Metabolomics Course

Visitor of the Week: Neetika Jaisinghani


Meet Neetika Jaisinghani of SUNY, Stony Brook. Neetika recently joined as a postdoctoral fellow in Jessica Seeliger’s lab and is finishing up her training at our Metabolomics course. This is her first course at CSHL and we suspect to have her back on campus participating in our future metabolism and immunology meetings.

What are your research interests? What are you working on?
Metabolism plays an important role in the host pathogen interaction of tuberculosis (TB). My research interests pertain specifically to how altered lipid metabolism in the host as well as the pathogen perturb the pathology of the disease. During my PhD, I worked on how infection of macrophages alters their lipid metabolism which finally affects their inflammatory response. And now I am excited to start studying pathogen’s lipid metabolism in Dr. Seeliger’s lab.

How did you decide to make this the focus of your research?
During my initial training at Dr. Sheetal Gandotra’s lab at CSIR IGIB, India, I learnt that tuberculosis infection leads to formation of lipid-rich macrophages in granulomas, the mechanism of which was not clearly understood. I started with a biochemical approach and found out that, contrary to common belief, bacterial infection of macrophages actually did not increase synthesis of lipids in macrophages. This was when I became drawn towards understanding metabolism in tuberculosis infection. I then went on to identify necrotic cell death as the metabolic stimulus responsible for lipid-rich macrophage formation in tuberculosis granulomas.

How did you scientific journey begin?
My interest towards research developed during my PhD in Gandotra’s lab at CSIR IGIB, where I was working with a great group of people who came from different scientific backgrounds. The discussions with my PI and my fellow lab mates kept me up-to-date on the recent discoveries as well as the history of scientific revelations in TB.

Was there something specific about the Metabolomics course that drew you to apply?
While my PhD training helped me gain expertise in studying host and pathogen lipid metabolism with techniques such as biochemical pathway analysis using metabolic labelling, lipid analyses using thin layer chromatography, and confocal microscopy, I lacked mass spectrometry training essential to understanding bacterial lipid metabolism as a whole. The Metabolomics course at CSHL will be beneficial in filling that technique gap and help me answer the unanswered questions from an omics perspective.

What is your key takeaway from the course?
This is a very intensive course on metabolomics, which helped me think about the various techniques of metabolomics that I can use to answer the questions about mycobacterial metabolism. Apart from that, I really enjoyed interacting with the other students, teaching assistants, organizers and the guest speakers. I learnt a lot from their experiences.

If someone curious in attending this course asked you for feedback or advice on it, what would you tell him/her?
I am thankful to the organizers Amy Caudy, Adam Rosebrock and Justin Cross for considering my participation. The organizing team is always available and approachable to answer questions and give their insights on a specific problem. Additionally, the nature of the course is such that you learn a lot at the end of it. I strongly feel that this is the best thing there is for anyone who is beginning to study metabolism.

What do you like most about your time at CSHL?
I like the CSHL campus, it is very scenic and beautiful. The scavenger hunt, beach picnic and sailing trip made my stay such a memorable one. I remember telling my course mates at one point that I don’t want to leave here. CSHL is a wonderful location with a lot of history, just being here inspires me and I’ve heard many of the course mates say the same thing.

Neetika received a scholarship from the National Institute of General Medical Sciences (NIGMS) to cover a portion of her course tuition. On behalf of Neetika, thank you to NIGMS for supporting and enabling our young scientists to attend a CSHL course where they expand their skills, knowledge, and network.

Also, thank you to Jessica Seeliger for encouraging and supporting her lab members to take part in our training courses – and simultaneously. (Nuri Kim is currently training at our Advanced Bacterial Genetics course. [])Finally, thank you to Neetika for being this week’s featured visitor. To meet other featured scientists – and discover the wide range of science that takes place in a CSHL meeting or course – go here.

Visitor of the Week: Felix Chan


Meet Felix Chan of Brown University. Felix is a postdoctoral research associate in Judy Liu’s lab within the Department of Molecular, Cell Biology, and Biochemistry. He was on campus for three weeks last month participating in the third iteration of the Metabolomics course. 

What are your research interests? What are you working on?
My interest is in characterizing the metabolic activity of the brain during physiological and pathological brain activity. Currently, I am working to characterize the link between pathological seizure activity and sleep in the context of tissue metabolism. 

How did you decide to make this the focus of your research? 
The brain is a unique organ with a high metabolic demand - it only takes up about 2% of the body weight but consumes 20% of the body’s oxygen supply. Yet, not much is understood about the metabolic change that occurs in the brain during a period of intense brain activation, whether in a physiological condition (during cognition, for example) or pathological condition (during a seizure, for example). 

How did your scientific journey begin? 
I have always been interested in psychological theories and research, and the leap I took to study neuroscience stems from how the brain -- as a single organ -- can be responsible for many different functions from crude ones like movement, sensation, and speech to fine-tuned ones like emotion, cognition, and perception. I owe my commitment to an academic research career to the many researchers I interacted with as I earned my Masters and PhD in Newcastle University; particularly my graduate mentors Dr. Gavin Clowry and Professor Mark Cunningham

Felix with fellow coursemates Karin Mitosch and Smitha Pillai getting hands-on practice at operating and analyzing liquid chromatography.

Felix with fellow coursemates Karin Mitosch and Smitha Pillai getting hands-on practice at operating and analyzing liquid chromatography.

Was there something specific about the Metabolomics course that drew you to apply?
I was attracted to the course by the wide range of techniques listed on its overview (here); such as GC-MS to LC-MS, and even Seahorse metabolic flux analyzer. In addition to picking up new techniques, I acquired hands-on experience on instrumentation use and data analysis which was really helpful in learning the theory behind the instruments and practical applications of the techniques. 

What and/or how will you apply what you've learned from the course to your work? 
The knowledge and techniques I acquired from the course will be implemented to design a metabolomics experiment to answer my research question regarding metabolic changes in the brain. 

What is your key takeaway from the course?
I came into the course with a naive perception that metabolomics is an all-encompassing technique to dissect metabolism in a comprehensive manner. Whilst it remains a powerful technique, as with other techniques, it cannot measure every metabolite. Careful thought into the experimental design is what can lead to precise measurements of the metabolites in which you are interested. The course has well-equipped me with skills, knowledge, and techniques to consider my experimental design so that it can answer the scientific hypothesis I have in mind. 

How many CSHL courses have you attended?
This is the first CSHL course that I have attended and it hopefully won’t be the last! 

If someone curious in attending this course asked you for feedback or advice on it, what would you tell him/her?
Come in with an open mind and curiosity to learn about metabolomics. The instructors have worked really hard to design a comprehensive and meaningful course that addresses a wide range of aspects about metabolomics. The course schedule will be intense but with a strong passion in metabolomics, you will get the most out of this course.

What do you like most about your time at CSHL?
I enjoyed the fact that I am learning cool science in a beautiful, serene, and picturesque place that has a rich history in advancing science and technology. You can easily walk around CSHL and see the many evidences of their involvement in advancing biomedical sciences. It helps also that the food served is top-notch and you can eat your meals on a balcony overlooking the beautiful Cold Spring Harbor - never gets old!

Thank you to Felix 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.

A Word From: Adam Rosebrock


Last week, we met with Adam Rosebrock to chat about the CSHL Metabolomics course. Founded in 2016 by Adam, Amy Caudy, and Eyal Gottlieb, Metabolomics is one of our newer courses. The second iteration of the course this summer saw the addition of a fourth lead instructor – Justin Cross – as well as a broader applicant pool and a refinement of how trainees rotate through the instruments.

It’s been a fun trajectory watching the students go from really thinking of metabolomics as a black box to understanding how it works. We have students from computational backgrounds, biology backgrounds, even chemists merging together in this one science. They’ve been working together as a team and it’s fun to watch!
I think of these courses like science summer camp: participants have great shared experiences, become disconnected from the outside world, and build a group of friends with whom they stay in contact for years to come. 

Are there any new developments in the field that are reflected in the course?  

Metabolomics is an actively changing and growing field. And ‘Metabolomics’ means many things to many people; it’s a catch-all word that is incredibly overloaded. Each time we set up this course, we have to think about what metabolomics means in that specific year. We’ve shifted from discovering new compounds every time we do an experiment to accurately measuring a known list of compounds. The changes in these known compounds -- that we thought we knew everything about -- are the meat of the biological story. The regulation of metabolism is really what defines different cell types and different physiological states. Students are now having to turn their thinking from “I want to discover a new compound” to “How do I measure a large swath of chemical matter that’s inside the cell?”
Another major change is the development of new software tools. One of the reasons students from computational backgrounds are great to have in the course is because they can get a better idea of how the data they analyze are generated. 
The course is very technology-driven. Metabolomics is underpinned by mass spectrometry, and instrument vendors are actively changing their offerings as this science becomes a larger part of what we do in the biological community. Every year we have to learn, as instructors, the new toys and tools out there to ensure the course stays current. It's a fantastic opportunity to see first-hand how vendors improve their offerings to suit the changing needs of science.

We have about $2.5 million worth of loaned instrumentation that students get to use hands-on during this course. So what we have is sort of like a flash-mob version of a core facility with high-end, top-of-the-line instruments. It’s a fantastic way for students to come in and have expert practitioners in the field – the instructors – set up machines for them to use. Although a lot of metabolomics is mass spectrometry, we have stuff that people who don’t have mass spectrometers can do, too; you don’t have to have a mass spec in your own lab to do the analyses we teach in the course.

We requested a description of a day-in-the-life of a Metabolomics trainee and, by the sound of it, they are kept quite busy!

The Metabolomics course is intense – science starts at 9 AM and many students don’t head home until nearly midnight. The goal this year was to have a common, defining thread: Students can see how the many different tools of metabolomics analysis play into a single experiment.   
At the beginning of the course, students are asked to give a two-slide pitch on why they chose the course, what metabolomics means to them, and what they want to get out of it in terms of the science. There’s a significant amount of lecture-based learning from my co-instructors and myself where students learn fundamental technologies, applications of different tools and algorithms to biological questions, hands-on time on high-end instruments, and the basic processes in designing and executing metabolomics experiments. The 16-student cohort is split off into smaller groups so that everybody has a lot more hands-on time with both instructors and instruments.
But that’s only part of what we do here. On top of the hands-on and lecture-based learning, students hear talks from more than a dozen invited speakers in metabolism. Each speaker gives a gloves-off chalk talk in the evening after dinner that is meant to be interactive, so the students are able ask questions and figure out tools the speaker used to enable his/her research. The students usually see these invited chalk talks at a time in the course when they’ve just learned the tools from us. The next day, the same speaker gives a more formal 50-minute talk that provides a distillate of the technologies, tools, and ideas into a formal scientific package. 
We’ve also designed a good amount of time for students to propose projects that they would like to execute back in their home institutions. The capstone of the course is for students to tell us what experiment they’re going to do first back home with the tools they currently have, as well as what they would like to do at their home institution but can’t. The idea is to foster collaboration; together, the cohort of students can critique ideas and designs given what they’ve all learned in the course.

We switched gears and talked about the students themselves:

This year, we wanted to bring in a wide range of scientists from different disciplines. I was really stunned by the quality of applications we received: they all asked how they could apply small-molecule metabolism analysis to their science. We have students from the National Institute of Standards and Technology, cancer biologists, and also scientists involved in microbiology and biofuel production. 
The applicant pool was also diverse in age this year. We have students who are as young as first-year graduates or MD-PhD students, and they bring a totally unbiased perspective to science, a real love for learning. They’re able to keep up with the senior graduate students, postdocs, and faculty who make up the rest of the class. They’re all getting along very well, and the age disparity that I initially thought might be a problem has turned out to be fantastic. It created a balance in the student body: the younger students add a spark while the older scientists provide perspective. 

We then looked forward to next year’s application process and applicant pool:

We would love to take twice as many students next year if we could. Unfortunately, we don’t have the bandwidth to do so. I think having a mix of computational and wet biologists is critical. Having a mix of young, fresh faces and grizzled scientists - like myself - is also critical. And certainly a mixture of model systems and kinds of biology is very important. So instead of just being a cancer metabolism course this really has, from the start, been a course about general methods for metabolism measurement and ways of computationally and directly measuring what happens biochemically inside the cell.  

For those interested in attending the 2018 iteration of this course, Adam offers the following advice:

The biggest criteria my fellow instructors and I use in evaluating student applications is “Can you make use of this in your current projects?” Or “Are you turning to projects that will immediately use these tools?” Cold Spring Harbor Laboratory Meetings & Courses Program has a very selective course admission process and we can only take roughly 16 students a year. There are many who would love to learn the theory and perhaps the practice behind this science just to have that added to their knowledge set. But as much as we love teaching and learning, our main goal is to train the next generation of scientists who can take these tools into the greater scientific community.

The Metabolomics course may have just finished its second iteration, but it has already been mentioned and recognized in publications.

I recently attended the American Society for Mass Spectrometry meeting which is an international meeting of a diverse range of mass spectrometrists, including metabolomists. At that meeting and many others I’ve been to over the last year, it’s been fantastic to see alumni from our 2016 course presenting talks and posters, demonstrating the power of this course and its effects on the greater science community. We’ve already been acknowledged in 1 publication, with another in the final phase of revisions.

We concluded our conversation discussing how Adam sees the field of metabolomics evolving, and the overall goal he and his co-instructors have for course alumni. 

While we do our best to present students with a wide range of different scientific approaches and technologies, there’s no way to encapsulate all of metabolomics into a 2- or 3- week course. Our main goal is to foster independent, metabolomics-empowered scientists.  

As metabolomics becomes a more mature field, it will be easier to have the actual measurements done by somebody else. Therefore, we try to teach students how to think about the design of an experiment -- to make a proper contrast to ask the question they want and then, with the raw data, figure out what’s inside and make their own scientific interpretation. That way, in a future where the mass spectrometry happens in some distant core facility, the students are still empowered to design proper experiments, generate biological samples that can be run through a mass spectrometer elsewhere, analyze the data, and make their own biological conclusions.

Thank you to Adam for taking the time to chat with us. For more conversations with our other meeting organizers and course instructors, go here. Also, to gain a trainee's perspective on the Metabolomics course, read our Q&A with Vita Stepanova.

Adam helping the Metabolomics course capture another Scavenger Hunt win.

Adam helping the Metabolomics course capture another Scavenger Hunt win.

Visitor of the Week: Vita Stepanova


Meet Vita Stepanova of the Skolkovo Institute of Science and Technology (Russia). Vita is a PhD student in Philipp Khaitovich’s group in the Skoltech Center for Data-Intensive Biomedicine and Biotechnology. She sets foot on CSHL for the first time to attend the second iteration of the Metabolomics course. Read on for more on her work and feedback regarding the course.    

What are your research interests? What are you working on? 
My research interests focus on autism spectrum disorder (ASD) and human brain developmental disorders. I've been studying ASD genetics and now I am switching my focus from genes to metabolites to investigate pathways affected in autism.

Was there something about the Metabolomics course that drew you apply? 
This course is comprehensive and it takes a systemic approach to cover the whole area so we, the trainees, return to our labs with an understanding of metabolomics and certain methodologies.
What is your key takeaway for the Course?
Metabolomics is a powerful tool to explore new compounds and biological strategies, as well as a fascinating area of research. 

How many CSHL courses have you attended?
This is my first time here at CSHL and I've already been thinking what other course I can participate in so I can come back. 

If someone curious in attending your course asked you for your feedback or advice on it, what would you tell him/her? 
I would tell him/her a detailed story of my experience, including application submission, my personal feelings about the course, and what I got out of the course.

What do you like most about your time at CSHL?
I appreciate how much our course instructors are engaged at our needs, at our comfort, and making sure we absorb as much of the course as possible. 

Vita received a stipend from the Howard Hughes Medical Institute to cover a portion of her course tuition. On behalf of Vita, 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 Vita 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.