Visitor of the Week: Patrick Capel

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Meet Patrick Capel of the University of Warwick. The SynBio CDT PhD student, co-supervised by Emzo de los Santos and Christophe Corre, is currently about halfway through his training at our annual course on Synthetic Biology.

What are your research interests? What are you working on?
I am interested in natural products – compounds that are derived from nature and are often very complex. More specifically I want to be able to use cell-free transcription-translation systems to investigate their biosynthesis and create new pathways in a way that is more similar to chemistry than it is biology!

How did you decide to make this the focus of your research?
I love organic synthesis, but I was drawn towards biosynthesis because biology allows us to do what we would need a myriad of reagents and conditions to do at physiological pH and with greater control. For me, cell-free transcription-translation is very similar to chemistry where you mix reagents together and let it go to get your protein of interest so it seemed like a good fit for me.

How did your scientific journey begin?
I was always encouraged to ask questions, and often taken to places like planetariums and the Natural History Museum in London (mainly to look at the dinosaurs) when I was young which made me fall in love with all things science.

Was there something specific about the Synthetic Biology course that drew you to apply?
I was drawn to the course as two of the main topics (DNA assembly and cell free transcription-translation) are things that I directly use in my PhD work. Also, microfluidics is something I can see myself using in the not-too-distant future.

What and/or how will you apply what you’ve learned from the course to your work?
I have learnt a lot about optimizing protocols for DNA synthesis, which I will be getting the lab to tinker with as soon as I get home. I have also explored some modeling whilst here which I am trying to apply to my own work too. 

What is your key takeaway from the course?
Give everything a go and talk to other people about what you are up too! Your idea about a potential experiment might sound a bit too crazy to you but it might be logically sound to someone else.

If someone curious in attending this course asked you for feedback or advice on it, what would you tell him/her?
I’d tell them to come if they can. You learn a lot about everything covered during the course and also get to talk about everything that surrounds science in the canteen, along with making connections with other people in a way that is very different from a conference or a short meeting. There is a real community feeling here and I already can’t wait to bump into my course mates and instructors at conferences later in my academic life. 

What do you like most about your time at CSHL?
S wimming in the harbor with my newfound friends and staying up late chatting about everything from local adventures to life philosophies.

Patrick received financial support from Howard Hughes Medical Institute (HHMI) and the Warwick Integrative Synthetic Biology Center to cover a portion of his course tuition. On behalf of Patrick, thank you to HHMI and the Warwick Integrative Synthetic Biology Center for supporting and enabling our young scientists to participate in training courses where they expand their skills, knowledge, and network.

Thank you to Patrick 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: Bartul Mimica

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Meet Bartul Mimica of the Norwegian University of Science and Technology (Norway). The Croatian national is part of Jonathan Whitlock’s lab within the Kavli Institute for Systems Neuroscience. A PhD student, Bartul has spent the last two weeks with us at the Neural Data Science course.

What are your research interests? What are you working on?
I am generally interested in the neurophysiological bases of behavior, i.e. how individual cells encode the moment-to-moment variability in what we or others are doing. I work on several projects, but my main focus was devoted to studying the cortical representation of posture with single-unit recordings and 3D tracking (our study was published in Science last year – you can read more about the research here)

How did you decide to make this the focus of your research?
A long, long time ago – I read about the discovery grid cells with extracellular recordings and became fascinated not only with the finding, but also the method. I went to Norway to learn the method, but also stumbled upon different questions about the methodology of tracking animal behavior, which got me into what I am doing today.

How did your scientific journey begin?
It was probably an amalgam of various thought processes across a lengthy span of time, the proclivity to ask questions and seek answers (however rough the road towards them was), and then channeling those inner drives to find a niche in the job market. I also always wanted to do a job which valued curiosity and intellectual honesty. I hope others agree with me on this, too.

Was there something specific about the Neural Data Science course that drew you to apply?
Data analysis is the bedrock of contemporary systems neuroscience. In my line of work, it spills over into almost every day-to-day activity in the lab, or outside it. The range of topics and quality of speakers were irresistible, so I decided to apply. And I’m happy to say that a day did not go by without my learning something I would be able to use in my work back home.

What and/or how will you apply what you’ve learned from the course to your work?
At my home institution, we analyze electrophysiological, imaging and behavioral data, so it is fair to say everything I learned from the course can be applied to some degree in my work. A lot of the methods for extracting spike or calcium signal data that we covered during the course are already implemented in our processing pipelines. However, I think implementing pose estimation from marker-less tracking videos and analogue signal analyses will be the next steps for me and my lab mates.

What is your key takeaway from the course?
It is hard to single one thing out, but I guess generally one could say that it is crucial to have a meticulous, well thought-out plan before analyzing data or writing a paper. In this day and age, a lot of sophisticated methods are only a button-click away for ordinary users, but it is really important to get the feeling for the raw data and understand the requirements for using different analyses before doing any actual work.

If someone curious in attending this course asked you for feedback or advice on it, what would you tell him/her?
The course is very, very useful, but also rather intense. It’s definitely worth considering if you want to improve your analytical skills, the smaller-sized groups increase focus and make you progress quicker.

What do you like most about your time at CSHL?
The new friendships I gained and certainly the weather, which has been merciful compared to the Norwegian one.

Bartul received financial support from Howard Hughes Medical Institute (HHMI) to cover a portion of his course tuition. On behalf of Bartul, thank you to HHMI for supporting and enabling our young scientists to attend a CSHL course where they expand their skills, knowledge, and network.

Thank you to Bartul 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: Tabita Ramirez-Puebla

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Meet Tabita Ramirez-Puebla of The Forsyth Institute. The Mexican national is a postdoctoral scientist in Gary Borisy’s lab. Tabita is on campus for her maiden meeting at CSHL – Microbiome – where she presented a poster entitled “Application of CLASI-FISH to visualize the micron-scale spatial structure of the microbiome of the kelp Nereocystis luetkeana.”

What are your research interests? What are you working on?
I am a biologist interested in the study of microbiomes. Particularly, I am interested in the ecological implications of the distribution of microbes in relation to the micron-scale features of their environment. The spatial arrangement plays a key role in the interaction of bacteria with other microbes, hosts and their environment. In my current project I am working to establish a method to visualize the dynamics of the bacterial biofilms in the human mouth.

How did you know you wanted to study this/make it the focus of your research?
In previous projects, I have worked with symbiotic bacteria of eukaryotic hosts and realized the relevance of microorganisms to both the host biology and functioning of the ecosystems. The importance of microbiomes is increasingly recognized and High-throughput ‘omics approaches allow us to study them in an effective way. However, in such techniques the spatial arrangement is destroyed during sampling. Visualizing the micron-scale spatial organization provides clues about micro-habitats, intertaxon associations and metabolic partners. I am using the human oral microbiome as a model to understand the dynamics of microbial communities at micron-scale. I want to study the micron-scale biogeography of microbiomes to obtain a more comprehensive understanding of their function and the ecological role of the different members in a microbial community.

How did your scientific journey begin?
I don’t remember a time in my life when I wasn’t interested in nature. When I was a child, I spent much time watching documentaries which helped to develop a curiosity that drove me to become a scientist.

I have been inspired by different scientists, but women in science made the biggest impact in my life. I remember how encouraging it was to read papers by women scientists because it made me realize that I could do it too. I have since had the opportunity to work and learn from strong, intelligent, and passionate women and continue to do so.  

Was there something specific about the Microbiome meeting that drew you to attend?
I was particularly interested in the topics of Host-microbe community assembly, Microbe-microbe interactions, and Spatial studies of the microbiome. These subjects are very relevant for my current research and attending this meeting provides me with the opportunity to discuss them – and exchange ideas – with other scientists.

As of today, what is your key takeaway from the meeting?
There are many scientists studying the human microbiome to develop therapies and there are already successful examples. I find this very interesting and inspiring.

What and/or how will you apply what you’ve learned from the meeting to your work?
I think that I can learn something new just by talking with other attendants about their projects. I have learned of eye-catching approaches that I would like to apply to my future research in microbiomes.

If someone curious in attending this meeting asked you for feedback or advice on it, what would you tell him/her?
I think this conference has an outstanding panel of speakers and the chairs organized this event in such a way that attendees have many opportunities to engage in high-level discussions that can generate a lot of feedback.

What do you like most about your time at CSHL?
The landscape of CSHL is gorgeous! It’s the perfect environment that fosters creativity. This is my first meeting at the CSHL and it is what I expected it to be: beautiful location, and attendants are enthusiastic and willing to talk.

Thank you to Tabita 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: Marek Svoboda

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Meet Marek Svoboda of Dartmouth College. Marek is a PhD Student in Quantitative Biomedical Sciences and a member of Dr. Giovanni Bosco’s lab. He is wrapping up his two-week training at our Single Cell Analysis course and is considering to attend our Single Cell Analyses meeting this fall.

What are your research interests? What are you working on?
I am using a mouse model of Autism Spectrum Disorder (ASD) with a mutation in a specific gene (PTEN) to characterize the molecular pathways responsible for the developmental abnormalities observed in humans. In my research, my goal is to move us closer to an effective treatment of ASD by combining medical knowledge with wet lab and computational techniques.

How did you decide to make this the focus of your research?
My main interests lie in neuroscience and genetics, both of which are essential for the study of Autism, an increasingly prevalent developmental disorder in children. In my future, I would like to become both a researcher discovering new ways to treat neurological diseases and a physician delivering those directly to patients.

How did your scientific journey begin?
I have always been interested in psychology and the inner workings of the human mind. At high school, I was inspired by my amazing Biology teacher and the more I learned about the human body, the more I wanted to understand the nervous system and the associated pathology. Later in college, I decided to become a physician-scientist with a focus on neuroscience.

Was there something specific about the Single Cell Analysis course that drew you to apply?
I am the only person doing single cell RNA sequencing (scRNA-seq) in my lab, and the only person doing scRNA-seq of neurons at my institution. Therefore, my primary motivation has been to acquire some of the more advanced wet lab and analytical skills for this technique. More generally, though, I personally believe that the ability to extract a wealth of information from individual cells bears an incredible potential for the future of personalized medicine. While I am using scRNA-seq in my own thesis research project, I hope to combine it with other single cell techniques in my future research and maybe even clinical practice.

What and/or how will you apply what you’ve learned from the course to your work?
I have already learnt some of the basic analytical processing steps for the data that I will obtain from my own experiments, which I am really excited about – though, I know more is yet to come! I really like the combination of wet lab and bioinformatics that this course offers. At Dartmouth, I am a member of the Single Cell Interest Group, and so I am also looking forward to sharing all the cool single cell techniques and other ideas with my colleagues back home.

What is your key takeaway from the Course?
There is so much more to single cell analysis than just RNA! Depending on the question, it may be a good idea to complement the transcriptomic data with the other ‘omics’ approaches, which are all fairly doable – with the right guidance and resources, of course.

If someone curious in attending this course asked you for feedback or advice on it, what would you tell him/her?
Make sure to have as few outside commitments during the course as possible, as the course itself is relatively intense and at the same time absolutely worth it. Come here ready to work hard, learn a lot, but also socialize and meet new people. Be mindfully present every second of the course, as the time spent here is extremely valuable!

What do you like most about your time at CSHL?
I really appreciate the fact that during the course, the conditions are perfectly conducive to what we are meant to focus on here. The course is extremely well-organized: one day we show up to lab and it is ready for RNA extraction. The next day, as if by a miracle (in fact, by tireless work of TAs, often into the late night), the lab is ready for confocal microscopy. Everything we need is available to us here all the time, and the atmosphere at CSHL feels very welcoming overall. As a result, taking a course at CSHL is a worry-free experience that creates a wealth of lasting memories.

Marek received financial support from Regeneron to cover a portion of his course tuition and a Research Alumni Award from Dartmouth to specifically attend this course. On behalf of Marek, thank you to Regeneron and the alumni of Dartmouth’s graduate program for supporting and enabling our young scientists to attend a CSHL course where they expand their skills, knowledge, and network.

Thank you to Marek 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

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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.