Core Facilities & Resources

BAC-Recombineering Core

The Center’s BAC-Recombineering core provides investigators affiliated with CBC schools the capability to dynamically image fluorescently tagged proteins in model organisms and measure the spatiotemporal expression of the protein of interest. Such tagged proteins can be further used to purify their associated partners, and to identify their chromatin binding sites. Using a pipeline developed by the White Lab, we are able to tag large numbers of genes of interest. The BAC construct contains the gene of interest in its native context, with associated regulatory elements and chromatin structure. A BAC transgene, therefore, typically expresses encoded genes at physiological levels similar to the endogenous gene.

Our Recombineering Core Director, Dr. Jennifer Moran is currently engaged in research to bring new Synthetic DNA technology into the repertoire of Core Facility technical services. Using commercially-available oligos as the raw material, we are able to synthesize virtually any DNA sequence we (or collaborators) can design in silico, up to about 1 kb. We have recently succeeded in joining three synthesized fragments (total length ~3 kb) and cloning them into an injectable integration vector (for Drosophila transgenics), using an efficient, one-step reaction.

As this process is refined, it will open up numerous possibilities for creative projects. For instance, we are currently synthesizing a construct to permit RNAi knockdown of multiple genes in Drosophila. Our goal is to test the multiple knockdown of putative "cancer genes" in a combinatorial fashion in this model organism. Dr. Moran and Recombineering Core scientist Alec Victorsen provide pre-experimental consultation to investigators who seek to incorporate advanced transgenic technology into their research programs.

Advanced Imaging Core

Dr. Dmitri Novikov is the Technical Director of the IGSB/CBC Advances Imaging Core (AIC). He is responsible for the operation and maintenance of the Digital Scanned Laser Light Sheet Fluorescence Microscope (DSLM), acquired from the European Molecular Biology Laboratory. This revolutionary microscope takes advantage of a new optical arrangement using one objective for specimen illumination generating a thin optical sheet, and another objective for collecting the image data at various angles. This way, phototoxicity is reduced a hundred folds and more, and high-resolution, fast live imaging of Drosophila embryonic development and other life processes becomes an exciting possibility.

The Center’s Advanced Imaging Core (AIC) is currently employing 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 above). A temperature step (T-step) is created within the microfluidic channel and around the embryo by the two different temperature flows.

Computational Core

Dr. Robert Grossman, Director of Informatics at IGSB, is leading the Center's CBC 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.
• Bionimbus: a cloud-based system for managing, analyzing and sharing genomic data
• Sector/Sphere: a cloud-based system for data intensive computing.

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.