist (I used to ask her a lot of questions!). Those careers have always been in the back of my mind and I chose the scientist path. I guess, in addition to the amazing scientific mentors I have had throughout my career, my father was my biggest inspiration. Even though he didn’t specifically want me to become a scientist, he always instilled in me the philosophy that ‘education/learning never ends, new knowledge always creates a way for more learning.’ That has been my life’s philosophy and what better profession to practice it than as a scientist exploring new – to create newer – things.

Was there something specific about the Workshop on Cereal Genomics that drew you to apply?
As I am switching my model system from soybean to maize, now is an ideal time for me to attend this workshop as it’ll allow me to more fully capitalize on its contents to help address the questions remaining in my research program. My research focuses on an emerging area of plant biology, and so I will benefit greatly from interacting with scientists from various backgrounds working on advanced techniques in cereals and comparative genomics.

What and/or how will you apply what you’ve learned from the course to your work?
It’s been just a few days into the course and already I feel like we (students) are speaking the cereal community’s lingo! The lectures and hands-on exercises on high-throughput transcriptomics and phenomics data analysis were very informative and will be something I will apply in my research. Also, the informal discussions with instructors and fellow coursemates have been invaluable. Learning from people with diverse research interests has been the biggest highlight.

What is your key takeaway from the Course?
First, I want to thank the instructors for putting together such an amazing list of speakers for the course. Also kudos to them for selecting such a diverse group of students; not just in gender balance but also geographic representation and, most importantly, diversity in research interests. An important take away from this course is that meaningful progress happens through great collaboration within the community, and the cereal genomics community is one of the best examples with everyone being supportive of each other’s work. 

If someone curious in attending this course asked you for feedback or advice on it, what would you tell him/her?
I highly recommend this and any other course at CSHL. There’s something special about the atmosphere at these courses that is very conducive for participants at all levels to take in and bring home a lot. I would recommend the CSHL Cereal Genomics Workshop to early career plant scientists who are or wish to work on cereals. It isn’t just about knowing the latest science but also getting to know the scientists at the forefront of cereal genomics.

What do you like most about your time at CSHL?
The environment here is so serene and inspiring. As a matter of fact, the first thing I did when I arrived at CSHL was take a walk along the beach! If I were to work here, I would always start my day with a walk along the beach, maybe read a couple of research papers there, get inspired, come up with ideas and run to the lab and turn ideas into reality!

Sunil received a travel award from The Michigan State University Plant Resilience Institute (PRI). On behalf of Sunil, thank you to PRI for supporting and enabling our young scientists to attend a CSHL course where they expand their skills, knowledge, and network.

Thank you to Sunil 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: Maira Almeida

Meet Maira Almeida of Iowa State University. A PhD candidate co-mentored in the labs of Dr. Maura McGrail and Dr. Jeffrey Essner, Maira just finished participating in Genome Engineering: Frontiers of CRISPR/Cas. The Brazilian national’s first meeting at CSHL included a poster presentation on “Short homology based CRISPR/Cas9 targeted integration for Cre/lox conditional gene inactivation tools in zebrafish”. The opportunity to explain her research to her peers and receive their feedback “went really well.” And those who approached her poster were “really surprised with the method…recently developed in [their] lab called GeneWeld. This method allows efficient CRISPR/Cas9-mediated integration directed by short homology.”

What are your research interests? What are you working on?
I am particularly interested in developing and applying genome engineering methods to understanding the molecular mechanisms behind developmental processes and diseases. I investigate how chromatin regulators control stemness and neural gene networks during neural development, and how their misregulation can lead to cell transformation and brain tumorigenesis.

How did you decide to make this the focus of your work?
Since high school, I knew I wanted to work with genetics focused on the cancer field. During my undergraduate studies and Masters, I worked on animal genetics and human genetics centered on numerical cognition, respectively. When I started my PhD, I finally got to work on what I’ve always been interested in: developmental genetics applied to the understanding of tumorigenesis. In the past 4 years I was introduced to the genome editing field, specifically CRISPR technology, and I quickly fell in love with it. Now, I have the opportunity to join both of these areas that I am passionate about, which makes me really excited about my research projects.

How did your scientific journey begin?
I have been interested in science since I was a child. In my first year of high school, I had a wonderful biology teacher, Prof. Paulo Flávio (better known by his nickname Paulinho), who introduced me to genetics and it was love at first sight. I remember my teacher talking about gene function and drawing pedigrees for genetic disorders and schemes depicting the different cell division steps. I was fascinated about everything. At that point, I already knew what I wanted to do for the rest of my life. I wanted to understand the molecular mechanisms involved in genetic disorders. My goal has always been to use my work to help others. Someday in the future, I hope to be able to apply all this genetics knowledge  I am acquiring to develop efficient therapies for patients in need.

Was there something specific about the Genome Engineering: Frontiers of CRISPR/Cas Meeting that drew you to attend?
The opportunity to learn about the latest in genome engineering and to share how I’ve applied CRISPR/Cas to create tools for recombinase genetics in zebrafish. Moreover, to meet leaders in the field including Dr. Fyodor Urnov, Dr. Jennifer Doudna, and Dr. Jonathan Weissman and learn about their exciting advances in CRISPR research.

What is your key takeaway from the meeting?
My key takeaway from this meeting is that the genome engineering field is rapidly evolving and its potential to revolutionize the medical field in the next few years is enormous. Currently, there are so many CRISPR systems already available or being described, and they represent a breakthrough in the understanding of molecular mechanisms behind genetic disorders and in the development of efficient therapies for diseases such as cancer.

What and/or how will you apply what you’ve learned from the meeting to your work?
On the second day of the meeting, Dr. David Liu gave an incredible talk where he described a technique called Prime Editing for introducing precise genome modifications. I was astonished by his results and I really would like to try this new technique in our model system, the zebrafish.

If someone curious in attending this meeting asked you for feedback or advice on it, what would you tell him/her?
I would greatly recommend this meeting to anyone interested in genome engineering. The Genome Engineering: Frontiers of CRISPR/Cas meeting is a wonderful opportunity, especially for young scientists like me, to learn from the leaders in the field and establish connections with other researchers that are developing similar work.

What do you like most about your time at CSHL?
I really enjoyed walking around the campus and the friends that I made. I met wonderful people from many different countries.

Thank you to Maira 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: Nabil Karnib

Meet Nabil Karnib of Bowling Green State University. The Lebanese national is a PhD student in Robert Huber’s Lab and is presently taking part in the 2019 meeting of Neurobiology of Drosophila. Nabil “heard a lot of positive reviews [about the Neurobiology of Drosophila meeting] from colleagues and though he “underestimated the engaging aspect of it,” it was up to his expectations. Our biennial fly meeting is his first meeting at CSHL and his inaugural experience included a poster presentation. This wasn’t his first time presenting a poster, but it was the first time he presented his work to such a targeted audience. The result? “Everyone was engaged and enthusiastic about [his] work [so] the feedback [he received] was highly constructive and gave [him] a lot of ideas to incorporate in [his] project trajectory.”

What are your research interests? What are you working on?
I am interested in substance abuse, in particular what makes an individual more prone to get addicted to a certain compound. I use the Drosophila to understand the underlying mechanisms for this susceptibility.

How did you decide to make this the focus of your research?
The ability to answer complex behaviors in a relatively simple model that could be translated clinically.

How did your scientific journey begin?
I was always intrigued by behavioral neuroscience: the fact that any normal or maladaptive behavior can be tracked and studied with the appropriate tools. Particularly, tracing the resilient/susceptible phenotype to depression to underlying epigenetic and genetic mechanisms and studying behavioral abnormalities following hypoxic seizures marked the beginning of my career in science.

Was there something specific about the Neurobiology of Drosophila meeting that drew you to attend?
My main reasons for attending the Neurobiology of Drosophila meeting were to know the state of the art in this field and establish collaborations. CSHL and the organizers provided the best platform for this. I identified and approached laboratories doing similar and complementary work to ours, laying foundations for future collaborations. 

What is your key takeaway from the meeting?
Collaboration makes science happen.

What and/or how will you apply what you’ve learned from the meeting to your work?
I was introduced to several techniques during the talks and the poster sessions that would be a great asset for my project. Also, it was insightful to see how different groups tackle the same questions using different approaches.

If someone curious in attending this meeting asked you for feedback or advice on it, what would you tell him/her?
I would definitely encourage them to attend. It’s a congenial environment to give and receive feedback on science. I return to the lab with a new understanding of novel techniques and approaches to expand my repertoire. The topics covered a vast range, from basic scientific questions to disease modeling and technological innovations done at the highest levels. The heterogeneity of the topics along with the fast pace of the sessions made the meeting highly engaging.

What do you like most about your time at CSHL?
The picturesque backdrop of Long Island, the chance to see the Big Apple and the new friendships I made.

Thank you to Nabil 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.