Two field experiments were conducted on sandy loam soils in OKhahlamba Local Municipality (OLM) (Bergville area), KwaZulu-Natal province in South Africa, during the rainy seasons of 2014/15 and 2015/16 to study the effect of calcium source (gypsum) fertilizer application on yield and quality of groundnut (Arachis hypogaea L.). The household economy of OLM is mostly dependent on agriculture and the majority of farmers in this area are small-scale farmers subsisting mainly on maize (constituting the staple diet) and groundnut production. Crop diversification, therefore, becomes an important aspect for farmers, and this is traditionally done using crops that are produced in almost similar agronomic circumstances to that of maize under dryland conditions. A large proportion of the OLM population depend on groundnut as a vital supplement to their daily food requirements, particularly as a cheap source of protein for resource-poor farmers. Therefore, any scientific approach to increase the yield of groundnut should be considered important in the livelihood of this community. Moreover, groundnut is an excellent rotational crop, since it responds well to fertilizer applied to previous crop and maize, as well as to crop, since it responds well to fertilizer applied to previous crop and maize, as well as to nitrogen left over by peanut. Thus, farmers save money because they use less fertilizer. The consideration for this study was based upon the above. The experiment was laid in a randomised complete block design with factorial arrangement, which was replicated three times in 48 plots. The factors studied were four levels of gypsum (CaSO4.2H2O) i.e. 0 kg/ha, 500 kg/ha, 750 kg/ha, and 1000 kg/ha and four levels of lime (MgCO3.CaCO3) i.e. 0 kg/ha, 250 kg/ha, 500 kg/ha, 750 kg/ha. Soil pH, cation exchange capacity (CEC), electrical conductivity (EC), pod yield, seed yield, 100 seeds weight, shelling percentage, dry shoot weight, seed moisture content percentage at harvest, and leaf calcium concentration data were collected prior to, and post harvesting. The application of 500 kg gypsum/ha alone acted as a liming factor for legumes, decreasing acid stress on nodulating bacteria, and improved soil chemical properties (increased soil pH), vegetative growth, yield, and quality of groundnut. The smallholder famers can afford this application rate, since gypsum acts both as a liming factor and as a calcium source to improve crop yield. The application of 1000 kg gypsum/ha improved seed yield, shelling percentage as well as kernel weight, which is yield, and quality of groundnut under dryland conditions. Since smallholder farmers practise dryland production, it is advisable to adopt the application of gypsum at the rate of 1000 kg/ha to improve yield and quality of groundnuts. It was also found to be more economical than using both gypsum and lime. The application of 500 kg gypsum per hectare in combination with 250 kg lime per hectare produced the highest shelling percentage. This combination of two calcium sources (gypsum and lime) is not recommended for small-scale farmers because it is not economical. The application of 500 kg gypsum per hectare in combination with 750 kg lime per hectare increased pod yield. However, this combination is also not recommended because it is not cost-effective. The application of 1000 kg gypsum per hectare in combination with 500 kg lime per hectare increased seed yield and produced sound mature kernel (SMK), whereas the application of 1000 kg gypsum alone per hectare also increased seed yield. This combination is also considered unacceptable due to the high increase in input costs. The application of 750 kg lime per hectare was more effective as an acid ameliorant and led to the improvement of the chemical composition of the soil (increased soil pH), resulting in a higher shoot weight of groundnut. This application also provided the catalyst for stimulating phosphorus production and enhancing the growth of an extensive root system for absorbing water and nutrients. The use of lime in acid soils is highly beneficial because it improves the chemical composition of the soil, ensures the availability of nutrients to plants, serves as an efficient calcium source, and ultimately leads to an improvement in yield. Results show that the application of gypsum at 1000 kg/ha and lime at 500 kg/ha respectively, significantly improved peanut yield and soil pH. The combination of gypsum and lime (500 kg/ha gypsum and 250 kg/ha lime) significantly improved shelling percentage (yield). Based on data on yield, yield components, and soil chemical properties, it is concluded that gypsum is the best calcium source fertilizer for groundnut production in OLM and lime should only be applied on acid soils to attain optimum groundnut yield in the region / Agriculture, Animal Health and Human Ecology / M. Sc. (Agriculture)

MSCFST / Department of Science and Technology / Heat-moisture treatment (HMT) is a physical modification that alters the physicochemical properties of starch without changing its molecular structure. The objective of the study was to investigate the influence of HMT on the functional, colour and thermal properties of bambara groundnut (BG) starch. A central composite rotatable design comprising two independent factors (temperature and time) was used for the study. The central composite rotatable design was generated using Design-Expert software version 8.0.1.0. Bambara starch extraction was done by milling BG into flour (5 Kg), suspension in 15 L, 0.3% sodium hydroxide and centrifugation followed by washing using distilled water. The starch was then HMT treated in an air oven at 80 - 120 °C for 30 - 90 min under 15 % moisture content (MC) (HMT 15), 25% MC (HMT 25) and 35% MC (HMT 35). The highest L* and WI values for HMT treated BG starch were observed at HMT 80 °C for 30 min under 15% MC; 100 °C for 60 min (25% MC); and 100 °C for 17.57 min (35% MC) while the lowest was observed in HMT 100 °C for 102.43 min (15% MC); 120 °C for 90 min (25% MC); and 120 °C for 90 min (35% MC). In HMT 15-BG starch, the gelatinisation parameters onset (To), peak (Tp) and concluding temperature (Tc) of the samples decreased as treatment time and temperature increased whereas gelatinisation enthalpy of BG starch increased with increase in HMT treatment temperature and time. In HMT 25-BG starch Tp, and gelatinisation enthalpy of the starch increased with increase in HMT treatment temperature and time. While in HMT 35-BG starch, To, Tp, Tc and gelatinisation enthalpy of the starches decreased with increase in HMT treatment temperature and time. In HMT 15-BG starch, the water absorption capacity (WAC), solubility and swelling power (SP) decreased as treatment time and temperature increased while oil absorption capacity (OAC) of the starch increased with increase in HMT treatment temperature and time. In terms of HMT 25-BG starch, the WAC and OAC increased as HMT treatment time and temperature increased while SP and solubility of the starch decreased with increase in HMT treatment temperature and time. In HMT 35-BG starch, OAC, solubility and SP decreased as treatment time and temperature increased while WAC of the starch increased with increase in HMT treatment temperature and time. The optimum HMT conditions for BG starch were found to be 80 °C for 30 min (HMT 15), 105.74 °C for 30 min (HMT 25), and 113.16 °C for 30 min (HMT 35). Desirability of the obtained optimum conditions were 0.63 (HMT 15), 0.56 (HMT 25) and 0.64 (HMT 35). Information obtained from scanning electron micrograph indicates oval and round shape for bambara starch granules, with varying sizes. The range of the granule size width was 4.2 – 4.7 mm and 10 μm for length. The modified starches showed some changes in granule morphology as they seem to disintegrate with application of HMT. Unmodified and HMT - BG starches showed characteristic FTIR bands linked with common starches. All the samples displayed complex vibrations in the region below 1000 cm-1 due to the skeletal vibrations of the glucose pyranose ring. Statistical analysis on colour, thermal and functional properties of HMT 15-BG, HMT 25-BG and HMT 35-BG starch showed that effects of temperature and treatment time had no significant (p ≥ 0.05) effect on these properties of HMT-BG starch. However, treatment time had a significant linear effect (p ≤ 0.05) on swelling power, for HMT 15-BG starch. In HMT 35-BG starch, WAC was significantly affected by quadratic effect of temperature and time while solubility was significantly affected by linear effect of time and quadratic effect of temperature. / NRF

Knowledge of the dissociation constants of the ionizable protons of weak acids in aqueous media is of fundamental importance in many areas of chemistry and biochemistry. The pKa value, or equilibrium dissociation constant, of a molecule determines the relative concentration of its protonated and deprotonated forms at a specified pH and is therefore an important descriptor of its chemical reactivity. Considerable efforts have been devoted to the determination of pKa values by different experimental techniques. Although in most cases the determination of pKa values from experimental is straightforward, there are situations where interpretation is difficult and the results ambiguous. It is, therefore, not surprising that the capability to provide accurate estimates of the pKa value has been a central goal in theoretical chemistry and there has been a large effort in developing methodologies for predicting pKa values for a variety of chemical systems by differing quantum chemical techniques. A prediction accuracy within 0.5 pKa units of experiment is the desirable level of accuracy. This is a non-trivial exercise, for an error of 1 kcal/mol in estimates of the free energy value would result in an error of 0.74 pKa units. In this thesis ab initio Car-Parrinello molecular dynamics (CPMD) has been used for investigating the Brϕnsted acid-base chemistry of weak acids in aqueous solution. A key issue in any dissociation event is how the solvating water molecules arrange themselves spatially and dynamically around the neutral and dissociated acid molecule. Ab initio methods have the advantage that all solvent water molecules can, in principle, be con- sidered explicitly. One of the factors that has inhibited the widespread use of ab initio MD methods to study the dissociation reaction is that dissociation of weak acids are rare events that require extremely long simulation times before one is observed. The metady- namics formalism provides a solution to this conundrum by preventing the system from revisiting regions of configuration space where it has been in the past. The formalism allows the system to escape the free-energy minima by biasing the dynamics with a history dependent potential (or force) that acts on select degrees of freedom, referred to as collective variables. The bias potentials, modeled by repulsive inverted Gaussians that are dropped during propagation, drive the system out of any free-energy minima and allow it to explore the configurational space by a relatively quick and efficient sampling. The the- sis deals with a detailed investigation of the Brϕnsted acid-base chemistry of weak acids in aqueous solutions by the CPMD-metadynamics procedure. In Chapter 1, current approaches for the theoretical estimation of pKa values are summarized while in Chapter 2 the simulation methodology and the metadynamics sampling techniques used in this study are described. The potential of the CPMD-metadynamics procedure to provide estimates of the acid dissociation constant (pKa) is explored in Chapter 3, using acetic acid as a test sys- tem. Using the bond-distance dependent coordination number of protons bound to the dissociating carboxylic groups as the collective variable, the free-energy profile for the dissociation reaction of acetic acid in water was computed. Convergence of the free-energy profiles and barriers for the simulations parameters is demonstrated. The free-energy profiles exhibit two distinct minima corresponding to the dissociated and neutral states of the acid and the deterrence in their values provides the estimate for pKa. The estimated value of pKa for acetic acid from the simulations, 4.80, is in good agreement with the experiment at value of 4.76. It is shown that the good agreement with experiment is a consequence of the cancellation of errors, as the pKa values are computed as the divergence in the free energy values at the minima corresponding to the neutral and dissociated state. The chapter further explores the critical factors required for obtaining accurate estimates of the pKa values by the CPMD-metadynamics procedure. It is shown that having water molecules sufficient to complete three hydration shells as well as maintaining water density in the simulation cell as close to unity is important. In Chapter 4, the CPMD-metadynamics procedure described in Chapter-3 has been used to investigate the dissociation of a series of weak organic acids in aqueous solutions. The acids studied were chosen to highlight some of the major factors that influence the dissociation constant. These include the influence of the inductive effect, the stabilization of the dissociated anion by H-bonding as well as the presence of multiple ionizable groups. The acids investigated were aliphatic carboxylic acids, chlorine-substituted carboxylic acids, cis- and trans-butenedioic, the isomers of hydroxybenzoic acid and ophthalmic acids and its isomers. It was found that in each of these examples the CPMD-metadynamics procedure correctly estimates the pKa values, indicating that the formulism is capable of capturing these influences and equally importantly indicating that the cancellation of errors is indeed universal. Further, it is shown that the procedure can provide accurate estimates of the successive pKa values of polypro tic acids as well as the subtle difference in their values for different isomers of the acid molecule. Changes in protonation-deprotonation of amino acid residues in proteins play a key role in many biological processes and pathways. It is shown that CPMD simulations in conjunction with metadynamics calculations of the free energy profile of the protonation- deprotonation reaction can provide estimates of the multiple pKa values of the 20 canonical α-amino acids in aqueous solutions in good agreement with experiment (Chapter 5). The distance-dependent coordination number of the protons bound to the hydroxyl oxygen of the carboxylic and the amine groups is used as the collective variable to explore the free energy profiles of the Brϕnsted acid-base chemistry of amino acids in aqueous solutions. Water molecules, sufficient to complete three hydration shells surrounding the acid molecule were included explicitly in the computation procedure. The method works equally well for amino acids with neutral, acidic and basic side chains and provides estimates of the multiple pKa values with a mean relative error with respect to experimental results, of 0.2 pKa units. The tripeptide Glutathione (GSH) is one of the most abundant peptides and the major repository for non-protein sulfur in both animal and plant cells. It plays a critical role in intracellular oxidative stress management by the reversible formation of glutathione disulfide with the thioldisulfide pair acting as a redox buffer. The state of charge of the ionizable groups of GSH can influences the redox couple and hence the pKa value of the cysteine residue of GSH is critical to its functioning. In Chapter 6, it has been reported that ab initio Car-Parrinello Molecular Dynamics simulations of glutathione solvated by 200 water molecules, all of which are considered in the simulation. It is shown that the free-energy landscape for the protonation - deprotonation reaction of the cysteine residue of GSH computed using metadynamics sampling provides accurate estimates of the pKa and correctly predicts the shift in the dissociation constant values as compared to the isolated cysteine amino acid. The dissociation constants of weak acids are commonly determined from pH-titration curves. For simple acids the determination of the pKa from the titration curves using the Henderson-Hasselbalch equation is relatively straightforward. There are situations, however, especially in polyprotic acids with closely spaced dissociation constants, where titration curves do not exhibit clear inflexion and equivalence stages and consequently the estimation of multiple pKa values from a single titration curve is no longer straightfor- ward resulting in uncertainties in the determined pKa values. In Chapter 7, the multiple dissociation constant of the hexapeptide glutathione disulfide (GSSG) with six ionizable groups and six associated dissociation constants has been investigated. The six pKa values of GSSG were estimated using the CPMD-metadynamics procedure from the free-energy profiles for each dissociation reaction computed using the appropriate collective variable. The six pKa values of GSSG were estimated and the theoretical pH-titration curve was then compared with the experimentally measured pH-titration curve and found to be in excellent agreement. The object of the exercise was to establish whether interpretation of pH-titration curves of complex molecules with multiple ionizable groups could be facilitated using results of ab initio molecular dynamics simulations.

Chapter 3 Groundnut Bud Necrosis Virus (GBNV) is a tripartite ambisense RNA plant virus that belongs to serogroup IV of Tospovirus genus. Non-Structural protein-m (NSm), which functions as movement protein in tospoviruses, is encoded by the M RNA. In this chapter, we demonstrate that despite the absence of any putative transmembrane domain, GBNV NSm associates with membranes when expressed in E. coli as well as in N. benthamiana. Incubation of refolded NSm with liposomes ranging in size from 200-250 nm resulted in changes in the secondary and tertiary structure of NSm. A similar behaviour was observed in the presence of anionic and zwitterionic detergents. Furthermore, the morphology of the liposomes was found to be modified in the presence of NSm. Deletion of coiled coil domain resulted in the inability of in planta expressed NSm to interact with membranes. Further, when the C-terminal coiled coil domain alone was expressed, it was found to be associated with membrane. These results demonstrate that NSm associates with membranes via the C-terminal coiled coil domain and such an association may be important for movement of viral RNA from cell to cell. Further NSm was shown to be phosphorylated by N. benthamiana and tomato crude sap as observed in other movement proteins. Chapter 4 This chapter deals with localization of NSm to PD and identification of domain involved in localization. For this purpose NSm and its mutants were cloned in pEAQ:GFP vector and transiently expressed in N. benthamiana by infiltration of transformed Agrobacteria. The GFP tagged NSm was visualized by confocal microscopy. The results demonstrated that NSm forms punctate structures and localizes to PD as confirmed by colocalization of mCherry: PDLP1a, a PD marker which resides in PD, with GFP:NSm. To find out the domain involved in PD localization, sequential deletion mutants were made. It was found that C-terminal domain is involved in PD localization. On the other hand, N-terminal unfolded region was dispensable for PD localization. This is the first report of a coiled coil domain shown to be involved in PD localization. It has also been demonstrated that GBNV NSm interacts with NP. Further, membrane floatation assay carried in presence of NP suggested that interaction of NSm and NP affected membrane association of NSm. These results were further confirmed by localization studies of NSm in presence of NP. It was found that there was considerable relocalization of both NSm and NP. NSm was observed to be present in cytoplasm as well as on the membrane. At the same time, NP was observed on membrane apart from being present in the cytoplasm. When N-terminal 50 amino acids (unfolded) region of NSm was deleted and colocalization studies were carried out, it was found that NSm and NP do not colocalize, suggesting that NSm interacts with NP via the unfolded region and helps in the relocalization of NP to the membrane. Chapter 5 This chapter deals with the pathway of targeting NSm to PD. To decipher the pathway, followed by NSm, an inhibitor of endomembrane or vesicle mediated transport, Brefeldin A (BFA) was used. When GFP-NSm was expressed it was observed to form punctate structure at PD as before. Upon treatment with BFA, green islands were observed in the cytoplasm suggesting that ER was involved in targeting NSm to PD. Similarly, LatB, inhibitor of actin mediated targeting of protein to membrane, also abrogated the localization of NSm to PD. In order to further understand the role of ER in targeting NSm to PD, an ER marker, ER-GFP (GFP fused to HDEL peptide that directs it to ER) was coexpressed with GBNV NSm fused to mCherry. It was observed that NSm colocalizes with ER-GFP as yellow puncta on PD. The puncta appeared as patches and the whole ER-network was converted to vesicles. This was further confirmed by coexpressing ER-GFP with NSm without any tag. The green fluorescent vesicles were observed preferentially near cell membrane. To delineate the region of NSm involved in vesicle formation, point mutants and deletion mutants of NSm were generated without the tag and coexpressed with ER-GFP. When N-terminal 203 amino acids were deleted, NSm was able to transform ER membranes to vesicles suggesting that these residues are dispensable for vesicle formation. Interestingly, the deletion of coiled coil domain leads to cytosolic location of NSm. Furthermore, the C-terminal coiled coil domain when expressed alone was capable of inducing vesicle formation. This is the first report of involvement of such a domain in ER membrane association and vesicle formation.

Les femmes, élément central de la vie économique et sociale, jouent un rôle important dans la société sénégalaise. Dans cette thèse nous avons voulu mettre en valeur le dynamisme et l'héroïsme quotidien des femmes sénégalaises, de la région de Diourbel en particulier. Ce dynamisme est étudié à travers leurs activités quotidiennes, la recherche d’autonomie économique, et leurs associations. Diourbel était le centre du bassin arachidier dont les contours se sont modifiés avec le développement de l’arachide et les mutations du milieu. Ces dernières ne manquent pas de conséquences sur la vie des populations, des femmes en particulier qui doivent trouver des moyens pour s'adapter et faire face au départ des hommes et à l'accroissement des charges familiales. En partant des difficultés multidimensionnelles du vieux bassin arachidier, étudiées à travers la mauvaise articulation des politiques agricoles coloniales et nationales, qui ont participé à la crise agricole qui a été aggravée par la combinaison de facteurs anthropiques et physiques, nous avons rappelé le rôle actif des femmes dans la sphère familiale, d’abord et rendu visibles les activités collectives ou individuelles qu’elles ont déployées. Ensuite, les associations féminines se caractérisent par leur diversité dans leurs formes, leurs objectifs, leurs moyens et leur tissu relationnel. Devant les mutations observées, elles sont devenues incontournables et sont perçues comme des réponses féminines. Devant tous ces changements, les femmes du Baol ont leur mot à dire et leur force à apporter pour que l'édifice familial et social reste debout. Face aux efforts déployés par les femmes, des perspectives s'ouvrent. / Women play an important role in Senegalese society occupying a central position in the economic and social life of the nation. In this thesis we will highlight the dynamism and the heroic levels of energy that Senegalese women invest in their daily tasks. Our observations will focus on the region of Diourbel. Their dynamism will be assessed throughout their daily activities, including their efforts to reach an economic self-sufficiency and their work within organizations. Diourbel used to be the center of the groundnut (peanut) basin. The borders of this region changed with shifts in the techniques of peanut farming and modifications in the environment. The latter has had effects on the living conditions of the inhabitants, particularly on women who had to find ways to adapt to such challenges as men migrating and increases in the cost of running a household. We highlight the active role women play within the family, demonstrating their collective and individual activities. These details are presented within the context of such multidimensional issues facing the old groundnut basin, as the incoherence of the colonial and national agricultural policies which have been aggravated by the combination of anthropogenic and physical factors. In addition the women´s associations are characterized by their variety, objectives, methods and internal relationships. The analysis will show them to be an inevitable feminine response to the observed social, economic and environmental changes. Women of Baol play a substantial role and exert significant influence on the process of maintaining both the social and familiar structures of their communities. As women carry out these efforts, our analysis will reveal how these efforts generate new perspectives.

MRDV / Institute for Rural Development / This study originated from the realisation that non-conventional crops such as Bambara nuts (Vigna subterranea) were becoming increasingly important in addressing food insecurity and malnutrition in the smallholder farming sector of countries in sub-Saharan Africa. Moreover, some of the smallholder crop farmers were observed to be continuing to rely on indigenous techniques to forecast rainfall and adapt agricultural activities in response to climate variability. However, it was not clear how climate change influenced the productivity of V. subterranea. Nor were the indigenous approaches that farmers used to forecast rainfall on this phenomenon well understood. Thus, a study was carried out to identify and document indigenous approaches that smallholder farmers used to forecast rainfall and adaptation practices relating to V. subterranea. The study was conducted in Xigalo and Lambani villages located in Collins Chabane Local Municipality of Vhembe District in Limpopo Province. The villages served as case study areas that helped to compare the native approaches that the Va-Tsonga and Vha-Venda used to forecast rainfall in the course of producing V. subterranea. A multi-case study research design, which was exploratory in nature was adopted. Convenience and snowball sampling techniques were used to identify and select respondents. The triangulation of participatory methods, techniques and tools guided the collection of qualitative data. Key informant interviews, learning circles, photovoice, one-on-one interviews and narrative inquiry techniques were applied during data collection. Smallholder farmers and the elderly members of communities were the respondents. Nine key informants in Xigalo and Lambani villages were interviewed. One retired and two currently serving government extension officers were also interviewed. Separate learning circles comprising mainly elderly men and women were also organised. Each learning circle was made up of 7-10 respondents. Atlas.ti version 7.5.7 software was used to analyse the qualitative data following the thematic content analysis approach. It was observed that the respondents were aware of climate variability events that affected V. subterranea. Some of the events were shifts in rainfall patterns, heavy rainfall, extreme temperatures, scarcity of summer rainfall, the disappearance of lunar signs and the seasonal cycle variations. Eighteen types of phenological signs used to predict rainfall were identified. The most common signs included the Milky Way Galaxy of stars, musical sounds of birds and frogs, moon shapes, cumulus and cumulonimbus cloud types. A close relationship between conservation of V. subterranea and adaptation strategies was said to exist. It was evident that most commonly used conservation strategies were rainmaking ceremonies, planting after the summer rains, hoeing weeds, soaking seeds before planting, hilling or earthing up around the base of the V. subterranea plant and storing the legumes in traditional vessels and sacks. The need for integrating western scientific knowledge with native forecasts to inform the production of V. subterranea was uncovered. In addition to this, the needs of Tsonga and Venda communities should inform local policy interventions. Lastly, adaptation strategies that address food insecurity with V. subterranea being part of the agro-ecosystem deserve attention in scientific investigation and policymaking. / NRF