Visitor of the Week: Erika Estrada

Meet Erika Estrada of the University of California, Davis! Erika is a PhD Student in Linda Harris’ lab who serendipitously “flew” into science. She took part in this week’s Advanced Sequencing Technologies & Bioinformatics Analysis virtual course – her first at CSHL. Erika shares her career plans and we look forward to her shepherding the next generation of scientists.

Tell us about your research.
My research focuses on enhancing microbial food safety with an emphasizing on produce, and tree nuts.

How did you decide to focus on this area/project?
Honestly, serendipity. While I was flying back from a conference, the person sitting next to me was working on a presentation. I peeked on his screen and saw pictures of microbes, soil and water samples. I asked him about his job, he was an extension faculty at UC Davis and he offered me a job in his lab. After just a couple days of working in his lab, I knew that I wanted to study foodborne pathogens for the rest of my life.

What and/or who is the inspiration behind your scientific journey?
My future students. In the near future, I would like to become a professor in hopes to inspire, mentor and guide students through their academic career. I hope my story can show them that if I did it (got a PhD and become a scientist) then so can they.

Erika receiving the Developing Scientist Award at the 2019 International Association of Food Protection (IAFP) Meeting.

Where do you see yourself in five years?
My ultimate career goal is to become an extension faculty and a professor for an academic institution. As an extension specialist, I want to generate, transmit, and apply knowledge for the direct benefit of the food industry, farmers, and my community. I hope that through my research I am able to develop practices that enhance produce food safety.

As a professor, I want to share my knowledge and academic journey with the younger generations, especially those from disadvantaged backgrounds, like myself, to motivate them to pursue careers in science.

What do you love most about being a researcher?

I think what I love most about being a researcher is that I get to study something that no one has studied before. I get to provide answers to questions that ultimately have a positive impact in my community, and the food industry.

What drew you to apply to this course?
Currently, I am working on a project aiming to do comparative genomic analysis of multiple Salmonella isolates obtained from a 3-year pistachio survey in California. The ultimate goal of this project is to understand the underlying reasons for unique microbial contamination profile in pistachios.  However, this is the first time during my academic career that I have to do use advanced Bioinformatics tools and techniques. During this quarantine, I have taken a couple of free online courses on UNIX, and read about different software that would be beneficial to process my sequences. Honestly, learning the basics of UNIX, NCBI databases, and data processing software using YouTube, online classes and different websites has been one of the most challenging and satisfying things I have done in my whole academic career. However, I believe that attending this course would be a valuable opportunity to obtain formalized training in the topic and to keep instilling my passion for learning about the application of sequencing technologies and bioinformatics analyses.

What feedback or advice would you share with someone considering to participate in this course?
Definitely try to get familiar with R and Unix so that you are able to truly focus on learning about the bioinformatics tools and technologies covered rather than focusing on understanding the code.

What’s the most memorable thing that happened during the Course?
I think the most memorable thing that happened during the course was learning about the power of R when we were building visual tool, such as graphs, plots and heat maps, to actually see the results of our analysis. After this course, I am committed to learn more about R.

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

Images provided by Erika Estrada

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.

Repeat Visitor: Diego Rodriguez Terrones

Meet Diego Rodriguez Terrones of Helmholtz Zentrum München (Munich, Germany). The Mexican national is a third-year PhD student supervised by Prof. Dr. Maria-Elena Torres-Padilla from the Helmholtz Zentrum München, and Dr. Juan Manuel Vaquerizas from the Max Planck Institute of Molecular Biomedicine. Diego made his CSHL debut this year and did so with quite the “bang”: first presenting a poster at the Transposable Elements meeting then the Advanced Sequencing Technologies & Applications course less than 48 hours later. We reached out to Diego to ask him of his experiences and if there were any other CSHL meetings or courses on his radar (and we may be welcoming him again for the Mouse Development, Stem Cells & Cancer and the Synthetic Biology courses!). We began by talking about his work and how he made it the focus of his research:

In the lab, we aim to understand the molecular basis of mammalian totipotency, which is the capacity of a single cell to give rise to an entire organism. For example, in the mouse, the one cell of the 1-cell embryo and each of the two cells from the 2-cell embryo are the only three totipotent cells that occur during development. What this essentially means is that if you let a 1-cell embryo develop to term you will get one mouse, and if you split up the 2 cells from the 2-cell embryo and let them develop independently, you will get two twin mice. Once the two cells from the 2-cell stage embryo divide once more to form the 4-cell stage embryo, totipotency is lost and it won’t be possible to initiate development from a single cell ever again during this round of development! Our goal is to understand what makes this particular set of three cells stand out from all others; specifically how the unique epigenetic landscape that arises at the beginning of development mediates this unique totipotent capacity.

Overview of mouse pre-impantation development. Image provided by Diego Rodriguez Terrones

Early on in my career, I realized that my main interests laid within the field of synthetic biology and that my long-term goal was to enable the engineering of biological systems that possess properties or exhibit behaviors not found in nature. However, I also understood at the time that any attempt to engineer life would most certainly fail without a thorough understanding of gene regulation, and all the epigenomic mechanisms that translate one unique genotype into the multitude of cellular phenotypes that exist throughout an organism. Under that logic, what better place to start than the early embryo where the mammalian developmental program and its epigenome are kick-started.

How did your scientific journey begin?

Actually, as far back as I can remember I’ve always wanted to be a scientist! When I was around 5 years old, for some reason, I started watching a lot of astronomy documentaries on TV and became absolutely fascinated by the idea of space exploration. Over the course of the next several years, however, I think I started to understand just how difficult space exploration really was, how little we were doing it, and just how much our biological limitations stood in the way of making space exploration a reality. Mainly because of this, and by the age of 12, I remember having had decided that I wanted to pursue a career in something involving biology or medicine, and was what eventually led me to start a career in genomics during my undergrad.

You recently joined the 200+ alumni of the Advanced Sequencing Technologies & Applications course. What attracted you to the course and what did you take away from it?

Advanced Sequencing Technologies & Applications Class of 2018

I was particularly interested in learning about the new long read sequencing technologies, and about genome assembly and the analysis of structural variants. These two topics were indeed two of the course’s central themes this year, so it was quite productive for me! I think it’s a fantastic course for primarily developing your bioinformatic skills, targeted towards the very latest technologies. I’m happy to have acquired a rather wide collection of new experimental and bioinformatic skills during this course, ranging from variant calling and genome assembly, all the way up to the preparation of single-cell RNA-seq libraries with 10X genomics. I’m in the process of incorporating the training in the analysis of RNA-seq data that I acquired at the course towards my current research project. If anything, I guess my key takeaway from this course -- of this year -- is that long read sequencing technologies are revolutionizing genomics! I think both beginner and intermediate bioinformatic users would benefit from the course equally, which is rather unusual for a course like this and speaks highly about its quality.

This year, you also attended the Transposable Elements meeting. Can you tell us what led you to register for this meeting in particular?

Diego at one of the 2018 Transposable Elements’ poster sessions.

Since I will be finishing my PhD relatively soon, I wanted to see where the field was heading and gather some ideas for my postdoctoral project. As a matter of fact, quite a few of the things that I learnt during the meeting are going to shape what I end up doing during my postdoc. This meeting represents ones of the best opportunities to get a global overview of the transposon field; so if you are working on repetitive elements, I would most definitely recommend it. Another group that I think would greatly benefit from it is anyone working on molecular biology or -omics method development: there are so many crazy molecular mechanisms going on with transposons that I think it would be rather inspiring!

One key takeaway was very neatly put forward by Cedric Feschotte during his keynote when he argued that the genome can only be understood as an ecosystem. I think this concept very elegantly puts together the idea that genomes are teeming with all sorts of selfish genetic entities that range from DNA transposon and endogenous retroviruses, all the way to parasitic repetitive elements that exploit other transposable elements for their own replication. However, the key point here is that while this interplay between host genome and transposable elements can give rise to genetic conflicts, it can also result in selective advantages to the host organism by providing a continuous source of novel regulatory sequences and even of novel regulatory proteins.

Since you’ve now experienced both meeting and course life at CSHL, did you pick up any differences or similarities between the two function types?

Well, long hours are definitely a constant between both!

What did you like most about your time at CSHL?

The course materials are perhaps my favorite general thing. They are of exceptional quality and permit us to come back to them for further reference once we start applying what we learnt! Also, the instructors were great, and it was really easy to approach them to discuss how to best address the specific challenges we are encountering in our own projects.

During the meeting, I really enjoyed the poster session. The quality of the posters were remarkable and there were tons of posters I was extremely interested in visiting! Fortunately, there was also a lot of time to mingle around during the poster session which is definitely not the case at every meeting). Also, the keynotes were spectacular!

Thank you to Diego for sharing with us his experience, and we look forward to having him back at the Laboratory again for the two courses he has his sights set on - Mouse Development, Stem Cells & Cancer and Synthetic Biology. Both annual courses are accepting applications until March 1, 2019 and April 1, 2019, respectively. The Advanced Sequencing Technologies & Applications course will again be offered at CSHL from November 5-17, 2019 (with applications due here by July 15, 2019); and the Transposable Elements meeting will return in October 2020.

Also, we would like to particularly thank Prof. Torres-Padilla, his institutions, HELENA (Helmholtz Graduate School Environmental Health), and Chromatin Dynamics (Integrated Research Training Group IRTG-SFB 1064) for providing Diego with the financial support that enabled him to participate at his CSHL meetings and courses this year.

To meet other featured scientists - and discover the wide range of science that takes part in a CSHL meeting or course - go here and here.

Visitor of the Week: Tianhao Xu

Meet Tianhao Xu of Rosalind Franklin University. The Chinese national is a Ph.D. candidate working in Dr. Gustavo Martinez’s lab within the Center for Cancer Cell Biology, Immunology, and Infection. He made his CSHL debut by training at this year’s Advanced Sequencing Technologies & Applications course.

What are your research interests? What are you working on?
My research interest is to understand the molecular mechanism of CD8+ T cell differentiation. I’m currently working on understanding the role of two transcription factors, NFAT1 and NFAT2, in CD8+ T cell differentiation and function.

How did you decide to make this the focus of your research?
The truth is I didn’t know of my current research field until my rotation in Dr. Martinez’s lab. In the first year of our graduate program, we are able to rotate with different PIs before deciding which lab to join. During my rotation in the immunology lab, I knew I had found my research focus because, I felt excited and rewarded every time I did the hands-on manipulation of CD8+ T cells!

How did your scientific journey begin?
My interest in science developed at a very young age during the hours and hours I spent playing with my childhood friends in gardens and wild fields. I also like to read science and nature books. This may sound boring or cliché, but the high school biology class brought me onto the biological science path and I still clearly remember the very first day I prepared slides and saw the onion cellular structures.

Was there something specific about the Advanced Sequencing Technologies & Applications course that drew you to apply?
The next-gen sequencing technology, especially RNA-seq and ATAC-seq are powerful tools unveiling the transcriptome and chromatin accessibility changes that bridge transcription factor changes and phenotypic changes in any given cell. Therefore, this course is perfect for me to further study the mechanisms behind NFAT dependent phenotypic changes in CD8+ T cell differentiation.

What and/or how will you apply what you've learned from the course to your work?
I’m still navigating my way in bioinformatics. However, I think I’m getting a more in-depth understanding of the potential application as well as the limitation of next-gen sequencing technology. I can’t wait to bring my knowledge about next-gen sequencing to my lab mates and home institution; and I hope to set up an Amazon Machine Images (AMI), using bioinformatics tools presently available to us, dedicated to all Rosalind Franklin graduate students.

What is your key takeaway from the course?
Leaving your research comfort zone and learning new things can be terrifying. However, you shouldn’t be. The course lecturers and your classmates will be there to help you achieve your goal. A part of becoming a scientist is having the drive to learn and discover new things continuously.

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

1. The course will be intense. Make sure to read all the guidelines (especially those related to the course pre-requests), and become familiar with the layout of CSHL to easily navigate the buildings and available facilities.

2. Do not be afraid to ask questions.

3. Make sure to bring a heavy jacket.

What do you like most about your time at CSHL?
It is “almost” freezing during this time of the year, but I did enjoy the autumnal feeling and seeing the tree leaves change colors. Most importantly, I have to say the food was fantastic. I never felt this happy eating in the cafeteria before.

Tianhao received a scholarship from the Helmsley Charitable Trust to cover a portion of his course tuition. On behalf of Tianhao, thank you to the Helmsley Charitable Trust for supporting and enabling our young scientists to attend a CSHL course where they expand their skills, knowledge, and network.

Thank you to Tianhao 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: Paola Silveira

Photo provided by Paola Silveira

Meet Paola Silveira of the Federal University of Rio de Janeiro (Brazil). Paola is a member of Amilcar Tanuri's molecular biology lab in the Department of Genetics and in March 2018 will be defending her thesis. Paola is on campus to attend her first CSHL course, 2017 Advanced Sequencing Technologies & Applications.

What are your research interests? What are you working on?
I'm interested in HIV and other endemic viruses affecting Brazil. Currently, I’m working on the next generation sequencing technologies to elucidate the origins and epidemiology of Zika virus, and determining whether there is a viral genetic basis of adverse fetal outcomes resulting from in utero ZIKV infection. 

Was there something specific about the Advanced Sequencing Technologies & Applications course that drew you to apply?
I wanted to gain more knowledge on new sequencing platforms and applications; particularly learn data processing and master bioinformatic tools that are available to me but I wasn't familiar with. The course met these needs and has since broadened my view of the genomics field. I have acquired data analysis know-how, and will confidently apply these new skills when I return to my home institution.

What is your key takeaway from the Course?
I’m looking forward to the next years of the genomic era. The advancements in DNA sequencing technologies and in the bioinformatics field are expanding our knowledge, and turning previously-unimaginable scientific and novel biological applications into achievements.

If someone curious in attending a future iteration of Advanced Sequencing Technologies & Applications course asked you for feedback or advice on it, what would you tell him/her?
For those interested in this course, I would strongly recommend this amazing opportunity. You will learn and you will be learning from the best who are each enthusiastic, supportive, and vested in your learning.  

What do you like most about your time at CSHL?
I’m delighted with the landscape of CSHL campus. Here you're surrounded by green and always be surprised by science sculpture. Additionally, I have met a great group of people here.

Paola received a stipend from the Howard Hughes Medical Institute (HHMI) to cover a portion of her course tuition. On behalf of Paola, we want to thank HHMI for continuing to support and enable young scientists to attend a CSHL course to expand their skills, knowledge, and network. 

Thank you to Paola 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.