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.

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|

Collaborator profile

Collaborator profile

5 minutes with visiting Research Assistant Professor, Adnan Halim, PhD

Adnan, where are you visiting from?
I’m visiting from the Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Copenhagen University

What are your research interests?
I’m interested in the regulation and functions of O-linked mannose (O-Man) glycosylations in eukaryotes. This post-translational modification (PTM) is conserved throughout evolution and servers essential cellular functions in organisms ranging from yeast to humans. However, identification of O-Man proteins and their modified sites remains technically challenging, and these limitations hamper our ability to fully understand the cellular functions of O-Man glycosylations. My research involves the use of advanced mass spectrometry to study structures, map site-specific locations and quantify changes of protein O-Man glycosylations on a proteome-wide scale.

Why have you come here to collaborate with the NCDIR in NYC?
We (my lab) recently described a new type of O-Man glycosylation found on yeast nucleocytoplasmic proteins (e.g. nucleoporins) and our hypothesis suggests that this PTM is involved in a myriad of cellular processes, mirroring the signaling- and regulatory functions of the mammalian O-GlcNAc system. We aim to explore the functions and regulations of these O-Man glycosylations, including their cross-talk with other PTMs (e.g. phosphorylation), using the yeast nuclear pore complex (NPC) as a model system.

The Rout lab is world-renowned for their pioneering structural work on the yeast NPC and their innovative interactomics platform. My visit in the Rout lab allows me to acquire key knowledge and skills in the field of interactomics. I am currently undergoing rigorous training and learning how to apply state-of-the-art methods/tools in my research related to O-Man glycosylation and the yeast NPC. The training-through-research approach is supervised by Prof. Michael P. Rout and Dr. Javier Fernandez Martinez and supported by all lab members. My long-term goal is to integrate interactomics with our main research activities focused on O-Man glycosylations upon my return to Copenhagen. We envision that this unique combination of techniques will enable major breakthroughs in mass spectrometry-based glycoproteomics and glycobiology.

Thanks Adnan! All the best for your research endeavors!

October 4th, 2018|
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