Proteomics Course

Visitor of the Week: Modesta Akoth

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Meet Modesta Akoth of Egerton University (Kenya)! She is a graduate student in the Protozoology and Molecular Biology labs within the Biotechnology Research Institute, KALRO (KARLO-BioRI). Modesta spent last week with us at the Proteomics virtual course, her first course at CSHL, the format to which she found “convenient in reaching out to a wider audience globally.”

Tell us about your research.
My research entails using proteomic approaches to identify the mechanism(s) of drug resistance in African trypanosome, the hematophagous parasite that causes sleeping sickness in man and Nagana in animals.

How did you decide to focus on this area/project?
From the reported records on upsurge of drug resistance in African trypanosomiasis by other researchers as well as a gap identified from a related study by one of the students in our labs led to this area of study.

What and/or who is the inspiration behind your scientific journey?
The inspiration has been self-driven since I have always been enthusiastic about research. Dr. Paul Mireji, a senior research scientist at KALRO-BioRI has also been instrumental in my scientific journey.

What impact do you hope to make through your work?
I am hopeful that my work will identify potential target sites which will provide insight into the development of novel drugs. This will improve disease management hence, better quality of life among the affected marginalized population. 

What do you love most about being a researcher?
The ability to explore and discover something that can be beneficial if implemented is very fulfilling to me.

What is your key takeaway from the Course; and how do you plan to apply it to your work?
My key takeaway from the course is to work with what works best for me because there will always be working environment factors to consider like the possible limitation in the equipment available. Also, ensure credibility and reproducibility of the generated results.

What feedback or advice would you share with someone considering to participate in this course?
The course is very informative and has competent facilitators with vast knowledge in the area of proteomics, therefore, s/he should not be hesitant to apply if the opportunity avails.

What’s the most memorable thing that happened during the Course?
The prompt elaborate responses by the lecturers towards the questions raised as well as being able to cover almost all aspects of proteomics within four days was remarkable.

Modesta received financial support from Regeneron to cover her course tuition. On behalf of Modesta, thank you to Regeneron for supporting and enabling our young scientists to participate in training courses where they expand their skills, knowledge, and network.

Thank you to Modesta 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.

Image provided by Modesta Akoth

Visitor of the Week: Timothy Licknack

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Meet Timothy Licknack of Arizona State University! Tim is a member of Michael Lynch’s lab within the Biodesign Center for Mechanisms of Evolution. Over the past few days, he joined an international cohort for our virtual Proteomics course -- the first CSHL course for the graduate research assistant. 

Tell us about your research.
My research is broad ranging into the evolution and physiology of Paramecium, which is a genus of single-celled eukaryotes with some unique properties that make it ideal for evolutionary and cell-biological studies. I have focused on gene expression at the level of transcription initiation and am moving into the world of proteomics to look at how the proteome localizes into distinct subcellular compartments and how it’s remodeled in various growth and temperature conditions.

How did you decide to focus on this area/project?
My projects have all been natural byproducts of the people around me; almost all resulted from chance conversations with lab mates and colleagues with shared interests. My PI has given me a lot of leeway to mold my projects in whatever direction gives me the best chance to produce useful and interesting data. 

What and/or who is the inspiration behind your scientific journey?
I can’t really say that I have a scientific or personal inspiration that has affected my research path in any meaningful way. I can only say that a consistent person who has shown me unconditional support has been my mom, who might not understand what I do, but she tries hard to express how proud she is of my journey, even when I myself don’t agree with her assessment. 

What impact do you hope to make through your work?
I really hope to make a meaningful contribution to the scientific community at the level of my nascent field of Evolutionary Cell Biology and more broadly in my Paramecium and Ciliate Genetics/Genomes community. I don’t think my work will be groundbreaking, but I think my data will help researchers to better understand the generality and universality of cell biological features. I’d like my Ph.D. to result in a comprehensive analysis of gene expression across Paramecium at the mRNA and protein levels that can be coupled with rigorous evolutionary studies to understand the forces that shape phenotypic variation. 

Where do you see yourself in five years?
Like most new Ph.D. students, I had grand plans to publish heavily, get a great postdoc, and start a lab centered around solving the questions that most interest me. Recently, I’ve become less committed to this route and don’t really even imagine doing a postdoc, unless a really perfect opportunity presents itself. My exact route will play itself out over the next year or so, but I’d really like to work in biotech or in biosecurity. I think I bring a unique background that might make me well-positioned to examine phenomena in different contexts than are currently predominant. 

What do you love most about being a researcher?
I really love the research environment most of all. I joined my lab in part to have at least 5 years dedicated to picking my PI’s brain on diverse topics. The community of researchers in my lab and center have really driven my understanding of topics previously foreign to me. I think my understanding of biological systems is richer because of those interactions. I do love when experiments work, but it’s the people and connections that provide the most obvious benefits to my everyday life.

What drew you to apply to this course? I think there’s no substitute to learning directly from experts. I’m new to proteomics, and I have an excellent colleague with whom I communicate frequently about mass spectrometry inquiries, but I have not received direct training on the ins and outs of this process, its limitations, and its possibilities. I want to know the standard methods and the conditions under which one might deviate from those. I want the tools to better think like a mass spectrometrist, and I hope that is reflected in the quality of data I manage to produce.

What is your key takeaway from the Course; and how do you plan to apply it to your work?
My key takeaway is that this process is filled with uncertainty at every level, and in some cases that uncertainty can propagate downstream, such that biological interpretation must only be done when the appropriate conditions are met. In terms of application, I think this will manifest itself in how I perform my pre-LC/MS steps via a consistent sample prep and in how I order multiple samples to reduce technical variation confounding biological variation.  

What feedback or advice would you share with someone considering to participate in this course?
I came into this course with a pretty specific project in mind and interpreted all the lectures through that lens. I wish that I had prepared more questions in advance, so that I could check them off and bring them up when appropriate. The condensed nature of this course made things a bit trickier, but I think it would be a good general rule to know what you want out of this experience before beginning. There’s a lot of information, and it’s very easy to get lost. A specific project and specific goals can help orient you through this maze. 

Anyone considering attending a CSHL course should consider how their research projects might be advanced from the lectures and activities provided in the course. They’ll need to understand just how packed these lectures are with information and come prepared to absorb as much of that as possible. They should come in with specific goals in mind and specific topics that they want to clarify. They will also want to find a quiet place in their house or office where they can really focus, because even a moment of relaxed attention can displace you for the entire lecture. I highly recommend attendance for anyone who doesn’t have access to experts in their field of study or who do and want to see another perspective. 

What’s the most memorable thing that happened during the Course?
I love history, both in general and with respect to scientific disciplines. I always like to start off talks by going back to the roots of a topic, finding the first person to do this or the inventor of that. So my most memorable experiences usually involved Daryl Pappin bringing that perspective into each lecture through his pointed comments. Whenever a seemingly random topic appeared on the slide, the lecturer usually did a great job to explain it, but Daryl had a knack for connecting that topic to some other topic previously discussed, typically through shared authorships or academic connections. That way of thinking really helps me understand the genesis of a field and its methodology, so I noted names, connections, and collaborations whenever possible.

Due to the pandemic, this course was transformed into a virtual course -- what do you think of the virtual format?
I would not have been able to attend this course had it not been virtual. Putting this material online was a great idea and surely made it far more accessible to many more researchers. In terms of execution, I think it went about as well as most Zoom meetings we’ve all had over the last few months. Minor technical difficulties, but the information was still there.

Thank you to Tim 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.

Visitor of the Week: Camille Trinidad

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Meet Camille Trinidad of the University of Kansas Medical Center. A member of Dr. Andrew K. Godwin’s lab, the fourth-year PhD student is currently with us training at the Proteomics course. This is Camille’s first course at CSHL and the Filipina is interested in eventually adding the Programming for Biology course to her CSHL course repertoire.

What are your research interests? What are you working on?
I study the role of extracellular vesicles in ovarian cancer development and metastasis. Part of my work also involves looking for potential biomarkers in extracellular vesicles for the early detection of ovarian cancer, which is a significant unmet clinical need in this area.

How did you decide to make this the focus of your research?
I have always been interested in immunology, specifically in cancer immunotherapy. I initially wanted to work on CAR-T cells but due to unforeseen events I had to move to a different area. I do appreciate working on the early detection of ovarian cancer, since treatment has been shown to be more effective if this disease is detected earlier.

How did your scientific journey begin?
I am from the Philippines, and was initially interested in science because of my teachers back in grade school and high school. In college, I really enjoyed the experience of working in a translational lab, in spite of all the difficulties one can imagine, conducting science in a resource-limited environment. I think that having a string of good mentors and labmates was a big factor in my decision to pursue science. 

Was there something specific about the CSHL Proteomics course that drew you to apply?
Mass spectrometry has recently become a very attractive and interesting method for profiling the vesicles that I study. This course covers both the theoretical and practical aspects of MS really well, so it was an easy decision to apply.

What and/or how will you apply what you’ve learned from the course to your work?
The course has been amazingly helpful for both experimental design and working with the current algorithms for proper and rigorous data analysis/interpretation. By taking this course, I can definitely better set up experiments for our lab’s current and future projects.

What are your takeaways from the course?

  1. Experimental design is crucial.

  2. There are many ways to interpret the humongous data sets we generate, but we must be very careful in analyzing the results and be transparent with how we arrive at any conclusions.

 If someone curious in attending this course asked you for feedback or advice on it, what would you tell him/her?
I highly recommend taking this course if you want to delve into proteomics work, since this covers everything; it is really intense. The best part is that the instructors are all very approachable and knowledgeable. We run several programs that are instrumental in both data acquisition and analysis. Also, the instructors are very accommodating when you have several questions about your own projects

What do you like most about your time at CSHL?
CSHL is absolutely beautiful. With tons of space right next to the water, I really enjoy walking around and fishing.

Camille received financial support from Regeneron to cover a portion of her course tuition. On behalf of Camille, thank you to Regeneron for supporting and enabling our young scientists to participate in training courses where they expand their skills, knowledge, and network.

Thank you to Alison 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: 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 tripPhoto: 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.