Research Cores

The COBRE CMADP brings together physical and biological scientists and engineers in a unique manner by combining cutting-edge enabling technologies for the analysis of disease-related molecular pathways. The CMADP's three core laboratories enable a variety of research applications that allow investigators to explore new pathways of the disease process:

  • The Genome Sequencing Core (GSC) provides researchers with next-generation sequencing technologies, as well as experimental design and analysis of sequence data. The GSC is involved in the identification of genetic (genotypic) elements that underlie the disease and disease pathways. Projects in the GSC include whole genome assembly, genome re-sequencing for identification of mutations important in development and disease, transcriptome analysis (RNA seq), variant mapping and genotyping, and identification of transcription factor interaction sites using chromatin immunoprecipitation combined with DNA sequencing (ChIP seq).
  • The Microfabrication and Microfluidics Core (MMC) makes resources and personnel available for the production of micro- and nano-scale devices to be used by project investigators for their studies. Equipment and training are available to investigators for the fabrication of devices for biomedical, biophysical, and bioanalytical studies related to disease pathways. Research applications for such devices include clinical diagnostics, pharmaceutical analysis, single-cell analysis, imaging, sensing, and biophysical applications, and broader applications in engineering, physics, and chemistry.
  • The Synthetic Chemical Biology Core (SCBC) offers expert design of molecular probes and synthesis of both small molecules and peptides, with an emphasis on the generation of fluorescent and other tagged molecules, as well as bioassays of molecular probes, including in vitro whole cell assays and in vivo assays using zebrafish. As needed, in addition to fluorescent probes, the SCBC can synthesize known but commercially unavailable compounds necessary for biochemical studies.
    • This core laboratory was previously known as the Molecular Probes Core, established by the CMADP upon its inception in 2012. In July 2016, the CMADP's Molecular Probes Core was combined with the medicinal chemistry core laboratory of KU's COBRE Center for Chemical Biology of Infectious Disease to form this joint Synthetic Chemical Biology Core. The SCBC leverages resources from both COBRE grants to best provide investigators with comprehensive synthetic chemistry capabilities.

    Microfabrication & Microfluidics Core

    These core facilities are designed to operate synergistically: imaging of model organisms treated with fluorescent probes developed through the SCBC are facilitated by the use of microfabricated devices developed in the MMC; screening of mutant organisms against these probes are used to discover novel disease-related phenotypes that can be precisely mapped to identify specific targets through the next generation sequencing offered by the GSC. These technologies are then made available to biomedical scientists through collaborations, publications, and potential commercialization.

    Together, the CMADP's cores seek to catalyze research that spans the chemistry-biology interface, empowering investigators to identify and solve important interdisciplinary research problems in the life sciences. Core personnel provide a wide range of expertise spanning numerous fields including synthetic organic chemistry, computational chemistry, bioinformatics, analytical chemistry, genetics, and imaging technologies.

     


Recent News

February 2017
CMADP Project Investigators co-author Top Downloaded article in Lab on a Chip

CMADP Co-I awarded R01 from NIH National Cancer Institute

CMADP Graduate's research featured on cover of Genetics and in other journals

October 2016
CMADP Co-I receives Mathers Foundation grant

View all news »

Upcoming Events
Special seminar by Dr. James P. Landers
Commonwealth Professor in Chemistry,
Mechanical Engineering & Pathology
University of Virginia

Wednesday, May 17, 2017 at 3:00pm
Simons Auditorium, HBC, West Campus

"Integrated Microfluidic Systems for Forensic DNA Analysis"
In 2006, we demonstrated that microfluidic technology could provide a ‘lab-on-a-chip’ solution for real-world genetic analysis. Sample-in/answer-out functionality was shown for the detection of bacteria in mouse blood and in a human nasal swab, with a sub-30 minute analytical time for DNA extraction, amplification, electrophoretic separation and detection. We extrapolated these technology developments to the analysis of short tandem repeats (STR) in human DNA; these clinically-insignificant (presumably) tetranucleotide sequences function effectively for statistically-relevant matching in human identification. Our efforts led to the development of a commercializable system designed for implementation in crime labs for STR profiling convicted felons or, in some states, profiling arrestees in booking stations. An intricate but functional microfluidic architecture allowed sample-to-profile to be achieved from a cheek swab in less than 80 minutes, using nanoliter flow control, infrared thermocycling and rapid electrophoretic separation of DNA with 5-color fluorescence detection. We have since demonstrated the fabrication of hybrid microdevices composed of inexpensive polymeric materials, many of these commercial-off-the-shelf. We have designed, built and functionalized fully-integrated DNA analysis chemistry/microfluidics on a rotationally-driven system the size of a compact disc. With this system, DNA can be extracted from a swab, PCR amplified to generate an abundance of DNA fragments of the STR loci, followed by resolution of those fragments in a separation in a 4 cm Leff channel that is complete in <300 sec with a 2-base resolution. The processes that allow for swab in–profile out microfluidics are carried out on an instrument that can be carried in one hand and weighs ~14 lbs, ultimately allowing for facile rapid human identification/screening in the field.
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