DNA Sequencing and Analysis Core Facility

1
DNA Sequencing and Analysis Core Facility
Original Goals

• improve the infrastructure for research at CMU
• assist researchers using molecular techniques
• impact researchers across campus
• increase engagement of undergraduates in
  research
• integrate new equipment into existing and new
  curricula

2
Original Timeline
Advertise and interview for technician position
June 2006

• Interviewed 4 candidates in August 2006
• Dr. Janet Miller started work in October 2006
• Noteworthy successfully recruited a PhD
  scientist to fill a position that preferred a
  masters degree

3
Original Timeline
Advertise and interview for technician position
Purchase major and supporting equipment
June 2006
July 2006
4
Equipment
Existing ABI 310 - DNA sequencer
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Equipment
Existing ABI 310 - DNA sequencer Refrigerated
centrifuge
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Equipment
Existing ABI 310 - DNA sequencer Refrigerated
centrifuge ABI 7500 real-time PCR machine
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Equipment
Existing ABI 310 - DNA sequencer Refrigerated
centrifuge ABI 7500 real-time PCR
machine Purchased GenePix 4000B microarray
scanner
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Equipment
Existing ABI 310 - DNA sequencer Refrigerated
centrifuge ABI 7500 real-time PCR
machine Purchased GenePix 4000B microarray
scanner
9
Equipment
Existing ABI 310 - DNA sequencer Refrigerated
centrifuge ABI 7500 real-time PCR
machine Purchased GenePix 4000B microarray
scanner KODAK Gel Logic 2200 Digital Imaging
System
10
Equipment
Existing ABI 310 - DNA sequencer Refrigerated
centrifuge ABI 7500 real-time PCR
machine Purchased GenePix 4000B microarray
scanner KODAK Gel Logic 2200 Digital Imaging
System
11
Equipment
Existing ABI 310 - DNA sequencer Refrigerated
centrifuge ABI 7500 real-time PCR
machine Purchased GenePix 4000B microarray
scanner KODAK Gel Logic 2200 Digital Imaging
System Eppendorf Mastercycler
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Equipment
pics here - microarray scanner chemiDoc, move ABI
310 and mention CST paid as match
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Original Timeline
Advertise and interview for technician position
Purchase major and supporting equipment
Biotechnology course uses facility
Announce opening of facility
Molecular genetics course
June 2006
July 2006
Sept. 2006
Fall 2006
Spring 2007

• Grand opening and open house November 2006
• Integration of new technologies into existing
  courses, BIO 325, Fall 2006
• BIO 545, Spring 2007

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Original Timeline
Advertise and interview for technician position
Purchase major and supporting equipment
Biotechnology course uses facility
Announce opening of facility
Purchase additional equipment
June 2006
July 2006
Sept. 2006
Fall 2006
Sept. 2007
CST Purchased ABI 3130 - 4 capillary DNA sequencer

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Equipment
New purchases ABI 3130 - 4 capillary DNA
sequencer
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Equipment
New purchases ABI 3130 - 4 capillary DNA
sequencer Nanodrop ND-1000 uv-vis
spectrophotometer
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Original Timeline
Advertise and interview for technician position
Purchase major and supporting equipment
Biotechnology course uses facility
Purchase additional equipment
Announce opening of facility
1 year evaluation
June 2006
July 2006
Sept. 2006
Fall 2006
Sept. 2007
Sept. 2007

• Evaluation of 4 measures of effectiveness at 1
  year mark
• Brief report, July 2007
• Evaluation, December 2007

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1. Impact of DNA-SACF on Grant activity

• Grants awarded
• Jon Kelty NIH R15 (2007) 190,000
• Janet Miller STARS Kids (2007) 38,400

• Grants pending
• Elizabeth Alm NSF (co-PIs at MSU and UMN)
• Michelle Steinhilb American Federation for Aging
  Research
• NIH R15
• Steve Juris NIH R15
• Cynthia Damer NIH R15

• Grants submitted/ not funded
• Anna Monfils NIH/R21 (co-PIs Juris,
  Steinhilb, Mueller (CHM)

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Impact of DNA-SACF on Grant activity (predicted
impacts)

• Current Grants of Users of DNA-SACF
• Ash (CHM) current NIH grant
• Colores current NSF grant
• Linton current NSF grant
• Schisa current NIH R15 grant
• Swanson DNR and contracts
• Current Grants of potential future users of
  DNA-SACF
• Oh-Lee (PSY) NIH grant

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2. Impact of DNA-SACF on Alumni giving
Currently None yet Potential Current donors/
supporters of molecular equipment Louisell
family has donated 15,000/ yr for 3 yrs to
Biology Department to upgrade molecular
equipment in teaching labs
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3. Impact of DNA-SACF on Student participation
in molecular-based research
Student presentations at international and
national conferences (2006-2007)

• Alm lab 4
• Colores lab 3
• Hertzler lab 1
• Linton lab 1
• Monfils lab 2

• Schisa lab 7
• Swanson lab 8

Total 26
Molly Jud in Los Angeles, July 2007 International
C. elegans Conference
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Impact of DNA-SACF on Student participation in
molecular-based research

• 7 Summer Scholars (2007) awarded to students
  using molecular techniques
• 15 BIO 403 independent, undergraduate research
  projects completed by students using molecular
  techniques
• 6 Posters at the Capitol presented by students
  using molecular techniques, Spring 2007
• 13 SRCEE posters at CMU presented by students
  using molecular techniques, Spring 2007

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Impact of DNA-SACF on Student participation in
molecular-based research
Student co-authors on papers
Jud, M., Razelun, J., Bickel, J., Czerwinski, M.,
and J.A. Schisa (2007). Conservation of large
foci formation in arrested oocytes of
Caenorhabditis nematodes Development, Genes, and
Evolution 217 221-226. Jud, M., Czerwinski,
M., Wood, M., Young, R., Bickel, J., and J.A.
Schisa (2008). Large P body-like RNPs form in C.
elegans oocytes in response to arrested
ovulation, heat stress, and osmotic stress and
are regulated by the Major Sperm Protein Pathway.
Developmental Biology. Millions, D. G., and B.
J. Swanson. (2007). Evaluation of habitat
fragmentation on population structure in bobcats.
Journal of Wildlife Management 71 96 102.
Vibber, L.L., M.J. Pressler and G.M. Colores.
(2007) Isolation and characterization of
atrazine-degrading microorganisms from an
agricultural soil. Applied Microbiology and
Biotechnology 75921-928.
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4. Impact of DNA-SACF on Increased academic
challenge in coursework
BIO 325 - Biotechnology BIO 620 - Advanced
Biotechnology BIO 597 - Microbial Ecology BIO
545 - Molecular Genetics BIO 544 - Developmental
Biology
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Overall Progress Report on DNA - SACF at 1 year
mark
Priority III Enhance the infrastructure for
research Strategies 2 (increased level of
funding) and 4 (increased engagement of
undergraduates in research) Strategy 2 KPI
increase grant and contract funding KPI
increase alumni giving Strategy 4 KPI enrich
students educational experiences
KPI increase students using molecular
methods at SRCEE, honors theses,
publications, presentations KPI
increase academic challenge in courses
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Overall Progress Report on DNA - SACF at 1 year
mark

• Added value recruiting faculty who use
  molecular techniques
• Cynthia Damer, new cell/molecular biologist
• current search for Fisheries Geneticist
• New web site http//dnasaf.bio.cmich.edu/index.ht
  ml

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Original Timeline
Advertise and interview for technician position
Purchase major and supporting equipment
Biotechnology course uses facility
Purchase additional equipment
Announce opening of facility
1 year evaluation
5 year
June 2006
July 2006
Sept. 2006
Fall 2006
Sept. 2007
Sept. 2007
Sept. 2011

The Future
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Future of DNA SACF
Predict increased use internally and
externally new user from Alma
College Challenge for sustainability beyond
2009 salary for technician