Abstracts G1-G3

Category G.  Enabling Technologies


G1.  Next Generation Genome Sequencing Core Lab at KU-Lawrence

Hackett, Jennifer L.1,2,3,4, Melinda A. Branin1,2,3,4, Erik A. Lundquist1,2,4, Susan M. Lunte1,5,6

1Center for Molecular Analysis of Disease Pathways, 2Genome Sequencing Core, 3Higuchi Biosciences Center, 4Department of Molecular Biosciences, 5Department of Chemistry, 6Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, KS, USA

The Genome Sequencing Core (GSC) is one of three research core labs in the newly established NIH COBRE Center for Molecular Analysis of Disease Pathways (CMADP) at KU.  The major mission of the GSC is to provide researchers with next-generation sequencing (NGS) technologies. NGS, carried out in a massively parallel fashion, has been revolutionizing bio-medical research and used in a growing list of applications. Projects supported by the GSC include de novo genome assembly, genome re-sequencing for identification of mutations and polymorphisms, transcriptome analysis (RNA-Seq), epigenomic and gene regulation studies such as ChIP-Seq, Methyl-Seq, small RNA discovery and analysis. The Genome Sequencing Core enhances the genomics infrastructure already at KU by bringing the astronomically high-throughput Illumina HiSeq 2500 sequencing capabilities to researchers at KU-Lawrence and across Kansas and the region. This next-generation sequencer has the capacity to generate 3-6 billion reads of 100bp per run on two eight-lane flow cells (600Gb data). In its rapid mode, it can generate 1.2 billion reads of 250 bp per run on two two-lane flow cells (300Gb data) in 60 hours. To capture the full power of NGS, we provide a whole range of project support, from project consultation, sample QC, library construction, cluster generation, data generation, to preliminary data analysis.  For latest pricing, current job queue, or other info, visit the Core’s website: https://gsc.ku.edu/.



G2.  The KU Molecular Probes Core Facility (KU-MPC):  A Resource for Research in Chemical Biology

Chamani Perera, Digamber Rane, Kelsey Knewtson, Matthew Meinig, and Blake Peterson

Department of Medicinal Chemistry, Higuchi Biosciences Center, The University of Kansas, Lawrence, KS, USA

The scientific discipline of chemical biology integrates chemistry and biology and applies synthetic chemical tools to the study of biological processes. The University of Kansas Molecular Probes Core Facility (KU-MPC), part of the Center for Molecular Analysis of Disease Pathways (CMADP) COBRE, was created to improve access of investigators to chemical biology approaches, tools, and techniques. A major focus of this core is to offer custom synthesis of both known and novel molecular probes for interrogation of a wide variety of biological targets. This core additionally provides access to the model organism Danio rerio (zebrafish), and allows investigators to image embryonic and adult zebrafish treated with molecular probes for phenotypic drug discovery and other projects. The KU-MPC currently houses both wild-type zebrafish as well as an inbred, pigmentation-deficient mutant strain known as casper. Because the casper strain is nearly completely transparent, investigators can more readily observe the pharmacokinetics (particularly the uptake and distribution) of fluorescent compounds in adult animals in vivo. Imaging equipment of the KU-MPC includes a Zeiss Axio Zoom.V16 stereomicroscope (11x-412x magnification) equipped with a Hamamatsu Orca Flash 4.0 CMOS camera and Sutter DG4 fast filter switching illumination system for ratiometric and other fluorescence-based assays. This core offers molecular probes, model organisms, and imaging services to a wide range of investigators.



G3.  Ultrasensitive Microfluidic Analysis of Circulating Exosomes Using Nanostructured Graphene Oxide/Polydopamine Coating

Peng Zhang1, Mei He2 and Yong Zeng1,3 *

1Department of Chemistry, University of Kansas, Lawrence, KS, USA; 2Department of Biological and Agricultural Engineering and Terry C. Johnson Cancer Research Center, Kansas State University, Manhattan, KS, USA; 3University of Kansas Cancer Center, Kansas City, KS, USA

Exosomes are cell-derived nanosized vesicles that have been recently recognized as new mediators for many cellular processes, such as cellular communication, and hold promising potentials for disease diagnosis. Despite their biomedical significance, progress in the field is severely hampered by the challenges in isolation and analysis of such small vesicles with diverse molecular properties. Herein we developed to develop a new microfluidic exosome analysis platform functionalized with a 3D nanostructured coating of graphene oxide (GO) and self-polymerized polydopamine (PDA). It was demonstrated such nanostructured GO/PDA coating presents a unique nano-interface to greatly improve the efficiency of exosome immuno-capture while effectively suppressing non-specific exosome adsorption. Based on this nano-interface, an ultrasensitive exosome ELISA assay was developed to afford a very low detection limit of 50 μL-1 with a 4-log dynamic range, which is orders of magnitude better than the existing methods. We demonstrated the ability of this platform to discriminate ovarian cancer patients from healthy controls by ultrasensitive detection of exosomes directly from 2-μL plasma without sample processing. Thus, this platform could provide a useful tool to facilitate exosome research and clinical utilities for non-invasive disease detection and precision treatment.



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