Proteomics Course

Repeat Visitor: Leila Rieder

Photo provided by Leila Rieder

Photo provided by Leila Rieder

The next scientist to be featured in the 2018 edition of our Repeat Visitor series is Leila Rieder. Leila is a K99 postdoctoral fellow in Erica Larschan’s lab in Brown University with a visiting appointment at Princeton University. And, next April, she will take on her new role as Assistant Professor in the Biology Department of Emory University. Leila made her CSHL Meetings & Courses debut in August 2017 when she trained at the Proteomics course. She returned for this year’s Quantitative Imaging: From Acquisition to Analysis course (QICM) followed by a poster presentation at the Nuclear Organization & Function meeting a few weeks later. We caught up with Leila to chat about her experience at our meetings and courses, and if she has any plans of participating in a near future meeting or course.

Tell us about your research interests and how you decided to make it the focus of your research.

I’m most interested in how genes are coordinately regulated -- turned on and off at the same time. Cells are remarkably good at this and we don’t know how they do it! I first began by focusing on how sex chromosomes are singled out for unique regulation, a process called dosage compensation. In these systems, basically all the genes carried on a single chromosome are coordinately regulated. However, it’s not simply the chromosomal location that leads to this coordinated regulation; there are other signals. While researching the role of a known dosage compensation protein on the male X-chromosome, I discovered the same protein was involved in regulating another group of coordinated genes: the histones. These genes are often clustered together within genomes and are notable and unique for many reasons. Every time a cell divides, it needs a huge output of histone proteins in the right ratios so they are incredibly important genes!

How did your scientific journey begin?

My father is a cell biologist and, to be honest, because it was important to me to forge my own path, I tried very hard to be anything other than a biologist! But because of my father’s research, I spent my childhood summers at the Marine Biological Laboratory and sat through so many meals where the entertainment (the entire conversation!) was dominated by my father and his colleagues debating their newest results. They couldn’t get together without “talking science” and I wanted to have those conversations myself -- and now I do!

Quantitative Imaging: From Acquisition to Analysis Class of 2018

Quantitative Imaging: From Acquisition to Analysis Class of 2018

This year, we hosted 26 meetings and 34 courses - how did you narrow down which ones to attend?

I taught myself most of the microscopy I know, and was intensely aware that I was probably doing 50% of it incorrectly. (After the course, I realized I was closer to 90%.) I knew that if I wanted to perform experiments correctly, I needed formal guidance and a background in theory. I’ll soon be in a position to guide my trainees through their own research, and will make sure to never suggest they do sloppy or ignorant microscopy!

As for the meeting, I decided it was important to understand how my favorite genes and loci were situated in the nucleus. I had been working in the field of coordinated gene regulation but without deeply considering higher-order organization and genomic context.

What is your key takeaway from QICM? Also, what advice would you give to someone interested in this course?

Quantitative microscopy is incredibly powerful when used correctly, but there are many ways to use it to find false positives and red herrings. Most of all, I will never apply a quantitative microscopy technique without first researching all the ways in which it can go wrong. I think the best time to take this course is when you have some basic microscopy experience but haven’t yet significantly applied it to your biological question. Be prepared to hear about the different ways your past experiments were sub-par. It’s not a great feeling, but it’s better to learn sooner rather than later!

For Nuclear Organization & Function, what feedback can you provide for those interested in participating in its 2020 iteration?

Leila during her poster presentation at the 2018 Nuclear Organization & Function meeting.

Leila during her poster presentation at the 2018 Nuclear Organization & Function meeting.

The field of nuclear organization and function is much broader than I imagined! It focused on specific topics that were not as relevant to my work as I had expected but, due to it, I now read more broadly. The meeting itself is a great opportunity to meet people—both those who are everyday names as well as those you might not have heard of but are doing really interesting work. I presented a poster entitled “Dynamic identification of the dosage-compensated Drosophila male X-chromosome during early embryogenesis,” and the experience was intense, as many poster sessions are, but friendly. I liked that the meeting was small so it was neither difficult to find people nor for them to find me.

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

Since you basically live and work with your course mates for two straight weeks, you really get to know them. We come from so many backgrounds and different countries, and are using what we learn during the course for wildly different purposes. This diversity really adds to the experience. This is all true of the meeting participants as well, but you don’t get to know them to the same extent since the meetings are only four days long.

Our readers are always eager to learn of ways to fund registration. Can you share how you were able to fund your CSHL meeting and course participation?

Since I am located at Brown and Princeton Universities - neither of which are far from CSHL - transportation to CSHL is easier and less costly for me than for most. For tuition and registration support, I received small grants from my home institution, NCI for QICM, and CSHL generously delayed payment for the course tuition until my K99 grant was available. I was also provided tuition support by NICHD when I took the Proteomics course in 2017.

What did you like most about your experience at CSHL?

Overall, I enjoyed meeting so many interesting people from backgrounds so different than mine. At the meeting, what I liked the most was the chance to sit next to someone new at dinner. As for the course, the instructors, TA’s, and vendors were really fantastic and you can absolutely tell they love teaching the course—they live and breathe it even more than the students do! And they had boundless energy. They never got tired of answering questions and, when the students finally shuffled out at the end of a long evening, they stayed to set up for the next day. They are amazing!

Do you have a future CSHL course or meeting on your radar?

Yes! Now that I am about to begin my own research group, I plan on taking the Workshop on Leadership in Biosciences this coming March. And, someday if I have time, I’d like to take the Programming for Biology course. I’m also planning to attend the Mechanisms of Eukaryotic Transcription meeting in 2019.

Both the Quantitative Imaging: From Acquisition to Analysis and Proteomics courses will return to the Laboratory in 2019; and applications are already being accepted. Apply to QICM by January 31, 2019 here, and to Proteomics by April 1, 2019 here.

Thank you to Leila for sharing with us her experience, and we look forward to having her back at the Laboratory again. 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: Viraj Doddihal

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Meet Viraj Doddihal of the Stowers Institute for Medical Research. The Indian national is a graduate student in Alejandro Sanchez Alvarado’s lab and, for two weeks, was on campus for the Proteomics course. 

What are your research interests? What are you working on?
I am studying animal tissue regeneration, using the planarian flatworm as a model system. My project focuses on studying the role of protein phosphorylation in the planarian regeneration. 

How did you decide to make this the focus of your research? 
I was introduced to regeneration biology during my undergraduate studies at the Indian Institute of Science Education and Research in Pune, India. I was fascinated by this phenomenon and worked a semester with Dr. Girish Ratnaparkhi studying Hydra regeneration. I next worked on planarian regeneration with Dr. Dasaradhi Palakodeti at the Institute for Stem Cell and Regenerative Medicine (inStem) at NCBS in Bengaluru, India. These early experiences in regeneration biology helped me choose my current project at the Stowers Institute for Medical Research.     

How did your scientific journey begin? 
I think it is to a large extent because of my parents and my family. They have always allowed me to question and explore as per my curiosity. In addition, they made sure I received the best possible education which led to me attending high school at Sri Ramakrishna Vidyashala in Mysuru. My very inspirational high school teachers laid the foundation for my career in science.

Searching for proteins. Photo: Viraj Doddihal

Searching for proteins.
Photo: Viraj Doddihal

Was there something specific about the Proteomics course that drew you to apply?
The course has a good balance of theory, experiments, and data analysis. I wanted to learn how to use mass spectrometers (MS), and analyze the big data sets generated from discovery proteomics experiments.  

What and/or how will you apply what you've learned from the course to your work? 
The course gave me an in-depth understanding of MS and other techniques that are available to study proteins in conjugation with MS. I plan to utilize these techniques as a new tool kit to probe regeneration in planarians.  

What is your key takeaway from the course?
In addition to understanding the power of mass spectrometry to study proteins in cells and tissues, the key takeaway for me was to always design orthogonal experiments to address any question. We, the students of the course asked a variety of fundamental biological questions, but are all using proteomics as an approach. This helped me appreciate the power of proteomics to answer questions in biology.

Sailing trip Photo: Viraj Doddihal

Sailing trip
Photo: Viraj Doddihal

If someone curious in attending this course asked you for feedback or advice on it, what would you tell him/her?
I would strongly encourage them to attend the course. Anybody interested in understanding the workings of MS and design of proteomics experiments should definitely attend the course. Additionally, the course provides a good balance of academia and industry thus giving students an opportunity to explore both the fields. 

What do you like most about your time at CSHL?
I really enjoyed our walks to the beach and the student gatherings we had there. We all enjoyed our sailing trip. The daily hike up the beautiful hill for the classes made sure that I got some exercise after sumptuous meals. 

I would like to thank the instructors and TAs for relentlessly answering all our questions and making the course fun and fruitful. Also, a big thank you to all my friends from this course who made it a memorable experience. 

Thank you to Viraj 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: Nyaradzo "Nyari" Chigorimbo-Tsikiwa

Photo by Constance Brukin

Photo by Constance Brukin

Meet Nyaradzo "Nyari" Chigorimbo-Tsikiwa of the University of Cape Town (South Africa) in the Desmond Tutu HIV Foundation and Division of Immunology. The early career fellow makes her first visit to the Laboratory to participate in the Proteomics course.

What are your research interests? What are you working on?
I am working on understanding how HIV transmission takes place in males in order to prevent its transmission. 

Was there something specific about the Imaging Structure & Function in the Nervous System course that drew you to apply? 
I applied to this course because I want to learn how to perform targeted proteomics and label-free quantification for use in biomedical research. I am happy to say that I have learnt both, as well as other methods including quantitative labeling from the method's inventor, Darryl Pappin.

What is your key takeaway from the course?
Proteomics is an exciting field with many possibilities and challenges; such as designing robust experiments that are reproducible especially for clinical applications.

If someone curious in attending your course asked you for feedback or advice on it, what would you tell him/her?
Anyone interested in understanding the history, present and future of proteomics should attend this course. It is a great place to learn new techniques and grow from others .

What do you like most about your time at CSHL?
I especially liked meeting different people from all over the world and in different stages of their academic careers. There was a great sense of camaraderie as a result of shared common experiences and frustrations, and the realization that our challenges and aspirations are the same regardless of our geography.

Nyari received a stipend from the Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD) to cover a portion of her course tuition. On behalf of Nyari, we would like to thank NICHD for supporting and enabling our young scientists to attend a CSHL course where they expand their skills, knowledge, and network. 

Thank you to Nyari 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.