Core Facilities & Resources

BAC-Recombineering Core

Transgenic Drosophila embryo carrying a YFP-tagged even-skipped gene on a recombineered BAC.
Image provided by Dr. Misha Ludwig (UofC).

The Center’s BAC-Recombineering Core can provide investigators affiliated with CBC schools the capability to dynamically image fluorescently tagged proteins in model organisms and measure spatiotemporal expression of protein of interest. Such tagged proteins can be used further to purify their associated partners, and to identify their chromatin binding sites. The Core currently uses the “recombineering” pipeline developed in the White lab to simplify the generation of cell lines and system model organisms that express fusion proteins from tagged transgenes or carry modified regulatory sequences by using bacterial artificial chromosomes (BACs). The genetic information carried on a BAC will generally include both the coding sequence and all upstream and downstream regulatory elements. A BAC transgene, therefore, typically expresses encoded genes at physiological levels similar to the endogenous gene of interest (see figure, above right).

Center Scientists employed and affiliated with the BAC-Recombineering Core can design and conduct experimental protocols and provide pre-experimental consultation to investigators who seek to incorporate this advanced transgenic technology into their research programs.

Advanced Imaging Core

The Center’s Advanced Imaging Core (AIC) is currently employing a confocal imaging system coupled to a microfluidics platform to measure spatiotemporal expression of fluorescence tagged transcription factors in live embryos. The spatiotemporal expression of various transcription factors is currently investigated in the Center in different temperature regimes and mutational backgrounds using a precisely controlled microfluidics environment. One example of a microfluidics device developed by Center investigator Dr. Rustem Ismagilov is a dual laminar flow, which is used to supply two different temperature streams over a live Drosophila embryo within a microfluidic channel (see figure below). A temperature step (T-step) is created within the microfluidic channel and around the embryo by the two different temperature flows.

Development of each half of a live Drosophila embryo in a microfluidic device.
Figure provided by Dr. Rustem Ismagilov (UofC).

Drosophila embryonic development was affected by the T-step — the cool side of the embryo developed more slowly than the warm side of the embryo, as seen by the lower density of nuclei in the cool half of the embryo relative to the warm half of the embryo.

Computational Core

Dr. Robert Grossman, Senior CCSB investigator & Director of the National Center for Data Mining (NCDM) at the University of Illinois at Chicago (UIC) is leading the Center’s Computational Core. This Core relays on standard bioinformatics tools as well as specialized tools such as:

• Cistrack: Cistrack is a repository for transcriptional network studies.
• Flynet: Flynet provides an integrated view of Drosophila melanogaster transcription regulation and makes genome wide in vivo protein-DNA interactions data available to the scientific community as a whole.
• The Chicago Utility for Biological Sciences (CUBioS): The CBC/CUBioS project is an open-source cloud-based bioinformatics platform. Cistrack is CUBioS instance. CUBioS is available from Source Forge and can be customized to support a variety of bioinformatics applications.

IGSB/CBC Cellular Screening Center (CSC)

CSC houses a state-of-the art high throughput cellular screening facility which opened in 2007. Support from the Chicago Biomedical Consortium and The University of Chicago Biological Sciences Division enabled the creation of the CSC. The CSC 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. Automation is present for all aspects of the screening process. Without automation a 300 plate screen would take as long as 2 months. With the automation present in the CSC the same screen can be performed in as little as 2 days. CSC facilities are available to a broad network of Chicago area investigators on a collaborative basis established through internal and external funding. The Center has attracted a significant number of collaborations with area scientists in fields as diverse as cancer biology, diabetes and ophthalmology.

IGSB High-Throughput Genome Analysis Core (HGAC)

HGAC is a state-of-the-art facility providing resources and services for ultra-high-throughput sequencing and large-scale microarray processing. Operated by the Institute for Genomics and Systems Biology, the HGAC facility is available to University of Chicago and Argonne National Laboratory investigators and their collaborators.