Resource Center

A key component of the Strategic Research Initiative is investing in the latest resources and tools that can benefit biomedical researchers across campus and beyond. Click on the components of the Resource Center, below, to learn more.

In Silico Protein Analysis Module

Motor neurons
Motor neurons

The In silico protein analysis module, directed by Dr. Santiago Schnell (schnells@umich.edu), helps PFD investigators make predictions about protein structure, analyze proteome data and model biochemical pathways related to the causes, control and prevention of PFDs.

The module provides four types of services:

Reaction Kinetics is widely applied to study reaction mechanisms and their engineering at the molecular level.  The mechanistic information is valuable in the context of the development of therapeutic strategies to combat diseases.

Mathematical and Computational Modeling is used to formulate several hypothetical model mechanisms in parallel, which are compared with independent experimental data.  The resulting comparisons satisfying statistical measures of similarity will be used to make new experimental predictions, which can be tested experimentally.

Bioinformatics tools can be used to predict systemic features of proteins with the aim of understanding the determinants modulating protein aggregation and making qualitative predictions of protein structure.

Proteomic Analysis Service assists with the analysis of mass spectrometry-based proteomics data generated in the Pathology Proteomics Resource facility.

For more information or access to the services of this module, please complete this on-line form.

PFD Reagent Library

PFD reagent library facilitates research by sharing critical reagents: plasmids, validated antibodies and protein quality control reporter vectors relevant to PFD studies.

  • Antibodies - The catalog contains validated antibodies which have been complied from various PFDI investigators for the purpose of lowering the barriers to explore new ideas in research.  Antibodies are available to any PFDI members laboratory and can be requested by completing this form.  Once the form is completed, please email it to Cathy Bearman at cniemiec@umich.edu.  The form will then be logged and sent off to Matthew Perkins who will be responsible for purchasing and distributing the antibodies.  Each laboratory can request and receive one (1) aliquot of a given antibody.  An aliquot will typically, but not always, represent one tenth of the purchased commerical antibody.  Each PFDI member can receive a maximum of one aliquot per each antibody listed in the catalog.
    To view the list of antibodies, click on the catalog
    We want to continually expand the antibody catalog, so please continue to send any PFD related antibodies to Cathy Bearman at cniemiec@umich.edu.  If you have questions on the antibody, please contact the investigator.  For other questions, contact Matthew Perkins at perkmd@umich.edu.

Mouse Tissue Bank

Mouse tissue bank will maintain a bank of fixed tissue blocks and frozen tissue from a range of PFD mouse models. This resource will facilitate PFD investigators’ ability to test novel ideas across disease platforms rapidly and at low cost.

Human Disease Brain Bank

Human disease brain bank facilitates analysis of human disease tissue by PFD investigators.

  • The brain bank contains frozen and fixed brain tissue from several hundred individuals with age-dependent neurodegenerative PFDs or similarly aged, cognitively normal controls. Most cases are linked to detailed clinical information, which is stored and disseminated in a manner that ensures patient confidentiality.
  • Access to tissue and clinical information will occur by request through the brain bank web portal. We anticipate that the PFD human tissue bank will expand to bank additional organs relevant to PFDs as the PFD initiative grows.

Please contact Matthew Perkins with any questions, perkmd@umich.edu

Posttranslational Modifications Core

Equipment from an Orbitrap Fusion Tribrid
Component from an Orbitrap Fusion Tribrid

The Posttranslational Modifications Core will enhance the ability of PFD investigators to detect posttranslational modifications of relevance to PFD’s. To accomplish this goal, the PFD initiative has invested in the Proteomics Resource Facility (PRF) maintained by the Department of Pathology at U of M and directed by Dr. Alexey Nesvizhskii.

The services offered by the PRF include:

  • Qualitative identification of proteins from multiple sources such as Coomassie and MS-compatible silver-stained gels, shot-gun proteomics analysis of complex mixtures using two-dimensional liquid chromatography and mass spectrometry (2D-LC/MS)
  • Identification of post-translational modifications such as phosphorylation, ubiqutination, acetylation, (mono-, di-, tri-) methylation, glycosylation etc.
  • Quantitative proteomic profiling using isotope labeling (SILAC, cICAT), and label-free (spectral counting) strategies
  • In addition, the PRF can flexibly provide specific functionalities to aid PFD investigators achieve aims that relate to their unique biological questions
  • PFD investigators will receive extensive support in terms of experimental design, technical training (related to sample prep for MS analysis), data interpretation and bioinformatics analysis

The PRF is equipped with four Thermo Scientific mass spectrometers devoted exclusively for proteomic analysis.  These include:

  1. Orbitrap Fusion Tribrid with ETD (obtained through PFD funding)
  2. Orbitrap (LTQ Orbitrap XL)
  3. Linear ion-trap with ETD (LTQ-XL ETD)
  4. Triple quadrupole mass spectrometer (TSQ Quantum Ultra)

PFD has funds available on a first come, first serve basis, up to a maximum of $2,500 per PFD investigator, to facilitate proteomics studies performed by PFD investigators within this core.  To be eligible, compose a paragraph describing the proposed study and estimated cost, utilizing this form, and submit, via email, to Cathy Bearman (cniemiec@umich.edu).  Studies must be relevant to the focus of the PFD Initiative, and will be reviewed by Dr. Venky Basrur from the Proteomics Resource Facility.  Before approval of any proposal, discussions should occur between the PFD investigator and the Proteomics Resource Facility staff to ensure the feasibility and best strategies to carry out the study. 

For more information about the PRF, please visit their website.

 

 

 

 

High Throughput Screening Core

High throughput screening core will leverage resources in the University of Michigan Center for Chemical Genomics (CCG), with experienced staff, modern instrumentation, chemical libraries, RNAi collection, and a track record of success, having performed over 80 screens for U-M faculty, external academic groups and both large and small pharmaceutical companies.

PFD has funds available to fund four high throughput screening projects, up to a maximum of $15,000 per PFD investigator.  To be eligible, compose a one to two page proposal outlining the proposed study and estimated cost, utilizing this form, and submit, via email, to Cathy Bearman (cniemiec@umich.edu), by April 1, 2015.  Studies must be relevant to the focus of the PFD initiative.  These funds are not for assay development, but rather for small molecule or siRNA screening with the CCG. Proposals will be reviewed by the Leadership Council during their regularly scheduled meetings.  Before approval of a proposal, it is expected the Center for Chemical Genomics (CCG) will sign off on the feasibility of the screen. To begin working with the CCG, click on this Request Project link.

Mouse Model Library

The mouse model library holds a compendium of model systems that are available across campus.  The list includes models of specific diseases, mutants of components of the protein quality control machinery, sensors of proteostasis, or other models that are of interest to the PFD community.  We believe the availability of this resource will facilitate new collaborations and speed scientific discovery.   If you are interested in sharing your model/s, please complete this form and email it to Cathy Bearman at cniemiec@umich.edu.  

For the current list of mouse models, click here.