A Word From: David Jackson, Todd Mockler & Jane Parker

In late 2017, we hosted the eleventh biennial CSHL meeting on Plant Genomes & Biotechnology: From Genes to Networks. The meeting debuted in 1997, and there have been monumental advances in the field during the intervening two decades. We met with meeting organizers David Jackson, Todd Mockler, and Jane Parker for a quick chat to hear their thoughts on the field’s evolution.

Jane: One obvious advance to me, and it struck me at this meeting particularly when compared to the one two years ago, is this merging of computation and high-end sequencing. It’s transforming biology and bringing together different disciplines that center around it.

Todd: I would echo the point that sequencing has changed all of biology. I don’t think there’s a single talk at this meeting that hasn’t been impacted by cheap, fast, genome sequencing. The 1997 meeting was when the Arabidopsis genome was the first plant genome to be sequenced.

David: It wasn’t even finished.

Todd: And now just about every plant that’s been discussed here has a sequenced genome. That’s been revolutionary. It’s changed everything.

David: I will add CRISPR. It’s a more recent advance, but it allows us to use all of this genome sequencing data to go in and modify plant genomes and find out what they’re doing. We had a session dedicated to CRISPR this year and we heard CRISPR talks in several other sessions.

Having had attended the 1997 Plant Genomes meeting, David took us on a quick trip down Memory Lane before the organizers collectively listed what’s changed – and stayed the same – about the meeting. 

David: During the first meeting in 1997, I remember driving into Huntington in the back of someone’s pickup truck and it was absolutely freezing. It’s a lot warmer this year, the climate has gotten warmer. And the food’s a lot better. There’s also less focus on Arabidopsis, although it’s still incredibly important as a model. With the new tools, we’ve seen really impressive talks using other plants that five years ago wouldn’t have been possible.

Jane: I would endorse that. Less focus, perhaps, on individual components but a broader focus on trends and processes that are enabled by new tools and technologies.

Todd: My perspective is shorter because I’ve only come for the last four meetings. I think the caliber of science is the same but the topics have changed, because there’s this march of technology. There’s a lot more research that has computational aspects, bioengineering, ‘omics, and all kinds of genomic analysis. It’s just the nature of where science is going. In my memory, we had more engineering and modeling this year – almost purely computational things – and that’s really interesting. Those are some of the coolest presentations that I’ve seen.

Jane: And presented in such a way that people who are not in computation can understand. The communication is what I found really impressive this time.

Technology was a clear theme throughout the conversation, so we asked their thoughts about it:

Todd: It’s a net good but – even as I made the comment about fast, cheap sequencing being revolutionary – you can’t answer every question with sequencing, right? There’s still a place for biochemistry and other basic biological techniques.

David: They go hand in hand. The more you can do in science, the more need you have to develop the technology, and that invents more science. I’ve had this concern that as science moves more quickly, as CRISPR did, people may become less interactive because it’s much easier to get scooped. I work in maize and at the Maize Meeting we talk about genetic projects that may take 2 or 3 years to get to a certain point, so you don’t feel bad talking about it before publication. But with CRISPR, I can go to my lab now and design a construct in about a month. But I haven’t seen that occur much; people are still interactive so this isn’t yet an issue.

An intimate meeting, the organizers commented on how Cold Spring Harbor plays a major role in the overall atmosphere at Plant Genomes & Biotechnology.

Jane: I think a lot of people come here because they appreciate the breadth of topics. I certainly do.

Todd: I think the breadth and the small size.

Jane: And the informality that goes with the small size. The students and postdocs don’t feel too intimidated and so there’s lots of discussion.

Todd: During the breaks, there’s always lots of conversation.

David: It’s quite a diverse meeting. I was commenting to one of my non-plant colleagues that it’s very diverse and they said, “But it’s all on plants!” And I said, “Well, you don’t have a meeting called ‘Animals’, you have a meeting on one pathway in animals!”

Our discussion concluded on their attendee wish list; specifically, who they would like to see more of at the next meeting. 

Jane: As many postdocs and students as we can get in, really getting labs to support them coming.

David: It’s always great to get lots of young people. I think this meeting is especially great for graduate students who are close to finishing. They can present their work and also look for a postdoc position, because they can meet lots of different people in different areas.

Todd: A type of attendee that I’d like to see more of is program officers from funding agencies. This year, we had someone from the Gates Foundation and in the past we’ve had people from NSF attend.

David: Yeah, they hear about the science which helps them in future rounds of funding. It’s also great for faculty - especially junior faculty - to interact with program officers because it helps their grant proposals.

The Plant Genomes & Biotechnology: From Genes to Networks meeting returns to the Laboratory in 2019. Also, every summer, we offer the Frontiers and Techniques in Plant Science course.

For more conversation with other meeting organizers, check out the rest of our A Word From series. 

A Word From: Fiona Watt, Marius Wernig & Ken Zaret

L to R: Ken Zaret, Fiona Watt, Marius Wernig; Photo by Constance Brukin

The fifth biennial meeting on Stem Cell Biology was held at Cold Spring Harbor Laboratory September 25-29, 2017. We spoke with the meeting’s organizers Fiona Watt, Marius Wernig, and Kenneth Zaret, about changes the field and meeting have experienced over the past decade.

Fiona: At huge stem cell meetings, all constituencies are represented and there’s usually a focus on the translational aspect: getting cells into therapies and patients. That’s really important, but here we’re mainly focused on mechanism.

Kenneth: I’ve heard from a lot of people this year that they really enjoyed the program because the emphasis is on understanding mechanism and how things work. There was a period when the stem cell field and meetings were often characterized by more descriptive stuff: “Let me show you what I can differentiate my stem cells into and how well that works.” But there's been a sort of resurgence of the basic science underlying those processes, and that has made this meeting more interesting. 

Marius: Yeah, now there’s much more understanding. The protocols have improved, and the cells have actually gotten useful for various purposes. In addition, there is a lot of new technology, particularly single cell approaches. I think we had some spectacular talks at this meeting on the new directions taken. 

Fiona: The other thing I like is that, in the past, you would be interested only in your own stem cell, your own experimental model. As mechanism has come to the fore, there’s so much you can pick up regardless of what the experimental system is. 

Kenneth: More general principles.

Fiona: Exactly. 

Marius: Stem cell biology is a great glue that can bring together people from completely different disciplines. For example, I would never normally talk to someone who studies livers. But with stem cells as a common denominator, the liver person and I may use similar experimental approaches, and so we can learn from each other technically and conceptually.

Kenneth: And that’s all enabled by talking about the underlying mechanisms and processes rather than descriptive phenomena surrounding them. 

With these changes in the field, we were curious to learn of the developments they personally found most exciting: 

Marius: At this point, the single cell technology is only descriptive but it’s still exciting. People are now realizing that they have to partner it with functional assays.

Kenneth: In addition to single cell analysis, we heard exciting new ways to do lineage labeling, and to map fields of cells based on their polarity in 3D, which I thought was a neat technological advance. 

Fiona: People are also getting more rigorous with their terminology. Christopher Lengner gave a really interesting talk about quiescent stem cells in the gut that started off by defining exactly what it means. It’s that rigor and good experimentation which I’ve really enjoyed. 

Kenneth: Another dimension is that the new technologies require sophisticated math and statistical analysis that a lot of biologists don’t have. It’s resulted in an influx of people from physics, statistics, and math to the field, which has been great. 

Our chat concluded with who they thought would benefit most from attending the meeting, and what makes the CSHL Stem Cell Biology meeting unique:

Kenneth: People studying disease could benefit from the sophistication now in our field, to model human disease using stem cells -- genetic disease, susceptibility or response to drugs, things like that. As Marius said, we’ve gotten so much better at making different types of cells, organoids, and higher-order structured tissues, and using them in assays. Those who might have thought that anything other than an animal study would be difficult, are now enabled by technology in the stem cell field.  

Fiona: There’s something for everybody but I think it’s important to give postdocs and PhD students exposure to the best stuff going on in the field, because that inspires them. We also made a big effort in 2017 to ensure a lot of early-career, independent researchers presented their work. 

Marius: Folks who just started their own lab or are about to start one could benefit from attending this meeting. They not only stay current with new content, but they also meet people in the field. Networking is really important.

Fiona: I brought three PhD students to the meeting this year, and two gave posters in the same session. They were shocked that anybody would want to look at their posters, and were exhausted by the level of questions. There were a lot of good questions in all the sessions, very good-natured and constructive questions.

Kenneth: I got feedback that the small size of this meeting and its intimacy allowed people to talk directly to one another. It was easier for younger participants to talk to the more established people. 

Marius: I also heard from participants that the setting here is just so supportive of interactions and discussions.

Kenneth: You’re sequestered , if you will, on a single site, and you’re cloistered in a way that makes it very, very concentrated. The geography encourages you to be with people, talk science, and make it as meaningful as possible. That’s what distinguishes a Cold Spring Harbor meeting from many other venues. Also there’s so much history here: You walk around and see pictures where scientists are made to be heroes. Where else can you go where scientists are heroes? For young people, it’s very inspiring. I came to my first CSHL meeting in the late 1970’s, I gave my first talk here - ever - in 1980, and I couldn’t have been more scared or thrilled. 

The Stem Cell Biology meeting returns to the Laboratory in 2019. Visit our website for a list of the meetings and courses taking place in 2018.

For more conversation with other meeting organizers, check out the rest of our A Word From series. 

Repeat Visitor: Sumangala Shetty

Every so often, we host a course trainee multiple times in a year. One such trainee from 2017 is Sumangala “Suma” Shetty, a research and teaching specialist at Paul Copeland’s lab in Robert Wood Johnson Medical School – Rutgers University. 

Suma made her debut at CSHL Meetings & Courses six years ago when she attended the 2012 Translational Control meeting. She still clearly remembers being surprised by the “talks [going] past 10 PM” and that “attendance was still at its peak during the evenings”. Last year, Suma returned to CSHL to attend three courses – The Genome Access Course, Scientific Writing Retreat, and Computational Genomics – and from our conversation it doesn’t seem like we’ve seen the last of her. 

Tell us about your research interests and what you’re working on. 
My research focuses on understanding the mechanism of synthesis for a specialized group of proteins referred to as selenoproteins. Selenoproteins play a crucial role in cellular homeostasis, thyroid hormone metabolism, redox regulation, storage and transport of selenium, protein folding, and signaling skeletal muscle regeneration.

The Genome Access Course, Fall Session, 2017

We offer roughly 30 courses per year and you participated in three of those courses last year. How did you decide which courses to apply for?
In concert with my want to transition into an independent scientist, I have been focusing on developing new skill sets to keep pace with emerging data mining techniques and high-throughput screening methods for genomic data analysis. Since independent research relies on grant funding, I was interested in a workshop that focused on grant writing. Similarly, I surveyed for courses on bioinformatics and data analysis tools. There are several online tools and resources, and I have acquired several online certificates for data analysis as well as developed programming skills using Python. But I was longing for face-to-face interaction with fellow beginners to discuss pitfalls and potentials, and, most importantly, get feedback. 

Keeping in mind my two goals and learning environment criteria, I consulted my mentors for advice. In addition, in December 2016, I attended a CRISPR workshop by NIH where I met Dr. Vielka Selezar. At that point in time she had just joined Cape Breton University (Canada) as a new faculty member and was in a similar situation as me so I asked her for advice. She shared with me her learning experience at CSHL’s Computational Genomics course and highly recommended it. Interestingly, when I visited the CSHL website, I found several other courses that suited my needs and I narrowed down the list to the three most relevant for my career. 

What is your key takeaway from each of the three courses?
I totally enjoyed each of the courses, especially given their highly-interactive setups. The Genome Access Course exposed me to a rich collection of databases and tools. It was so engrossing and involved that I didn’t even need my second shot of caffeine in the afternoon! Totally loved it and, in fact, I think The Genome Access Course should be made mandatory for all graduate students.

Scientific Writing Retreat, 2017

My second course was the Scientific Writing Retreat. This workshop was an eye opener for several reasons: 1) It taught me how to overcome writer’s block and clean a draft for clarity; 2) I learned inside information on how a manuscript submitted to a journal is reviewed and how to improve the chances of it being accepted; 3) I chatted with a grant writing expert; and 4) The one-on-one review of my manuscript draft was, in my opinion, the best feature of this course. At the end, I felt like my fellow participants, the mentors, and I had become a tight-knit network that I could always approach with any of my tough writing issues. Charla and Steve thank you very, very much. 

And finally, Computational Genomics was the most intense and most exciting seven-day course I have ever attended. We were in class almost all day till midnight and still every one of us showed up at 9:00 the next morning. It was highly informative and full of new tools to explore. My favorite part was working in teams on our take-home midterm exam and also on our final project, because I learnt a lot from my course mates. Also, through an online course on genomic data analysis by Johns Hopkins University, I had heard lectures from James Taylor and Jeff Leek but it was cool and an honor to meet and hear them in person at the course. They were extremely helpful, very humble, and the course was much more fun than an online course. 

One similarity I noticed that was consistent in the three courses is that all of the course mentors were highly motivated and inspiring. They were extremely helpful, always available, and their enthusiasm was infectious.

Have you already applied what you learned from each course to your work?
I am using the data analysis tools on our pre-existing RNA-seq and proteomics data, and currently, we are storyboarding some new applications for our project using genome analysis tools. Also, tips from the Scientific Writing Retreat enabled me to finish my manuscript. 

Computational Genomics, 2017

If someone interested in a CSHL course asked you for advice, what would that be?
After my experience, I strongly believe that CSHL courses are a crucial resource for learning current techniques under the direct supervision of the experts. I think a stronger awareness about CSHL courses should be raised among graduate students and postdocs; and therefore, I would strongly encourage those interested in a CSHL course to apply. A number of the courses post their past lectures online so it’s easy to browse the content and analyze if the course will suit your needs.

Our readers are curious about how course tuitions are funded. Would you like to share how you were able to pay for three courses in one year? 
I am fortunate in that my PI, Paul Copeland, strongly supports my career growth. We both agreed that expanding my skill set will add new insights to our current projects and, therefore, I received financial support for my courses from Paul.

What did you like most about your time at CSHL? 
The intensity and enthusiasm of everyone I met. More importantly, the one-on-one interaction and personalized discussion with experts on our individual projects.

Do you have any future plans to attend another course or, perhaps, a meeting at CSHL?
Absolutely yes. The CSHL Meetings & Courses website is in my browser favorite list, and I am already planning to apply for the Statistical Methods for Functional Genomics course. 

Thank you to Suma for sharing with us her experience. We look forward to having her back at the Laboratory soon. 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: Denise Monack, Raphael Valdivia & Malcolm Whiteway

In September 2017, Denise Monack, Raphael Valdivia, and Malcolm Whiteway organized the eleventh meeting of Microbial Pathogenesis and Host Response at the Cold Spring Harbor Laboratory. We met with them to talk about how the meeting has changed and the role that scientific inclusivity plays in its growth.

Raphael: When I was a starting faculty member, my view was that there are categories of microbial pathogenesis that you always have to cover. But over the last few years – and probably since I’ve become a meeting organizer – one of the goals has been to expand into areas where we think the field is moving, or perhaps where the exciting new advances will be happening. Rather than being stuck in a “this is what we need to cover” framework, it’s become more about “where is the future of the field?” 

Denise: I agree with that. The first time I attended this meeting was as a graduate student and I remember a lot of the talks were on the pathogen side, with maybe an infection slide here and there. Now it’s both, and the 2017 meeting in particular covered both sides. People are using Collaborative Cross mice and infecting them to get at host genetics. And with CRISPR/Cas9 you can make mutants much more easily, so I think the host side is getting more coverage. 

Raphael: Also, since we work with people who are outside of what’s considered the standard microbial pathogenesis field, another goal for the meeting is to bring some of those individuals into this field of study because we’ll learn from them. 

Denise: Exactly. That’s why I intentionally invited Isaac Chiu, a neuorimmunologist from Harvard, to give a talk. Since he isn’t a microbiologist, he was really nervous about his lecture. But people in this audience want to hear about neuroimmunology, not take apart his microbiology, so he felt welcome and comfortable. 

Malcolm: Those talks where someone says “nerves for pain are connected to the immune system,” they open a lot of eyes.

Raphael: Similarly, we invited Lawrence David from Duke to give a talk in 2017. He doesn’t work on pathogens but on microbial ecology in the gut, so the perspective he gave was very, very different than what most people in the audience are used to thinking. Getting out of your comfort zone and thinking about your research problems from a different view point is always useful. 

Malcolm: Two years ago, I invited Hendrik Poinar from McMaster University to give a talk. He looked at the plague from an ancient pathogenesis angle that was really cool and well-received. Those are the kinds of things you go back to and think about.

Raphael: That’s right, because they just stick with you. We only know what we know, and sometimes it's what we don’t know that we find most interesting. The 2017 meeting had a session focused on imaging technologies for this reason. A lot of people had not heard of the techniques presented in that session but now they can ask, “How can I apply this technology in my own research questions?” 

Denise: Some of the pathogenesis meetings I go to are almost exclusively on bacteria, so we’ve made this meeting much more multi-organismal. In the future, I’d like to have it be not just for bacterial or fungal pathogens, but maybe invite some specialists in eukaryotic parasites as well. That would make this the go-to meeting for pathogenesis in general.

As the meeting continues to evolve, we wanted to know who they thought would benefit the most from attending: 

Malcolm:  If I was an advanced graduate student looking for a postdoc, I’d want to go to a meeting like this. Besides seeing a lot of different research perspectives, graduate students will also be introduced to people who are at the top in the field, people they’ll want to do postdocs with. 

Raphael: Postdocs looking for faculty positions can also benefit from this meeting because PIs who come here represent departments looking for talent. And for junior faculty, the ability to network and have one-on-one interactions with others in the field is key. That’s one of the reasons why, at the beginning of the meeting, we remind everyone to step out of their comfort zones and make sure they’re not only listening to the science, but also getting into those one-on-one interactions. The science is the hook that allows you to engage a person; if you’re interested in what they’re doing, it is likely that they’re doing a bunch of other things you’ll also find interesting. You never know what opportunities or collaborations will emerge. 

We closed our discussion chatting about what made their meeting different from other pathogenesis meetings:  

With CSHL Meetings & Courses Executive Director David Stewart at the meeting's Wine & Cheese event. Photo: Constance Brukin

Raphael: Well, the organizing team is top-notch.

Malcolm: And the venue is top-notch too.

Raphael: There is something about the environment here. I remember when I first came to the meeting, I just walked around the halls and saw pictures of heroes in science interacting in this setting. It’s a vibe you don’t feel in many places; it’s hard to replicate.

Malcolm: I completely agree. I’ve been coming to Cold Spring Harbor for decades and I loved it from the very beginning. It just has so much history that’s central to molecular biology. It’s great to be in a place with that historical connection…that vibe. 

The Microbial Pathogenesis and Host Response meeting returns to the Laboratory in 2019, where Anita Sil will join Denise Monack and Raphael Valdivia as meeting organizers. If you’re looking for a meeting in the years that Microbial Pathogenesis and Host Response is not at CSHL, the Gene Expression & Signaling in the Immune System meeting is a great alternative.

For more conversations with other meeting organizers, check out the rest of our A Word From series.

Visitor of the Week: Irene Faravelli

Meet Irene Faravelli of Università degli Studi di Milano (Italy) where she is part of the Neural Stem Lab led by Stefania Corti. The fourth-year resident in Neurology, however, is currently spending a year in Columbia University in Serge Przedborski's lab under Francesco Lotti's guidance. Irene made her inaugural trip to the Lab to participate in the 2017 Development and 3D Modeling of the Human Brain.  

What are your research interests? What are you working on?
My main focus has always been neuromuscular disorders of both childhood and adulthood. I use different cell and animal models to dissect the pathogenetic mechanisms underlying these diseases.

Was there something specific about the Development and 3D Modeling of the Human Brain meeting that drew you to attend?
I was particularly interested in the cerebral organoid topic as this is my main field of research back in Italy. In addition, as soon as I knew that Paola Arlotta (whose lab I’ve had the chance to visit for a brief period of time) was among the organizers, I knew this would be an incredibly interesting meeting.

What is your key takeaway from the Meeting?
The rapid speed in which the organoid field has grown in recent years, and how cutting-edge technologies have been applied to different aims with increasing and fascinating complexity.

If someone curious in attending a future iteration this meeting asked you for feedback or advice on it, what would you tell him/her?
I would tell him/her that this is a marvelous opportunity to keep updated in the advances of this rapidly evolving field and, also, to interact with the most important exponents of research on organoids.

What do you like most about your time at CSHL?
I really enjoyed the feasibility of meeting people from different countries and laboratories, and with varying backgrounds in a friendly and lovely context. 

Thank you to Irene 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.