Training with the NCDIR

The NCDIR currently has over 60 active collaborations from over 40 institutions. If you are a scientist seeking in-depth training, typically we ask that you seek to collaborate with one of our scientists, and then visit one of the labs on a longer-term basis (i.e. several months). Our Center places great value in scientists training scientists and this training provides direct scientist-to-scientist training for trainees who want to learn and/or apply a tool (method, technology) to their own science.

If you are interested in collaborating with one of our researchers, visit our About Us page to contact the four PI’s directly or contact!

Training with the NCDIR can also be done virtually via our video links which can be accessed here.

Visiting Student Profile

5 minutes with visiting Masters student, Lars ter Morsche

Lars, where are you visiting from?
I’m an MSc student from the University of Groningen/University Medical Center Groningen in the Netherlands.

What are your research interests?
Being only at the very start of my research career, those interests have started to take shape but are at the same time yet to be completely defined. The well-defined foundation for me was an interest in the molecular basis of life (and disease), which I was able to explore partly during a previous internship in molecular oncology. Having completed that I wanted my current internship to shift more towards a biochemical and protein angle. I am currently interested in studying the endogenous interactome of the LINE-1 RNP. LINE-1 (or L1) is a retrotransposon that can copy-and-paste itself into the human genome via an mRNA intermediate. This mechanism relies on the interaction of the mRNA with its two self-encoding proteins, and this self-proliferative capacity has led to the fact that over the course of evolution, LINE-1 has been able to multiply to occupy 17% (!) of the human genome today.

How did you come to learn and work with the NCDIR?
The research Master’s program that I’m enrolled in provides the opportunity to pursue a 6-months research internship in a lab of choice, after which I plan to pursue a PhD. In Groningen I met Dr. John LaCava, and together we set up this collaboration of me working under his supervision in the Rout lab.

What do you hope to learn?
Working in the Rout lab, in a world-renowned institution such as The Rockefeller University, and under the direct supervision of Dr. John LaCava provides me with a set of skills and knowledge that I will cherish for the rest of my scientific career. Coming to the Rout lab I expected an environment of distinguished researchers that could help me broaden my knowledge in the field of biochemistry and protein biology, and yet also one that would challenge me and help me develop the skills to become an independent researcher.

How has your time been so far?
The knowledge base in the lab is enormous, as is the willingness to share that knowledge. I’m also given the opportunity to independently search for the path of scientific progress, and – perhaps most importantly – learn from my mistakes. I’m confident that I will step out of the Rout lab with a solid base for starting a PhD, and I would be very glad to collaborate with the Rout lab or any of its members in the future.

February 26th, 2020|

Introducing our 2019 NCDIR Fellow – María Benítez Guijarro

The 2019 NCDIR fellow is Ms. Maria Benitez Guijarro, PhD candidate and member of Garcia-Perez lab, GENYO, Pfizer-University of Granada-Junta de Andalucía, Centre for Genomics and Oncological Research in Spain. Maria has spent 9 months at The Rockefeller University working within the LINE-1 research team of Dr. John LaCava. She received advanced training in protein interactomics and leveraged resources and assistance provided by Profs. Michael Rout and Brian Chait and their lab members to explore endogenous LINE-1 interactomes in embryonal carcinoma cells (PA-1).

 Class-1 Long INterspersed Elements (LINE-1s or L1s) are abundant human active retrotransposons (comprise >17% of our genome) that move using a copy-and-paste mechanism, generating new insertions during early human embryogenesis which can sporadically result in the generation of new genetic disorders. Previous research from Garcia-Perez lab demonstrated that new LINE-1 insertions in Pluripotent Cells (PCs) are silenced epigenetically shortly after/during insertion, using a novel but otherwise completely uncharacterized mechanism. LINE-1 silencing only occurs in PCs, and this restriction mechanism is absent in isogenic Differentiated Cells (DCs). The main goal of Maria’s project in collaboration with the NCDIR is to discover the mechanism of LINE-1 insertion silencing in PCs, as this restriction mechanism may mitigate the mutagenic potential of LINE-1 during evolution and development. As L1s are known to impact the genomes of human embryonic stem cells, with potential in regenerative medicine, understanding how L1 is regulated is important to guarantee their safety for clinical use.

To interrogate the above-described mechanism and identify factors linked to LINE-1 insertion silencing, Maria carried out co-immunoprecipitation studies of the LINE-1 ORF1 protein and its interactors in PCs and DCs from PA-1 cells. For this she worked together with other NCDIR scientists, including Ms. Hua Jiang, Ms. Kelly Molloy, and Dr. Mehrnoosh Oghbaie, to capture LINE-1 ribonucleoprotein particles and conduct mass spectrometry-based protein interaction studies on them. As a result of this work, they identified a list of factors that will be subsequently validated by Maria using CRISPR/Cas9 genome editing and retrotransposition activity assays. During her visit, Maria also worked to develop a ‘capillary western’ (Protein Simple: simple western) assay for the combined detection of ORF1p and ORF2p, the two proteins encoded by LINE-1. Her aim is to easily facilitate future, rapid quantitation of LINE-1 proteins across different samples.

Maria Benitez Guijarro’s visit was funded by an EMBO short-term fellowship and the Fellowship for temporary transfers for FPU from the Spanish Government.
January 18th, 2019|
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