Development of a 3D bioprinting and standalone bioreactor unit for the production and maintenance of bioscaffolds in vitro
- Authors: Hundling, Jethro Daniel
- Date: 2021-10-29
- Subjects: Bioreactors , Tissue scaffolds , Cell culture , Polyethylene glycol Biotechnology , 3D bioprinting , Poly(ethylene glycol) diacrylate (PEGDA)
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10962/192063 , vital:45192
- Description: The most common method for in vitro cell culture currently is to grow a specific cell type in isolation, in monolayer format, adhered to a 2D culture surface. This brings about many limitations in comparison to in vivo models due to altered cell phenotypes, as caused by the culturing technique itself, and the lack of naturally occurring cell-to-cell interactions. Three dimensional mammalian cell culture technologies have the potential to overcome these limitations, and provide models more representative of natural systems. Unfortunately, the cost and difficulty associated with achieving sustainable and useful 3D mammalian cell culture is still very high, preventing its widespread adoption across scientific platforms. In this research, we investigate the feasibility of developing and producing a visible light-based 3D stereolithographic bioprinter to produce 3D scaffolds for cell culture. Furthermore, we investigate the possibility of developing and implementing a forced perfusion bioreactor system, which would support the produced scaffold and improve longer-term culture conditions. The developed 3D bioprinter, and bioreactor designs were developed and tested alongside Poly (ethylene glycol) diacrylate (PEGDA), a versatile synthetic scaffold material. PEGDA itself was also evaluated for its printability, robustness in culture conditions over time, and its ability to maintain 3D mammalian cell culture. This research showed that both the developed 3D bioprinter, and bioreactor unit were capable of producing and maintaining an easily modifiable PEGDA scaffold, in culture conditions. In addition, the PEGDA formulation developed was shown to allow for the effective and reproducible 3D cell culture conditions over the medium term, with automated media feeding. The research presented here aimed to illustrate a proof of concept that the low-cost development and production of 3D culture scaffold production and maintenance systems was feasible to the scientific research environment. This technology can then be built upon, into a system that would then allow for the broader adoption and investigation of 3D cell culture as a tool within the scientific community. , Thesis (MSc) -- Faculty of Science, Biotechnology Innovation Centre, 2021
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- Date Issued: 2021-10-29
In silico identification of natural inhibitory compounds against the Mycobacterium tuberculosis Enzyme Pyrazinamidase using high-throughput virtual screening techniques
- Authors: Kenyon, Thomas
- Date: 2021-10-29
- Subjects: Mycobacterium tuberculosis , Pyrazinamide , Molecular dynamics , High throughput screening (Drug development) , Mutagenesis , South African Natural Compounds database (SANCDB)
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10962/192074 , vital:45193
- Description: Tuberculosis (TB) is most commonly a pulmonary infection caused by the bacterium Mycobacterium tuberculosis. With the exception of the COVID-19 pandemic, TB was the most common cause of death due to an infectious disease for a number of years up until 2020. In 2019, 10 million people fell ill with TB worldwide and 1.4 million people died (WHO, 2020a). Additionally, multidrug-resistant TB (MDR-TB) remains a public health crisis and a health security threat. A global total of 206 030 people with multidrug- or rifampicin-resistant TB (MDR/RR-TB) were reported in 2019, a 10% increase from 186 883 in 2018. South Africa is ranked among the 48 high TB burden countries, with an estimated 360 000 people falling ill in 2019, resulting in 58 000 deaths, the majority of which being among people living with HIV. Unlike HIV, however, TB is a curable disease when managed correctly with long durations of antitubercular chemotherapy. Pyrazinamide (PZA) is an important first-line tuberculosis drug unique for its activity against latent TB. PZA is a prodrug, being converted into its active form, pyrazinoic acid (POA) by the Mtb gene pncA, coding for the pyrazinamidase enzyme (PZase). TB resistance to first-line drugs such as PZA is commonly associated with mutations in the pncA/PZase enzyme. This study aimed to identify potential novel inhibitors that bind to the active site of PZase. By making use of molecular docking studies and molecular dynamics (MD) simulations, high throughput virtual screening was performed on 623 compounds from the South African Natural Compounds database (SANCDB; https://sancdb.rubi.ru.ac.za). Ligands that selectively bound to the PZase active site were identified using docking studies, followed by MD simulations to assess ligand-PZase complex stability, Finally, hit compounds identified from the first round of MD simulations were screened again against PZase structures with high confidence point mutations known to infer PZA resistance in order to identify any novel compounds which had inhibitory potential against both WT and mutant forms of the PZase enzyme. , Thesis (MSc) -- Faculty of Science, Biochemistry and Microbiology, 2021
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- Date Issued: 2021-10-29
Remote fidelity of Container-Based Network Emulators
- Authors: Peach, Schalk Willem
- Date: 2021-10-29
- Subjects: Computer networks Security measures , Intrusion detection systems (Computer security) , Computer security , Host-based intrusion detection systems (Computer security) , Emulators (Computer programs) , Computer network protocols , Container-Based Network Emulators (CBNEs) , Network Experimentation Platforms (NEPs)
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10962/192141 , vital:45199
- Description: This thesis examines if Container-Based Network Emulators (CBNEs) are able to instantiate emulated nodes that provide sufficient realism to be used in information security experiments. The realism measure used is based on the information available from the point of view of a remote attacker. During the evaluation of a Container-Based Network Emulator (CBNE) as a platform to replicate production networks for information security experiments, it was observed that nmap fingerprinting returned Operating System (OS) family and version results inconsistent with that of the host Operating System (OS). CBNEs utilise Linux namespaces, the technology used for containerisation, to instantiate \emulated" hosts for experimental networks. Linux containers partition resources of the host OS to create lightweight virtual machines that share a single OS kernel. As all emulated hosts share the same kernel in a CBNE network, there is a reasonable expectation that the fingerprints of the host OS and emulated hosts should be the same. Based on how CBNEs instantiate emulated networks and that fingerprinting returned inconsistent results, it was hypothesised that the technologies used to construct CBNEs are capable of influencing fingerprints generated by utilities such as nmap. It was predicted that hosts emulated using different CBNEs would show deviations in remotely generated fingerprints when compared to fingerprints generated for the host OS. An experimental network consisting of two emulated hosts and a Layer 2 switch was instantiated on multiple CBNEs using the same host OS. Active and passive fingerprinting was conducted between the emulated hosts to generate fingerprints and OS family and version matches. Passive fingerprinting failed to produce OS family and version matches as the fingerprint databases for these utilities are no longer maintained. For active fingerprinting the OS family results were consistent between tested systems and the host OS, though OS version results reported was inconsistent. A comparison of the generated fingerprints revealed that for certain CBNEs fingerprint features related to network stack optimisations of the host OS deviated from other CBNEs and the host OS. The hypothesis that CBNEs can influence remotely generated fingerprints was partially confirmed. One CBNE system modified Linux kernel networking options, causing a deviation from fingerprints generated for other tested systems and the host OS. The hypothesis was also partially rejected as the technologies used by CBNEs do not influence the remote fidelity of emulated hosts. , Thesis (MSc) -- Faculty of Science, Computer Science, 2021
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- Date Issued: 2021-10-29