Molecular Biology Module

Director: Steven Abcouwer, Ph.D.
Staff: David Reed, Ph.D.
Email: dmreed@umich.edu
Phone: 734-647-5843
Fax: 734-232-8021

This Module facilitates and expedites vision research by providing an array of services involving molecular biology technologies, statistical genetics, and bioinformatics. The facility also provides access to large equipment that would be impractical for a single lab to acquire or maintain.

Project Priority

  • NEI-funded investigations
  • Generation of pilot data for vision grant proposals
  • Collaborative investigations involving vision research

Primary Services

  • Maintenance/oversight of Module equipment
  • Training and certification for experimentation involving Module equipment and protocols
  • Facilitating MCORES usage
  • Gene expression, statistical, analytical experiment support and analysis
  • ‘OMICS data storage (as needed)
  • Emergency and defrosting freezer storage

Experimentation/Protocols

  • SNP and GWAS analysis
  • Gene expression data analysis
  • Quantitative PCR assay design and analysis
  • RNA-Seq sequence data processing pipeline, differential expression and bioinformatic analysis
  • Other molecular biology protocols, depending on availability

Module Equipment

Some pieces of equipment must be reserved for use. Reserve Equipment here.

RNA, DNA, Protein, Quantification and ELISA

  • Agilent 2200 Tape Station
  • Agilent Bioanalyzer 2100
  • BioTek Epoch plate Spectrophotometer
  • Thermo Fisher Scientific Nanodrop 1000 Spectrophotometer
  • Beckman DU530 Spectrophotometer
  • PerkinElmer Lambda Bio20 UV/Vis Spectrophotomer
  • Shimadzu Spectrophotometer
  • Molecular Devices SpectraMax 190 Microplate Reader
  • Turner BioSystems Veritas Microplate Luminometer

Quantification PCR

  • BioRad CFX96
  • BioRad CFX384

Digital Imaging

  • Azure Biosystems C500 Imaging System
  • GE Typhoon FLA 9000
  • UVP Biospectrum 500 image station
  • AFP X-ray Film Processor  

Sample Preparation

  • Large capacity centrifuges
    • Beckman Avanti J-26 centrifuge
    • Beckman Coulter Opima L-90K ultracentrifuge
    • Sorvall Super T21 centrifuge
    • Benchtop centrifuges
  • Vacuum concentrators
    • Savant ISS 110 Integrated SpeedVac System (2)
  • Ultrapure water purification systems
    • Milli-Q Reference
    • Seimens/US Filter ELGA Purelab Ultra
  • Other sample preparation
    • Thermo Spectronic French Press
    • Thermo Scientific MaxQ 5000 Shaker incubator

Other devices

  • Bectin-Dickenson Flow Cytometer
  • Waters HPLC System with Radiodetector
  • Perkin-Elmer WinSpectral 1414 Scintillation Counter
  • Tuttnauer-Brinkman 3870E tabletop autoclave

Past Projects

Microarray Analysis

Statistical analysis heat map

Statistical analysis

 

Statistical Genetics

Statistical Genetics Meta-Analysis

Meta-Analysis
Ayala-Lugo RM, Pawar H, Reed DM, Lichter PR, Moroi SE, Page M, Eadie J, et al. Variation in optineurin (OPTN) allele frequencies between and within populations. Mol Vis 2007;13:151–63. PMCID: PMC2533035

 

 

Molecular Genetics

Molecular Genetics Statistical analysis

Statistical analysis
McLaren N, Reed DM, Musch DC, Downs CA, Higashi ME, Santiago C, Radenbaugh PA, Allingham RR, Richards JE, Moroi SE. Evaluation of the beta2-adrenergic receptor gene as a candidate glaucoma gene in 2 ancestral populations. Arch Ophthalmol2007;125:105–11. PMID: 17210860

 

 

Physiology

 

Physiology Statistical modeling

Statistical modeling
Radenbaugh PA, Goyal A, McLaren NC, Reed DM, Musch DC, Richards JE, Moroi SE. Concordance of aqueous humor flow in the morning and at night in normal humans. Invest Ophthalmol Vis Sci 2006;47:4860–64. PMID: 17065499

 

 

Immunology

Immunology: Experimental design, cytokine levels, categorical data analysis

 

Experimental design, cytokine levels, categorical data analysis

  • Bucher RS, Hall E, Reed DM, Richards JE, Johnson MW, Zacks DN. Effect of intravitreal triamcinolone acetonide on susceptibility to experimental bacterial endophthalmitis and subsequent response to treatment. Arch Ophthalmol 2005;123:649–53. 
    PMID: 15883284
  • Comer GM, Miller JB, Schneider EW, Khan NW, Reed DM, Elner VM, Zacks DN. Intravitreal daptomycin: a safety and efficacy study. Retina 2011;31:1199–206. PMID: 21522040
 

Structural bioinformatics

Structural bioinformatics: Ab initio tertiary structure

Ab initio tertiary structure
Hemati N, Feathers KL, Chrispell JD, Reed DM, Carlson TJ, Thompson DA. RPE65 surface epitopes, protein interactions, and expression in rod- and cone-dominant species. Mol Vis2005;11:1151–65. PMID: 16379027