The application of representational difference analysis and plant differentiation

Please read the abstract in the section 00front of this documentDissertation (MSc (Botany))--University of Pretoria, 2005.Plant Scienceunrestricte

Using whole genome comparison to detect sequence similarities between plants and microbes

With an increasing amount of whole genome sequence data becoming available on a daily basis we have an opportunity to study the interactions and dynamics of different organisms on a whole genome level. In the past, reports of horizontal gene transfer have focused mainly on the identification of single genes that show distorted phylogenetic profiles to that of the organism it was isolated from. This study firstly did whole genome comparisons between the rice nuclear and plastid genomes to determine the level and dynamics gene transfer and insertion of the chloroplast ad mitochondrial genomes into that of the nuclear genome of rice. Secondly, it looked to identify sequence similarities between the rice genome and microbial genomes by performing whole genome comparisons between the rice genome and that of several microbial genomes. These sequences were analyzed further to identify possible instances of horizontal transfer of DNA from microbes to the rice genome. Using this approach, this study reports several fragments in the rice genome with significant sequence similarity to that of microbial DNA fragments. This study also provides evidence supporting horizontal transfer of several of these fragments. This study provides valuable information regarding intra- as well as inter-genome DNA transfer dynamics.Thesis (PhD)--University of Pretoria, 2009.Plant Scienceunrestricte

Reclamation of ultra-fine coal with scenedesmus microalgae and comprehensive combustion property of the Coalgae® composite

Combustion of South African discard ultra-fine coal (i.e. coal dust), charcoal, microalgae biomass, and composites of the three under air were studied. The study involves to find out the effect of Scenedesmus microalgae biomass on the comprehensive combustion characteristics of the ultra-fines. Coal dust is considered as waste material, but it could be modified and combusted for energy. The composites were designed with Design Expert, and unlike blending with the dry microalgae biomass, fresh slurry was blended with the ultra-fine coal and charcoal. Non-isothermal combustion was carried out at heating rate of 15 C/min from 40 – 900 ºC and at flow rate of 20 ml/min, O2/CO2 air. Combustion properties of composites were deduced from TG-DTGA and analysed using multiple regression. On combustion, the interaction of coal-charcoal-microalgae was antagonistic (b = - 1069.49), while coal-microalgae (b = 39.17), and coal-charcoal (b = 80.37), was synergistic (p = 0.0061). The coal-microalgae (Coalgae®) indicated first order reaction mechanism unlike, coal, and the charcoal. Comprehensive combustion characteristics index of Coalgae®, (S-value = 4.52E8) was superior relative to ultra-fine (S-value = 3.16E8), which indicated high quality fuel. This approach to combusting ultra-fine coal with microalgae biomass is partly renewable, and it would advance the production of heat and electricity. Key words: coal-dust, combustion, s-value, Coalgae®, renewable

Palmer amaranth : a threat to soya bean production in South Africa

Palmer amaranth is the latest addition to South Africa’s growing list of Amaranthus species (commonly known as pigweed or marog). Some of these Amaranthus species are indigenous to Africa, while others originate from other continents.http://reference.sabinet.co.za/sa_epublication/vp_oilseedsam2023Plant Production and Soil Scienc

Growth-stage and temperature influence glyphosate resistance in Conyza bonariensis (L.) Cronquist

Glyphosate, currently the world's most extensively used herbicide was on the market for more than 20 years since its introduction in 1975 without reported evolution of resistant weed cases. Glyphosate is the only reported herbicide to inhibit 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS), and endogenous accumulation of shikimic acid has been used as a biomarker for the herbicide's activity in plants after spraying. Increased levels of shikimic acid indicate sensitivity or injury while a lack or limited accumulation of shikimic acid shows resistance to glyphosate. Conyza bonariensis seed germinates in flushes in South Africa and its emergence is staggered throughout the year under conducive temperature conditions. This variability in growth stages in the same field poses a challenge in chemical control. Glyphosate herbicide efficacy is affected by environmental conditions, particularly temperature. A glyphosate resistance screening study was carried out based on reports from farmers that C. bonariensis has become increasingly difficult to control especially in conservation tillage systems. This study has confirmed the occurrence of glyphosate-resistant C. bonariensis (hairy fleabane) cases in the western and southern Cape regions of South Africa. A glasshouse screening experiment of 24 biotypes indicates resistance levels ranging from 0.6 to 26.9-fold, with GR50 values of up to 3908.42 g.ae.ha− 1 being reported in a population collected from a vineyard in the Piketberg district of the western Cape. The influence of growth stage and temperature on glyphosate resistance in hairy fleabane was evaluated by using a shikimate assay. Results from this study have shown that response of hairy fleabane to glyphosate is influenced by the phenological stage, with sensitivity or injury decreasing with growth stage. The significant statistical tests verified the dependence of the shikimate pathway on temperature, with more shikimic acid accumulating at 15 °C compared to 27 °C across all biotypes, regardless of origin and glyphosate tolerance status. More tolerance to the herbicide was demonstrated under warm temperature conditions. Possible outcomes of applying glyphosate at the bolting stage and under warm temperature conditions are escapes and no control of susceptible and resistant plants, respectively.The Organization for Women in Science for the Developing World (OWSD), the Swedish International Development Cooperation Agency (Sida), National Research Foundation (NRF), South Africa and Monsanto South Africa.http://www.elsevier.com/locate/sajbhj2020Forestry and Agricultural Biotechnology Institute (FABI)Plant Production and Soil Scienc

Plant Vacuolar Processing Enzymes

Plant proteomes contain hundreds of proteases divided into different families based on evolutionary and functional relationship. In particular, plant cysteine proteases of the C1 (papain-like) and C13 (legumain-like) families play key roles in many physiological processes. The legumain-like proteases, also called vacuolar processing enzymes (VPEs), perform a multifunctional role in different plant organs and during different stages of plant development and death. VPEs are similar to animal caspases, and although caspase activity was identified in plants almost 40 years ago, there still remains much research to be done to gain a complete understanding of their various roles and functions in plants. Here we not only summarize the current existing knowledge of plant VPEs, including recent developments in the field, but also highlight the future prospective areas to be investigated to obtain a more detailed understanding of the role of VPEs in plants

Factors facilitating sustainable scientific partnerships between developed and developing countries

International scientific partnerships are key to the success of strategic investments in plant science research and the farm-level adoption of new varieties and technologies, as well as the coherence of agricultural policies across borders to address global challenges. Such partnerships result not only in a greater impact of published research enhancing the career development of early and later stage researchers, but they also ensure that advances in plant science and crop breeding technologies make a meaningful contribution to society by brokering acceptance of emerging solutions to the world problems. We discuss the evidence showing that despite a lack of funding, scientists in some African countries make a significant contribution to global science output. We consider the criteria for success in establishing long-term scientific partnerships between scientists in developing countries in Southern Africa (“the South”) and developed countries such as the UK (“the North”). We provide our own personal perspectives on the key attributes that lead to successful institutional collaborations and the establishment of sustainable networks of successful “North-South” scientific partnerships. In addition, we highlight some of the stumbling blocks which tend to hinder the sustainability of long-term “North-South” scientific networks. We use this personal knowledge and experiences to provide guidelines on how to establish and maintain successful long-term “North-South” scientific partnerships.National Research Foundation of South Africa, Winter Cereal Trust and African Union Research Grant Programme funded by the European Union.http://journals.sagepub.com/home/oaghj2021Forestry and Agricultural Biotechnology Institute (FABI)Plant Production and Soil Scienc

Harnessing the functional diversity of plant cystatins to design inhibitor variants highly active against herbivorous arthropod digestive proteases

Please read abstract in the article.Natural Sciences and Engineering Research Council of Canada.https://febs.onlinelibrary.wiley.com/journal/17424658hj2023Plant Production and Soil Scienc

A chimeric affinity tag for efficient expression and chromatographic purification of heterologous proteins from plants

The use of plants as expression hosts for recombinant proteins is an increasingly attractive option for the production of complex and challenging biopharmaceuticals. Tools are needed at present to marry recent developments in high-yielding gene vectors for heterologous expression with routine protein purification techniques. In this study, we designed the Cysta-tag, a new purification tag for immobilized metal affinity chromatography (IMAC) of plant-made proteins based on the protein-stabilizing fusion partner SlCYS8. We show that the Cysta-tag may be used to readily purify proteins under native conditions, and then be removed enzymatically to isolate the protein of interest. We also show that commonly used protease recognition sites for linking purification tags are differentially stable in leaves of the commonly used expression host Nicotiana benthamiana, with those linkers susceptible to cysteine proteases being less stable then serine protease-cleavable linkers. As an example, we describe a Cysta-tag experimental scheme for the one-step purification of a clinically useful protein, human α1-antitrypsin, transiently expressed in N. benthamiana. With potential applicability to the variety of chromatography formats commercially available for IMAC-based protein purification, the Cysta-tag provides a convenient means for the efficient and cost-effective purification of recombinant proteins from plant tissues.A Discovery grant from the Natural Science and Engineering Research Council (NSERC) of Canada to DM, and by an Australian Research Council (ARC) Discovery Early Career Research Award to FS (DE140101553).PJ was the recipient of an AgroPhytoSciences NSERC–FONCER scholarship and of a BMP graduate scholarship funded by NSERC, the Fonds de Recherche Québec Nature et Technologies and our private research partner Medicago Inc.http://www.frontiersin.orgam2016Plant Production and Soil Scienc

Proteolysis of recombinant proteins in bioengineered plant cells

Plants are increasingly used as alternative expression hosts for the production of recombinant proteins offering many advantages including higher biomass and the ability to perform posttranslational modifications on complex proteins. Key challenges for optimized accumulation of recombinant proteins in a plant system still remain, including endogenous plant proteolytic activity, which may severely compromise recombinant protein stability. Several strategies have recently been applied to improve protein stability by limiting protease action such as recombinant protein production in various sub-cellular compartments or application of protease inhibitors to limit protease action. A short update on the current strategies applied is provided here, with particular focus on sub-cellular sites previously selected for recombinant protein production and the co-expression of protease inhibitors to limit protease activity.http://www.tandfonline.com/loi/kbie20hb201