Doctor of Philosophy

dissertationChronic myeloid leukemia (CML) is caused by the constitutive kinase activity of the fusion oncoprotein BCR-ABL. Conventional therapy in CML utilizes tyrosine kinase inhibitors (TKIs), small molecules that target the ATP-binding pocket in the BCR-ABL kinase domain. Despite their success in treating this disease, continued use of TKIs can lead to drug resistance due to point mutations in the kinase domain. Additionally, non-specific (non-BCR-ABL) kinase inhibition by these TKIs can cause toxic off-target effects. To function as an aberrant kinase, BCR-ABL must first homo-oligomerize via a coiled-coil (CC) domain located at its N-terminus. Thus, inhibiting BCR-ABL oligomerization abolishes its function as an oncoprotein. Designing an inhibitor of the 72-amino acid BCR-ABL CC domain is the focus of this dissertation. To engineer a construct capable inhibiting oligomerization, strategically designed mutations were incorporated into an isolated BCR-ABL CC domain with the goal of promoting higher affinity binding to endogenous BCR-ABL while at the same time disfavoring binding to our isolated CC construct. The designed construct, called CCmut3, was tested in vitro in leukemia cells containing both wild-type and mutant BCR-ABL. Overall, in vitro treatment with CCmut3 resulted in a decrease in BCR-ABL kinase activity, induction of apoptosis, and a reduction in the proliferation and transformative ability of CML cells. Next, combining CCmut3 with ponatinib, a recently approved BCR-ABL TKI, was also explored. This combination resulted in improved BCR-ABL inhibition and a lowering of the dose of ponatinib necessary for efficacy. Finally, the later chapters in this dissertation focus on possible methods in which the deliverability and stability of CCmut3 can be improved. Truncation and helical capping were both attempted, however, neither provided an inhibitory advantage over the full-length CCmut3 construct. Thus, current designs are focusing on creating a hydrocarbon stapled and truncated CCmut3 peptide, expected to result in a translatable product for wild-type and therapy-resistant CML

3D Mapping with an Unmanned Aerial Vehicle

Missionary aviation pilots often have to land their planes on remote airstrips that might be unsafe due to runway obstructions such as encroaching vegetation or large objects that were unknowingly placed on the runway. The Falcon Unmanned Aerial Vehicle (UAV) team is partnering with ITEC to develop an imaging system using a UAV to scan these airstrips to detect these obstructions. ITEC was founded by Steve Saint, the son of martyred missionary Nate Saint, to develop technologies to aid missionaries in their work. This video highlights the work of the Falcon UAV team and the basic terms and definitions for understanding the work of the team. The Falcon UAV team focuses primarily on the use of automated 3D mapping and photogrammetry by drones to help identify obstructions to pilots landing on remote airstrips. In this video, we will explore 3D mapping and compare different options for drones to purchase and software to use in the process of mapping information.https://mosaic.messiah.edu/engr2020/1007/thumbnail.jp

Ternatin and improved synthetic variants kill cancer cells by targeting the elongation factor-1A ternary complex.

Cyclic peptide natural products have evolved to exploit diverse protein targets, many of which control essential cellular processes. Inspired by a series of cyclic peptides with partially elucidated structures, we designed synthetic variants of ternatin, a cytotoxic and anti-adipogenic natural product whose molecular mode of action was unknown. The new ternatin variants are cytotoxic toward cancer cells, with up to 500-fold greater potency than ternatin itself. Using a ternatin photo-affinity probe, we identify the translation elongation factor-1A ternary complex (eEF1A·GTP·aminoacyl-tRNA) as a specific target and demonstrate competitive binding by the unrelated natural products, didemnin and cytotrienin. Mutations in domain III of eEF1A prevent ternatin binding and confer resistance to its cytotoxic effects, implicating the adjacent hydrophobic surface as a functional hot spot for eEF1A modulation. We conclude that the eukaryotic elongation factor-1A and its ternary complex with GTP and aminoacyl-tRNA are common targets for the evolution of cytotoxic natural products

A case of acute myeloid leukemia with promyelocytic features characterized by expression of a novel RARG-CPSF6 fusion

Key Points Novel RARG-CPSF6 fusion in an AML case with promyelocytic features and no evidence of PML-RARA or X-RARA fusion. Gene fusions involving RARG can initiate AML with promyelocytic morphological features.</jats:p

Isotopic composition of stratospheric ozone

We present a kinetic calculation for the isotopic composition of stratospheric ozone. The calculated enrichments of ^(49)O_3 and ^(50)O_3 are in agreement with atmospheric measurements made at midlatitudes. Integrating the kinetic fractionation processes in the formation and photolysis of ozone, we obtain enrichments of ∼7.5–10.5 and ∼7.5–12.5% (referenced to atmospheric O_2) for δ^(49)O_3 and δ^(50)O_3, respectively, at altitudes between 20 and 35 km; the photolysis in the Hartley band of ozone is responsible for the observed altitude variation. The overall magnitude of the ozone enrichments (∼10%) is large compared with that commonly known in atmospheric chemistry and geochemistry. The heavy oxygen atom in ozone is therefore useful as a tracer of chemical species and pathways that involve ozone or its derived products. For example, the mass anomalies of oxygen in two greenhouse gases, CO_2 and N_2O, are likely the consequences of the transfer of heavy oxygen atoms from ozone

Glycaemic index, glycaemic load and risk of endometrial cancer: a prospective cohort study

Objective High-glycaemic-load diets may increase endometrial cancer risk by increasing circulating insulin levels and, as a consequence, circulating oestrogen levels. Given the paucity of epidemiological data regarding the relationship between the dietary glycaemic index and glycaemic load and endometrial cancer risk, we sought to examine these associations using data from a prospective cohort study. Design, setting, and subjects We examined the association between dietary glycaemic load and endometrial cancer risk in a cohort of 49 613 Canadian women aged between 40 and 59 years at baseline who completed self-administered food-frequency questionnaires between 1982 and 1985. Linkages to national mortality and cancer databases yielded data on deaths and cancer incidence, with follow-up ending between 1998 and 2000. Results During a mean of 16.4 years of follow-up, we observed 426 incident cases of endometrial cancer. Hazard ratios for the highest versus the lowest quartile level of overall glycaemic index and glycaemic load were 1.47 (95% confidence interval (CI) = 0.90–2.41; P for trend = 0.14) and 1.36 (95% CI = 1.01–1.84; P for trend = 0.21), respectively. No association was observed between total carbohydrate or total sugar consumption and endometrial cancer risk. Among obese women (body mass index \u3e 30 kg m−2) the hazard ratio for the highest versus the lowest quartile level of the glycaemic load was 1.88 (95% CI = 1.08–3.29; P for trend = 0.54) and there was a 55% increased risk for the highest versus the lowest quartile level of glycaemic load among premenopausal women. There was also evidence to support a positive association between glycaemic load and endometrial cancer risk among postmenopausal women who had used hormone replacement therapy. Conclusions Our data suggest that diets with the high glycaemic index or high glycaemic load may be associated with endometrial cancer risk overall, and particularly among obese women, premenopausal women, and postmenopausal women who use hormone replacement therapy

Genotypic diversity effects on biomass production in native perennial bioenergy cropping systems

Citation: Morris, G. P., Hu, Z., Grabowski, P. P., Borevitz, J. O., de Graaff, M. A., Miller, R. M., & Jastrow, J. D. (2016). Genotypic diversity effects on biomass production in native perennial bioenergy cropping systems. GCB Bioenergy. doi:10.1111/gcbb.12309Article: Version of RecordThe perennial grass species that are being developed as biomass feedstock crops harbor extensive genotypic diversity, but the effects of this diversity on biomass production are not well understood. We investigated the effects of genotypic diversity in switchgrass (Panicum virgatum) and big bluestem (Andropogon gerardii) on perennial biomass cropping systems in two experiments conducted over 2008-2014 at a 5.4-ha fertile field site in northeastern Illinois, USA. We varied levels of switchgrass and big bluestem genotypic diversity using various local and nonlocal cultivars - under low or high species diversity, with or without nitrogen inputs - and quantified establishment, biomass yield, and biomass composition. In one experiment ('agronomic trial'), we compared three switchgrass cultivars in monoculture to a switchgrass cultivar mixture and three different species mixtures, with or without N fertilization. In another experiment ('diversity gradient'), we varied diversity levels in switchgrass and big bluestem (1, 2, 4, or 6 cultivars per plot), with one or two species per plot. In both experiments, cultivar mixtures produced yields equivalent to or greater than the best cultivars. In the agronomic trial, the three switchgrass mixture showed the highest production overall, though not significantly different than best cultivar monoculture. In the diversity gradient, genotypic mixtures had one-third higher biomass production than the average monoculture, and none of the monocultures were significantly higher yielding than the average mixture. Year-to-year variation in yields was lowest in the three-cultivar switchgrass mixtures and Cave-In-Rock (the southern Illinois cultivar) and also reduced in the mixture of switchgrass and big bluestem relative to the species monocultures. The effects of genotypic diversity on biomass composition were modest relative to the differences among species and genotypes. Our findings suggest that local genotypes can be included in biomass cropping systems without compromising yields and that genotypic mixtures could help provide high, stable yields of high-quality biomass feedstocks. © 2015 John Wiley & Sons Ltd

Linking goniometer measurements to hyperspectral and multi-sensor imagery for retrieval of beach properties and coastal characterization

In June 2011, a multi-sensor airborne remote sensing campaign was flown at the Virginia Coast Reserve Long Term Ecological Research site with coordinated ground and water calibration and validation (cal/val) measurements. Remote sensing imagery acquired during the ten day exercise included hyperspectral imagery (CASI-1500), topographic LiDAR, and thermal infra-red imagery, all simultaneously from the same aircraft. Airborne synthetic aperture radar (SAR) data acquisition for a smaller subset of sites occurred in September 2011 (VCR\u2711). Focus areas for VCR\u2711 were properties of beaches and tidal flats and barrier island vegetation and, in the water column, shallow water bathymetry. On land, cal/val emphasized tidal flat and beach grain size distributions, density, moisture content, and other geotechnical properties such as shear and bearing strength (dynamic deflection modulus), which were related to hyperspectral BRDF measurements taken with the new NRL Goniometer for Outdoor Portable Hyperspectral Earth Reflectance (GOPHER). This builds on our earlier work at this site in 2007 related to beach properties and shallow water bathymetry. A priority for VCR\u2711 was to collect and model relationships between hyperspectral imagery, acquired from the aircraft at a variety of different phase angles, and geotechnical properties of beaches and tidal flats. One aspect of this effort was a demonstration that sand density differences are observable and consistent in reflectance spectra from GOPHER data, in CASI hyperspectral imagery, as well as in hyperspectral goniometer measurements conducted in our laboratory after VCR\u2711

Lesioning of the Striatum Reverses Motor Asymmetry in the 6-Hydroxydopamine Rodent Model of Parkinsonism

In the rat several paradigms of grafting of adrenal medulla into the striatum were studied following the induction of a parkinsonian model, using a unilateral 6-hydroxydopamine (6-OHDA) lesion of the substantia nigra . Direct autologous grafting of adrenal medulla into the caudate-putamen complex, a radiofrequency lesion of the striatum alone, and a radiofrequency lesion followed by delayed grafting of adrenal medulla were compared by analyzing rotational behavior. Direct grafting of adrenal medulla produced an overall reduction in apomorphine induced turning behavior by 43.5% when compared with controls. Radiofrequency lesioning of the striatum without graft showed the best improvement over control animals with a 92% reduction in the total number of rotations induced by apomorphine. Delayed grafting into the caudate lesion cavity also produced a dramatic reduction in motor asymmetry but did not improve the behavioral outcome over that of the lesion alone. Animals receiving only radiofrequency lesions exhibited a band of increased tyrosine hydroxylase like immunoreactivity bordering the lesion cavity. Graft survival was limited in the nonlesioned animals but appeared enhanced in the animals whose striatum was previously lesioned. Lesion location within the striatum influenced the behavioral outcome. Large reductions in apomorphine-induced rotations could result from small lesions of the dorso-lateral striatum. These findings indicate that selective destruction of the caudate-putamen complex without tissue transplantation produces a dramatic reduction in the motor asymmetry of 6-OHDA treated rats. Suggested explanations for the decrease in induced rotational behavior with radiofrequency lesions include a decrease in the number of striatal dopamine receptors following cell destruction and lesioninduced recovery of host dopaminergic afferents. Striatal damage in critical areas can reverse some of the motor behavior associated with the 6-OHDA model and needs to be considered when evaluating the effects of neural grafting in this model

What Powers the 3000-Day Light Curve of SN 2006gy?

SN 2006gy was the most luminous supernova (SN) ever observed at the time of its discovery and the first of the newly defined class of superluminous supernovae (SLSNe). The extraordinary energetics of SN 2006gy and all SLSNe (>10^(51) erg) require either atypically large explosion energies (e.g. pair-instability explosion) or the efficient conversion of kinetic into radiative energy (e.g. shock interaction). The mass-loss characteristics can therefore offer important clues regarding the progenitor system. For the case of SN 2006gy, both a scattered and thermal light echo from circumstellar material (CSM) have been reported at later epochs (day ∼800), ruling out the likelihood of a pair-instability event and leading to constraints on the characteristics of the CSM. Owing to the proximity of the SN to the bright host-galaxy nucleus, continued monitoring of the light echo has not been trivial, requiring the high resolution offered by the Hubble Space Telescope (HST) or ground-based adaptive optics (AO). Here, we report detections of SN 2006gy using HST and Keck AO at ∼3000 d post-explosion and consider the emission mechanism for the very late-time light curve. While the optical light curve and optical spectral energy distribution are consistent with a continued scattered-light echo, a thermal echo is insufficient to power the K′-band emission by day 3000. Instead, we present evidence for late-time infrared emission from dust that is radiatively heated by CSM interaction within an extremely dense dust shell, and we consider the implications on the CSM characteristics and progenitor system