Thesis (M.Sc. Agriculture (Soil Science)) -- University of Limpopo, 2019 / Nutritional water productivity (NWP) is an assessment tool, which describes the amount of water that has been used to produce selected mineral malnutrition (MMN) elements and micronutrient malnutrition (MNMN) substances. Therefore, it links agricultural production to human nutrition. Deficiencies in MMN elements and/or MNMN substances in human nutrition referred to as malnutrition, had been linked with fatal diseases. Agricultural soils could be affected by soil-borne pathogens such as plant-parasitic nematodes, which could limit the availability of MMN elements and MNMN substances. In some communities, vegetable crops, including chilli are regarded as a major source of MMN elements and MNMN substances. Effects of root-knot (Meloidogyne species) nematodes on NWP of chilli (Capsicum annuum L.) have not been documented. The objective of the study was to determine the effects of increasing population densities of M. incognita race 2 and M. javanica on the NWP of hot chilli plants. A microplot trial was conducted at the Green Biotechnologies Research Centre of Excellence (GBRCE), University of Limpopo, South Africa. Pots were filled with 10-L steam-pasteurised (300oC) sandy clay loam soil sourced from GBRCE and Hygromix-T (Hygrotech, Pretoria North) growth medium in the ratio 3:1 (v/v). Thereafter, three-week-old hot chilli cv. 'Serrano' seedlings were transplanted into each pot, with inoculum prepared by extracting eggs and second-stage juveniles (J2) of M. incognita race 2 and M. javanica from roots of grown nematode susceptible tomato cv. 'Floradade' (Solanum lycopersicum L.) in a 1% NaOCl solution. Fourteen days after transplanting, treatments 0, 50, 125, 250, 625, 1250 and 2000 eggs and second-stage juveniles (J2) of M. incognita race 2 and M. javanica were separately inoculated using a 20 ml plastic syringe into 5-cm-deep holes in pots. At 56 days after the initiation of the treatments, Meloidogyne species xiv decreased soil pH and increased organic carbon, contributing 29 and 43% in total treatment variation (TTV) of the respective variables. Treatment effects caused the pH to decrease. NWP variables against increasing nematode numbers exhibited quadratic relations, with coefficients of determination ranging from 59 to 86% for M. incognita race 2 trial and 80 to 98% for M. javanica trial. Meloidogyne species population densities against plant variables did not show any significant relationship, except for root galling and chlorophyll content where treatments contributed 76, 98 and 47% TTV of the respective variables. Generally, root galling increased with increase in Meloidogyne species population densities, whereas chlorophyll content decreased with increasing inoculum levels. Nematode variables against their increasing population exhibited quadratic relationship with the model explained by 44 to 95% for M. incognita race 2 and 28 to 82%, association, respectively for M. javanica. In conclusion, Meloidogyne species interfered with NWP of mineral elements in chilli plant and therefore, nematode management practices should be done to reduce the nematode population densities that would confer quality to agricultural produce for human health benefits.

Thesis (M. Sc. (Plant Protection)) -- University of Limpopo, 2021 / Worldwide, root-knot (Meloidogyne species) nematodes are considered to be the most important and damaging genus in crop husbandry. The existence of a wide host range, over 2000 plants, and several biological races, makes the management of this nematode genus difficult with nematode-resistant crop Hybrid Sorghum Sudan grass (Sorghum bicolor × Sorghum Sundanese) has been classified as being resistant to certain Meloidogyne species and races, with a wide range of uses in crop rotation intended to manage nematode population densities. However, due to the ability of nematodes to enter chemiobiosis when gradually exposed to chemicals, this hybrid might not be effective in managing nematode population densities for the subsequent highly susceptible sweet potato (Ipomoea batatas L.) cultivars. The objective of the study was to determine whether hybrid Sorghum-Sudan grass would suppress M. javanica (Trial 1), M. incognita race 2 (Trial 2) and M. incognita race 4 (Trial 3) population densities, allowing a nematode susceptible sweet potato cv. ′Beauregard′ as successor crop to be cultivated without suffering nematode damage. The hybrid Sorghum-Sudan grass study was conducted under greenhouse conditions, with seven inoculation levels, namely, 0; 5; 25; 125; 625; 3 125 and 15 625 eggs and second-stage juveniles (J2) of each nematode species or race, arranged in randomised complete block design, with six replications and validated in time. Plant growth, foliar nutrient elements and nematodes were collected at 56 days after inoculation and prepared for analysis using standard methods. The reproductive factor (RF) at all levels was zero, whereas nematode inoculation at all levels did not have any effect on plant growth of the hybrid Sorghum-Sudan grass. However, the nematode levels affected the accumulation of nutrient elements and the quality of forage. After cultivating the susceptible sweet potato cultivar in pots xxx previously with hybrid Sorghum-Sudan grass at increasing levels of M. javanica alone, that is in Trial 1, similar results were observed with respect to RF and lack of nematode damage to plant growth. Consequently, the hybrid was suitable for use in crop rotation with sweet potato for the purpose of managing nematode population densities of thermophilic Meloidogyne species and/or races. / National Research Foundation of South Africa (NRF) and the Agricultural Research Council (ARC)

No description available.

Thesis (PhD)--Stellenbosch University, 2014. / ENGLISH ABSTRACT: In this dissertation we address the conservation of topological states in polymer knots. Topological constraints are frequently included into theoretical descriptions of polymer systems through invariants such as winding numbers and linking numbers of polynomial invariants. In contrast, our approach is based on sequences of manipulations of knots that maintain a given knot's topology; these are known as Reidemeister moves. We begin by discussing basic properties of knots and their representations. In particular, we show how the Reidemeister moves may be viewed as rules for dynamics of crossings in planar projections of knots. Thereafter we consider various combinatoric enumeration procedures for knot configurations that are equivalent under chosen topological constraints. Firstly, we study a reduced system where only the zeroth and first Reidemeister moves are allowed, and present a diagrammatic summation of all contributions to the associated partition function. The partition function is then calculated under basic simplifying assumptions for the Boltzmann weights associated with various configurations. Secondly, we present a combinatoric scheme for enumerating all topologically equivalent configurations of a polymer strand that is wound around a rod and closed. This system has the constraint of a fixed winding number, which may be viewed in terms of manipulations that obey a Reidemeister move of the second kind of the polymer relative to the rod. Again configurations are coupled to relevant statistical weights, and the partition function is approximated. This result is used to calculate various physical quantities for confined geometries. The work in that chapter is based on a recent publication, "Conservation of polymer winding states: a combinatoric approach", C.M. Rohwer, K.K. Müller-Nedebock, and F.-E. Mpiana Mulamba, J. Phys. A: Math. Theor. 47 (2014) 065001. The remainder of the dissertation is concerned with a dynamical description of the Reidemeister moves. We show how the rules for crossing dynamics may be addressed in an operator formalism for stochastic dynamics. Differential equations for densities and correlators for crossings on strands are calculated for some of the Reidemeister moves. These quantities are shown to encode the relevant dynamical constraints. Lastly we sketch some suggestions for the incorporation of themes in this dissertation into an algorithm for the simulated annealing of knots. / AFRIKAANSE OPSOMMING: In hierdie tesis ondersoek ons die behoud van topologiese toestande in knope. Topologiese dwangvoorwaardes word dikwels d.m.v. invariante soos windingsgetalle, skakelgetalle en polinomiese invariante in die teoretiese beskrywings van polimere ingebou. In teenstelling hiermee is ons benadering gebaseer op reekse knoopmanipulasies wat die topologie van 'n gegewe knoop behou - die sogenaamde Reidemeisterskuiwe. Ons begin met 'n bespreking van die basiese eienskappe van knope en hul daarstellings. Spesi ek toon ons dat die Reidemeisterskuiwe beskryf kan word i.t.v. reëls vir die dinamika van kruisings in planêre knoopprojeksies. Daarna beskou ons verskeie kombinatoriese prosedures om ekwivalente knoopkon gurasies te genereer onderhewig aan gegewe topologiese dwangvoorwaardes. Eerstens bestudeer ons 'n vereenvoudigde sisteem waar slegs die nulde en eerste Reidemeisterskuiwe toegelaat word, en lei dan 'n diagrammatiese sommasie van alle bydraes tot die geassosieerde toestandsfunksie af. Die partisiefunksie word dan bereken onderhewig aan sekere vereenvoudigende aannames vir die Boltzmanngewigte wat met die verskeie kon- gurasies geassosieer is. Tweedens stel ons 'n kombinatoriese skema voor om ekwivalente kon gurasies te genereer vir 'n polimeer wat om 'n staaf gedraai word. Die beperking tot 'n vaste windingsgetal in hierdie sisteem kan daargestel word i.t.v. 'n Reidemeister skuif van die polimeer t.o.v. die staaf. Weereens word kon gurasies gekoppel aan relevante statistiese gewigte en die partisiefunksie word benader. Verskeie siese hoeveelhede word dan bereken vir beperkte geometrie e. Die werk in di e hoofstuk is gebaseer op 'n onlangse publikasie, "Conservation of polymer winding states: a combinatoric approach", C.M. Rohwer, K.K. Müller-Nedebock, and F.-E. Mpiana Mulamba, J. Phys. A: Math. Theor. 47 (2014) 065001. Die res van die tesis handel oor 'n dinamiese beskrywing van die Reidemeisterskuiwe. Ons toon hoe die re els vir kruisingsdinamika beskryf kan word i.t.v. 'n operatorformalisme vir stochastiese dinamika. Di erensiaalvergelykings vir digthede en korrelatore vir kruisings op stringe word bereken vir sekere Reidemeisterskuiwe. Daar word getoon dat hierdie hoeveelhede die relevante dinamiese beperkings respekteer. Laastens maak ons 'n paar voorstelle vir hoe idees uit hierdie tesis geï nkorporeer kan word in 'n algoritme vir die gesimuleerde vereenvoudiging van knope.

The cyclotides are a family of naturally occurring peptides characterized by cyclic cystine knot (CCK) structural motif, which comprises a cyclic head-to-tail backbone featuring six conserved cysteine residues that form three disulfide bonds. This unique structural motif makes cyclotides exceptionally resistant to chemical, thermal and enzymatic degradation. They also exhibit a wide range of biological activities including insecticidal, cytotoxic, anti-HIV and antimicrobial effects. The cyclotides found in plants exhibit considerable sequence and structural diversity, which can be linked to their evolutionary history and that of their host plants. To clarify the evolutionary link between sequence diversity and the distribution of individual cyclotides across the genus Viola, selected known cyclotides were classified using signature sequences within their precursor proteins. By mapping the classified sequences onto the phylogenetic system of Viola, we traced the flow of cyclotide genes over evolutionary history and were able to estimate the prevalence of cyclotides in this genus. In addition, the structural diversity of the cyclotides was related to specific features of the sequences of their precursor proteins, their evolutionary selection and expression levels. A number of studies have suggested that the biological activities of the cyclotides are due to their ability to interact with and disrupt biological membranes. To better explain this behavior, quantitative structure-activity relationship (QSAR) models were developed to link the cyclotides’ biological activities to the membrane-interactive physicochemical properties of their molecular surfaces. Both scalar quantities (such as molecular surface areas) and moments (such as the distributions of specific properties over the molecular surface) were systematically taken into account in the development of these models. This approach allows the physicochemical properties of cyclotides to be geometrically interpreted, facilitating the development of guidelines for drug design using cyclotide scaffolds. Finally, an optimized microwave-assisted Fmoc-SPSS procedure for the total synthesis of cyclotides was developed. Microwave irradiation is used to accelerate and improve all the key steps in cyclotide synthesis, including the assembly of the peptide backbone by Fmoc-SPPS, the cleavage of the protected peptide, and the introduction of a thioester at the C-terminal carboxylic acid to obtain the head-to-tail cyclized cyclotide backbone by native chemical ligation.

This thesis investigates the structure and properties of hyperbolic 3-manifold groups (particularly knot and link groups) and arithmetic Kleinian groups. In Chapter 2, we establish a stronger version of a conjecture of A. Reid and others in the arithmetic case: if two elements of equal trace (e.g., conjugate elements) generate an arithmetic two-bridge knot or link group, then the elements are parabolic (and hence peripheral). In Chapter 3, we identify all Kleinian groups that can be generated by two elements for which equality holds in Jørgensen’s Inequality in two cases: torsion-free Kleinian groups and non-cocompact arithmetic Kleinian groups. / text

Plant parasitic nematodes cause billons of dollars in annual crop losses. One of the most damaging is the root-knot nematode, Meloidogyne incognita, which is known to attack more than 3000 plants. This research will contribute to the understanding of host-plant resistance through characterization of the early infection processes of Meloidogyne incognita race 3 in susceptible (Lahontan) and resistant (Moapa) alfalfa cultivars by light microscopy and transmission electron microscopy. Neither differential penetration of M. incognita J2 into Lahontan, nor migration of J2 from Moapa, played a significant role in the resistance mechanism(s). Coiled nematodes in the cortex were observed in greater numbers in the Moapa 48 hours after inoculation. This position was interpreted as a sign of disorientation and starvation. By 96 hours after inoculation, no coiled nematodes were observed in Lahontan. In Moapa, resistance probably depends not only on the failure of the J2 to identify a suitable feeding site and initiate giant cells, but also on its inability to maintain the giant cells, once they are initiated. At the ultrastructural level, 48 hours after inoculation, the most evident change in both cultivars was the appearance of a uniform interstitial material (IM) between the nematode cuticle and the root cell wall. At 96 hours, IM in Moapa was completely agglutinated while in Lahontan it was still uniform or only slightly agglutinated. Due to these clear differences between both cultivars I propose that the IM plays a role in the resistance of Moapa to M. incognita. Immunolabeling techniques were employed to determine if the distribution of the nematode's surface coat, deposited in host tissues, differs in resistant and susceptible alfalfa cultivars. At 72 hours after inoculation, labeling of surface coat epitopes in Moapa was stronger than at 24 and 48 hours after inoculation. Labeling was observed on the nematode's cuticle, the plant cell wall, and the IM. In Lahontan, 72 and 96 hours after penetration, labeling of the surface coat epitopes was observed on the nematode's cuticle, the root cell walls, and the cell wall junctions of cells near the nematode, but not in direct contact with the cell.

<p>For any Legendrian knot in R^3 with the standard contact structure, we show that the existence of an augmentation to any field of the Chekanov-Eliashberg differential graded algebra over Z[t,t^{-1}] is equivalent to the existence of a normal ruling of the front diagram, generalizing results of Fuchs, Ishkhanov, and Sabloff. We also show that any even graded augmentation must send t to -1.</p><p>We extend the definition of a normal ruling from J^1(S^1) given by Lavrov and Rutherford to a normal ruling for Legendrian links in #^k(S^1\times S^2). We then show that for Legendrian links in J^1(S^1) and #^k(S^1\times S^2), the existence of an augmentation to any field of the Chekanov-Eliashberg differential graded algebra over Z[t,t^{-1}] is equivalent to the existence of a normal ruling of the front diagram. For Legendrian knots, we also show that any even graded augmentation must send t to -1. We use the correspondence to give nonvanishing results for the symplectic homology of certain Weinstein 4-manifolds.</p> / Dissertation

Knot nullification is an unknotting operation performed on knots and links that can be used to model DNA recombination moves of circular DNA molecules in the laboratory. Thus nullification is a biologically relevant operation that should be studied. Nullification moves can be naturally grouped into two classes: coherent nullification, which preserves the orientation of the knot, and incoherent nullification, which changes the orientation of the knot. We define the coherent (incoherent) nullification number of a knot or link as the minimal number of coherent (incoherent) nullification moves needed to unknot any knot or link. This thesis concentrates on the study of such nullification numbers. In more detail, coherent nullification moves have already been studied at quite some length. This is because the preservation of the previous orientation of the knot, or link, makes the coherent operation easier to study. In particular, a complete solution of coherent nullification numbers has been obtained for the torus knot family, (the solution of the torus link family is still an open question). In this thesis, we concentrate on incoherent nullification numbers, and place an emphasis on calculating the incoherent nullification number for the torus knot and link family. Unfortunately, we were unable to compute the exact incoherent nullification numbers for most torus knots. Instead, our main results are upper and lower bounds on the incoherent nullification number of torus knots and links. In addition we conjecture what the actual incoherent nullification number of a torus knot will be.

Thesis advisor: Julia E. Grigsby / "Ozsváth, Stipsicz and Szabó define a one-parameter family {ϒᴋ(t)}t∈[₀,₂] of Heegaard Floer knot invariants for knots K ⊂ S³ . We generalize ϒᴋ (t) to knots in any" "rational homology sphere. We study the ϒ−invariant of a fibered knot. We prove that the ϒ−invariant can never reach its minimum slope if the monodromy of the fibration is not right-veering. / Thesis (PhD) — Boston College, 2018. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Mathematics.