Visitor of the Week: Chirayu Chokshi

Meet Chirayu Chokshi of the Stem Cell and Cancer Research Institute at McMaster University (Canada). The graduate student, who’s working towards a PhD in Biochemistry with a focus on brain tumor stem cells, is a part of the Brain Tumor Stem Cell Research Program led by Sheila K. Singh. Chirayu is on campus participating in his first CSHL meeting – Genome Engineering: The CRISPR/Cas Revolution – and also presented a poster titled “Discovery and validation of genes essential for survival of recurrent Glioblastoma brain tumor initiating cells”.

What are your research interests? What are you working on?
My research focuses on discovering novel therapeutic targets responsible for therapy resistance in glioblastoma, the most common and a highly aggressive form of malignant brain tumor in adults. I use CRISPR-Cas technology to probe brain tumor initiating cells for context-specific genetic vulnerabilities. 

How did you decide to make this the focus of your research?
Glioblastoma remains a therapeutic challenge. Despite the use of gold standard therapy, patients face a median survival rate of less than 15 months. Previous research heavily focused on using multiomic analyses to capture snapshots of glioblastoma progression and inform therapeutic efforts. Through a collaboration between my current supervisor, Dr. Sheila K. Singh and Dr. Jason Moffat at University of Toronto, I learned about the potential of CRISPR-Cas technology to functionally direct target discovery in glioblastoma in an unbiased manner. Today, I utilize this genetic engineering tool in combination with multiomic data to identify novel therapeutic targets in treatment-resistant glioblastoma. 

How did your scientific journey begin? 
My scientific journey began during a lecture I attended in 2014 by Saul Perlmutter at UC Berkeley. Going in with little knowledge about astrophysics, I was blown away by his research which led to the discovery of the accelerating expansion of the Universe. At that lecture, I realized the potential of science to answer seemingly impossible questions about the world around us. I was especially inspired by Dr. Perlmutter’s use of supercomputers to analyze light emitted by supernovae and arrive at the conclusion that the universe is expanding at an accelerating rate. 

Was there something specific about Genome Engineering: The CRISPR/Cas Revolution meeting that drew you to attend?
The main reason I attended this meeting is to learn about new applications of CRISPR Cas technology from the world leading experts.

What is your key takeaway from the meeting?
My key takeaway from this meeting is that CRISPR Cas technology is constantly evolving and leading to an infinite amount of applications to gain insight into various diseases.  

What did you pick up or learn from the meeting that you plan to apply to your work?  
At this meeting, I was pleasantly surprised to see the many original, innovative applications of CRISPR Cas technology to answer important scientific questions. From the development of modulators of Cas activity to fate mapping with CRISPR technology, I am excited to apply these new technologies to gain insight into glioblastoma progression. Specifically, I would like to set-up CRISPR Cas screening experiments to ask specific questions about the regulation of stemness in glioblastoma cancer stem 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 that this meeting is a great way to learn about recent advances in CRISPR Cas technology, network with leading experts, and set-up future collaborations. 

How many CSHL meetings have you attended?
This is my first CSHL meeting and I would love to attend future CRISPR-Cas and cancer modelling meetings. 

What do you like most about your time at CSHL?
CSHL is a very special place. Irrespective of where you look around this campus, you’ll always see a beautiful view of historic architecture integrated with nature.

Thank you to Chirayu 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: Viraj Doddihal

Meet Viraj Doddihal of the Stowers Institute for Medical Research. The Indian national is a graduate student in Alejandro Sanchez Alvarado’s lab and, for two weeks, was on campus for the Proteomics course. 

What are your research interests? What are you working on?
I am studying animal tissue regeneration, using the planarian flatworm as a model system. My project focuses on studying the role of protein phosphorylation in the planarian regeneration. 

How did you decide to make this the focus of your research? 
I was introduced to regeneration biology during my undergraduate studies at the Indian Institute of Science Education and Research in Pune, India. I was fascinated by this phenomenon and worked a semester with Dr. Girish Ratnaparkhi studying Hydra regeneration. I next worked on planarian regeneration with Dr. Dasaradhi Palakodeti at the Institute for Stem Cell and Regenerative Medicine (inStem) at NCBS in Bengaluru, India. These early experiences in regeneration biology helped me choose my current project at the Stowers Institute for Medical Research.     

How did your scientific journey begin? 
I think it is to a large extent because of my parents and my family. They have always allowed me to question and explore as per my curiosity. In addition, they made sure I received the best possible education which led to me attending high school at Sri Ramakrishna Vidyashala in Mysuru. My very inspirational high school teachers laid the foundation for my career in science.

Searching for proteins.
Photo: Viraj Doddihal

Was there something specific about the Proteomics course that drew you to apply?
The course has a good balance of theory, experiments, and data analysis. I wanted to learn how to use mass spectrometers (MS), and analyze the big data sets generated from discovery proteomics experiments.  

What and/or how will you apply what you've learned from the course to your work? 
The course gave me an in-depth understanding of MS and other techniques that are available to study proteins in conjugation with MS. I plan to utilize these techniques as a new tool kit to probe regeneration in planarians.  

What is your key takeaway from the course?
In addition to understanding the power of mass spectrometry to study proteins in cells and tissues, the key takeaway for me was to always design orthogonal experiments to address any question. We, the students of the course asked a variety of fundamental biological questions, but are all using proteomics as an approach. This helped me appreciate the power of proteomics to answer questions in biology.

Sailing trip
Photo: Viraj Doddihal

If someone curious in attending this course asked you for feedback or advice on it, what would you tell him/her?
I would strongly encourage them to attend the course. Anybody interested in understanding the workings of MS and design of proteomics experiments should definitely attend the course. Additionally, the course provides a good balance of academia and industry thus giving students an opportunity to explore both the fields. 

What do you like most about your time at CSHL?
I really enjoyed our walks to the beach and the student gatherings we had there. We all enjoyed our sailing trip. The daily hike up the beautiful hill for the classes made sure that I got some exercise after sumptuous meals. 

I would like to thank the instructors and TAs for relentlessly answering all our questions and making the course fun and fruitful. Also, a big thank you to all my friends from this course who made it a memorable experience. 

Thank you to Viraj 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: Koen Schipper

Meet Koen Schipper of the Netherlands Cancer Institute. A PhD student in a group led by Jos Jonkers. He is at Cold Spring Harbor Laboratory for his first CSHL meeting – Mechanisms & Models of Cancer – where he presented a poster titled “Actomyosin relaxation enables tumor formation upon loss of E-cadherin expression in the mammary gland”.

What are your research interests? What are you working on?
My current research focuses on the process of tumor initiation in lobular breast cancer. We primarily use mouse models and cell culture approaches to determine the driving forces behind tumor development. 

How did you decide to make this the focus of your research?
I have always found the transformation of a normal cell into a tumor cell very interesting; especially since a small alteration in a single cell can have such tremendous impact on an entire organism. Mouse models are particularly suitable to study tumor development since you have the optimal environment to study the early phases of tumor initiation. 

How did your scientific journey begin? 
I did a bachelor study in bio-pharmaceutical sciences during which I discovered an interest for courses about signal transduction and how it is altered in disease. As a result, for my masters I decided to delve deeper into the signaling routes frequently deregulated in tumorigenesis and, during my research internships, I truly understood how much we still don’t know in this field and how much there is left to discover.   

Was there something specific about Mechanisms & Models of Cancer meeting that drew you to attend?
Several former lab members have been to this meeting and all of them highly recommended it as one of the best meetings they have attended; and so I had to experience it as well. The meeting also has a nice format with a number of short talks giving young scientists ample opportunities to present their work. 

What is your key takeaway from the meeting?
Discussing your research with those outside of your own field is very useful. You are able to see how they interpret your results and think about potential future directions. It can really open up new avenues for your own project. 

What did you pick up or learn from the meeting that you plan to apply to your work?  
The main thing I plan to apply to my research is to broaden how I look at the effects I see in our mouse model in human patients with germline CDH1 mutations. This way, I am able to validate our findings and identify possibilities to prevent cancer development in these families.

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?
Just like the people who recommended I attend, I would encourage them to come and experience this great meeting and venue for themselves. 

How many CSHL meetings have you attended?
This was my first CSH meeting but, if I get the opportunity, I will definitely attend future meeting(s) or a course. 

What do you like most about your time at CSHL?
I really liked the atmosphere of the CSH campus. Compared to most institutes located in big cities, it is calm and helps you to relax and think about your research from a different perspective.

Thank you to X 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.

Photo: Koen Schipper

Visitor of the Week: Salma Ferdous

Meet Salma Ferdous of Emory University. A PhD candidate and member of John Nickerson’s lab in the Emory Eye Center, Salma made her CSHL debut via the Chromatin, Epigenetics and Gene Expression course. 

What are your research interests? What are you working on?
My research is focused on the visual system, specifically the retina which is a neurosensory tissue in the back of the eye responsible for vision. I study an epigenetic protein called Lsd1 and its role in proper retinal development because it could be a therapeutic target for a pediatric ocular cancer called retinoblastoma.  

How did you decide to make this the focus of your research? 
During college, I did a summer internship at The Retina Foundation of the Southwest in Dallas, TX where I tested patients with blinding disorders for visual problems. That internship made me realize how few treatment options are available for different forms of blindness and visual disorders. Emory University has an outstanding ophthalmology department and Dr. Nickerson was looking for a graduate student to explore a new project in the lab so it was a perfect fit!  

How did your scientific journey begin? 
My 8th grade science teacher Ms. Roden was a huge inspiration. She always encouraged me to ask questions outside of the scope of the assignment or project and really fostered my scientific curiosity. Afterwards, that curiosity was enhanced by my high school IB science teacher, Ms. Katavic, who taught me for 2 years and ultimately encouraged me to pursue a neurobiology degree in college.  

Was there something specific about the Chromatin, Epigenetics and Gene Expression course that drew you to apply?
The course covers specific techniques that I wanted to learn and apply towards my own project: Chromatin immunoprecipitation (ChIP) combined with DNA sequencing (ChIP-seq) and Electrophoretic Mobility Shift Assays (EMSAs). These are techniques not currently used in my laboratory but would be very valuable for my project. Also, the invited lecturers for this course are game-changers in the fields of genetics and epigenetics so learning about their research firsthand was a fantastic opportunity.  

What and/or how will you apply what you've learned from the course to your work? 
The two techniques I mentioned above will allow me to determine exactly where the Lsd1 protein binds to DNA and how tightly this binding occurs. Ultimately, I will be able to determine which genes are being controlled by Lsd1 and in the case for retinoblastoma, how the inhibition of Lsd1 may decrease gene expression to prevent the spread of the tumor.  

What is your key takeaway from the course?
The key takeaway from this course for me were the new techniques that I learned. In theory, you can learn a technique by reading a protocol or the method section of a paper, but having someone show you step-by-step how to complete the experiment makes the entire learning process so much easier. The instructors and TAs of the course were very friendly and helpful, and always willing to answer questions. Now I feel confident in my ability to perform experiments solo when I’m back at Emory.  

If someone curious in attending this course asked you for feedback or advice on it, what would you tell him/her?
Whether they are looking to learn specific techniques for their project or general information about genetics and epigenetics, I would highly encourage anyone to attend this course. It is very intense with long hours, but you have the very rare opportunity to engage with people who are trailblazers in their respective fields. The quality of seminar speakers and instructors is unparalleled, and having the chance to listen to their presentations--and afterwards have dinner with them--is truly unique to this course. 

What do you like most about your time at CSHL?
CSHL is located on a beautiful campus and, during the course, the instructors scheduled a boat trip where we spent an entire Saturday afternoon soaking up the sun and swimming! We also participate in a friendly “Plate Race” against the Yeast Genetics & Genomics course where we ran a relay race carrying 40 yeast agar plates. Though we lost the race, it was so much fun cheering for each other and chanting “GeneX, GeneX!”

Salma received a scholarship from the National Cancer Institute (NCI) to cover a portion of her course tuition. On behalf of Salma, thank you to NCI for supporting and enabling our young scientists to attend a CSHL course where they expand their skills, knowledge, and network. 

Thank you to Salma 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.

Photo: Salma Ferdous

Visitor of the Week: Nick Weilinger

Meet Nick Weilinger of the University of British Columbia (Canada). The postdoctoral fellow is a member of Brian MacVicar’s lab in the Centre for Brain Health and is on campus training at his first CSHL course: Imaging Structure & Function in the Nervous System. 

What are your research interests? What are you working on?
My work focuses on understanding how the brain swells (called cerebral edema) during stroke and traumatic brain injury. I approach this by imaging movement of chloride ions, which are crucial in controlling the volume of nerve cells by regulating their solute content. 

How did you decide to make this the focus of your research? 
Despite cerebral swelling being a hallmark consequence of brain trauma and a major cause of death in patients with large infarctions, we have no direct way to treat the underlying changes in cell volume. In the MacVicar lab, we are highly motivated to identify novel targets for therapeutic intervention. We have developed new ways of measuring the chloride changes that trigger cell swelling under these conditions, and hope to pinpoint the key routes of chloride entry as potential drug targets. 

How did your scientific journey begin? 
I kind of fell into it. I didn’t know what to do after undergrad, so I looked back on which courses interested me most; and my neurobiology courses stood out. I was lucky to start as a MSc student in a terrific lab without any prior experience and that led to a PhD in Neuroscience! 

Was there something specific about the Imaging Structure & Function in the Nervous System course that drew you to apply?
The neuroimaging course provides students with a unique opportunity to build custom microscopes: advanced microscopy theory can be taught anywhere, but getting hands-on experience with all the equipment needed to build a microscope from scratch is a rare thing. 

What and/or how will you apply what you've learned from the course to your work? 
My classmates and I will be leaving this course with the practical know-how to build, repair, and modify microscopes to answer niche scientific questions that would otherwise be difficult to address. I am confident that I will be well-positioned to teach my labmates what I’ve learned here so that we can improve upon our data acquisition methods. 

What is your key takeaway from the course?
CSHL brings in a world-class lineup of lecturers and teaching assistants who are on the leading edge of their respective fields. Not only did the course offer tremendous learning opportunities, but the one-on-one interactions over the past weeks have fostered a new network with both instructors and students. I leave campus with new colleagues whom I look forward to collaborating with throughout my career. 

How many CSHL courses have you attended? Will you be attending another CSHL course or meeting in the near future?
This is my first time at CSHL and I don’t have anything else scheduled, but after visiting the campus firsthand I can say that I will certainly return for a future meeting! 

If someone curious in attending this course asked you for feedback or advice on it, what would you tell him/her?
The neuroimaging course was personally recommended to me by colleagues who have attended in the past. It is a fully immersive, challenging and, most importantly, fun experience. I would not hesitate to recommend the neuroimaging course to a colleague.  

What do you like most about your time at CSHL?
What stood out to me the most was developing new friendships with trainees from across the globe - and enjoying a frisbee/football break at lunch!

Thank you to Nick 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.