Pilot Projects (2013-2014)

Mechanisms of genome instability induced by transposable elements

Justin P. Blumenstiel
Assistant Professor, Dept. of Ecology & Evolutionary Biology
University of Kansas


Transposable elements (TEs) are selfish replicating elements that comprise about half of the human genome. Due to their proliferative and repetitive nature, they are a significant source of new mutation and chromosomal rearrangement. Studies over the past few years have provided growing evidence for TEs, through their mutator capacity, being an important contributor to cancer. Recent studies have also demonstrated that a genome defense mechanism mediated by small, silencing RNAs (piRNAs), limits potential TE damage by targeting TE transcripts for destruction. Under some circumstances, however, this mode of genome defense fails to control TE proliferation. In Drosophila, the mobilization of one single element family can result in global failure of TE control, chromosome damage and sterility. This syndrome of genome destabilization is known as hybrid dysgenesis. It is not clear how the mobilization of one element family can lead to cascading mobilization of other elements. A critical question is how this mobilization causes the machinery of genome defense by small RNAs to become compromised. The goal of this project is to test two specific models for how the piRNA machinery loses efficacy when TEs become mobilized. One model is that DNA damage itself is directly responsible for TE mobilization. A second model is that, as has been demonstrated with viruses, TEs encode suppressors of small RNA silencing. Thus, when one TE mobilizes, the piRNA machinery becomes directly antagonized, leading to the mobilization of other TEs. By testing these two models, we will provide significant insight into the mechanisms by which genome instability can be induced by TEs. In addition, by testing the TE encoded suppressor model, we may identify new potential mechanisms of oncogenesis.

Transcriptomic analysis of disease pathways in animal models of Tourette syndrome

Marco Bortolato
Associate Professor, Dept. of Pharmacology and Toxicology, School of Pharmacy
University of Kansas


Tourette syndrome (TS) is a neurodevelopmental disorder with marked male predominance (M:F=4:1). The disease is characterized by multiple motor and vocal tics, which have a disrupting impact on social and occupational functioning. The current available therapies for TS have variable efficacy and induce significant side effects, highlighting the need for novel treatment and diagnostic biomarkers that can predict treatment response.The objective of this pilot NIH/COBRE grant is to study the molecular bases of the gender differences in TS and the mechanisms of action of finasteride in this disease. Finasteride is the inhibitor of 5J-reductase (5AR), the enzyme catalyzing the conversion of testosterone and other steroid precursors into their neuroactive metabolites. Recent evidence from our group suggests that FIN may be a highly efficacious therapy for TS with limited side effects.
The proposed studies will be focused on transcriptomic changes in the animal model of TS with highest degree of homology, the D1CT-7 transgenic mice, which exhibit tic-like manifestations. The results of these studies will set the stage for future large-scale NIH-funded translational studies aimed at the development of new therapeutic strategies for TS with limited side effects.

Multicellular evolution by reprograming cell cycle regulation

Bradley Olson
Assistant Professor, Division of Biology
Kansas State University


The long term objective of this project is to better understand the genetic basis of multicellular evolution. Despite multicellular evolution being a fundamental, and cancer relevant process, the genetic pathways required for multicellularity to evolve are poorly understood. This project will determine the genes important for multicellular evolution in a novel, metazoan relevant multicellular model system, the Volvocine algae, whose members include closely related unicellular and multicellular species. Importantly, the Volvocine algae regulate their cell cycle with homologs of the retinoblastoma (RB) tumor suppressor, where evolutionary changes in its function are linked to multicellular evolution. In Aim 1 of this proposal, cell cycle regulated gene expression will be determined by deep sequencing all messenger RNA (RNA-seq) in unicellular Chlamydomonas compared to multicellular Gonium. Second, RNA-seq will also be performed in Chlamydomonas and Gonium strains lacking RB (encoded by the MAT3 gene) to determine which genes have expression defects compared to wild-type and between the two species. This process will then be repeated in a pseudo-multicellular Chlamydomonas strain caused by the presence of the Gonium RB.
In Aim 2, the promoter occupancy by the RB protein in Chlamydomonas and Gonium will be determined by chromatin immunoprecipitation, followed by deep sequencing (ChIP-seq) of RB bound genetic loci. These RB bound loci will be compared between Chlamydomonas and Gonium as well as to the expression data from Aim 1.
In summary, this project will make significant advancements in our understanding of the genetic determinants of multicellularity, as well as determine the genome-wide architecture of the RB pathway in unicellular Chlamydomonas compared to multicellular Gonium.

Single wall carbon nanotube platforms as near-infrared fluorescent sensors

Shenqiang Ren
Assistant Professor, Department of Chemistry
University of Kansas


The research objective of this proposal is to establish the single wall carbon nanotubes (SWCNTs) platformfor adenosine 5’-triphosphate (ATP) and glucose sensing. Molecular recognition plays an important role in the design of therapeutics and sensing platforms. The research strategy is to explore functionalized singlechirality SWCNT platforms as new type molecular recognition motif, by using a binding pocket or interface to recognize the specific molecule. The project will be comprised of the following interrelated sub-programs: (1) Explore the design rules for building single-chirality SWCNT NIR fluorophore biosensor; (2) Understand the mechanism and relationship between structure and fluorescent emission changes of SWCNT by the target analyte binding, such as the wavelength and intensity changes due to charge-transfer, exciton quenching or solvatochromism. Biosensors based on the modulation of single-chirality SWCNT photoemission will demonstrate real time spatio-temporal detection.

Upcoming Events

Spring 2016 CMADP Group Meetings
- Wednesday, February 10
- Wednesday, March 30
both 12:30-2:00pm in 100C MRB, West Campus

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