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CBC Summer Workshop in Proteomics and Informatics, August 2-6, 2010

August 23, 2010
The Fourth Annual CBC Summer Workshop in Proteomics and Informatics took place at the CBC/UIC Proteomics and Informatics Service Facility (PISF) on August 2-6, 2010. The workshop, organized by Dr. Larry Helseth, the Associate Director of the PSIF, and Dr. Kolla Kristjansdottir of The University of Chicago, was a combination of lectures, demonstrations, hands-on laboratory training in multiple mass spectrometry techniques, and computer training in data analysis. In addition, the five-day course offered lectures and training in protein separation followed by trypsin digestion, peptide separation, mass spectrometry, database searches, isotope labeled sample analysis, identifying and analyzing post-translational modifications, top down proteomics and complex data analysis. As with past workshops, the number of applicants far exceeded the capacity of the workshop; the 28 students, faculty and staff that attended the workshop included 7 from The University of Chicago, 6 from Northwestern University, 14 from the University of Illinois at Chicago and 1 from industry.

Proteomics and informatics specialists from all three CBC affiliated universities contributed to the workshop. In addition to lectures by Drs. Alex Schilling, Hua Xu and Larry Helseth from the PISF at UIC, Dr. Kolla Kristjansdottir, University of Chicago, a co-organizer of the meeting, presented multiple lectures and participated in sample prep demonstrations and tutorials in data analysis software applications during the 5-day workshop. Dr. Carrie Crot and Mr. Rod Davis from the PISF demonstrated the use of several of the instruments in the facility and helped participants interpret raw mass spectrometry data. Dr. Paul Thomas, Northwestern University, organized sections on top-down proteomics, gave lectures in this area and demonstrated top-down proteomics on the PISF LTQ-FT Ultra.

The workshop also featured an invited speaker from the University of Wisconsin - Madison, Dr. Josh Coon, who gave a lecture on using iTRAQ for quantitative proteomics and presented a seminar discussing on-going research in his lab. The final day of the workshop included presentations by all attendees. The workshop members were divided into 3 groups that outlined a preparative strategy, analyzed data, and then proposed an interesting biological question and how they would investigate it using proteomic and informatic techniques learned during the week. The day concluded with workshop participants meeting one-on-one with PISF staff members to discuss individual research projects.

   

LEFT: Kolla Kristjansodotti using systems biology software to analyze mass spectrometry results. CENTER: Paul Thomas acquiring top-down data on the LTQ-FT Ultra. RIGHT: Alex Shilling describing advanced proteomics strategies. (Photos: CBC)

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High-Throughput Cellular Screening Workshop introduces Chicago research community to resources available at the Cellular Screening Center

June 14, 2010
The High-Throughput Cellular Screening Workshop organized by the Institute for Genomics & System Biology (IGSB) at the University of Chicago took place on June 8, 2010. Approximately 30 researchers attended the workshop that aimed to familiarize scientists with the high-throughput RNAi and chemical screening technologies available at the Cellular Screening Center (CSC). The CSC, opened in 2007 with support form the Chicago Biomedical Consortium and the University of Chicago Biological Science Division (BSD), facilitates drug discovery and development by defining the complex genetics underlying disease, isolating chemical compounds that affect specific cellular activities, and developing potential therapeutics to target disease pathways.

The morning events, held at the Knapp Center for Biomedical Discovery (KCBD), began with an overview of the technology and instrumentation available at the CSC presented by Sam Bettis, the Technical Director of the CSC. In his seminar, Sam discussed the screening reagents (RNAi and small compound libraries), screening guidelines, assay development, formatting assays for automation, and readout parameters. Subsequently, three current users of the CSC presented their research overviews:

Ruby Dhar: “Genome-wide RNAi screening to elucidate estrogen-receptor signaling in breast cancer”
John Barkinge: “A high throughput solution-phase strategy for quantifying thousands of protein-protein interactions”
Michael Thirman: “Screening for small molecule inhibitors for specific genetic subtypes of acute leukemia”

Following lunch, Sam Bettis led a tour of the CSC, which is located in the Gordon Center of Integrative Science at the UChicago campus. The CSC consists of a 900 square foot laboratory and includes three filtered air space rooms to reduce the number of air-borne particles and thus reduce the risk of contamination: certified 10,000 (anteroom), 1000 (storage and tissue culture room) and 100 (Tecan Freedom EVO 200 and Thermo F3 robotic arm system rooms). During the tour, workshop participants had an opportunity to observe the precise and complex maneuvers performed by the robotic arm on the CSC robotic deck during a mock run. The robotic arm is integrated with 3 readers allowing multiple different reads within a single screen. More information on CSC technology can be found here.

  

LEFT: A group of workshop attendees at the Cellular Screening Center. CENTER AND RIGHT: Workshop participants observe the robotic arm during a mock run. (Photos: CBC)

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Quantitative Insights, Inc wins CBC Business Plan Competition

May 26, 2010
The CBC held its Third Annual Business Plan Competition on May 17, 2010, at the University of Chicago Gleacher Center in Chicago, IL. Five graduate student-led teams from the business and management schools at the three CBC affiliated institutions presented business plans describing their biomedical companies and products to a panel of judges. The judges were selected from Chicago-area venture capital firms, angel investors, biotechnology and pharmaceutical companies and included:

Bob Altman (Marathon Pharma)
George Arida (Venture Investors)
Tom Churchwell (Midwest Venture Partners)
Ron Kirshner (Heartland Angels)
John Larson (Abbott Laboratories)
Donna Williamson (Ceres Venture Fund)

The three business and management schools and the plans they presented were:

  • Northwestern University, Kellogg School of Management, Center of Biotechnology Management
    • Barron, Inc
    • UroVention
  • The University of Chicago Booth School of Business, Polsky Center for Entrepreneurship
    • Quantitative Insights, Inc
  • The Liautaud Graduate School of Business, UIC Institute for Entrepreneurial Studies
    • Apana
    • MMPe Technologies

At the conclusion of the half-day program, the University of Chicago team’s business plan for Quantitative Insights, Inc was announced the winner of the competition and received a $10,000 CBC prize. Quantitative Insights, Inc is developing a computer-aided diagnostic (CAD) software platform that assists radiologists during breast cancer diagnosis. The software, QuantX, provides new and expanded diagnostic information and uses an advanced neural network to assist radiologists in characterization and assessment of identified lesions, leading to fewer missed and incorrectly diagnosed cancers. As the company moves forward, it plans to extend the QuantX platform to a variety of cancers and imaging modalities and ultimately create the industry’s first integrated multi-modality CAD solution. The team members include:

James Krocak: CEO
Brian Luerssen: President
Maryellen Giger, PhD: Co-Founder, Scientific Advisor
Yading Yuan, PhD: Scientific Officer
Ryan Richardson: VP Marketing
Shailesh Agarwal, MD: Medical Officer

 

LEFT: Katie Stallcup, the CBC Executive Director and the Quantitative Insights, Inc team members (from left to right: James Krocak, Ryan Richardson, Brian Luerssen, Yading Yuan). RIGHT: The judges listening to the presentations. (Photos: CBC)

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Illinois Governor Pat Quinn visits the Chicago Biomedical Consortium exhibit at the 2010 BIO International Convention

May 7, 2010
Illinois Governor Patrick Quinn presided over the BIO 2010 International Convention ribbon cutting ceremony on May 4. The convention was held at McCormick Place and it is the largest biotechnology event in the world. During his tour of the Illinois Pavilion, Governor Quinn (right) visited the Chicago Biomedical Consortium booth and met with Katie Stallcup (left), the CBC Executive Director, and Brenda Russell (middle), the Scientific Director from the University of Illinois at Chicago. (Photo: CBC)

Norbert Riedel, Corporate Vice President and Chief Scientific Officer of Baxter International, talks about the Chicago Innovation Pipeline, a collection of technologies available for licensing from 6 of the top research institutions in the Chicago region. The pipeline was developed by UChicagoTech for the 2010 BIO International Convention. (see video clip - QuickTime; see also UChicagoTech)

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