https://commons.ru.ac.za/vital/access/manager/Index en-us 5 https://commons.ru.ac.za/vital/access/manager/Repository/vital:41933 Wed 28 Sep 2022 14:29:44 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:37900 Wed 12 Oct 2022 08:55:28 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:34104 Wed 12 May 2021 23:39:51 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:37914 Wed 12 May 2021 23:07:48 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:38467 Wed 12 May 2021 23:07:00 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:38465 Wed 12 May 2021 22:48:02 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:37968 Wed 12 May 2021 22:47:28 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:37896 Wed 12 May 2021 22:34:50 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:37671 A in exon 41 is the most prevalent LRRK2 variation which causes a substitution of glycine to serine in G2019S in the highly activated loop of its MAP kinase domain. The LRRK2 G2019S variant is the most common genetic determinant of Parkinson’s disease identified to date. This work focused on building accurate 3D models of the LRRK2 kinase domain, that were used for large-scale in silico docking against South African natural compounds from the South African Natural Compounds Database (SANCDB; https://sancdb.rubi.ru.ac.za/). Molecular docking was performed to identify compounds that formed interactions with the active site of the protein and had the lowest binding energy scores. Molecular dynamics simulations showed different movements of the protein-ligand complexes and behavioural difference of the wildtype and the variants, all three structures proved to be compact. Network analysis was done to study residue interactions, contact maps, dynamic cross correlations, average BC and average L were used to study the residue interactions and general residue contribution to the functioning of the protein..]]> Wed 12 May 2021 22:17:40 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:34655 Wed 12 May 2021 21:03:14 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:38592 Wed 12 May 2021 20:24:50 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:37917 Wed 12 May 2021 20:11:11 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:34592 Wed 12 May 2021 19:35:55 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:37954 Wed 12 May 2021 19:34:51 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:37603 Wed 12 May 2021 19:27:38 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:38553 Wed 12 May 2021 18:48:16 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:37955 Wed 12 May 2021 18:47:46 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:35855 Wed 12 May 2021 18:47:06 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:37827 Wed 12 May 2021 18:41:00 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:38575 Wed 12 May 2021 18:39:05 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:37880 Wed 12 May 2021 18:14:02 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:38420 Wed 12 May 2021 17:54:33 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: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:38540 Wed 12 May 2021 16:46:03 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:37959 Wed 12 May 2021 16:43:17 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:37956 Wed 12 May 2021 16:37:10 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:37920 Wed 12 May 2021 16:30:53 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:35371 Wed 12 May 2021 16:26:36 SAST ]]> https://commons.ru.ac.za/vital/access/manager/Repository/vital:37983 Wed 12 May 2021 16:21:49 SAST ]]> 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