Visitor of the Week: Oscar Perez

Meet Oscar Perez, director of the Developmental Biology Laboratory 113 in the Pontificia Universidad Católica del Ecuador’s School of Biological Sciences, a graduate student in Dr. Federico Brown’s lab at the University of Sao Paulo, and the Ecuadorian representative in the Latin American Society for Development Biology Board. Oscar was on campus for two courses this year – Scientific Writing Retreat followed by Computational Genomics – but his history with CSHL started twelve years ago when he took his first CSHL course. We caught up with him to ask what keeps him coming back.

What are your research interests? What are you working on?
I am interested in the evolutionary comparison of reproductive strategies and early development of Ecuadorian chordates. My research is currently focused in the plasticity of oocyte organization and how this can modify the embryological events. I apply the comparative method in order to find molecular variations in oogenesis and embryogenesis of the Ecuadorian megadiverse fauna.

How did you decide to make this the focus of your research?
Since an early age, I was always interested in nature and I was fortunate to have a childhood surrounded by forests and open fields. I clearly remember hearing the Quito frogs singing in the cold nights and looking for bugs under the stones in the morning. I have to thank my mother for showing me a marvelous chicken birth and what I consider my very first exposure to embryology. Every child should have a similar opportunity.

How did your scientific journey begin?
I had the great fortune of working with great mentors with Dr. Eugenia del Pino, Dr. Richard Elinson, and Dr. Luis Coloma being the most influential to my scientific formation. I became extremely interested in embryological events while working with the outstanding Ecuadorian embryologist Dr. Eugenia del Pino. In her lab, I had the opportunity to be involved – for the first time – in the diverse and fascinating area of embryology by studying the embryos of Ecuadorian frogs which began my fascination for this almost unknown field of biology. My love for molecular techniques, evolution, and direct development came from Dr. Elinson’s expertise, and my passion for reproductive biology and ecology came from scientific interaction with the brilliant herpetologist Dr. Luis Coloma.

Was there something specific about the Computational Genomics course that drew you to apply?
There were three main reasons I applied for the Computational Genomics course in CSHL: 1) My previous experience in the CSHL Xenopus and live imaging training courses were brilliant; 2) The outstanding instructors listed for the genomics course; and 3) CSHL is considered one of the most prestigious scientific institutes in the world.

What and/or how will you apply what you've learned from the course to your work?
Undoubtedly, all the information I acquired from the course will be of great help in my research and institution. I have to say that my research in the non-model science world. Ecuadorian alternative models such as frogs, ascidians, and sea slugs do not have standardized molecular tools as in mice, Xenopus, or the human. Fortunately, in this course I learned of alternative ways to take advantage of modern computational tools to analyze transcriptomic data from my non-model species and still get informative results despite the absence of reference genomes and other existing tools that are easily obtained in human and mouse. Institutionally, my Computational Genomics training is very important because these skills can be shared with other laboratories and groups in collaborative investigations.

What is your key takeaway from the course?
The take-home message from the Computational Genomics course is that genomics is a flexible tool that can offer several alternative strategies to solve one single question. The experience of the genomics experts and mentors were extremely useful to learn how to effectively extract many hidden results from your data.

If someone curious in attending this course asked you for feedback or advice on it, what would you tell him/her?
My answer would say to complete all the homework sent by the instructors before the course. Even when you are not required to be an expert in the field, you must have a certain level of knowledge in order to get in the fast lane of learning. Also, bring data. If you have an unsolved problem in this regard, the Computational Genomics course is the right place to solve it.

How many CSHL courses have you attended?
Computational Genomics, 2018
Scientific Writing Retreat, 2018
Immunocytochemistry, In Situ Hybridization & Live Cell Imaging, 2009
Cell & Developmental Biology of Xenopus, 2006

Thinking back on your course at CSHL (Cell & Developmental Biology of Xenopus in 2006), did you notice differences or similarities between that course and Computational Genomics?
I still clearly remember how intense and diverse the training was at the Xenopus course in 2006 and, even after 12 years, that same level intensity and high quality of the courses in CSHL has remained the same. Although, considering the tasks sent weeks before the course started, preparation of a poster, and the mid-term test, I could even say that Computational Genomics might be more demanding than the 2006 course.

Since your first two CSHL courses, your career stage has changed. Given your present position, did your experience in the course change in any way?
Course features such as intensity and quality of the knowledge offered are contrastable; however, it is without doubt that CSHL offers first-rate courses instructed by leaders in the field of science. Over the years, my capacity of appreciating this knowledge has evolved. When I was a younger researcher, I did not fully appreciate how great an opportunity it was to train and be trained in one the most prestigious scientific institutes in the world. But, as my experience has expanded, I have become more aware of the magnitude of having opportunities to learn and to learn from such a source.

What do you like most about your time at CSHL?
The confidence that you acquire by mastering specific techniques. The rate of learning in CSHL is very high as is the demand and complexity of the courses. It is great to have the opportunity to ask your questions to pioneers, leaders, and scientific experts that collaborate with CSHL to teach and share their knowledge. 

Oscar received a fellowship from Pontificia Universidad Catolica del Ecuador (PUCE). On behalf of Oscar, thank you to the PUCE for supporting and enabling our scientists to attend a CSHL course where they expand their skills, knowledge, and network.

Thank you to Oscar 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: Paul Marcogliese

Meet Paul Marcogliese of Baylor College of Medicine (BCM) and the Jan and Dan Duncan Neurological Institute. He is a postdoctoral associate in HHMI Investigator Hugo Bellen’s lab within the Department of Molecular and Human Genetics of BCM. Paul was on campus for the tenth Neurodegenerative Diseases: Biology & Therapeutics meeting where he presented a poster entitled: “Loss-of-function variants in IRF2BPL are associated with neurological phenotypes”.

What are your research interests? What are you working on?
I am interested in the use of model organisms, particularly the fruit fly, to functionally assess candidate disease causing genes in human neurological disease; specifically, unraveling the molecular and cellular pathogenic mechanisms driving neuronal cell death in two movement disorders: IRF2BPL-linked neuroregression and Parkinson’s disease.

How did you decide to make this the focus of your research?
We are in the era of genomic sequencing that is progressing towards what has been called ‘personalized or precision medicine’. However, the identification of disease causing variants (even with access to large control databases) can be a challenge in light of the amount of natural genetic variation and variation of unknown significance. To bridge this gap, we can use genetically tractable model organisms, like the fruit fly, to help the human genetics diagnosis effort. Humanization strategies in model organisms that allow the functional assessment of a candidate disease variant and compare it to the human reference gene can support disease diagnosis and shed insight on biology. Added to this, the brain and its related disorders still remain a substantial challenge to understand. I feel that model organisms can be used in identifying and unraveling the function of genes causing these disorders. This will also lead to the identification of therapeutic targets thus helping both patients and families.

How did your scientific journey begin?
It has been an interesting journey for me. After completing a BA in criminology at 23 years old, I went to adult high school to complete 3 science credits that I initially avoided. This was due to an increasing interest in science primarily through understanding the evolutionary mechanisms underlying the diversity of life. Then, while completing a BSc in forensics, I was fortunate to work in the lab of David Park at the University of Ottawa studying animal models of Parkinson’s disease. It was here where my love of the scientific process really developed and what led me to conducting my doctoral studies in the Park lab. Not only did I work on mouse and fly models of Parkinson’s disease, but I met inspiring patients.

Now that I am a postdoc in the Bellen lab, I get to be part a large collaborative effort: the Undiagnosed Diseases Network (UDN). The UDN employs next-generation sequencing and model organism studies to help diagnose individuals with rare, undefined diseases. Our newly discovered human disease gene, IRF2BPL (Marcogliese et al., AJHG, 2018), which we originally deposited to bioRxiv has led to meeting a handful of patient families that inspire me to determine a more mechanistic understanding of the gene/disease in hopes of potential therapy.

Was there something specific about Neurodegenerative Diseases: Biology & Therapeutics meeting that drew you to attend?
I have kept a high interest in the role of glia in the pathogenesis of neurodegenerative disorders. There was a substantial portion of the meeting focused on this topic. Additionally, as part of a team studying rare diseases, it was important for me to be able to present our recent work identifying IRF2BPL-linked neuroregression to this audience. While the audience may be focused on more common neurodegenerative diseases, their input and advice on tackling novel diseases/genes will only help.

What is your key takeaway from the meeting?
Not all neurons are the same and there is differential susceptibility across neurodegenerative diseases. Additionally, glial cells -- specifically microglia -- are clearly critical players in neurodegenerative disease development and progression. Hence, from a therapeutic standpoint, there are multiple cell types and potential targets to ameliorate or slow disease progression.

What did you pick up or learn from the meeting that you plan to apply to your work?
The Bellen lab excels at model organism work in vivo, but the CSH meeting has allowed me to make collaborative connections with experts in the iPSC field that could allow us to translate our findings to human cells.

If someone curious in attending a future iteration of this meeting asked you for feedback or advice on it, what would you tell him/her?
I would tell them it was a great experience. The two main reasons why I enjoy CSHL meetings are that the topics are focused enough to attract major players in the field to attend, and there is a substantial discussion of unpublished and novel ideas in the field.

What do you like most about your time at CSHL?
CSHL is located on a beautiful campus. The smaller size of the meeting allows for an intimate atmosphere where everyone is very approachable and inclusive. It not only builds networks but also friendships.

Thank you to Paul 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: Tatiana Moiseeva

Meet Tatiana Moiseeva of the University of Pittsburgh. The Russian national is a postdoctoral associate in Dr. Christopher Bakkenist’s lab. She returned to campus for her first CSHL course: Scientific Writing Retreat.

What are your research interests? What are you working on?
I study how human cells initiate the replication of their DNA and how they suppress the majority of the available replication origins that should only be used in the event of stress. Certain drugs that are currently in clinical trials can induce excessive replication initiation and make cells more prone to toxic DNA damage.

How did you decide to make this the focus of your research?
I have always been interested in basic science questions. The Bakkenist lab focuses on using certain kinase inhibitors to sensitize cancer cells to ionizing radiation, and we found an unexpected effect of a drug that was supposed to be inert in the absence of DNA damage. My natural curiosity took over and I had to figure out what happens exactly, and it turned out that I can use this drug to answer some basic science questions, so I couldn’t resist.

How did your scientific journey begin?
I completed my undergraduate and graduate degrees in St. Petersburg, Russia. I had amazing professors in the Polytechnical University who inspired me, encouraged discussion, critical thinking, taught me the importance of constant self-education, and really shaped my scientific mind. Doing research in Russia was not easy but they, by example, showed me that nothing is impossible if you put your mind to it. I have switched a few research topics since then, but I think my education is what defined my scientific path.

Was there something specific about the Scientific Writing Retreat course that drew you to apply?
Scientific writing is a critical part of working in academia. To date, I have written multiple manuscripts and grant proposals that I asked my PIs to look over. They always provided feedback but they weren’t always able explain why I should write something in a certain way. My goal in attending this course is to become more independent in my writing and improve this valuable skill for future work as an independent researcher.

What and/or how will you apply what you've learned from the course to your work?
Ask several people to read your text before submitting it. Getting feedback, even from non-experts, can help a lot.

What is your key takeaway from the course?
For any piece of scientific writing, proper structure is key. Whether it is a seven-figure paper or three-sentence abstract, the order of the messages is what matters the most.

How many CSHL courses have you attended? How about meetings at CSHL?
This is my first course but I am very curious about the Workshop on Leadership in Bioscience. I attended the Cell Cycle meeting in 2012 and DNA Replication meetings in 2015 and 2017. I am planning to attend the 2019 Eukaryotic DNA Replication & Genome Maintenance meeting.

If someone curious in attending this course asked you for feedback or advice on it, what would you tell him/her?
This course is very useful, informative, and intensive. Before coming to the retreat, think about the general and specific writing problems you are having because the time at the retreat is very tight. Anything can be solved, you will see the progress immediately. Also, the course is always the week before Thanksgiving - be ready for the snow!

What do you like most about your time at CSHL?
A chance to meet new people from very different backgrounds (that we don’t really get at scientific conferences), learn about their experiences and make new friends. Also, very good dinners. 

Thank you to Tatiana 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: Tianhao Xu

Meet Tianhao Xu of Rosalind Franklin University. The Chinese national is a Ph.D. candidate working in Dr. Gustavo Martinez’s lab within the Center for Cancer Cell Biology, Immunology, and Infection. He made his CSHL debut by training at this year’s Advanced Sequencing Technologies & Applications course.

What are your research interests? What are you working on?
My research interest is to understand the molecular mechanism of CD8+ T cell differentiation. I’m currently working on understanding the role of two transcription factors, NFAT1 and NFAT2, in CD8+ T cell differentiation and function.

How did you decide to make this the focus of your research?
The truth is I didn’t know of my current research field until my rotation in Dr. Martinez’s lab. In the first year of our graduate program, we are able to rotate with different PIs before deciding which lab to join. During my rotation in the immunology lab, I knew I had found my research focus because, I felt excited and rewarded every time I did the hands-on manipulation of CD8+ T cells!

How did your scientific journey begin?
My interest in science developed at a very young age during the hours and hours I spent playing with my childhood friends in gardens and wild fields. I also like to read science and nature books. This may sound boring or cliché, but the high school biology class brought me onto the biological science path and I still clearly remember the very first day I prepared slides and saw the onion cellular structures.

Was there something specific about the Advanced Sequencing Technologies & Applications course that drew you to apply?
The next-gen sequencing technology, especially RNA-seq and ATAC-seq are powerful tools unveiling the transcriptome and chromatin accessibility changes that bridge transcription factor changes and phenotypic changes in any given cell. Therefore, this course is perfect for me to further study the mechanisms behind NFAT dependent phenotypic changes in CD8+ T cell differentiation.

What and/or how will you apply what you've learned from the course to your work?
I’m still navigating my way in bioinformatics. However, I think I’m getting a more in-depth understanding of the potential application as well as the limitation of next-gen sequencing technology. I can’t wait to bring my knowledge about next-gen sequencing to my lab mates and home institution; and I hope to set up an Amazon Machine Images (AMI), using bioinformatics tools presently available to us, dedicated to all Rosalind Franklin graduate students.

What is your key takeaway from the course?
Leaving your research comfort zone and learning new things can be terrifying. However, you shouldn’t be. The course lecturers and your classmates will be there to help you achieve your goal. A part of becoming a scientist is having the drive to learn and discover new things continuously.

If someone curious in attending this course asked you for feedback or advice on it, what would you tell him/her?

1. The course will be intense. Make sure to read all the guidelines (especially those related to the course pre-requests), and become familiar with the layout of CSHL to easily navigate the buildings and available facilities.

2. Do not be afraid to ask questions.

3. Make sure to bring a heavy jacket.

What do you like most about your time at CSHL?
It is “almost” freezing during this time of the year, but I did enjoy the autumnal feeling and seeing the tree leaves change colors. Most importantly, I have to say the food was fantastic. I never felt this happy eating in the cafeteria before.

Tianhao received a scholarship from the Helmsley Charitable Trust to cover a portion of his course tuition. On behalf of Tianhao, thank you to the Helmsley Charitable Trust for supporting and enabling our young scientists to attend a CSHL course where they expand their skills, knowledge, and network.

Thank you to Tianhao 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: Zhou "Jason" Shi

Meet Zhou “Jason” Shi of the Gladstone Institutes at UCSF. Working as a postdoc in the lab of Katherine Pollard, who is among the 47 Chan Zuckerberg Investigator selected in 2017, Jason is also a junior research scholar at the Chan Zuckerberg Biohub. He is on campus for the third iteration of Biological Data Science. He marked his first CSHL meeting with a talk titled “Comprehensive and ultra-rapid identification of genetic variants in human gut microbiome”.

What are your research interests? What are you working on?
My general research interest is to better address biological problems by developing computational methods and bioinformatics tools. My current project involves developing a computational method to quickly identify specific microbes from any huge, messy pool of microbes in the human gut.

How did you decide to make this the focus of your research?
Due to having an interest in broad research topic, I only recently centralized the focused my research: microbiome. Microbiome is something I am passionate about and the more time I spend in studying microbiomes, the more I am amazed by how they impact human health, especially in "surprising" or unexpected ways.

How did your scientific journey begin?
I come from a software engineering background. During a software process class in my senior year, my instructor shared a translated version of a quote from a great computer scientist, Donald Knuth: “I can’t be as confident about computer science as I can about biology. Biology easily has 500 years of exciting problems to work on.” At that time, I was in working on an unchallenging project so was easily convinced by the quote and then applied to a microbiology graduate program.

Was there something specific about Biological Data Science meeting that drew you to attend?
I chose to attend this meeting mainly because it is one of the most exciting meetings with a clear focus on data science for biology. The meeting this year included multiple topics I am personally and highly interested in; e.g., algorithms and deep learning.

What is your key takeaway from the meeting?
One key takeaway I found very inspiring is that transfer learning allows the use patterns learnt from developing retina cells to recognize cell types in adult mouse.

What did you pick up or learn from the meeting that you plan to apply to your work?
I learned a technique that further breaks down k-mers to l-mers then only indexes minimizers of l-mers for efficient algorithms. I found this technique very intriguing because I may be able to apply it to my project to improve the data structure behind the bioinformatics tool I am building.

If someone curious in attending a future iteration of this meeting asked you for feedback or advice on it, what would you tell him/her?
I would be happy to tell him/her of my personal great experience at this meeting. Also, for anyone who enjoy method intensive talks and want to take back to their lab a great variety of cool ideas handling biological data, then this is a meeting they should consider and definitely enjoy.

What do you like most about your time at CSHL?
The ease of communicating with anyone during the meeting was truly amazing.

Thank you to Jason 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.