Browsing by Author "Clase, Kari L."

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    Isolation and Analysis of a Mycobacteriophage Specific to Mycobacterium Smegmatis
    (2015-12-15) Collins, Angela J.; Ghazali, Danish M.; Li, Yi; Ha, Soo; Clase, Kari L.; Hatfull, Graham
    BACKGROUND: Bacteriophages are viruses that kill bacteria. It is estimated that there are roughly 1031 types of bacteriophages in the world, and that every bacterium has an average of 10 bacteriophages that can infect it. A mycobacteriophage is a type of bacteriophage which has a mycobacterial species as its host. There are 30 known clusters, or types, or mycobacteriophages which all contain very distinct genetic structures, but there are still countless mycobacteriophage populations that need to be isolated. Now that microorganisms are becoming resistant to many antibiotics, the study of bacteriophages is increasingly important because they have an incredibly untapped potential to treat resistant bacteria, eradicate bacterial contaminants in food products, promote ulcer healing, control bacterial growth during fermentation, and much more. The goal of this project was to discover new bacteriophages that might contribute to novel medical solutions. MATERIALS AND METHODS: We plated 29 agar plates for 8 different samples. One sample resulted in plaque growth, from which we performed 9 streak tests, underwent a dilution series and filtration to eliminate the contamination, and harvested a High Titer Lysate. After isolating and purifying the phage genomic DNA, we analyzed the sample and quantified the DNA using a Nanodrop spectrophotometer, and we used agarose gel electrophoresis to separate and analyze the DNA fragments. Finally, we used electron mycrocopy to visualize the physical structure and confirm the successful isolation of a single mycobacteriophage population. DISCUSSION: The cloudiness of the plaque produced by the bacteriophage suggests it is a temperate phage, meaning it switchs between two behavior types regarding replication and survival. Analysis of the physical structure of the mycobacteriophage reveals more information about its genomic DNA; its large capsid diameter suggests lengthy indwelling genomic DNAand its relatively long tail suggests a large tape-measure gene. We were unble to analyze the agarose gel electrophoresis results due to time constraints. However, the results of the genomic DNA sequence will hopefully prove that our bacteriophage is a distinct population. CONCLUSION: We successfully captured, isolated, and purified a single bacteriophage species from the local environment of West Lafayette, Indiana. Upon isolating a single bacteriophage species, we then isolated, purified, restricted, and analyzed the genomic DNA of the phage. Finally, we documented our findings on the Bacteriophage Database as FelixElFago (http://phagesdb.org/phages/FelixElFago/) and sent our DNA to the Sequencing Center.
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    Lipidomic Analysis of Glioblastoma Multiforme Using Mass Spectrometry
    (Bentham Science Publishers, 2014-04-01) Ha, Soo Jung; Showalter, Gordon; Cai, Shanbao; Wang, Haiyan; Liu, Wei Michael; Cohen-Gadol, Aaron A.; Sarkaria, Jann N.; Rickus, Jenna; Springer, John; Adamec, Jiri; Pollok, Karen E.; Clase, Kari L.; Department of Neurological Surgery, IU School of Medicine
    Glioblastoma multiforme (GBM) is the most common and malignant form of primary brain tumors. It is highly invasive and current treatment options have not improved the survival rate over the past twenty years. Novel approaches and technologies from systems biology have the potential to identify biomarkers that could serve as new therapeutic targets for GBM. This study employed lipid profiling technology to investigate lipid biomarkers in ectopic and orthotopic human GBM xenograft models. Primary patient cell lines, GBM10 and GBM43, were injected into the flank and the right cerebral hemisphere of NOD/SCID mice. Tumors were harvested from the brain and flank and proteins, metabolites, and lipids extracted from each sample. Reverse phase based high performance liquid chromatography coupled with Fourier transform ion cyclotron resonance mass spectrometry (LC-FTMS) was used to analyze the lipid profiles of tumor samples. Statistical and clustering analyses were performed to detect differences. Over 500 lipids were identified in each tumor model and lipids with the greatest fold effect in the comparison of ectopic versus orthotopic tumor models fell predominantly into four main classes of lipids: glycosphingolipids, glycerophoshpoethanolamines, triradylglycerols, and glycerophosphoserines. Lipidomic analysis revealed differences in glycosphingolipid and triglyceride profiles when the same tumor was propagated in the flank versus the brain. These results underscore the importance of the surrounding physiological environment on tumor development and are consistent with the hypothesis that specific classes of lipids are critical for GBM tumor growth in different anatomical sites.