Visitor of the Week: Sessaly Reich

Meet Sessaly Reich of the College of Veterinary Medicine in the University of Missouri-Columbia. The second-year veterinary medical oncology resident and PhD student in the Comparative Oncology Radiobiology and Epigenetics Laboratory is two weeks into our three-week training course on Advanced Sequencing Technologies & Applications to increase her understanding of the various next generation sequencing platforms available for her to sequence her sizable datasets. This is her first course at CSHL has been a “positive experience” and we look forward to having her back again.     

What are your research interests? What are you working on?
My research interests are the epigenetic signature of cancers in dogs, specifically lymphoma. I’m also interested in translational aspects of immunotherapy treatment in canine osteosarcoma (bone cancer), which closely mirrors the genetic landscape and clinical behavior of pediatric osteosarcoma.

How did you decide to make this the focus of your research?
The University of Missouri Veterinary Health Center Oncology Service participates in a variety of clinical trials. We are able to enroll client-owned dogs and cats with spontaneously occurring cancers in order to promote translational research, while directly benefiting animals who otherwise do not have available treatment options. The results from our studies have provided enough evidence to move treatments forward to development in humans.

How did your scientific journey begin?
I became interested in the genetic risk for disease and translational research during veterinary school, where I enrolled in a dual DVM/MS program. I initially studied the relationships between genetic polymorphisms in a phase II detoxification enzyme (glutathione S-transferases), enzyme activity, and lymphoma risk in dogs. When my own dog developed lymphoma during my veterinary curriculum, I was further inspired to learn more about treating and even preventing this disease.

Was there something specific about the Advanced Sequencing Technologies & Applications course that drew you to apply?
The subject of my research is defining the epigenetic landscape of lymphoma in dogs, with specific stratification according to breed and lymphoma subtype. We hope to use this information to provide prognostic information, select different treatments, and predict which dogs are at a higher risk of developing -- or will soon develop -- lymphoma. Understanding all of the next generation sequencing platforms, along with their individual strengths and weaknesses, is essential when dealing with massive amounts of sequencing data.

What and/or how will you apply what you’ve picked up from the course to your work?
The next stage of my PhD project will revolve around analyzing whole genome bisulfite sequencing (WGBS, DNA methylation) and bulk RNA sequencing (RNAseq). While the benchtop portion of these techniques has been optimized in my lab, I personally have limited bioinformatics data processing experience. I want to analyze my own data in order to filter results according to biological relevance and applicability, rather than relying exclusively on an outside bioinformatician. The University of Missouri-Columbia is also beginning collaborative efforts with the bioinformatics team at Washington University, and I want to be able to effectively communicate and grasp both the clinical and bioinformatics aspects of larger translational projects moving forward.

What is your key takeaway from the Course?
While I’m far from being an expert in bioinformatics, this Course has provided me with the groundwork to begin processing my own NGS data. I also know where to go for further training/education and how to use the many resources available to researchers. 

If someone curious in attending this course asked you for feedback or advice on it, what would you tell him/her?
Do as much preparation with the materials provided prior to arrival. It will help you get the most out of the Course. That being said, be prepared to be very busy and be pushed outside of your comfort zone.

What do you like most about your time at CSHL?
My favorite thing about being at CSHL is meeting peers from a wide variety of specialties with an incredible array of skillsets. This provided a unique environment for changing your perspective in order to learn as a group, in addition to fostering collaboration and collegiality.  

Thank you to Sessaly 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: Sam Nicholls

Meet Sam Nicholls of the University of Birmingham (United Kingdom). The postdoctoral fellow in Nick Loman’s group is currently at CSHL participating in his first meeting: Genome Informatics. In addition to giving a talk, titled "Detecting microbial transmission and engraftment after faecal microbiota transplants with long-read metagenomics and reticulatus" during the Microbial and Metagenomics session, Sam’s work was featured as the front cover of the meeting’s abstract book. He has also been taking advantage of the chance to “meet in person a bunch of familiar Twitter avatars that [he’s] been messaging over the past year or so.”

What are your research interests? What are you working on?
I'm currently working on computational methods to analyse clinical microbiome samples. We're interested in determining whether we can identify and characterise species and strains that are transferred from donors to recipients in faecal microbiota transplants.

How did you decided to make this to focus of your research? 
This project is a natural follow-on from my PhD, which I finished a little over a year ago. My PhD was concerned with recovering haplotypes for particular genes of interest from the rumen (stomach) of a cow. We were interested in cataloguing the haplotypes of different hydrolases used to break down natural grasses in the stomach, with a view to investigate these for their potential use in the manufacture of biofuels. Now, I'm applying these skills and my experience to catalogue the genomes (and their haplotypes) that are transplanted from the gut of a healthy donor to the gut of an unwell recipient via faecal microbiota transplant, to characterise what it is about the procedure that makes it work as a successful therapy.

As part of my PhD, I created a data structure (called Hansel) for holding all possible pairwise observations of SNP variants on a set of short sequencing reads; and an algorithm (called Gretel) to use this matrix as crumbs for navigating a graph-like structure representing all possible ordered combinations of SNPs that make up the haplotypes for a region of interest. Although we didn't get so far as to test the recovered haplotypes for biofuel capabilities, as part of my final year I was able to put on a white coat and get in the lab to gain some wet lab experience of my own. I think it's important for bioinformaticians to know where their data comes from!

How did your scientific journey begin?
In the second year of my Computer Science and Statistics undergraduate degree with no plans for summer, I recall an e-mail being sent around the Computer Science Department at Aberystwyth University (United Kingdom) looking for someone who had knowledge of Perl, tree algorithms, and proteins for a placement at the Wellcome Trust Sanger Institute. Undeterred by ticking none of those boxes, I applied. The trip to Cambridge was awfully long from Aberystwyth and I didn't feel like the interview had gone particularly well. Good practice at least, I thought, but a few days later I was surprised to find that I'd been offered the summer job! On my first day, I remember someone dropping off a bunch of genetics textbooks to my desk and saying that I'd have to pick up a lot of new concepts quickly, which was a little intimidating, but I was keen to learn something completely new.

 Ultimately that short placement had more of an effect on me than I had expected. I was not really aware that my skills in computing could be applied to interesting, difficult real-world problems like those we find in biology. It was nice to be writing code that wasn't just a website, or an app, or something to sell. I liked that I could tell people about my work and even post it online as it was being written, something that was definitely not part of the ethos of my previous experience in industry.

 That placement led me to change my modules in my final year and to go on and pursue a PhD in bioinformatics, rather than returning to industry.

Was there something specific about the Genome Informatics meeting that drew you to attend?
As a bioinformatician, I always find myself a little lost at conferences that focus heavily on biology. I'm excited to be at Genome Informatics as this finally feels like a conference where everything makes sense to me! I was also happy at the prospect of finally meeting a bioinformatics hero of mine: Heng Li.

What is your key takeaway from the Meeting?

A takeaway in the literal sense: I'll be flying home this weekend with one of the Genome Informatics 2019 meeting posters, which features artwork that I submitted! The picture is an assembly graph from one of our complex clinical samples. It's a wonder to look at, but actually a rather terrible assembly...

What and/or how will you apply what you’ve picked up from the Meeting to your work?
Yesterday's morning session on sequencing algorithms, variant calling and genome assembly was a highlight for me so far. I'm quite interested in exploring some of the techniques for genome sketching that were discussed, and how we can apply these to our own clinical metagenomic data sets. 

If someone curious in attending this meeting asked you for feedback or advice on it, what would you tell him/her?
I'm not sure how I feel about coffee at 9 in the evening, but this meeting has been full of excellent presentations that I'm going to have to go and read up more about. I'd definitely recommend Genome Informatics if you want to know what the cutting edge techniques and hot topics of bioinformatics are right now.

What do you like most about your time at CSHL?
I grew up in Swansea, Wales and moved to Aberystwyth for eight years to study my undergraduate and PhD; so I've spent most of my life near the sea. I enjoy the hustle and bustle of the city of Birmingham but I do miss the seaside. I've been enjoying walks around the campus and the views of the water. It's very calm and picturesque here. Thanks for having me!

Thank you to Sam 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: Hossein Davarinejad

Meet Hossein Davarinejad of the University of Ottawa. The second-year PhD student is a member of Dr. Dr. Jean-François Couture’s lab within the Department of Biochemistry, Microbiology, and Immunology, and he recently wrapped up his training at the annual three-week course on X-Ray Methods in Structural Biology.

What are your research interests? What are you working on?
I am interested in studying enzymes that modify the interaction of DNA with DNA-packaging proteins as these important processes affect gene expression.

How did you decide to make this the focus of your research?
When I began my undergraduate studies, epigenetics had gained a spotlight in cellular and molecular biology. The field was relatively new and introduced the histone code with many enzymatic modifications with unmapped individual or combinatory effects on gene expression. It was an attractive puzzle with a lot of room for identifying new pieces.

How did your scientific journey begin?
I enrolled in the biology program with an interest in dentistry or medicine at first. I was not performing well during my first year as courses were very broad and I learn better with more depth and needed to have a good understanding of the applications to engage. During my undergrad second year, my biochemistry and cell biology professor really raised my interest in how life works at the molecular level. I was fascinated with the understanding of how mutations cause changes in the structure and function of macromolecules which contribute to disease. That course paved my path in molecular biology leading to epigenetic studies for MSc and eventually to structural biology in my PhD program.

Was there something specific about the X-Ray Methods in Structural Biology course that drew you to apply?
My PhD studies rely substantially on understanding the structure of the protein complexes which I study in order to understand how they assemble and initiate or inhibit their functions. We have an X-ray source at my home lab which is used extensively by our group for solving protein structure using X-ray crystallography. The X-ray course at CSHL is the most extensive program to my knowledge that covers a wide variety of topic related to this technique including biochemical and lab techniques and strategies for obtaining high quality protein crystals, methods in sample preparation and mounting of the instrument, mathematics and physics at play behind the scenes while using an X-ray source to collect crystallographic refraction data, data processing and analysis using variety of popular software, and information for validation of data for publication. All of the topics covered are directly beneficial to structural biologists using X-rays.  

What is your takeaway from the Course?
There is no single key takeaway from this course. The course covers a large volume of material on very related topics. The majority of topics were important, indispensable, and taught us things to consider ranging from chemical reagents and lab work to instrument function and data processing. In this field, there are many pieces that need to fall into place for obtaining a high-resolution structure and the course teaches you how to optimize the work at each step.

What and/or how will you apply what you’ve picked up from the Course to your work?
Before attending the course, I thought I had an idea of what I didn’t know and what I needed to learn. This course introduced me a lot of new material conceptually and technically. Having attended the course, I have filled in many gaps in my knowledge and my list of things to continue to learn has grown substantially. The sections on laboratory work are readily understandable, relatable, and translatable to my own work such as techniques on better understanding the stability of the protein that I work with and ways to re-evaluate whether my preps can negatively impact my sample before data collection stage. We had training on using many software and this course helped me understand what the application parameters really do, and this can enhance my data processing.

If someone curious in attending this course asked you for feedback or advice on it, what would you tell him/her?
I would say the volume and the difficulty of the material would make it suitable for a 4-credit university course which would normally be covered in a full semester (at least by Canadian standards). The 15-day period makes this course very intensive and it could be challenging as lectures are back to back. For a junior researcher, with little time to take them in, it can be exhausting. I think the best strategy to keep up is to keep good track of what you don’t understand and use the short coffee breaks, food breaks, Q/A sessions, and any other time you find to go up to the instructors and resolve the ambiguities as soon as you can since the lectures build on each other to a good extent. If allowed, maybe recording the lectures could be useful as you’d definitely need to come back to the material. The great thing about the course is that there are many instructors and experts around at all times. The instructors are fun, approachable, and genuinely like to be “bothered” with your questions. There were many instructors who are major contributors to the field, and some are the actual developers of the computational software used or leading structural biologists so you will be talking to the best sources. Being able to network with the instructors is invaluable.

It is great to come here with structure problems from your own work and consult the instructors on how to improve your data.

What did you like most about your time at CSHL?
This is a beautiful campus and unlike any laboratory campus I had ever seen. The course directors and instructors were really fun, you can talk to them about anything in science or beyond. Being in the same rooms as all the instructors and other students for a long period made it feel warm and friendly as you get to know each other. The stray cat roaming the campus made it even better.

Thank you to Hossein 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: Ioanna Myronidi

Meet Ioanna Myronidi of Stockholm Univeristy. The Greek national is a PhD student in Professor Per. O Ljungdahl’s lab within the Department of Molecular Biosciences, Wenner-Gren Institute who is currently taking part in the 2019 biohistory meeting on Yeast Research: Origins, Insights & Breakthroughs. This is her first meeting at CSHL and it included a poster presentation on “The ER membrane chaperone Shr3 co-translationally assists biogenesis of related polytopic membrane protein substrates” (a collaboration between Andreas Ring, Per Ljungdahl, and Ioanna). Thought his wasn’t the first time she presented a poster, “it was definitely the one [she] enjoyed the most.” Here is what else Ioanna said about her experience:

Given the history that comes with CSHL I had imagined that it would be a very inspiring place to be. It absolutely lived up to my expectations. I would recommend this meeting to everyone working with yeast, not only for the high-quality science that was presented and discussed but also for the opportunity to hear firsthand about some of the discoveries that laid the groundwork for establishing yeast as a model system.

We hope to have her back for Yeast Genetics & Genomics – a course she “would love to attend”.

What are your research interest? What are you working on?
My research interests focus on the mechanisms that govern the biogenesis of complex polytopic membrane proteins, i.e. how proteins that span a membrane multiple times manage to fold into a proper three-dimensional structure in the extremely crowded cellular environment and reach the target membrane compartment. With the use of yeast as a model eukaryotic system, I am studying how membrane chaperones at the endoplasmic reticulum assist complex polytopic membrane proteins -- such as amino acid transporters -- to fold correctly as they are being synthesized and destined for functional expression at the plasma membrane.

How did you decide to make this the focus of your research?
During a series of lectures on transporter protein biogenesis, function and regulation given by Professor George Diallinas at the University of Athens (Greece) I found myself fascinated by the mechanisms that drive the journey of membrane proteins through the secretory pathway of cells. Later on, I got the opportunity to work on a six-month project on amino acid transporter biogenesis in Professor Per Ljungdahl’s lab at Stockholm University where I came to work with Saccharomyces cerevisiae, a beautiful eukaryotic system to study membrane protein biogenesis among a broad spectrum of other cellular processes. This experience was so motivating and inspiring that I knew the puzzle was complete: the question, the system, the place.

How did your scientific journey begin?
I find the “Why?” of curious kids evolving into the “How?” of motivated scientists most intriguing. I guess for some people the curiosity about how life works can only be satisfied as a scientist – and that is me.

Was there something specific about the Yeast Research: Origins, Insights & Breakthroughs meeting that drew you to attend?
There are two points that immediately drew me to attend the meeting: The excellent list of invited speakers and the opportunity to visit CSHL.

This is a historical meeting that brought together scientists that did groundbreaking work based on yeast genetics. Thus, for young scientists such as myself, I found it very motivating to be so encouraged to discuss our work and put it into perspective.

What is your key takeaway from the Meeting?
I got very useful feedback on our work and I look forward to trying out some of the suggested experimental approaches that allow the investigation of protein-protein interactions.

What do you like most about your time at CSHL?
Aside from science talks and discussions, I mostly liked hanging out in this wonderful place with people that come from every place on earth.

Thank you to Ioanna 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: 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.