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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.

Visitor of the Week: Roberto Hernandez

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Meet Roberto Hernandez of the Florida Atlantic University. A member of Gregory Macleod’s lab, the second-year graduate student returns to CSHL for another drosophila­-centric program. In 2017, Roberto took part in the Neurobiology of Drosophila meeting and is training at our Drosophila Neurobiology: Genes, Circuits & Behavior course this time around.

What are your research interests? What are you working on?
I am currently investigating how neuronal pH changes during synaptic activity and the impact these changes have on neurotransmission.  

How did you decide to make this the focus of your research?
I became interested in this topic while helping Michal Stawarski collect neurophysiological data while disturbing pH homeostasis during neurotransmission. This project drove me to question how many untreatable neurological disorders may be related to pH imbalance in the central nervous system. However, the lack of research on pH dynamics in neurons and its effects on neurotransmission makes it difficult to venture into this topic. But this didn’t stop me. The lack of information and unique challenges presented by this project gave me an inexplicable sense and passion to discover the unknown as well as provide others with some insight into this field. 

How did your scientific journey begin?
The application of scientific knowledge to understand how humans and the world functions has always been a source of wonder to me. Inspired by the many scientific documentaries I have watched and the ambition to one day either make a discovery or treat individuals led me to pursue a career in the STEM field. There was a point in time when I aspired to become a medical doctor specializing in neurology and scientific research was nowhere on my radar. My organic chemistry professor at Miami Dade College, Dr. Carlos Fernandez introduced me to scientific research and had often hinted that the qualities I possess were that of a scientist. Upon graduating with an A.A., I moved to the Harriet L. Wilkes Honors College of Florida Atlantic University and was still very much interested in the medical tract. However, I became more curious about research and joined Dr. Gregory Macleod’s lab which was where I grew to further appreciate scientific research, found a deep passion for neuroscience, and decided to pursue a PhD in Integrative Biology-Neuroscience. 

Was there something specific about the Drosophila Neurobiology course that drew you to apply?
I found the Drosophila Neurobiology course of interest because the lab techniques it covers will take my current skill set to the next level and see me through my PhD and scientific career. Further, this course provides me with the unique opportunity to learn about the ongoing research in the Drosophila community and network with the students also attending the courses. 

What and/or how will you apply what you’ve learned from the course to your work?
This course provides many benefits for unraveling disruptions to the anatomy and physiology of the fly. Being trained in high-speed fluorescent imaging, immunohistochemistry, and electrophysiology will enable me to assess differences in signaling mechanisms or structures as well as elucidate distinct neurophysiological phenotypes caused by acid-base imbalances. Learning the proper methods of studying specific behaviors will help me to determine how the mutation is affecting the memory and motor functions of the fly, linking a molecular phenotype to a behavioral response. I hope to apply these skills to investigate genetic mutations that disrupt acid-base homeostasis during neurotransmission (a concept poorly researched to date) by transferring such mutations to Drosophila via CRISPR in conjunction with other molecular techniques.

What is your key takeaway from the course?
The different perspectives and approaches of application that are available to my research. 

If someone curious in attending this course asked you for feedback or advice on it, what would you tell him/her?
This course is phenomenal; the techniques you will learn are valuable in neuroscience and required for any lab using Drosophila as a model organism. Further, you get the rare opportunity of learning taught these techniques from the best scientists in the field. Also important is the opportunity to make connections with others within the field, connecting you to the greater Drosophila community. 

What do you like most about your time at CSHL?
What I like most about my time at CSHL is the opportunity I have in making friendships with fellow course members and network with guest speakers.

Roberto received a scholarship from the International Brain Research Organization (IBRO) to cover a portion of his course tuition. On behalf of Roberto, thank you to IBRO for supporting and enabling our young scientists to attend a CSHL course where they expand their skills, knowledge, and network.

Thank you to Roberto 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: Natasha Pacheco

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Meet Natasha Pacheco of the Inova Translational Medicine Institute where she is a postdoctoral research fellow. Natasha is on campus for this summer’s Statistical Methods for Functional Genomics course which makes this her fourth time at the Laboratory. Her CSHL course and meeting history includes the 2015 Biology of Genomes, 2016 Programming for Biology course, and 2017 meeting of Genome Informatics.

What are your research interests? What are you working on?
I’m broadly interested in using bioinformatics applications to understand how genetic variants contribute to different diseases. My current research project focuses on characterizing noncoding DNA regulatory elements in congenital heart disease (CHD), with the ultimate goal of identifying genetic variants within noncoding DNA elements in CHD patients.

How did you decide to make this the focus of your research?
The need to understand the functional roles of noncoding DNA elements has long been recognized, yet it’s fascinating to me how little we know about basic concepts like what defines a noncoding DNA element. Before we can begin to address how different genetic variants could affect a noncoding DNA element’s functional role, we need better definitions of what noncoding DNA elements are and what their targets are under normal biological conditions.

How did your scientific journey begin?
I first got inspired in 8th grade when my science teacher played the movie Lorenzo’s Oil. This movie is based on a true story about a young boy diagnosed with the genetic disorder Adrenoleukodystrophy (ALD). I was so amazed by how such a seemingly small change in a single gene could cause such a devastating disorder like ALD. I knew then that I wanted to understand how genetics influences health and disease.

Was there something specific about the Statistical Methods in Functional Genomics course that drew you to apply?
My research project requires the integration of different types of bioinformatics tools and large “omics” data sets. I quickly realized that I needed a more solid foundation of the underlying statistics for many of the bioinformatics tools I need to use, and how to pick and use the best bioinformatics tools for my research needs.

What and/or how will you apply what you’ve learned from the course to your work?
So far I’ve learned how important it is to understand your data set and the question(s) you’re trying to ask, as well as great tools in R and Bioconductor to analyze and visualize different types of data.

What is your key takeaway from the course?
Really spend time to understand the statistics behind different bioinformatics tools, as different statistics can address different questions and affect how you interpret your results.

If someone curious in attending this course asked you for feedback or advice on it, what would you tell him/her?
I would say ask lots of questions, take advantage of all the great instructors’ expertise, and get plenty of rest before arriving for the course!

What do you like most about your time at CSHL?
I love walking around the campus and taking in the beautiful landscape, it’s a great way to clear my mind and come back to class refreshed and ready to learn.

Thank you to Natasha 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: Steven Chen

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Meet Steven Chen of the Indiana University School of Medicine. A third-year PhD student in the Medical Scientist Training Program, Steven is also a member of Yunlong Liu’s lab in the Center for Computational Biology and Bioinformatics. He is on campus for his very first course at CSHL – Advanced Techniques in Molecular Neuroscience – and is considering coming back for the next Genome Informatics meeting.

What are your research interests? What are you working on?
I am interested in the regulation of messenger RNA splicing by RNA-binding proteins in the brain. I am taking an informatics approach to understand these splicing mechanisms that affect posttranscriptional processes.

How did you decide to make this the focus of your research?
I have been interested in RNA processing since my time in Amy Gladfelter’s lab when she was at Dartmouth College. We studied how cells are organized in time and space, specifically how RNA transcripts are trafficked and partitioned within the cell. As my interests developed during undergrad, I became more interested in genomics and how they can inform new hypotheses on molecular mechanisms. With the advent of RNA sequencing, we can now profile thousands of splicing profiles at once. I have made my focus to study RNA processing in the brain since it is particularly enriched in posttranscriptional regulation.

How did your scientific journey begin?
My scientific journey began as a little kid joining my parents on weekend trips to the lab during their postdocs. To pass the time, I would assist my mom in labeling tubes. During my senior year of high school, I worked in Irina Petrache’s lab studying how e-cigarettes and nicotine can damage lung endothelial cells. I would also shadow Dr. Petrache when she saw chronic obstructive pulmonary disease patients in clinic, and this inspired me to become a physician-scientist.

Was there something specific about the Advanced Techniques in Molecular Neuroscience course that drew you to apply?
I was primarily drawn to the Advanced Techniques in Molecular Neuroscience course by the scientific reputation of the instructors and guest speakers. I knew I was here to learn, and it is a blessing to be able to do so from such great minds. In addition, I had been analyzing data from the techniques taught in the course, and I wanted to be able to design and implement these on my own.

What and/or how will you apply what you’ve learned from the course to your work?
Since I come from a largely computational background, I have already learned a lot about the time and effort it takes to carry out experimental techniques like culturing astrocytes, single nuclei isolation, and making bacterial artificial chromosomes. I have also gained more scientific insight into neuroscience and have learned so much about the role of glia. Furthermore, I have acquired newfound appreciation for the history of how we have accumulated all this knowledge in the field. This will inform my critical thinking in discussions with my colleagues at home.

What is your key takeaway from the course?
The culture of being in Cold Spring Harbor almost magically allows course participants to freely speak about scientific ideas and even question canonical thinking. The people here are so inquisitive – it is almost like an incubator for new theories of molecular neuroscience. The guests come from all over the globe, but we all share a passion for understanding even the most basic of molecular mechanisms. It is a really special place to be at even if only for just two weeks.

If someone curious in attending this course asked you for feedback or advice on it, what would you tell him/her?
I think it is definitely worth the time spent here. You will not only form many new connections but also lifelong friends! But make sure you come prepared to work hard and be challenged in thinking critically (and also maybe with some late nights in the lab).

What do you like most about your time at CSHL?
The people here are awesome! Among the four courses running concurrently, there is always someone new to meet. It is easy to strike up a new conversation since we are all visitors. And we are constantly able to learn new things since everyone comes from a unique (cultural and scientific) background. The (unlimited) food is also great, so I have to control myself sometimes.

In addition to the Eli Lilly - Stark Neurosciences Fellowship in Neurodegeneration awarded to Steven, he received a fellowship from the Helmsley Charitable Trust to cover a portion of his course tuition. On behalf of Steven, thank you to the Helmsley Charitable Trust and Indiana Clinical and Translational Sciences Institute for supporting and enabling our young scientists to attend a CSHL course where they expand their skills, knowledge, and network.

Thank you to Steven 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.