NCDIR COLLABORATORS – Current Projects (Grant ID: P41 GM109824)

Driving Biological Projects (DBPs)

The NCDIR’s DBP partnerships and collaborations are used to synergistically develop and advance state-of-the art methods, as well as being the first stage of providing access to the NCDIR’s emerging tools. DBPs are linked to the TR&Ds to drive advances into new areas of high biomedical importance and translational potential. DBPs are selected to develop and validate our methods on different biological systems. Thus, projects are selected to collectively meet the following criteria:

• Present specific technological roadblocks that have been generally acknowledged by the field, allowing us to refine our technologies by determining how to overcome these roadblocks.
• Cover many different kinds of model organisms, tissues, and disease types. Thus, any new DBP should complement these, by adding a new model organism, tissue, or disease of significant biomedical importance.
• Address macromolecular systems spanning different representative subcellular systems, thus ensuring their robust utility upon further dissemination. Thus, a new DBP will be considered if it allows the NCDIR to expand its pipeline technologies into new macromolecular and dynamic subcellular systems.
• Sufficient resources and laboratory investment of funding and effort are in place.
• Mechanisms are in place to ensure continued two-way engagement with the PIs of these projects, and NCDIR

“The role of the Center in our collaborators’ work is acknowledged through listing the P41 as grant support in their publications or acknowledge the fact that they got help for the NCDIR funded by the P41 grant.”

If you are interested in collaborating with the NCDIR, email the key NCDIR Principal Investigators directly, or email admin@ncdir.org.

Below is the list of ongoing and completed DBPs (Grant ID: P41 GM109824)

Collaboration and Service Projects (C&SPs)

C&SP provide opportunities for high-level collaborative support to researchers in the biomedical community. Distinct from DBPs, C&SPs support research with technologies that are already addressed by our Center’s pipeline. Thus, they “beta-test” our technologies to remove remaining minor issues that may be unique to the experimental challenge at hand. C&SPs thus are an important aspect of community engagement, enabling biomedical researchers to adopt existing and newly-developed TR&D technologies.

We continue to actively seek new C&SPs as part of our commitment to community engagement and those interested are encouraged to email the key NCDIR Principal Investigators directly, or email admin@ncdir.org.

Below is the list of ongoing and completed C&SPs (Grant ID: P41 GM109824)

C&SP 1 – Identification of Nuclear Transport Cargos and their Nuclear Targeting Signals
Collaborating PI(s): Yuh Min Chook
Collaborating Institution(s): University of Texas, Southwestern Medical Center, USA
NCDIR personnel: Andrej Sali

C&SP 2 – Capturing dynamic protein-protein interactions in Toxoplasma gondii autophagy
Collaborating PI(s): Vernon Carruthers
Collaborating Institution(s): University of Michigan, USA
NCDIR personnel: John Aitchison & Arti Navare

C&SP 3 – LINE-1 Retrotransposition in the Human Genome (Completed)
Collaborating PI(s): Jeff Boeke
Collaborating Institution(s): NYU Grossman School of Medicine, NYU Langone Health, USA
NCDIR personnel: John LaCava & Michael Rout

C&SP 4 – Degenerative and Dementing Diseases of Aging
Collaborating PI(s): Stan Prusiner
Collaborating Institution(s): UCSF, USA
NCDIR personnel: Andrej Sali & Dibyendu Mondal

C&SP 5 – Characterization of Human Disease Related RNA-Protein Complexes (Completed)
Collaborating PI(s): Torben H. Jensen
Collaborating Institution(s): Aarhus University, Demark
NCDIR personnel: John LaCava & Michael Rout

C&SP 6 – Elucidating the Structure of Dysferlin and its Interactome
Collaborating PI(s): Kevin Sonnemann
Collaborating Institution(s): University of Wisconsin-Madison, USA
NCDIR personnel: Brian Chait, Michael Rout & Peter Fridy

C&SP 7 – A New Technology for Cancer Therapy: From Pilot to Pipeline
Collaborating PI(s): Hans-Guido Wendel
Collaborating Institution(s): Memorial Sloan Kettering Cancer Center, USA
NCDIR personnel: Brian Chait, Michael Rout & Peter Fridy

C&SP 8 – Integrative structure modeling of HIV-human protein complexes
Collaborating PI(s): Ignacia Echeverria
Collaborating Institution(s): UCSF, USA
NCDIR personnel: Andrej Sali 

C&SP 9 – Volume tissue imaging using fluorescent nanobodies
Collaborating PI(s): Marc Tessier-Lavigne
Collaborating Institution(s): Stanford University / The Rockefeller University
NCDIR personnel: Brian Chait, Michael Rout & Peter Fridy

C&SP 10 – Mapping the Interactome of Mycobacterium tuberculosis (Sherman, Aitchison)
Collaborating PI(s): David R. Sherman
Collaborating Institution(s): University of Washington, USA
NCDIR personnel: John Aitchison & Fred Mast

C&SP 11 – Characterization of Malaria host-parasite interactions
Collaborating PI(s): Alexis Kaushansky
Collaborating Institution(s): Seattle Children’s Research Institute, USA
NCDIR personnel: John Aitchison

C&SP 12 – CRISPR interference (CRISPRi) platform to accelerate the genetic interrogation of Mycobacterium tuberculosis pathogenesis
Collaborating PI(s): Jeremy Rock
Collaborating Institution(s): The Rockefeller University, USA
NCDIR personnel: Brian Chait & Wenzhu Zhang

C&SP 13 – Structure, Function and Specificity of RNA Editing Complexes
Collaborating PI(s): Kenneth Stuart
Collaborating Institution(s): Seattle Children’s Research Institute, USA
NCDIR personnel: John Aitchison

C&SP 14 – Nanobodies against Trypanosome Conserved Surface Antigens as Therapeutics
Collaborating PI(s): Mark Field
Collaborating Institution(s): University of Dundee, UK
NCDIR personnel: Michael Rout, Natalia Ketaren & Samson Obado

C&SP 15 – The structure and function of the bacterial PCAT1 transporter (Completed)
Collaborating PI(s): Jue Chen
Collaborating Institution(s): The Rockefeller University
NCDIR personnel: Brian Chait & Dom Olinares

C&SP 16 – Structural modeling of the eukaryotic replicative helicase CMG in complex with essential replication factor Mcm10
Collaborating PI(s): Mary O’Donnell
Collaborating Institution(s): The Rockefeller University
NCDIR personnel: Brian Chait &Tanmoy Sanyal

C&SP 17 – Architecture of the Human γ-Tubulin Ring Complex
Collaborating PI(s): Tarun Kapoor
Collaborating Institution(s): The Rockefeller University
NCDIR personnel: Brian Chait & Dom Olinares

C&SP 18 – DNA Replication and Nucleotide Excision Repair
Collaborating PI(s): David Jeruzalmi
Collaborating Institution(s): City University of New York, USA
NCDIR personnel: Brian Chait & Dom Olinares

C&SP 19 – A spatiotemporal multi-scale model of the human pancreatic β-cell
Collaborating PI(s): Raymond Stevens, Kate White, Carl Kesselman
Collaborating Institution(s): University of Southern California
NCDIR personnel: Andrej Sali &Tanmoy Sanyal

C&SP 20 – Determining the structure and functions of the SEA Complex (completed)
Collaborating PI(s): Svetlana Dokudovskaya, Yi Shi
Collaborating Institution(s): Institut de Cancérologie Gustave Roussy, France (Dokudovskaya); University of Pittsburgh (Shi)
NCDIR personnel: Michael Rout & Andrej Sali

C&SP 21 – Atomic Structures of the Eukaryotic Ribosome (Completed)
Collaborating PI(s): Sebastian Klinge
Collaborating Institution(s): The Rockefeller University
NCDIR personnel: Brian Chait & Kelly Molloy

C&SP 22 – Structural characterization of Bm86 homolog antigens to accelerate understanding of mammalian anti-tick immune response
Collaborating PI(s): Erica Jacobs
Collaborating Institution(s): St. John’s University
NCDIR personnel: Brian Chait

C&SP 23: Investigating a structural basis for cross-reactive antibodies between ATR1 and SARS-CoV-2 (Completed)
Collaborating PI(s): Whitney Harrington and Lisa Frenkel
Collaborating Institution(s): Seattle Children’s Research Institute, USA
NCDIR personnel: John Aitchison & Fergal Duffy

C&SP 24 – Nanobodies for the Development of Lyme Disease Diagnostic Tests
Collaborating PI(s): Margaret MacDonald
Collaborating Institution(s): The Rockefeller University
NCDIR personnel: Michael Rout, Brian Chait & Peter Fridy

COLLABORATORS OF THE NCDIR