University of Colorado Denver

• Directors
• Core Objectives
• Staffing
• Instrumentation
• Services
• Fees

Director: Frank Frerman, PhD

Co-Director:  Tamim Shaikh, PhD

Core Objectives:

The objective of the Molecular Discovery Core is to provide advice, training and service in molecular IDD research, from hypothesis generation to characterization of macromolecules. This includes: genome, transcriptome, proteome and metabolome analysis; vector construction; and access to shared instrumentation, such as centrifuges and fluorescence imaging. Advice on biomolecular structure analysis also is available.

Staff:   

• Tamim Shaikh, PhD (Comparative Genomic Hybridization)
• Wallace Chick, PhD (Vector construction)
• Kristina Williams, BS (Vector construction; quantitative PCR)
• Kirk Hansen, PhD (Proteomics)
• Natalie Serkova, PhD (Metabolomics)
• Frank Frerman, PhD ( Molecular Structure)

Services: 

Investigators:  Please remember to acknowledge your Colorado IDDRC affiliation and your use of the cores in all your published papers. For an example see the For Investigators web page.

VIDEO: Molecular Discovery core 

Mass spectrometry (MS)/proteomics.  
Contact:  Kirk Hansen, PhD
Proteomics Core Website 

Goals:  To provide high-throughput, qualitative and quantitative analysis of proteins from tissues, cells, and fluids that can change with respect to time, physiology, and pathology.  In addition to proteomic studies, the MS section of the facility also contributes to investigations involving small molecule analysis. 

The Mass Spectrometry/Proteomics core is operated by the Program in Biomolecular Structure and the Colorado Cancer Center.

VIDEO:  Proteomics Core

Quantitative (QPCR).  
Contact, Quantitative PCR:  Kristina Williams, BS  

Goals:  To provide quantitative (real-time) PCR services, including gene expression, copy number variation (CNV) and single nucleotide polymorphism (SNP) analysis.  Related sample preparation services are also available.  

 

Comparative genomic hybridization (CGH).  
Contact:  Tamim Shaikh, PhD

Goals: To analyze copy number variation (CNV) in the genome using array
CGH with high-resolution oligonucleotide microarrays. IDDRC members will
have access to all the necessary equipment and technical expertise for
array CGH. Additionally, consultation services will be available for the
design of array CGH experiments.

High-throughput DNA sequencing (HTS)
Contact:  Tamim Shaikh, PhD

Goal: To provide IDDRC members access to state-of-the-art sequencing technologies for high-throughput sequencing applications. Consultation services will also be available for the design and application of appropriate technologies to specific projects.

The sequencing equipment and technical expertise is available through the High Throughput Sequencing and the Genomics and Microarray Cores. 
  

Vector construction.
Contact: Wallace Chick, PhD

Goals:  To provide the IDDRC members with state-of-the-art services for the design and generation of genetically engineered mouse models of IDD.  The vector facility constructs vectors to generate transgenic, knockout and knockin animals and vectors with tissue-specific promotors.  The IDDRC has teamed with the NINDS-funded Vector Core of the RMND Center to provide these services.  W. Chick designs the constructs that are subsequently engineered by K. Williams. 

VIDEO:  Vector Construction  

Metabolomics
Contact Person: Natalie Serkova, PhD (Natalie.Serkova@ucdenver.edu).

Metabolomics Core Website

Metabolomics refers to technologies that detect and quantify the low- molecular weight molecules or metabolites (constituents of the metabolome) produced by active, living cells under different conditions and times in their life cycles. The metabolomics facility offers IDDRC investigators the opportunity to analyze genotype-phenotype as well as genotype-envirotype relationships. The following metabolomic technologies are available through the Cancer Center's core:

High-resolution one-dimensional metabolic analysis (including 1H-, 13C-, and 31P-NMR analysis). Over 50 metabolites are quantified simultaneously from a single tissue biopsy/cell extract:

• From 1H-NMR: neuronal markers, such as neurotransmitters, amino acids, ketone body, and lipid metabolism;
• From 13C-NMR: glucose and fatty acid fluxes;
• From 31P-NMR: high-energy phosphates and phospholipid precursors.

High-resolution two-dimensional NMR analysis (2D-COSY, NOESY, HSQC) for structural elucidation of metabolites (see above for the list of metabolites, or identification of unknown metabolites.

VIDEO:  NMR Metabolomics

Molecular Structure Analysis. 
Contact: Frank Frerman, PhD
Biomolecular Structure Program Website 

Goals:  To provide advice regarding the use of biophysical methods  for the determination of molecular structure and interactions.  Facilities are available through the Biophysics Laboratories, a user facility operated by the Program in Biomolecular Structure at the University of Colorado Denver (directed by R. Hodges).   The Biophysics Laboratories offer training (group and one-on-one) for a fee.  After training, instrument user fees are assessed. Assistance also is available for peptide synthesis, purification by HPLC, and composition analysis. More extensive structure analyses may be arranged through collaborations with x-ray crystallographers and NMR spectroscopists in the Biomolecular Structure Program.

IDDRC Shared Instrumentation 

The major, shared instrumentation that is currently available to Colorado IDDRC members is listed below.  The Center maintains these instruments.   The equipment is located on the 4th floor, RC1 North.  For access to equipment and further information, contact Frank Frerman.

For fluorescence imaging Colorado IDDRC members have access to a General Electric Typhoon 9410 multi-mode fluorescence laser scanner/phosphorimager.  This instrument, equipped with three lasers and capable of scanning gels, blots, storage phosphor screens, tissue sections, and multi-well plates is located in the area occupied by the Biomolecular Structure Program and easily accessible to Center members.

Fees:  

Vector Construction: $1,500-$3,000/construct (depending on complexity)

QPCR: $80/sample set of 10 (investigator provides primers)

Array CGH: $160/array. Fee includes array scan (but not array cost) plus analysis with Agilent's DNA Analytics Software

Metabolomics: Discounted Cancer Center rates apply.

Proteomics: Fees cover only instrument time in the proteomics core.

HTS: Fees cover supply costs only.