Visitor of the Week: Jackson Tonnies

Meet Jackson Tonnies of the University of Washington! A member of the Christine Queitsch/Josh Cuperus lab in the Department of the Genome Sciences, the graduate student joined us at last week’s Plant Photobiology – ISPP 2021 meeting. At his first CSHL meeting, Jackson presented a poster entitled “Synergy between functional elements drives activity of light-responsive enhancers”.

Tell us about your research.
I currently work on understanding the rules that regulate DNA expression in crop plants. Recently, I have been focused on picking apart a few pieces of DNA that help plants respond to light.

How did you decide to focus on this area/project?
I decided to go into plants because I want to help ensure the food supply continues in spite of future changing climates.

What and/or who is the inspiration behind your scientific journey?
Before college I wanted to work in solar power, battery creation, or biotech with an emphasis on agriculture as those were the areas that I thought to be important. I chose plant biotechnology because I like studying plants the most.

What impact do you hope to make through your work
By illuminating regulatory rules in plants my research will enable improved crop breeding and reduce the land acreage required to feed the world’s population.

What do you love most about being a researcher?
The best part of being a researcher is the ability to continue to learn and have access to those who are also passionate about what they are studying.

What drew you to attend this meeting?
Finding and connecting with researchers with a deep knowledge of light responses in plants.

What is your key takeaway from the Meeting; and how do you plan to apply it to your work?
The key takeaway is that light response is a multifaceted, deep area of study. I learned a lot about the players on the protein side of plant regulation and will try to use this viewpoint to inform my genomics analysis in the future.

What feedback or advice would you share with someone considering to participate in this meeting?
I would recommend trying to balance focusing on the speakers that most interest you with exploring areas of the conference that are outside of your usual interests. It can be daunting with the number of talks/posters but it makes for a great collection of cool science.

What’s the most memorable thing that happened during the Meeting?
I really enjoyed the session on optogenetic tools. It encouraged me to think about new ways that these tools could be used. Tools such as green light receptors and systems that ignore day/night cycles open up a lot of possibilities in plants.

Thank you to Jackson 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 Jackson Tonnies

Visitor of the Week: Sunil Kumar Kenchanmane Raju

Meet Sunil Kumar Kenchanmane Raju of Michigan State University! A research associate in Chad Niederhuth’s lab within the Department of Plant Biology, Sunil returns to CSHL for another plant science-centric course. In 2015, Sunil trained at the annual summer course on Frontiers & Techniques in Plant Science. This year, he is back for the week-long Workshop on Cereal Genomics where he is picking up techniques he’ll use to help analyze his ATAC-seq data. Sunil has also been a CSHL course ambassador of sorts, informing his fellow workshop trainees that the course goes beyond the lecture room: Speak with everyone in the course and build your network – including the instructors and lecturers. 

What are your research interests? What are you working on?
My research focuses on how plants adapt to changing climates and how genomic interactions with the environment shape complex trait evolution. Currently, I’m working on utilizing comparative epigenomics to understand variations in low temperature tolerance in maize and its close relative, temperate-adapted Tripsacum dactyloides.

How did you decide to make this the focus of your research?
Temperatures in my native South India typically range between 70 and 90 degrees Fahrenheit. When I first arrived to Lincoln, Nebraska for my grad school, it was a cold December night. I was immediately cold stressed and that frigid experience became the motivation behind my want to study cold stress. <Fun emoji> Jokes aside, the changing climate is threatening our ability to produce enough food for the growing population. Food security depends on the ability of plant scientists to develop climate-resilient crops that withstand the challenges of the changing climates. We don’t have to re-invent the wheel: some crop-wild relatives are naturally adept to stressful environments. My motivation is to understand stress adaptation of crop-wild relatives at the genomic and epigenomic levels, and translate stress-resilience into major crops.

How did your scientific journey begin?
When I was a kid, my pediatrician used to tell my parents that I will grow up to be a politician or a scientist (I used to ask her a lot of questions!). Those careers have always been in the back of my mind and I chose the scientist path. I guess, in addition to the amazing scientific mentors I have had throughout my career, my father was my biggest inspiration. Even though he didn’t specifically want me to become a scientist, he always instilled in me the philosophy that ‘education/learning never ends, new knowledge always creates a way for more learning.’ That has been my life’s philosophy and what better profession to practice it than as a scientist exploring new – to create newer – things.

Was there something specific about the Workshop on Cereal Genomics that drew you to apply?
As I am switching my model system from soybean to maize, now is an ideal time for me to attend this workshop as it’ll allow me to more fully capitalize on its contents to help address the questions remaining in my research program. My research focuses on an emerging area of plant biology, and so I will benefit greatly from interacting with scientists from various backgrounds working on advanced techniques in cereals and comparative genomics.

What and/or how will you apply what you’ve learned from the course to your work?
It’s been just a few days into the course and already I feel like we (students) are speaking the cereal community’s lingo! The lectures and hands-on exercises on high-throughput transcriptomics and phenomics data analysis were very informative and will be something I will apply in my research. Also, the informal discussions with instructors and fellow coursemates have been invaluable. Learning from people with diverse research interests has been the biggest highlight.

What is your key takeaway from the Course?
First, I want to thank the instructors for putting together such an amazing list of speakers for the course. Also kudos to them for selecting such a diverse group of students; not just in gender balance but also geographic representation and, most importantly, diversity in research interests. An important take away from this course is that meaningful progress happens through great collaboration within the community, and the cereal genomics community is one of the best examples with everyone being supportive of each other’s work. 

If someone curious in attending this course asked you for feedback or advice on it, what would you tell him/her?
I highly recommend this and any other course at CSHL. There’s something special about the atmosphere at these courses that is very conducive for participants at all levels to take in and bring home a lot. I would recommend the CSHL Cereal Genomics Workshop to early career plant scientists who are or wish to work on cereals. It isn’t just about knowing the latest science but also getting to know the scientists at the forefront of cereal genomics.

What do you like most about your time at CSHL?
The environment here is so serene and inspiring. As a matter of fact, the first thing I did when I arrived at CSHL was take a walk along the beach! If I were to work here, I would always start my day with a walk along the beach, maybe read a couple of research papers there, get inspired, come up with ideas and run to the lab and turn ideas into reality!

Sunil received a travel award from The Michigan State University Plant Resilience Institute (PRI). On behalf of Sunil, thank you to PRI for supporting and enabling our young scientists to attend a CSHL course where they expand their skills, knowledge, and network.

Thank you to Sunil 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: Sanjay Joshi

Meet Sanjay Joshi of the University of Kentucky. The Nepali national is a Ph.D. candidate in the Department of Plant and Soil Sciences and a graduate research assistant in Prof. Sharyn Perry’s lab. He is on campus for the first time, training at the Frontiers & Techniques in Plant Science course and is interested in returning for our Programming for Biology course.

What are your research interests? What are you working on?
I am interested in understanding the development of plants. The knowledge in plant growth and development can be utilized in improving the productivity of crops. Currently, I am working on understanding the gene regulation in seed embryogenesis in Arabidopsis.

How did you decide to make this the focus of your research?
After completing my undergraduate studies, I had the opportunity to pursue a master’s degree in The Hebrew University of Jerusalem (Israel). The unique experience allowed me to learn innovative science and technologies, and exposed me to different agriculture (compared to what I was accustomed to in Nepal). I did my masters research on the post-harvest management of apples -- but from a molecular perspective -- which inspired and opened an entirely new window into agriculture as a whole. I became fascinated with understanding new techniques and methods related to genes and proteins which I can eventually apply to improving the productivity and sustainability of plants.

How did your scientific journey begin?
Having grown up in the countryside of Nepal where farming is the main profession, I was into growing crops since my childhood. My interest in gaining knowledge on cultivating crops through a systematic and scientific approach led me to join the Institute of Agriculture and Animal Sciences in Chitwan, Nepal for my undergraduate studies. I always enjoyed doing experiments and liked finding solutions.

Was there something specific about the Frontiers & Techniques in Plant Science course that drew you to apply?
When I read the course curriculum and the labs techniques, I was excited since this course can help me in understanding plant biology better and learning new techniques like TRAP, INTACT, CRISPR. It is providing me with an opportunity to be exposed to different flavors and aspects of research in the plant world. 

What and/or how will you apply what you’ve learned from the course to your work?
This course has certainly changed my views on research and experiments; encouraging and motivating me to incorporate new techniques in my research – such as the TRAP method – so that I can explore at a new level.

I am happy to share my experience and techniques learned here to my colleagues in my institution.

What is your key takeaway from the course?
The plant science field is evolving. A large number of interesting things have been discovered yet a big portion of plant biology is still a mystery. Newly emerging techniques and tools will enable us to answer questions that have yet to be addressed.

If someone curious in attending this course asked you for feedback or advice on it, what would you tell him/her?
I would encourage and recommend the Frontiers & Techniques in Plant Science course to all my friends and colleagues interested in plant science. It is an excellent platform for learning and professional development;. providing exposure to both theoretical and practical demonstrations which enhance your professional skills.  This course also gives you the opportunity to meet many renowned scientists in the plant field thereby helping you join the community and build a network.

What do you like most about your time at CSHL?
CSHL is a wonderful place to live, with a peaceful ambiance and greenery all around. I have a lot of happy and fun memories to take home from this course, and loved all the social events thoroughly:. the scavenger hunt, course picnic, the totally relaxing and enjoyable sailing trip, having ice cream after the sailing trip, and hosting the fly course at the totally entertaining Venus flytrap party.

Sanjay received financial support from the National Science Foundation (NSF) and Regeneron to cover a portion of his course tuition. On behalf of Sanjay, thank you to NSF and Regeneron for supporting and enabling our young scientists to attend a CSHL course where they expand their skills, knowledge, and network.

Thank you to Sanjay 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: Sonia Chin

Meet Sonia Chin of Friends’ Central School. After earning her PhD from Johns Hopkins University in 2016, Sonia joined the independent and co-educational Quaker day school as an Upper School Science Teacher and just completed her first year teaching Biology I Advanced and Biology II Advanced Genetics Super Lab. She is on campus for the Frontiers & Techniques in Plant Science course where she is gathering material for a plant biology course she would like to begin offering her high school students.

Before becoming a teacher, what were your research interests? What were you working on?
Before becoming a teacher, I was interested in sensory neuroscience - particularly how animals sense the environment and what their brains do to generate an appropriate behavioral response. My graduate work in Chris Potter’s lab involved studying how the female fly brain processes olfactory stimuli to decide where to lay eggs, an important choice that impacts the survival of her offspring. I completed my PhD in October 2016 from Johns Hopkins University Department of Neuroscience; and I’m excited to say that on July 4th (during this course) my thesis work identifying a brain region specifically geared towards recognizing and avoiding smells associated with bacterial infection and larval parasites was accepted for publication!

As a teacher, what are your science interests and goals for your students?
I aim to introduce my students to how wonderfully weird biology can be and challenge them to use what they know to form novel and interesting ways to ask questions and problem solve. By incorporating practices rooted in the training of a scientist – such as the scientific method, frequently posing open-ended questions, and troubleshooting inquiry-based labs – I hope to help my students achieve these goals and make biology relevant and interesting. Most importantly, I hope that the skills they work so hard to hone in my class transfer to the other domains of their lives to logically evaluate information they encounter out in the world.

How did you know you wanted to become a teacher (as opposed to continuing to work in the lab)? What factor(s) helped/led you to make the career decision?
Typical of any young scientist’s developmental progress, I had an existential crisis at the beginning of my third year of graduate school. This, along with the added stress of a health scare, motivated me to take off a couple of months from graduate school to work on my mental and physical health. During that time, I found summer employment at a nonprofit called the Biotechnical Institute of Maryland teaching Baltimore City high schoolers interested in biomedical sciences to work in the lab. It was there that I discovered a love for teaching high schoolers.

While I love the life of the mind that professional scientists live, upon graduation, I thought hard about what to do next and determined that there are plenty of newly-minted PhDs who will become great scientists and, perhaps, relatively fewer PhDs who joyfully see teaching high school biology as a viable, first choice career path. Having just completed my first year of teaching, I love it. Teaching high school is equally dynamic to doing science day-to-day, puts me in contact with endlessly interesting people, and has been incredibly rewarding.

How did your scientific journey begin? 
I think I have a classic story here: During senior year of high school, I remember looking at a neuron slide and thinking how cool it was that I could see cells and measure things to understand how they work. More importantly, my high school biology teacher, Karen Shepherd, encouraged us to read popular science books, and a book called Dr. Tatiana’s Sex Guide to All Creation by Olivia Judson really captured my imagination about evolutionary biology and the weird behaviors in the animal world. 

Was there something specific about the Frontiers & Techniques in Plant Science course that drew you to apply?
I constantly think about what I can offer to my students not only through the curriculum but also from my experiences as a scientist. Presently, I teach a fall semester course, Genetics SuperLab which covers epigenetics and optogenetics, followed by an independent project by the students. I would like to expand my curriculum by offering a more molecular biology and experiments-based plant biology course in the spring (which will complement the botany course my colleague teaches in the fall).

Also, since earning with my PhD in October 2016, I miss working with my hands and doing science so I thought a CSHL course would be an amazing opportunity to hang out with scientists and bring new skills back to my school.

What and/or how will you apply what you've learned from the course to your work? 
I already plan to replace one of my labs with a technique I learned in the Plants course. When a pollen grain contacts the stigma of a flower with female anatomy, the single-celled grain of pollen extends a tube (up to one meter long in corn!) to deliver two sperm cells inside the ovary. One of the two sperm ultimately fuses with an egg cell to form an embryonic plant while the other fuses with a large cell, called the central cell, which eventually grows into endosperm, the part of a seed that provides nutrition for the new plant. In foods like beans and corn, endosperm is where we gain the most nutrition from eating. I like this system because it is dynamic and I think my students would really enjoy learning about some of the cell biology and signaling involved in double fertilization in plants. And to watch the process in real time would (literally and figuratively) help the lesson come alive for them. 

I will also probably use some of the bioinformatics tools covered in the course to talk about gene expression and how understanding evolution and phylogenetic trees can inform hypotheses about biological phenomena.

What is your key takeaway from the course?
Plants have evolved to address evolutionary pressures that are very different than animals, and their biology is both similar and different to animal biology in some pretty profound ways. Because of some major differences from animal biology, it has been interesting - to me - to see how differently plant biologists use inferences derived from the similarities in genetic sequences across species to support their hypotheses and conclusions. 

How many CSHL courses have you attended? Have you participated in a CSHL meeting? 
This is my first course at CSHL, and I would never have predicted that I would be taking this course as a high school teacher. Also, I attended the Neurobiology of Drosophila meeting in 2011 and 2015. 

If someone curious in attending this course asked you for feedback or advice on it, what would you tell him/her?
Frontiers & Techniques in Plant Biology is an excellent course for someone who wants to quickly get up to speed on plant science. I have really enjoyed hearing talks and learning from scientists  in their areas of expertise; it feels a bit like being at a really long conference because it includes such a diversity of topics and types of techniques. Learning to use computational tools and programming would have been tremendously useful at the beginning of my PhD which leaned more towards animal behavior and genetics. I am happy to see my fellow students, who are mostly early-year graduate students, getting such a well-rounded training covering multiple levels of research.  
 
What do you like most about your time at CSHL?
How welcoming the students, instructors, and scientists have been to answering my (probably) naive questions!

Sonia received funding support from the National Science Foundation (NSF) and from an endowment created by an alumnus dedicated and passionate about science education at Friends' Central School. On behalf of Sonia, thank you to NSF and to the alumnus for supporting and enabling our young scientists to attend a CSHL course where they expand their skills, knowledge, and network.

Also, thank you to Sonia 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: 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.