Escherichia coli (E. coli) is a gram-negative bacteria found in the intestinal system of humans that can also contaminate food, drinking water, as well as lakes and rivers. While not all strains are pathogenic, some including O157:H7 can cause severe illness. Conventional methods of detecting E. coli contamination in water samples often have limitations for on-site testing applications, which can include their slow detection time or need for expensive laboratory equipment. While several fluorescent biosensors for the detection of E. coli have been developed in the Didar lab, there is increased interest in colourimetric biosensors whose signal can be interpreted with the naked eye. This thesis will describe the development and performance of a hydrogel biosensor, that is made of polyacrylamide chains crosslinked by an E. coli detecting Deoxyribozyme (DNAzyme) and its substrate. In the presence of E. coli, the DNAzyme cleaves its substrate and crosslinking breaks down, resulting in the visible dissolution of the hydrogel. Paired with the use of bacteriophage induced cell lysis to amplify the target protein, detection sensitivity to the order of 10^1 CFU/mL has been achieved using this platform with an incubation time of 18 hours. A convolutional neural network (CNN) trained on optical images of the platform was able to classify samples as contaminated or uncontaminated with a validation accuracy of over 93%. / Thesis / Master of Applied Science (MASc) / Microbial contamination of water sources including surface water, groundwater, and drinking water can pose risks to human health. One bacterial species that can sometimes contaminate these sources is Escherichia coli (E. coli). To determine if E. coli is present in a water sample, it often needs to be sent to a laboratory for testing, which can be time consuming and inconvenient. Therefore, researchers are working to develop new sensors that are able to detect E. coli from water samples, ideally being simple enough to use that testing could be done right away and without sending the sample to another location. In this research project, we have developed a new biosensor that can detect E. coli in water samples. To use the sensor, a water sample is added onto a small red gel in a tube, and this gel breaks apart if E. coli is present in the sample.

It is common knowledge that water is one of the basic needs for human beings. However, the consumption of contaminated water can lead to waterborne diseases and fatalities. It is, therefore imperative to constantly monitor the quality of potable water. There are numerous technologies used for water quality monitoring. These technologies are relatively effective however these tests are expensive and complex to use, which then require experienced technicians to operate them. Other tests are not rapid, making consumers of water susceptible to waterborne diseases. In this study, dye-doped, surface functionalized silica nanoparticles (SiNPs) and surface-functionalized magnetic nanocomposites (MNCs) were proposed as materials that can be applied in order to reduce the time taken to get results as well as to make the processes less complex and portable. The aim of this study was to synthesize and characterize surface functionalized dye-doped SiNPs and surface functionalized MNCs for detection and preconcentration of in water. Additionally, proof of concept had to be shown using the synthesized materials. SiNPs were the materials of choice due to their easily functionalized surfaces and their strong optical properties. SiNPs are photostable and they do not leach in solution due to the inert nature of the silica matrix in aqueous media. MNCs were chosen as materials of choice for preconcentration of E. coli in water because they are easy to synthesize and they can be applied in various biological applications due to their functional groups. SiNPs were synthesized using the water-in-oil microemulsion. The SiNPs were further functionalized with amine and carboxyl groups and avidin. Thereafter, they were bioconjugated with biotinylated anti-E. coli antibodies. The pure and surface functionalized SiNPs were characterized using ATR-FTIR spectroscopy, FE-SEM, HR-TEM, Zeta Sizer, UV-vis spectroscopy and spectrofluorometry. The application of the dye—doped surface functionalized SiNPs in E. coli detection was characterized using the fluorescence plate reader. The SiNPs were spherical and uniform in size. They increased in size as they were being functionalized, ranging from 21.20 nm to 75.06 nm. The SiNPs were successfully functionalized with amine and carboxyl groups as well as with avidin and antibodies. Two methods were investigated for carboxyl group attachment (direct and indirect attachment) and the direct attachment method yielded the best results with a surface charge of -31.9 mV compared to -23.3 mV of the indirect method. The dye loading was found to be 1% after particle synthesis. The optical properties of the Ru(Bpy) dye were enhanced 3 fold when they were encapsulated in the Si matrix. The SiNPs were binding to the E. coli cells and enabled detection. MNCs were synthesized through in-situ polymerization. The MNCs were characterized using ATR-FTIR spectroscopy, SEM, TEM and XRD. The MNCs were successfully functionalized with carboxyl groups. The increase in size of the nanocomposites as seen in SEM images proved that the Fe3O4 was successfully encapsulated in the polymer matrix. The MNCs were proven to be magnetic by a simple magnetism test whereby they were separated in an aqueous solution using an external magnetic field. The antibody-labelled MNCs were binding to the E. coli cells as shown in TEM images. E. coli cells were removed from water at varying concentrations of 1x106 CFU/mL to 1x109 CFU/mL at 10 mL volumes. This study has demonstrated that dye-doped SiNPs amplify the signal of E. coli cells using fluorescence. The study has also demonstrated that the MNCs can be applied in sample preconcentration and enrichment for E. coli detection. However, further studies should investigate and optimize the combination of the two techniques in a point of use device for water quality testing of 100 mL-samples as per the requirement of the SANS 241 standard. / Civil and Chemical Engineering / M. Tech. (Chemical Engineering)

It is common knowledge that water is one of the basic needs for human beings. However, the consumption of contaminated water can lead to waterborne diseases and fatalities. It is, therefore imperative to constantly monitor the quality of potable water. There are numerous technologies used for water quality monitoring. These technologies are relatively effective however these tests are expensive and complex to use, which then require experienced technicians to operate them. Other tests are not rapid, making consumers of water susceptible to waterborne diseases. In this study, dye-doped, surface functionalized silica nanoparticles (SiNPs) and surface-functionalized magnetic nanocomposites (MNCs) were proposed as materials that can be applied in order to reduce the time taken to get results as well as to make the processes less complex and portable. The aim of this study was to synthesize and characterize surface functionalized dye-doped SiNPs and surface functionalized MNCs for detection and preconcentration of in water. Additionally, proof of concept had to be shown using the synthesized materials. SiNPs were the materials of choice due to their easily functionalized surfaces and their strong optical properties. SiNPs are photostable and they do not leach in solution due to the inert nature of the silica matrix in aqueous media. MNCs were chosen as materials of choice for preconcentration of E. coli in water because they are easy to synthesize and they can be applied in various biological applications due to their functional groups. SiNPs were synthesized using the water-in-oil microemulsion. The SiNPs were further functionalized with amine and carboxyl groups and avidin. Thereafter, they were bioconjugated with biotinylated anti-E. coli antibodies. The pure and surface functionalized SiNPs were characterized using ATR-FTIR spectroscopy, FE-SEM, HR-TEM, Zeta Sizer, UV-vis spectroscopy and spectrofluorometry. The application of the dye—doped surface functionalized SiNPs in E. coli detection was characterized using the fluorescence plate reader. The SiNPs were spherical and uniform in size. They increased in size as they were being functionalized, ranging from 21.20 nm to 75.06 nm. The SiNPs were successfully functionalized with amine and carboxyl groups as well as with avidin and antibodies. Two methods were investigated for carboxyl group attachment (direct and indirect attachment) and the direct attachment method yielded the best results with a surface charge of -31.9 mV compared to -23.3 mV of the indirect method. The dye loading was found to be 1% after particle synthesis. The optical properties of the Ru(Bpy) dye were enhanced 3 fold when they were encapsulated in the Si matrix. The SiNPs were binding to the E. coli cells and enabled detection. MNCs were synthesized through in-situ polymerization. The MNCs were characterized using ATR-FTIR spectroscopy, SEM, TEM and XRD. The MNCs were successfully functionalized with carboxyl groups. The increase in size of the nanocomposites as seen in SEM images proved that the Fe3O4 was successfully encapsulated in the polymer matrix. The MNCs were proven to be magnetic by a simple magnetism test whereby they were separated in an aqueous solution using an external magnetic field. The antibody-labelled MNCs were binding to the E. coli cells as shown in TEM images. E. coli cells were removed from water at varying concentrations of 1x106 CFU/mL to 1x109 CFU/mL at 10 mL volumes. This study has demonstrated that dye-doped SiNPs amplify the signal of E. coli cells using fluorescence. The study has also demonstrated that the MNCs can be applied in sample preconcentration and enrichment for E. coli detection. However, further studies should investigate and optimize the combination of the two techniques in a point of use device for water quality testing of 100 mL-samples as per the requirement of the SANS 241 standard. / Civil and Chemical Engineering / M. Tech. (Chemical Engineering)

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