Visitor of the Week: Tabita Ramirez-Puebla

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

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

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

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

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.