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.

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)

DBP 1 – Structural Dynamics of the Nuclear Pore Complex
Collaborating PI(s): Javier Fernandez
Collaborating Institution(s): The Biophysics Institute (UPV/EHU, CSIC), Spain
NCDIR Personnel: Michael Rout, Brian Chait, Andrej Sali, Paula Upla & Trevor Van Eeuwen

DBP 2 – De Novo Peroxisome Biogenesis
Collaborating PI(s): Richard Rachubinski
Collaborating Institution(s): University of Alberta, Canada
NCDIR Personnel: John Aitchison, Michael Rout, Fred Mast & Max Neal

DBP 3 – Hierarchical Assembly of RNPs
Collaborating PI(s): Susan Wente, Marlene Oeffinger
Collaborating Institution(s): Vanderbilt University, USA (Wente), IRCM, Canada (Oeffinger)
NCDIR personnel: Michael Rout, Brian Chait, John Aitchison, Erica Jacobs, Peter Fridy & John LaCava

DBP 4 – Nuclear Organization in Trypanosomes
Collaborating PI(s): Mark Field
Collaborating Institution(s): University of Dundee, UK
NCDIR personnel: Michael Rout, John Aitchison, Samson Obado, Javier Fernandez, Erica Jacobs & Max Neal

DBP 5 – Surveying the Genome Landscape in Space and Time
Collaborating PI(s): Frank Alber
Collaborating Institution(s): University of Southern California, USA
NCDIR personnel: John Aitchison, Andrej Sali, Olivier & Ben Webb

DBP 6 – Architecture of Transcriptional Regulatory Complexes (Completed)
Collaborating PI(s): Jeff Ranish
Collaborating Institution(s): Institute for Systems Biology, USA
NCDIR personnel: Andrej Sali, John Aitchison, Seung Joong Kim & Fergal Duffy

DBP 7 – Dynamic Structure of the Spindle Pole Body (Completed)
Collaborating PI(s): Mark Winey
Collaborating Institution(s): UC Davis, USA
NCDIR personnel: Andrej Sali & Shruhti Viswanath

DBP 8 – The Host-Viral Interactome During Infection (Completed)
Collaborating PI(s): Charles Rice
Collaborating Institution(s): The Rockefeller University, USA
NCDIR personnel: John Aitchison, Michael Rout, Artem Serganov, Chris Carter & Arti Navare

DBP 9 – Structure and Function of the Malaria Plasmodial Surface Anion Channel, Required for Parasite Survival within Human Erythrocytes
Collaborating PI(s): Sanjay Arvind Desai
Collaborating Institution(s): NIH/NIAID, USA
NCDIR personnel: Michael Rout & Brian Chait

DBP 10 – Integrative modeling of ABC transporters (Completed)
Collaborating PI(s): Robert Stroud
Collaborating Institution(s): UCSF, USA
NCDIR personnel: Andrej Sali

DBP 11 – Molecular Architecture of Exocysts (Completed)
Collaborating PI(s): Mary Munson
Collaborating Institution(s): University of Massachusetts Medical School, USA
NCDIR personnel: Andrej Sali & Brian Chait

DBP 12 – The Prokaryotic Transcriptional Cycle (Completed)
Collaborating PI(s): Seth Darst
Collaborating Institution(s): The Rockefeller University, USA
NCDIR personnel: Brian Chait

DBP 13 – SARS-CoV-2 replication transcription complex
Collaborating PI(s): Seth Darst, Elizabeth Campbell
Collaborating Institution(s): The Rockefeller University, USA
NCDIR personnel: Brian Chait & Dom Olinares

DBP 14 – Nanobodies against the SARS-CoV-2 Spike and Nucleocapsid Proteins for Therapeutic and Diagnostic Purposes
Collaborating PI(s): Erica Jacobs, Paul Bieniasz, Jason Debley, Louis Herlands, Noah Sather, David Fenyö
Collaborating Institution(s): St. John’s University, USA (Jacobs); The Rockefeller University, USA (Bieniasz);  Seattle Children’s Research Institute, USA (Debley); University of Washington, USA (Sather); NYU Grossman School of Medicine, USA (Fenyo); AbOde Therapeutics Inc, USA (Herlands).
NCDIR personnel: Michael Rout, Brian Chait, John Aitchison, Andrej Sali, Fred Mast, Peter Fridy, Natalia Ketaren, Junjie Wang, Dom Olinares, Tanmoy Sanyal & Kelly Molloy.

DBP 15 – Yeast expression library screening for anti-COVID nanobodies
Collaborating PI(s): Fred Cross
Collaborating Institution(s): The Rockefeller University, USA
NCDIR personnel: Michael Rout

DBP 16 – Malaria Transcriptional Regulation
Collaborating PI(s): Alexis Kaushansky
Collaborating Institution(s): Seattle Children’s Research Institute, USA
NCDIR personnel: John Aitchison

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