Canadian Parliament Internship

STEP Category: Education AbroadAU18 STEP Expo poster of Conor Hayes, describing his experiences in the Canadian Parliament Internship education abroad program.The Ohio State University Second-year Transformational Experience Program (STEP)Academic Major: Astronomy and Astrophysic

Generation and application of recombinant antibody fragments for prostate cancer detection.

Prostate cancer (PCa) is the most prevalent adenocarcinoma and the second highest cause of cancer-related deaths in men. Early diagnosis is required to identify the development of PCa to reduce the risk of the disease metastasising to different regions of the body. Multiple biomarkers in serum have been identified for the diagnosis of PCa. However, prostate-specific antigen (PSA) and its isoforms remain the gold standard test for PCa detection. Many antibodies have been generated for the detection of PSA with good sensitivities and limits of detection. To ensure reliable assay performance a number of biomarkers for PCa are required to increase specificity and sensitivity thus reducing the number of false positive results upon initial examination. The overall aims of the work presented in this thesis were to generate, select and characterise antibodies to PSA, an important biomarker in PCa. The generation and selection of murine and avian recombinant antibody fragments to free PSA (fPSA) was performed. Animals were immunised, RNA extracted and cDNA synthesised. The antibody variable genes were amplified by PCR, gel-purified and cloned into a phagemid vector. Electrocompetent cells were transformed and library sizes of 2.02 x 106 cfu/mL and 3.10 x 108 cfu/mL were obtained for the murine and avian clones, respectively. Specific clones were isolated by ‗biopanning‘ which involved a selection process on fPSA-coated immunotubes, enrichment and affinity maturation. Five and three rounds of selection were performed on the murine and avian anti-fPSA single chain variable fragments (scFv) recombinant antibody libraries, respectively. Preliminary analysis by ELISA indicated a large panel of positive binding clones for both screened libraries with approximately 60% of the analysed clones binding to fPSA. The murine recombinant antibody fragments were reformatted and expressed as single chain antibodies (scAb). This construct greatly enhanced soluble protein expression and stability while also facilitating the rapid kinetic analysis of candidate antibodies by Biacore. A differential expression profile of an anti-fPSA scFv and reformatted scAb was performed by ELISA. Individual antibodies isolated from the ‗biopanning‘ process were then characterised. The murine anti-fPSA antibodies were further analysed using the Biacore 3000 in a capture assay format. This facilitates correct affinity ranking of the selected antibodies where the antibody fragment was captured using the appropriate secondary tag antibody (anti-human constant kappa Ab) and a fixed concentration of fPSA (1 g/mL) passed over the captured antibody fragment. Ninety four antibody fragments were evaluated and ranked on their percentage complex stability values after a 5 minute dissociation period. Eleven of the ninety four were subjected to further analysis and their affinities ranged from 3.99 x 10-9 M to 3.62 x 10-10 M. They were then expressed in host Escherichia coli (E. coli) cells on a large scale and purified by immobilised metal affinity chromatography (IMAC). The cell lysates were characterised by ELISA, SDS-PAGE and Western blotting. The antibodies were sequenced and analysed for variability and similarities between the coding regions of the variable domains. Inhibition ELISA-based assays with inter and intra-day analysis were performed on the purified antibodies and a reproducible and accurate assay format was demonstrated with a limit of detection of 2.6 ng/mL. The avian clones were analysed, ranked and affinities evaluated by Dr. Paul Leonard using the Biacore A100 employing the same assay format used for analysis of the murine antibody fragments. Imperative to assay design is the selection of optimal antibody candidates for improved performance. For assay development antibody pairs which bind different regions of the fPSA molecule were determined using the capture assay format on the Biacore 3000. One murine scAb, two avian Fabs and one avian scFv were shown to bind different epitopes of the fPSA molecule with no non-specific binding evident. Following the successful purification of the murine and avian antibody fragments immunohistochemistry studies were performed on PCa tissue samples. These antibodies were shown to bind to different zones of the prostate gland (epithelial and stromal regions) confirming that the antibodies were binding to different epitopes of the fPSA molecule. The purified murine anti-fPSA scAb was biotinylated and this was employed in a sandwich ELISA assay whereby the murine anti-fPSA biotinylated scAb was captured on a neutravidin-coated ELISA plate and fPSA sandwiched using the avian antibody fragments as the detection antibodies. The assay sensitivity was improved using this format with a limit of detection of 1.8 ng/mL in PBST solution. Female serum was spiked with fPSA and inter-day studies performed by sandwich ELISA. Patient serum samples with diagnosed PCa were evaluated by sandwich ELISA to determine levels of fPSA in the sample and data were compared to documented tPSA levels which were comparable to the levels obtained from a commercially available sandwich assay

Spectroscopic Confirmation of Four Ultra Diffuse Galaxy Candidates

Ultra diffuse galaxies (UDGs) are a type of low surface brightness galaxy that have gar- nered much interest in the astronomical community in recent years in part because their high dark to baryonic matter ratios make them ideal testing grounds for the assumptions of the ΛCDM cosmological framework. Measuring redshifts of these objects is of critical importance because it allows us to understand their physical properties and, through comparisons with established galaxy catalogues, the environments in which they live. In this work, I present redshift measurements for four UDG candidates. Through these measurements, I have determined that these objects exist in group environments. Because the number of UDGs in similar environments with confirmed distances is presently quite small, this represents an important addition to our catalogues of the low surface brightness universe.No embargoAcademic Major: Astronomy and Astrophysic

Life-Cycles and Mutual E_ects of Scientific Communities

AbstractCross-community e_ects on the behaviour of individuals and communities themselves can be observed in a wide range of applications. While previous work has tried to explain and analyse such phenomena, there is still a great potential for increasing the quality and accuracy of this analysis. In this work, we propose a general framework consisting of several di_erent techniques to analyse and explain cross-community e_ects and the underlying dynamics. The proposed methodology works with arbitrary community algorithms, incorporates meta-data to improve the overall quality and expressiveness of the analysis and identifies particular phenomena in an automated manner. We illustrate the benefits and strengths of our approach by exposing in-depth details of cross-community e_ects between two closely related and well established areas of scientific research. This work focuses on techniques for understanding, defining and eventually predicting typical life-cycles and events in the context of cross-community dynamics

One Star Shines on Many Worlds: Exploring Extraterrestrial Water Through Observations of Scattered Light on the Moon and Mars

We investigate interactions between scattered light and water on the Moon and Mars. On the Moon, we develop an illumination and thermal model to examine small-scale temperatures and the thermal stability of volatile molecules at the Lunar Crater Observation and Sensing Satellite (LCROSS) impact site. We find that small-scale surface roughness creates a maximum temperature spread of approximately 10 K. On Mars, we derive a scattering phase function for Aphelion Cloud Belt water-ice clouds (WICs) during Mars Years 34 36 using Mars Science Laboratory cloud movies. We compared our phase functions with seven previously-derived Martian WIC phase functions and two Martian dust phase functions, as well as modeled phase functions for seven different ice crystal geometries. We find poor to moderate agreement with our phase functions. We also investigate interannual and diurnal variability of our phase functions, finding that any variability is minimal, consistent with previous results

One Star Shines on Many Worlds: Exploring Extraterrestrial Water Through Observations of Scattered Light on the Moon and Mars

We investigate interactions between scattered light and water on the Moon and Mars. On the Moon, we develop an illumination and thermal model to examine small-scale temperatures and the thermal stability of volatile molecules at the Lunar Crater Observation and Sensing Satellite (LCROSS) impact site. We find that small-scale surface roughness creates a maximum temperature spread of approximately 10 K. On Mars, we derive a scattering phase function for Aphelion Cloud Belt water-ice clouds (WICs) during Mars Years 34 – 36 using Mars Science Laboratory cloud movies. We compared our phase functions with seven previously-derived Martian WIC phase functions and two Martian dust phase functions, as well as modeled phase functions for seven different ice crystal geometries. We find poor to moderate agreement with our phase functions. We also investigate interannual and diurnal variability of our phase functions, finding that any variability is minimal, consistent with previous results

SemStim at the LOD-RecSys 2014 challenge

Abstract. SemStim is a graph-based recommendation algorithm which is based on Spreading Activation and adds targeted activation and duration constraints. SemStim is not affected by data sparsity, the cold-start problem or data quality issues beyond the linking of items to DBpedia. The overall results show that the performance of SemStim for the diversity task of the challenge is comparable to the other participants, as it took 3rd place out of 12 participants with 0.0413 F1@20 and 0.476 ILD@20. In addition, as SemStim has been designed for the requirements of cross-domain recommendations with different target and source domains, this shows that SemStim can also provide competitive single-domain recommendations

Chemical species concentration measurement via wireless sensors

This paper describes studies carried out to investigate the viability of using wireless cameras as a tool in monitoring changes in air quality. A camera is used to monitor the change in colour of a chemically responsive polymer within view of the camera as it is exposed to varying chemical species concentration levels. The camera captures this image and the colour change is analyzed by averaging the RGB values present. This novel chemical sensing approach is compared with an established chemical sensing method using the same chemically responsive polymer coated onto LEDs. In this way, the concentration levels of acetic acid in the air can be tracked using both approaches. These approaches to chemical plume tracking have many applications for air quality monitoring