Toward an automated botnet analysis framework: a darkcomet case-study
- Authors: du Bruyn, Jeremy Cecil
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/2937 , vital:20344
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Towards an alternative spatial-based management approach for estuarine fisheries in South Africa, with a case study from the Sundays Estuary
- Authors: Kramer, Rachel
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/1007 , vital:20012
- Description: Estuaries are productive habitats and biologically important ecosystems which serve as juvenile nursery areas and feeding grounds for adults from a host of fish species. They are, however, threatened habitats, increasingly exposed to human disturbance and exploitation. The stocks of several South African estuary-dependent linefish species are now considered as either overexploited or collapsed. It is clear that their dependence on estuaries would warrant the inclusion of these ecosystems into marine reserve planning exercises. Since traditional management strategies (e.g. bag and size limit restrictions) have proven ineffective for estuarine fisheries, there is a need for alternative management measures, such as spatial and temporal restrictions, to ensure increased survival of juveniles and recovery of adult breeding populations. This thesis explored the potential for an ecosystem-based approach through the application of a rapid sustainability assessment technique, and a spatial-based management approach for an important fishery species, using conservation planning software. The Sundays Estuary, Eastern Cape, South Africa falls within the footprint of the Addo Elephant National Park, with a proposed expansion to include a marine protected area (MPA). However the estuaries resources were not considered during the planning of the proposed MPA. This study conducted an indicator-based sustainability assessment based on the principles of sustainable development. The results showed that present levels of exploitation, due to non-compliance and a lack of law enforcement are unsustainable. The sustainability of the Sundays Estuary had a low overall sustainability score of only 23.8%. With limited enforcement of estuarine fisheries regulations in South Africa, alternative management measures such as spatial regulations may provide a viable option forward. The sustainability of fishery resources depends on the comprehensive understanding of the fishery resource. Acoustic telemetry is a technique that has been widely adopted to infer habitat and area use patterns of fish species. The second component of this study made use of high resolution telemetry data collected on juvenile dusky kob Argyrosomus japonicus movements within the Sundays Estuary to conduct a scenario-based approach using Marxan conservation planning software. The best solution given by Marxan, in the form of a protected area for the conservation of juvenile A. japonicus in the Sundays Estuary was identified in the middle (starting 7km from the mouth) to the upper reaches (approximately 16km from the mouth) of the estuary, ultimately providing protection to tagged individuals for 61% of their time in the estuary. Although Marxan presented a best solution, the Sundays Estuary’s small size and shape, and minimal features used, was too simplistic to be included into a Marxan analysis. However, new methods and tools to analyse and plan spatial-based management options at this scale are currently being developed. Using the Sundays Estuary as a case study, a decision tree was then developed as a protocol to assist management address the challenges of effective estuarine management depending on the unique biological and socio-economic characteristics of individual estuaries in South Africa.
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Towards determining the dietary lysine requirement in the South African abalone, Haliotis midae
- Authors: Lloyd, Kyle Everett
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/1024 , vital:20014
- Description: Animals generally do not have a requirement for protein, but instead have a requirement for specific essential amino acids (EAAs) and non-essential amino acids (NEAAs). The NEAAs are those that can be synthesised by the animal, however, EAAs cannot be synthesised and must therefore be supplied as part of the diet. When these amino acids (AAs) are supplied in the correct ratios and with the correct level of digestible energy, nutritionists can maximise somatic growth from proteins. This has resulted in increased research into the use of crystalline AAs as a tool in feed formulation research in order to quantify the AA requirements in aquaculture species, and allow for alternative protein sources (other than fishmeal) to be utilised. In common with other water soluble nutrients, leaching of crystalline AAs from diets prior to ingestion is of concern in an aquatic environment. Microencapsulation techniques have been successfully employed to restrict micronutrient leaching, and improve ingestion rates. In this research, LysiPEARL™ (Kemin®) was used as a means to determine the lysine requirement in Haliotis. midae. This encapsulated lysine product is used in the dairy cattle industry as an effective source of rumen bypass for intestinal release of lysine. It has previously been proposed that crystalline AAs are not suitable for AA studies in H. midae due to the slow feeding rates of the species as well as the solubility of these AAs. However, 90.00 % of supplemented lysine was maintained in this study after a six hour period of leaching, showing that if effective microencapsulation techniques are used, it is possible to use crystalline amino acids to supplement protein bound lysine in abalone feeds. Six isoenergetic (15.90 MJ/kg), isolipidic (6.00 %) and isonitrogenous (29.00 %) diets enriched with 5.52, 6.40, 7.28, 8.14, 9.00 and 9.86 % lysine (as a % of protein) were fed to triplicate groups of 20 H. midae (20.41 ± 1.95 mm SL 1.51 ± 0.44 g w.wt) for 90 days. Wet weight and shell length measurements were taken every 30 days and specific growth rate (SGR) (% body weight.day-1), feed conversion ratio (FCR), protein efficiency ratio (PER), feed consumption (% body weight.day-1) and condition factor were calculated for each dietary treatment. Linear regression showed that FCR increased as dietary lysine increased (Regression analysis, p=0.031), and that PER reduced as dietary lysine increased (Regression analysis, p=0.026). Feed consumption also increased as dietary lysine increased (Regression analysis, p<0.001). The inclusion of lysine at 7.28 % of the total protein in the diet resulted in significantly superior SGR (0.57±0.01 % body weight.day-1) to that of 5.52 % (0.42±0.05 % body weight.day-1), FCR (1.51±0.05) to that of 8.14 % (1.99±0.21) and PER (2.45±0.07) to that of 8.14 % (1.99±0.18; ANOVA, p<0.05). There was a significant difference found in feed consumption (% body wt.d-1), with consumption increasing significantly between the first three dietary treatments and the last three dietary treatments (ANOVA, p<0.001). There was no significant improvement in SGR when dietary lysine increased above 7.28 % of the dietary protein in the diet, indicating that dietary lysine requirement was being met at 7.28 %, after which excess lysine promoted no growth response. The diet producing the best SGR, PER and FCR in this study was diet 3 which had a measured lysine content of 6.90 %. The results of the present study suggest that the lysine requirement in H. midae is in the range of 6.00 - 7.00 % of dietary protein. From these data amino acid ratios were used to estimate optimum inclusion levels of other essential amino acids. However, lysine availability in LysiPEARL™ may have resulted in over estimations due to the lipid encapsulation technique used, and haliotids limited ability to efficiently digest lipids. For this reason EAA requirements were suggested based on three different hypothetical scenarios of lysine availability from LysiPEARL™.
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Using bioinformatics tools to screen for trypanosomal cathepsin B cysteine protease inhibitors from the SANCDB as a novel therapeutic modality against Human African Trypanosomiasis (HAT)
- Authors: Mokhawa, Gaone
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/3304 , vital:20470
- Description: Human African Trypanosomiasis (HAT), also known as sleeping sickness, is a fatal chronic disease that is caused by flagellated protozoans, Trypanosoma brucei gambiense and Trypanosoma brucei rhodesiense. HAT is spread by a bite from an infected tsetse fly of the Glosina genus. Up to 60 million people in 36 countries in sub-Saharan Africa are at a risk of infection from HAT with up to 30 000 deaths reported every year. Current chemotherapy for HAT is insufficient since the available drugs exhibit unacceptable side effects (toxicity) and parasite resistance. Novel treatments and approaches for development of specific and more potent drugs for HAT are therefore required. One approach is to target vital proteins that are essential to the life cycle of the parasite. The main interest of this study is to explore Trypanosoma brucei cathepsin B-like protease (TbCatB) structural and functional properties with the primary goal of discovering non peptide small molecule inhibitors of TbCatB using bioinformatics approaches. TbCatB is a papain family C1 cysteine protease which belongs to clan CA group and it has emerged as a potential HAT drug target. Papain family cysteine proteases of Clan CA group of Trypanosoma brucei (rhodesain and TbCatB) have demonstrated potential as chemotherapeutic targets using synthetic protease inhibitors like Z-Phe-Ala-CHN2 to kill the parasite in vitro and in vivo. TbCatB has been identified as the essential cysteine protease of T. brucei since mRNA silencing of TbCatB killed the parasite and resulted in a cure in mice infected with T. brucei while mRNA silencing of rhodesain only extended mice life. TbCatB is therefore a promising drug target against HAT and the discovery and development of compounds that can selectively inhibit TbCatB without posing any danger to the human host represent a great therapeutic solution for treatment of HAT. To understand protein-inhibitor interactions, useful information can be obtained from high resolution protease-inhibitor crystal structure complexes. This study aims to use bioinformatics approaches to carry out comparative sequence, structural and functional analysis of TbCatB protease and its homologs from T. congolense, T, cruzi, T. vivax and H. sapien as well as to identify non-peptide small molecule inhibitors of TbCatB cysteine proteases from natural compounds of South African origin. Sequences of TbCatB (PDB ID: 3HHI) homologs were retrieved by a BLAST search. Human cathepsin B (PDB ID: 3CBJ) was selected from a list of templates for homology modelling found by HHpred. MODELLER version 9.10 program was used to generate a hundred models for T. congolense, T, cruzi and T. vivax cathepsin B like proteases using 3HHI and 3CBJ as templates. The best models were chosen based on their low DOPE Z scores before validation using MetaMQAPII, ANOLEA, PROCHECK and QMEAN6. The DOPE Z scores and the RMSD (RMS) values of the calculated models indicate that the models are of acceptable energy (stability) and fold (conformation). Results from the different MQAPs indicate the models are of acceptable quality and they can be used for docking studies. High throughput screening of SANCDB using AutoDock Vina revealed nine compounds, SANC00 478, 479, 480, 481, 482, 488, 489, 490 and 491, having a strong affinity for Trypanosoma spp. cathepsin B proteases than HsCatB. SANC00488 has the strongest binding to Trypanosoma spp. cathepsin B proteases and the weakest binding to HsCatB protease. Molecular dynamics (MD) simulations show that the complexes between SANC00488 and TbCatB, TcCatB, TcrCatB and TvCatB are stable and do not come apart during simulation. The complex between this compound and HsCatB however is unstable and comes apart during simulation. Residues that are important for the stability of SANC00488-TbCatB complex are Gly328 of the S2 subsite, Phe208, and Ala256. In conclusion SANC00488 is a good candidate for development of a drug against HAT.
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