Training with the NCDIR

Our Center represents an important resource of instrumentation, software, methods, and expertise that we have developed and optimized. The overarching goal of the NCDIR is to enable the widest range of researchers in the biomedical community to access our interactomics pipeline resource, and to transfer the pipeline technology to researchers’ laboratories. One major method to achieve this goal is to create a body of researchers from a wide diversity of fields who are trained in the use of NCDIR technology. These researchers will, in turn, act as nuclei to seed further spreading of our approaches in the community.

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. The NCDIR visiting scientist program trains scientists who desire to apply NCDIR science or technology directly to their research. Initially, to ensure quality control and standard operating procedures, this hands-on training occurs at one of the Center locations (Rockefeller University, UCSF, or Center for Infectious Diseases Research). Once the scientist is trained (i.e., knowledge transfer of NCDIR science or technology), NCDIR scientists continue to interact with the scientist remotely, or through additional direct interactions and further technology advancement at an NCDIR site or at the scientist’s home institution/lab. Thus, our cross-institutional training is one of the ways in which the expertise gained through the NCDIR is transferred to the community. Furthermore, providing training also has the added benefit of encouraging scientists to learn new techniques in a collaborative learning environment. The scientists in the Driving Biomedical Projects (DBPs) and Collaborations and Service Projects (C&SPs) also provide hands-on training for other scientists.

Since 2018 our labs have provided direct hands-on training to 93 investigators/students, including 75 scientists from 7 states in the US and 18 scientists from 5 foreign countries; representing a highly active and successful outreach of the Center through user training. 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). The role of the Center in our collaborators’ work is acknowledged through listing the P41 (P41 GM109824/GM/NIGMS NIH HHS/United States) as grant support in their publications or acknowledge the fact that they got help for the NCDIR funded by the P41 grant.

Visiting scientist and reciprocal training program. Generally, to set up training with the NCDIR, community scientists contact a NCDIR scientist (including the PIs) at the institution where the training should best occur. Alternatively, NCDIR personnel reach out to scientists to inform them of the potential contributions NCDIR can make to a project.  The training provided is based on the scientific challenge at-hand, and the current status of the NCDIR method or technology. Hands-on direct contact training will occur at one of the Center institutions to ensure quality control and standard operating procedures are followed. Fully equipped benches and adjacent workstations are dedicated and made available for NCDIR visiting scientists; surrounded by the interactomics equipment (cryomilling stations, 96-well solution handling and screening equipment, HPLCs and FPLCs, mass spectrometers, and computer workstations) needed to complete the training, as well as on-hand NCDIR members with the appropriate expertise. Thus, the NCDIR visiting researcher has everything they need within a few paces of their bench for being trained on taking their samples from frozen cells to multiple analytic stages. Once the research, technology, method, or software is proven to be robust within the Center, NCDIR scientists can then visit the trainee’s lab to train these scientists at their home institutions. In this way NCDIR scientists are able to provide hands-on training to teach trainees to directly apply our methods, technologies, and/or modeling to their own research.

The NCDIR Fellows Program. We have developed a Fellows program to provide trainees within the NCDIR the opportunity to receive hands-on training in a specific research, technology, method or computational tool to help further their own research. We have leveraged the framework of the Fellows program from within the NCDIR to trainees in the greater biomedical community. Our current and previous Fellows are listed below.

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.

410, 2018

Collaborator profile

October 4, 2018|

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!

402, 2018

Introducing our 2018 NCDIR Fellow – Dr. Maxwell Neal

February 4, 2018|

The NCDIR Fellows program provides is awarded to an exceptional scientist within the NCDIR, allowing them the opportunity to receive hands-on training in a specific research, technology, method or computational tool to help further their own research. We have leveraged the framework of the Fellows program from within the NCDIR to trainees in the greater biomedical community.

Dr. Maxwell Neal

The 2018 Fellow was Maxwell Neal, a postdoctoral fellow in John Aitchison’s lab (CGIDR). Within the Aitchison lab he worked on characterizing the functional role of the nucleoprin NUP170 in yeast. He also collaborated with members of Alexis Kaushansky’s lab to identify the determinants of hepatocyte susceptibility to infection by Plasmodium. He also collaborated with researchers at the University of Washington who focus on developing community standards for sharing computational, mechanistic models among biomedical researchers.
A computational biologist by training, Dr. Neal’s work focused on applying computational analyses to assist in various ongoing investigations within the NCDIR consortium. Working with members of the Aitchison lab, he developed an approach for functionally characterizing the NUP170 protein using a previously-published compendium of yeast transcriptome profiles assembled from over 1400 single-gene knock-out strains. By identifying the set of knock-out profiles that best match the NUP170 profile, Dr. Neal identified a set of putative functions associated with NUP170 along with a set of genes that may interact with NUP170 as participants in those functions. By cross-referencing Dr. Neal’s gene set with NUP170 protein-interaction data collected in the lab, we have been able to identify specific protein complexes that may participate with NUP170 in maintaining genome stability. Dr. Neal has also been responsible for analyzing RNA-seq data generated as part of the NUP170 project. These analyses helped identify the region of the NUP170 protein required for its subtelomeric gene silencing activity.
In collaboration with the Kaushansky lab, Dr. Neal has developed computational methods for determining how specific Ephrin receptors modulate hepatocyte infectivity by the malaria parasite. Using flow cytometry data collected by last year’s NCDIR Fellow Adam Lewis, Dr. Neal developed computational approaches for visualizing how infectivity changes with receptor amount and for determining the relative contribution of different Ephrin receptors (and their associated hetero- and homo-dimers) to infectivity. In addressing the latter challenge, Dr. Neal developed a mechanistic model of Ephrin receptor dimerization on the cell surface. Then, using a genetic algorithm, he identified the linear weighting factors for each Ephrin species that produced the best fit between model-based infectivity estimates and actual infectivity measured using flow cytometry. The resulting model not only shows good quantitative matches with data in terms of its infection rates, but also predicts a counter-intuitive biological finding – that adding receptor ligand to cell cultures increases infectivity.
As an NCDIR Fellow, Dr. Neal also collaborated with researchers at the University of Washington who focus on developing community standards for sharing and reusing computational models within biological research. Specifically, these researchers investigate the application of semantic annotations on computational models. Such annotations capture, in a computable way, the biological processes simulated in a model as well as the entities that participate in those processes. Semantic annotations are a critical ingredient for making models more discoverable and reusable among the broader scientific community, and with assistance from the NCDIR Fellowship program, Dr. Neal published two papers in 2018 focused on semantic annotations for computational models.

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