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.

Repeat Visitor: Tatiana Schnieder

Among the ~9,000 scientists we hosted this year, a number of them participated in multiple meetings and/or courses. Kicking off the 2018 edition of our Repeat Visitor series is Tatiana Schnieder, an assistant professor of clinical neurobiology at Columbia University and an adjunct assistant professor at Hunter College. Tatiana divides her work between two research labs – the neuropathology laboratory of Dr. Andrew Dwork at Columbia University Irvin Medical Center and epigenetics laboratory of Dr. Fatemeh G. Haghighi at Mount Sinai School of Medicine. This year, Tatiana took part in the 83rd CSHL Symposium on Quantitative Biology and joined the ranks of both the CSHL Protein course (Expression, Purification, & Analysis of Proteins & Protein Complexes) and The Genome Access Course (TGAC). Previously, she presented a poster during the Glia in Health & Disease meeting in 2016 as well as attended Blood Brain Barrier that same year. We reached out to Tatiana to chat with her about her experiences in CSHL meetings and courses, and to learn more about what keeps her coming back to campus.

Tell us about your research interests.

My research is focused on the question of brain-periphery interactions in psychiatric disorders. To be more specific, I am currently investigating whether or not the reported relationship between suicide and central and peripheral inflammation is mediated by changes in blood-brain barrier (BBB) permeability.

How did you decide to make this the focus of your research?

During my doctoral training, I investigated prefrontal white matter microglia in individuals who died by suicide; and although I did not find any significant differences in microglial activation between suicides and non-suicides, suicide decedents had significantly higher densities of juxtavascular phagocytic cells in dorsal white matter than diagnostically-matched non-suicide decedents. Interestingly, however, studies of animal models of psychiatric symptoms have attributed maladaptive behavior in rodents to peripheral inflammation and to the influx of peripheral immune cells into the brain parenchyma. These findings and my own findings in postmortem human brains prompted me to investigate the involvement of peripheral immune cells in pathology associated with completed suicide. Further research revealed that non-parenchymal immune cells do not contribute to the increase in perivascular cell density that we observed in suicide; which suggests that resident microglial cells -- rather than non-parenchymal immune cells -- cross-communicate immune responses between the periphery and central nervous system in suicide. Moreover, those who died by suicide had a lower surface area density of microvessels in dorsal white matter -- the same brain region where I found increased densities of perivascular phagocytes. Cumulatively, these findings indicated that changes in the properties of the neurovascular unit could be contributing to pathological changes that lead to suicide. This piqued my interest in the role of BBB in psychiatric disorders. The goal of my current project is to determine if completed suicide is associated with transcriptional, epigenetic, or protein changes in the neurovascular unit.

Expression, Purification & Analysis of Protein & Protein Complexes Class of 2018

What led you to apply for the Protein course and how has it contributed to your work?

I applied to the Protein course to find answers to the challenges I faced during the preparation of my samples for HPLC/mass spectrometry. To assess changes in the expression level of key proteins crucial for BBB function and identify novel differentially expressed proteins, I use HPLC/mass spectrometry proteomics to interrogate protein expression profiles in isolated microvessels. To investigate BBB changes in psychiatric disorders and suicide specifically, I wanted to optimize a microvessel isolation protocol from postmortem frozen human tissue. It was important for me to develop the best method for the extraction of cytosolic, membrane, and transmembrane proteins that seal a gap between the brain endothelial cells. The two-week course gave me a lot of hands-on practice in protein isolation and, through extensive communication with the Instructors and use of the course materials, I was able to come up with the optimal protocol for my project. My main takeaway from the course is that it is imperative to learn as much as possible about your protein/s of interest before you start your experiments. Know your target well because what may work for one protein can be detrimental to another.

How about TGAC? Why did you register for it and what is your key takeaway?

My BBB project involves data that will require knowledge of bioinformatics, and I want to understand what goes into the analyses of the data I produce at the bench. I took TGAC to start learning how to analyze high-throughput data obtained using next-generation sequencing methods and mass spectrometry. As for my key takeaway: Apply what you learn in the course without delay. To acquire a new skill, one needs to practice often – if not daily – therefore it is important to “play” with your data so as to avoid forgetting what you pick up from the course.

The two courses have very different formats: the Protein course consists of hands-on training in a laboratory setting while The Genome Access Course is purely computational. What can you share about the differences or similarities between your experiences in the two courses?

The Genome Access Course Class of 2018 (Spring)

The two courses I took were indeed very different: TGAC was a short two-day course, whereas Protein course was two weeks long and so requires a completely different level of commitment. What is expected of you is also different: TGAC course is mostly lecture-based with some hands-on computer work, and the Protein course is mostly lab-based with lectures sprinkled throughout the day and evening. You cannot really choose to opt out, and by the end of the first week you already feel like you are a part of a team. In fact, working in a team and as a team will be the main mode of learning in a longer course. Irrespective of which course you decide to take, you will be taught by the top experts in the field within a friendly and supportive learning environment, where you will always have the ability to discuss and clarify concepts that may be confusing. It was an amazing experience: I was challenged to step out of my comfort zone, which is how personal and professional growth happens.

The focus of the CSHL Symposium changes annually. This year its topic was “Brains & Behavior: Order & Disorder in the Nervous System,” with an emphasis on neuroscience and related technologies. Besides the overall topic, what attracted you to participate in it?

Once you graduate, it is easy to focus on your specific area of research and, sometimes, you lose sight of the bigger picture. I strive to prevent this from happening to me. As a college professor, I need to stay abreast of the new discoveries in the field of brain research, and attending the Symposium was a perfect way to catch up with the latest findings. It provided a diverse range of topics and speakers from top-notch brain research labs. When this Symposium hones in on this topic again, I would recommend aspiring neuroscientists to attend. If you haven’t yet decided what you want to dedicate your research to or are looking to expand your network, this is a great conference.

Since you’ve now experienced both meeting and course life at CSHL, what differences or similarities did you notice about the two program types?

The courses had a much more focused agenda and required a few prerequisites so you are more likely to meet people who share similar professional or academic experiences as you. The meetings, on the other hand, were eclectic and brought together people from very diverse backgrounds. But in both instances, expect to be surrounded by like-minded people enthusiastic about science and the discoveries it brings.

What did you like most about your meeting and courses this year?

I am very lucky to live a short train ride away from CSHL. Since the first CSHL meeting I attended in 2016 on Glia in Health and Disease, I keep coming back because the quality of the meetings and courses have always been stellar, and the content and organization of the events always meet my expectations. In fact, I am looking forward to attending the Blood Brain Barrier meeting in 2019.

Both the Protein course and TGAC will return to the Laboratory in 2019; and applications are already being accepted. Apply to the Protein course by January 31, 2019 here.

Thank you to Tatiana for sharing with us her experience, and we look forward to having her back at the Laboratory again. To meet other featured scientists - and discover the wide range of science that takes part in a CSHL meeting or course - go here and 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.

Visitor of the Week: Anastasia Teterina

Meet Anastasia Teterina of the University of Oregon. The Russian national is a postdoc in Patrick Phillips’ lab which is part of the Institute of Ecology and Evolution. Anastasia attended the Probabilistic Modeling in Genomics meeting (ProbGen) – her first meeting in CSHL – where she gave a talk on the impact of reproduction mode on polymorphism in roundworms entitled “Mode of reproduction drives the distribution of polymorphism across the genome: theory and empirical tests in Caenorhabditis nematodes”.

What are your research interests? What are you working on?
I’m interested in the population genomics of worms (nematodes), namely, how their mating system and recombination landscapes influence the genomic polymorphism patterns. Genotype-phenotype relationships and the ways to explore them is another personal research interest.

How did you decide to make this the focus of your research?
The study of natural variation can help to understand the biology and ecology of organisms and demonstrate how different factors – such as genomic organization, population demographics, and other aspects of population structure – change genetic diversity; an important theoretical problem that has various practical implementations.

How did your scientific journey begin?
When I was 5 years old, my grandfather, a nuclear physicist, told me that every tiny cell has information that encodes everything necessary to build an organism and maintain all its functions. Since then, I've been trying to understand how it works.

Was there something specific about Probabilistic Modeling in Genomics meeting that drew you to attend?
The announced meeting topics caught my attention as I am curious about the trends in this area and wanted to know more. The meeting was devoted to modeling methods in genetics and omics and approaches to explore specific parameters and their distributions. In my current project, I intensively apply evolutionary population simulation and a variety of bioinformatics methods, a majority of them implies the use of some models. And, last but not least, I wanted to meet and talk with those who developed the methods I use to discuss their application in specific projects.

What is your key takeaway from the meeting?
To find out the answer to your scientific problem, ask more questions, be curious and ask tricky ones; try different approaches and combine methods; and don’t forget to test with simulation how well you can explain the results.

What did you pick up or learn from the meeting that you plan to apply to your work?
At ProbGen, there were many talks on model development, genetic parameter estimation techniques, a lot of benchmarking of old/new approaches, very promising announcements of new algorithms, (of course) a ton of interesting research with detailed descriptions of the methods, and inspiring talks on the current state and future direction of the field. I’m going to recommend some of the algorithms to my labmates and apply several new-to-me methods on my datasets.

Additionally, the day before the ProbGen meeting, there was an amazing satellite meeting on population simulations, PopSim, during which we discussed the current issues in population genetics and ways to approach them.

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?
ProbGen is an excellent opportunity to meet with colleagues, discuss your project, and learn new methods.

What do you like most about your time at CSHL?
It was my first visit to the CSHL, and I really enjoyed the autumn colors and amazing nature. One morning, a few colleagues and I went to the Inner Harbor to watch the birds. Also, I liked the amusing sculptures scattered around the campus.

Thank you to Anastasia 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.