https://commons.ru.ac.za/vital/access/manager/Index en-us 5 https://commons.ru.ac.za/vital/access/manager/Repository/vital:38989 Wed 21 Jul 2021 13:20:55 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:38577 Wed 12 Oct 2022 12:44:54 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:41444 Wed 12 Oct 2022 11:47:03 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:37957 Wed 12 May 2021 23:45:28 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:38367 Wed 12 May 2021 23:40:00 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:38746 Wed 12 May 2021 23:03:20 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:37991 Wed 12 May 2021 22:19:41 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:38314 Wed 12 May 2021 21:04:16 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:38547 Wed 12 May 2021 20:57:26 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:37937 Wed 12 May 2021 20:49:13 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:38196 Wed 12 May 2021 20:32:21 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:39507 0.05). The HRAP produced more biomass (317.18±27.76 g/m3) than the AS (83.12±64.91 g/m3), which resulted in a significantly greater downstream production of biogas and fertiliser per volume of effluent treated. According to the LCA, this also resulted in the HRAP system having a higher terrestrial ecotoxicity, due to the greater volume of solids and thus heavy metals applied to the soil. This interpretation can be misleading, because the mass of heavy metals released into the environment is the same for both systems, with a greater portion being applied to the land in the HRAP scenario and discharged into fresh water in the case of AS. Future LCA models should clarify if these biomasses are going to be applied to a single piece of land or multiple sites as this will influence the risk of contamination via pollutant build up in the soil. The application of sludge or algae on soil increased the soil’s sodium concentration and sodium absorption ratio from 774.80±13.66 mg/kg to 952.17±34.89 mg/kg and 2.91±0.04 to 3.53±0.13, respectively. Regulations on the application of algae or sludge on agricultural soils should be altered to consider the limit values for sodium and future LCA’s associated with effluent treatment facilities should incorporate the possibility of soil contamination through sodium build-up. This work also conceptualised the importance of reporting water emissions in wastewater treatment LCA in as much detail as possible, because this had a significant influence on the eutrophication impacts on water systems. Reporting water emissions as total nitrogen underestimated downstream eutrophication impacts compared with those using nitrogen-species concentration (ammonia, nitrite, nitrate etc). A marine eutrophication sensitivity co-efficient should be included in future LCA models which accounts for the probability of nitrogen and phosphorus emissions entering the coastal environment as well as the vulnerability of the marine environment to eutrophication. Activated sludge systems are favourable for situations where space is limited, were there are inadequate options for biomass disposal (biomass not be used in agriculture or AD) and were electricity is generated from a renewable source; whereas, HRAP are more suitable under circumstances where electricity production relies on fossil fuel that carries a high environmental impact and where options are available to use the biomass for economic gain such as biogas and fertiliser production. This thesis contributes towards a zero-waste brewery effluent treated process. The HRAP and AS treated effluent for reuse in the brewery or in agricultural irrigation. The solids were anaerobically digested, and the carbon was recovered as a biogas, while the digestate was applied as an agricultural fertiliser. This allowed for the recovery of water, nutrients and carbon.]]> Wed 12 May 2021 20:28:34 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:38082 Wed 12 May 2021 20:25:24 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:35540 Wed 12 May 2021 20:16:31 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:38416 Wed 12 May 2021 20:04:46 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:38318 Wed 12 May 2021 19:43:08 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:37810 Wed 12 May 2021 19:28:59 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:34663 Wed 12 May 2021 19:23:48 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:37897 Wed 12 May 2021 19:08:27 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:38425 Wed 12 May 2021 18:38:04 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:38091 Wed 12 May 2021 18:26:49 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:38249 10, 000 km2) systems. However, there was variability in infertility response between lionesses including adverse reactions in a small proportion of treated individuals. The number of resident prides and male coalitions in a reserve affected lion social behaviour. Lionesses formed larger groups in reserves with a higher density of unknown adult female neighbours, likely driven by territory defence. Lion prides with resident cubs were generally more fragmented, likely in response to reduced competition from unknown adult males. However, in areas with a high density of unknown adult female neighbours, prides with cubs formed larger groups likely in response to heightened territory defence. Therefore, with smaller foraging group sizes, predation rate was increased in reserves with reduced competition from unknown lions. My study supports a metapopulation approach for the management of lions in small, fenced reserves, and the standardisation of lion management procedures and database management. Endorsed by the Biodiversity Management Plan for lions in South Africa, this will enhance the long-term conservation potential of isolated populations.]]> Wed 12 May 2021 18:16:51 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:39025 Wed 12 May 2021 18:11:47 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:37649 Wed 12 May 2021 17:51:01 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:38663 Wed 12 May 2021 17:37:38 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:37907 20-40mm), swimmers, flattened body shape, a preference for temporary attachment, crawling, respiration with aerial/vegetation, possession of breathing tubes, possession of strap or other apparatus for respiration, streamlined body, and a high sensitivity to oxygen depletion. Permanent attachment as an ecological preference associated with LIS was also positively correlated with increasing dissolved oxygen (DO) and was deemed a pollution sensitive ecological preference. The possession of very small body size (<5mm), associated with HIS, was deemed a pollution-tolerant trait and was negatively correlated with DO, confirming the deteriorating state of the urban and urban-agricultural rivers. The impact of urban-forestry pollution on the distribution pattern of macroinvertebrate traits and ecological preferences was also explored in the selected rivers. Traits and ecological preferences such as possession of hard-shell, large body size, and grazing as a feeding preference which were significantly positively associated with the LIS, were also either significantly positively correlated with DO, or significantly negatively correlated with increasing any two of flow velocity, water temperature, BOD5 and nutrient. These traits and ecological preferences were deemed sensitive in forested rivers receiving urban pollution. Further, burrowing, the pupa aquatic stage, and predation which were significantly positively associated with HIS on the RLQ ordination, were also significantly negatively associated with DO. These traits were deemed tolerant of forested systems receiving urban pollution. Multimetric indices (MMI) were developed, validated and applied for urban, urban-agriculture and urban-forested (MMI-urban, MMI-urban-agric and urban-forest) areas. Of the 26 metrics that satisfactorily discriminated between the LIS, the MIS, and the HIS for MMI-urban, only five metric were retained for integration into MMI-urban, they are log VeL, Hemiptera abundance, % Coleoptera + Hemiptera, % Chironomidae + Oligochaeta and Evenness index. Further, of the 18 metrics that satisfactorily discriminated between the LIS, the MIS, and the HIS for MMI-urban-agric, only 12 metrics were retained and nine proved to be redundant. The nine metrics represent different measures; two of them were retained in addition to Chironomidae/Diptera abundance, % Odonata and Oligochaeta richness. The two metrics selected in addition to the hironomidae/Diptera abundance, % Odonata and Oligochaeta richness were the Margalef index and the logarithm of relative abundance of sprawler. For the MMI-urban-forest, 14 metrics satisfactorily discriminated between the LIS, the MIS, and the HIS, and 12 metrics were retained and 11 proved to be redundant. The non-redundant metric was Trichoptera abundance. Three metrics were further selected in addition to the Trichoptera abundance which include % Chironomidae + Oligochaeta, Coleoptera + Hemiptera richness and Shannon diversity. The MMI-urban and MMI-urban-agric indices performed better for LIS designated stations compared to the MIS and HIS deignated stations. The developed indices proved effective as biomonitoring tools for assessing the ecological health of rivers in the urban and urban-agriculture catchments within the Niger Delta. Overall, the results of the macroinvertebrate traits and ecological preferences, and taxonomic approaches showed the strength in the complementarity of both approaches in developing biomonitoring tools for assessing levels of deterioration in riverine systems. The study contributes significantly to understanding the ecology of riverine systems in the Niger Delta, particularly those subject to urban stresses, agricultural activities and urban pollution in forested systems, and thus makes an important contribution to the science and practice of biomonitoring in Nigeria where such studies are sparse.]]> Wed 12 May 2021 17:31:44 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:34666 Wed 12 May 2021 17:23:45 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:37890 Wed 12 May 2021 17:19:11 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:38531 Wed 12 May 2021 17:09:49 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:38062 Wed 12 May 2021 16:25:36 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:38177 Wed 12 May 2021 16:20:35 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:38447 Wed 12 May 2021 16:10:18 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:38517 Wed 12 May 2021 16:07:51 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:41336 Wed 12 May 2021 15:11:47 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:41465 Wed 12 May 2021 15:08:05 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:41433 Wed 12 May 2021 15:07:12 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:41264 Wed 12 May 2021 15:06:53 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:41050 Wed 12 May 2021 15:05:06 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:41376 Wed 12 May 2021 15:04:43 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:41155 Wed 12 May 2021 15:03:14 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:41337 Wed 12 May 2021 15:02:23 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:41263 Wed 12 May 2021 15:01:47 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:40963 Wed 12 May 2021 14:58:07 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:41441 Wed 12 May 2021 14:56:40 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:41148 Wed 12 May 2021 14:54:29 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:41019 Wed 12 May 2021 14:53:50 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:41296 Wed 12 May 2021 14:52:01 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:41469 Wed 12 May 2021 14:51:15 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:41442 Wed 12 May 2021 14:50:34 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:41276 Wed 12 May 2021 14:47:27 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:41499 Wed 12 May 2021 14:45:58 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:41437 Wed 12 May 2021 14:45:54 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:40962 Wed 12 May 2021 14:43:59 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:41446 Wed 12 May 2021 14:43:25 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:41139 Wed 12 May 2021 14:43:20 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:41032 Wed 12 May 2021 14:40:25 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:41051 Wed 12 May 2021 14:34:28 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:40995 Wed 12 May 2021 14:34:04 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:41164 Wed 12 May 2021 14:30:41 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:41279 Wed 12 May 2021 14:24:39 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:41142 Wed 12 May 2021 14:21:50 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:41029 Wed 12 May 2021 14:19:55 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:41434 Wed 12 May 2021 14:19:11 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:41483 Wed 12 May 2021 14:17:23 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:41151 Wed 12 May 2021 14:11:42 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:42769 Tue 23 May 2023 11:45:11 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:38509 Thu 13 May 2021 15:55:13 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:37667 Thu 13 May 2021 10:59:19 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:33249 Thu 13 May 2021 07:39:35 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:38234 Thu 13 May 2021 07:19:35 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:34282 Thu 13 May 2021 07:18:46 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:34163 Thu 13 May 2021 06:59:15 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:34201 0.05 in all cases). Microplastic counts ranged on average from 55 ± 289 to 930 ± 462 microplastic particles.m-3. With the exception of two instances, microfibres constituted > 50 % (range: 47 to 97 %) of the total microplastic counts. Part two of this study assessed the size range of, and seasonal and spatial patterns in ingested microplastic. No significant differences were found in the number of microplastics ingested within seasons between the mussels Perna perna (Linnaeus, 1758) and Mytilus galloprovincialis (Lamarck, 1819), and the barnacles, Octomeris angulosa (Sowerby, 1825) and Tetraclita serrata (Darwin 1954) (Student’s t-test; d.f = 18; p > 0.05 in all cases), or between the two sites sampled, Kenton-on-Sea, Eastern Cape, and Wilderness, Western Cape (ANOVA; d.f. = 18; p > 0.05 in all cases). The nitric acid digestion technique was used to determine the presence of ingested microplastics. Microplastic loads ranged from 2 ± 1 to 33 ± 19 microplastics.g-1 wwt across all consumers, and the size of ingested microplastics ranged from 1 to 16 μm. Though highly variable, the absence of statistically significant differences in ingestion rates points to a ubiquity in the availability of microplastics within the water column over time and space.]]> Thu 13 May 2021 06:52:15 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:38464 Thu 13 May 2021 06:47:27 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:35576 Thu 13 May 2021 06:16:55 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:38211 Thu 13 May 2021 06:15:33 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:38548 Thu 13 May 2021 05:39:40 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:38635 Thu 13 May 2021 05:23:36 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:38497 Thu 13 May 2021 05:20:34 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:38461 Thu 13 May 2021 04:21:04 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:38089 3000 cases and controls) are required. Macrophage migration inhibitory factor (MIF) is a cytokine that is important in both innate and adaptive immunity that has been shown to play a role in T. brucei pathogenicity using murine models. A total of 27 missense SNVs were modelled using homology modelling to create MIF protein mutants that were investigated using in silico effect prediction tools, molecular dynamics (MD), Principal Component Analysis (PCA), and Dynamic Residue Network (DRN) analysis. Our results demonstrate that mutations P2Q, I5M, P16Q, L23F, T24S, T31I, Y37H, H41P, M48V, P44L, G52C, S54R, I65M, I68T, S75F, N106S, and T113S caused significant conformational changes. Further, DRN analysis showed that residues P2, T31, Y37, G52, I65, I68, S75, N106, and T113S are part of a similar local residue interaction network with functional significance. These results show how polymorphisms such as missense SNVs can affect protein conformation, dynamics, and function. Trypanosomes are auxotrophic for folates and pterins but require them for survival. They scavenge them from their hosts. PTR1 is a multifunctional enzyme that is unique to trypanosomatids that reduces both pterins and folates. In the presence of DHFR inhibitors, PTR1 is over-expressed thus providing an escape from the effects of DHFR inhibition. Both TbPTR1 and TbDHFR are pharmacologically and genetically validated drug targets. In this study 5742 compounds were screened using molecular docking, and 13 promising binding modes were further analysed using MD simulations. The trajectories were analysed using RMSD, Rg, RMSF, PCA, Essential Dynamics Analysis (EDA), Molecular Mechanics Poisson–Boltzmann surface area (MM-PBSA) binding free energy calculations, and DRN analysis. The computational screening approach allowed us to identify five of the compounds, named RUBi004, RUBi007, RUBi014, RUBi016 and RUBi018 that exhibited antitrypanosomal growth activities against trypanosomes in culture with IC50 values of 12.5 ± 4.8 μM, 32.4 ± 4.2 μM, 5.9 ± 1.4 μM, 28.2 ± 3.3 μM, and 9.7 ± 2.1 μM, respectively. Further when used in combination with WR99210 a known TbDHFR inhibitor RUBi004, RUBi007, RUBi014 and RUBi018 showed antagonism while RUBi016 showed an additive effect. These results indicate that the four compounds might be competing with TbDHFR while RUBi016 might be more specific for TbPTR1. These compounds provide scaffolds that can be further optimised to improve their potency and specificity. Lastly, using a systematic approach we derived CHARMM force-field parameters to accurately describe the TbrPDEB1 bi-metal catalytic center. For dynamics, we employed mixed bonded and non-bonded approach. We optimised the structure using a two-layer QM/MM ONIOM (B3LYP/6-31(g): UFF). The TbrPDEB1 bi-metallic center bonds, angles, and dihedrals were parameterized by fitting the energy profiles from Potential Energy Surface (PES) scans to the CHARMM potential energy function. The parameters were validated by means of MD simulations and analysed using RMSD, Rg, RMSF, hydrogen bonding, bond/angle/dihedral evaluations, EDA, PCA, and DRN analysis. The force-field parameters were able to accurately reproduce the geometry and dynamics of the TbrPDEB1 bi-metal catalytic center during MD simulations. Molecular docking was used to identify 6 potential hits, that inhibited trypanosome growth in vitro. The derived force-field parameters were used to simulate the 6 protein-ligand complexes with the aim of elucidating crucial protein-ligand residue interactions. Using the most potent ligand RUBi022 that had an IC50 of 14.96 μM we were able to identify key residue interactions that can be of use in in silico prediction of potential TbrPDEB1 inhibitors. Overall we demonstrate how bioinformatics tools can complement current disease eradication strategies. Future work will focus on identifying variants identified in Genome Wide Association Studies and partnering with wet labs to carry out further enzyme-ligand activity relationship studies, structure determination or characterisation of appropriate protein-ligand complexes by crystallography, and site specific mutation studies]]> Thu 13 May 2021 04:20:49 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:37906 Thu 13 May 2021 03:38:54 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:38472 Thu 13 May 2021 03:05:20 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:38554 Thu 13 May 2021 03:02:27 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:35424 Thu 13 May 2021 02:53:44 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:34291 Thu 13 May 2021 02:24:07 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:38546 Thu 13 May 2021 02:21:31 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:32315 Thu 13 May 2021 02:16:00 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:38844 Thu 13 May 2021 01:36:53 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:37930 Thu 13 May 2021 01:30:26 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:38100 Thu 13 May 2021 01:12:05 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:38545 Thu 13 May 2021 00:54:10 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:38423 Thu 06 Jul 2023 06:51:22 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:38741 Sat 04 Dec 2021 12:41:27 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:41020 Mon 18 Dec 2023 18:00:37 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:41490 Mon 17 Apr 2023 11:28:01 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:42896 Fri 28 May 2021 11:35:51 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:38991 Fri 14 Jul 2023 09:03:33 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:38581 Fri 14 Jul 2023 08:46:05 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:41327 Fri 08 Jul 2022 11:49:07 SAST ]]>