Queen's Science Undergraduate Research Journal 2017-03-08T16:22:52-05:00 Rhiannon Ng Open Journal Systems <p>The Queen’s Science Undergraduate Research Journal (QSURJ) is an online peer- reviewed and faculty-reviewed undergraduate research journal with a focus in biochemistry and life sciences.</p> Comparison of the inhibition of recombinant and native heme oxygenase-1 (HO-1) activity by the imidazoledioxolane compound QC-15 2017-03-08T15:17:58-05:00 Nick Stone Recombinant full-length and truncated forms of human heme oxygenase-1 (hHO-1) were compared with their native, microsomal HO-1 counterpart from rat spleen tissue, with respect to their inhibition by the imidazole-dioxolane HO inhibitor QC-15. Rat native HO-1 was maximally inhibited to the greatest extent (7.53 ± 1.51% of control activity), as compared to recombinant, full-length hHO-1 (55.55 ± 6.08%), and also truncated hHO-1 (72.17 ± 5.94%). The greater susceptibility of native HO-1 to QC-15 inhibition may be attributed to the presence of its C-terminal transmembrane domain (CTD) and its anchoring into the endoplasmic reticulum (ER). If so, membrane-anchored, recombinant, full-length hHO-1 may replace the current HO-1 microsomal model derived from rat spleen, in future in vitro inhibition studies. A better understanding of HO-1 inhibitors like QC-15 may lead to chemotherapeutics that prevent tumour cells from taking advantage of the cytoprotective nature of the HO system. ##submission.copyrightStatement## Assessing accuracy of automated segmentation methods for brain lateral ventricles in MRI data 2017-03-08T15:31:27-05:00 Mahadev Bhalla Haaris Mahmood The incidence of Alzheimer’s disease (AD) has steadily increased over the last few decades. AD leads to a decreased quality of life for those affected, hence, there is an urgent need to identify a reference point that can assist in early identification of the presence of AD. An objective and sensitive measure that may assist in the detection of AD is the lateral ventricle volume. In high-resolution magnetic resonance (MR) images, a relationship between lateral ventricle enlargement and AD progression can be examined. Volumetric data analyses for the ventricles require that they be segmented by neuro-anatomy experts using manual tracing. Since manual segmentation methods are impractical due to time requirements and rater variability, automated methods are frequently used to reliably and accurately segment brain regions. Thus, our goal was to compare the performance of two automated segmentation methods, FreeSurfer (FS) and FreeSurfer combined with Large Deformation Diffeomorphic Metric Mapping label propagation (FS+LDDMM), for the task of lateral ventricle segmentation. The Dice Similarity Coefficient (DSC) was used to evaluate the segmentation accuracy obtained by these two automated methods. When compared to the manual segmentation labels, the FS+LDDMM method had a greater mean DSC than the FreeSurfer method. Moreover, the manual vs. FS+LDDMM DSC values ranged from 99-100, while manual vs. FreeSurfer ranged from 73-92. Both of these results illustrate that FS+LDDMM is an automated method that has a high degree of accuracy and can be used in place of manual segmentation, while FreeSurfer should only be used as a preliminary automatic segmentation method. ##submission.copyrightStatement## The putative type I secretion sequence of a 1.5-MDa icebinding adhesin folds as a Ca2+-dependent β-rich structure 2017-03-08T16:22:52-05:00 Tony He Marinomonas primoryensis is a Gram-negative and strictly aerobic bacterium, an isolate of which was found in a brackish (half-strength seawater) lake in Antarctica. M. primoryensis produces a Ca2+-dependent 1.5-MDa ice-binding adhesin (MpAFP) that likely binds the bacterium to the underside of surface ice, where it may have better access to oxygen and other nutrients. The MpAFP is divided into five distinct regions that include the highly repetitive Region II (RII) and the moderately repetitive ice-binding Region IV (RIV). Region V (RV) is the C-terminal domain of MpAFP, and may serve as its non-cleavable signal sequence for the Type I Secretion System (TISS). The Protein Homology/analogY Recognition Engine (Phyre2) Server modeled RV as a Ca2+-bound β-rich structure. A previous study used a RV construct that started directly following the C-terminus of RIV, but the expressed protein aggregated and was unsuitable for further characterization. Here, we report the expression and purification of a fusion construct spanning RIV and RV. We defined the start of the RV domain by digesting the purified RIV-V fusion protein with trypsin in the presence of Ca2+. A soluble RV was then purified from the digestion mixture using anion-exchange chromatography, and its N-terminal residues were determined using Edman degradation sequencing. The folding of the newly designed RV construct was assessed by size-exclusion chromatography and circular dichroism (CD) spectroscopy. This work will provide insight into the structural relationship between RIV and RV, as well as how extremely large proteins are secreted via the TISS in Gram-negative bacteria. ##submission.copyrightStatement##