京都大学 / 0048 / 新制・課程博士 / 博士(農学) / 甲第22484号 / 農博第2388号 / 新制||農||1075(附属図書館) / 学位論文||R2||N5264(農学部図書室) / 京都大学大学院農学研究科応用生命科学専攻 / (主査)教授 小川 順, 教授 加納 健司, 教授 栗原 達夫 / 学位規則第4条第1項該当 / Doctor of Agricultural Science / Kyoto University / DFAM

京都大学 / 0048 / 新制・課程博士 / 博士(医学) / 甲第18138号 / 医博第3858号 / 新制||医||1002(附属図書館) / 30996 / 京都大学大学院医学研究科医学専攻 / (主査)教授 木村 剛, 教授 坂田 隆造, 教授 羽賀 博典 / 学位規則第4条第1項該当 / Doctor of Medical Science / Kyoto University / DFAM

Thesis (M.Sc. (Agriculture, Plant Protection)) -- University of Limpopo, 2020 / The unavailability of environment-friendly nematicides for managing root-knot (Meloidogyne species) nematodes in crop husbandry have led to various alternative methods being sort which includes the development of cucurbitacin-containing phytonematicides. The cited phytonematicides consistently suppressed nematode numbers on different crops under greenhouse, microplot and field conditions, although there is lack of information on how the products would affect susceptible Swiss chard infected by root-knot nematodes. Swiss chard is one of most nutritious vegetables, grown throughout the year and is well adapted to different soil types. However, these products have the potential to induce phytotoxicity on various crops, if applied improperly. Phytotoxicity of phytonematicides on different crops, has been resolved by deriving Mean Concentration Stimulation Point (MCSP). The MCSP, developed using the Curve-fitting Allelochemical Response Data (CARD) computer-based model, is crop-specific, hence it should be developed for every crop. The objectives of this study were to investigate (1) whether population densities of Meloidogyne species, growth and accumulation of selected nutrient elements in Swiss chard would respond to increasing concentration of Nemarioc-AL and Nemafric-BL phytonematicides under greenhouse and microplot conditions and (2) whether the nemarioc-group and nemafric-group phytonematicides in liquid and granular formulations would affect population densities of Meloidogyne species and the productivity of Swiss chard with related accumulation of nutrient elements in leaf tissues under field conditions. Parallel experiments for Nemarioc-AL and Nemafric-BL phytonematicides were conducted concurrently under greenhouse and microplot conditions. Greenhouse experiment was prepared by arranging 25-cm-diameter plasticpods on greenhouse benches, whereas microplot experiment was prepared by digging holes and inserting 30-cm-diameter plastic pots in the field. The four-week-old Swiss chard seedlings were transplanted into the pots, filled with steam-pasteurised loam, sand and Hygromix-T at 3:1:1 (v/v) ratio. Treatments comprised 0, 2, 4, 8, 16, 32 and 64% phytonematicides arranged in randomised complete block design (RCBD), with six replications. Treatments were applied seven days after inoculation, with 3000 eggs and J2 of M. incognita race 4 under greenhouse conditions, whereas under microplot conditions were inoculated with 6000 eggs and J2 of M. javanica. Under field conditions, treatments comprised untreated control (0), 2 g Nemarioc-AG and 3% Nemarioc-AL phytonematicides (nemarioc-group) or 0, 2 g Nemafric-BG and 3% Nemafric-BL phytonematicides (nemafric-group), arranged in RCBD, each experiment with 8 replications. At 56 days after initiation of treatments, eggs in roots, J2 in roots and Pf exhibited negative quadratic relations under both greenhouse and microplot conditions. Under greenhouse conditions, dry shoot mass (R2 = 0.81), dry root mass (R2 = 0.87) and leaf number (R2 = 0.91) over Nemarioc-AL phytonematicide exhibited positive quadratic relations. In contrast, dry shoot mass (R2 = 0.78), dry root mass (R2 = 0.93) and leaf number (R2 = 0.70) over Nemafric-BL phytonematicide exhibited positive quadratic relations. Under microplot conditions, dry shoot mass (R2 = 0.95) and gall rating (R2 = 0.96) over Nemarioc-AL phytonematicide, exhibited positive quadratic relations. Dry shoot mass (R2 = 0.84) and gall rating (R2 = 0.97) versus Nemafric-BL phytonematicide exhibited positive quadratic relations. Selected nutrient elements under greenhouse conditions K (R2 = 0.96), Ca (R2 = 0.79), Mg (R2 = 0.64), Fe (R2 = 0.78) and Zn (R2 = 0.77) over Nemarioc-AL phytonematicide exhibited positive quadratic relations. In contrast, only Ca (R2 = 0.90), Mg (R2 = 0.68) and Zn (R2 = 0.84) over Nemafric-BL phytonematicide exhibited positive quadratic relations, whereas K (R2 = 0.72) and Fe (R2 = 0.63) over the product exhibited negative quadratic relations. Under microplot conditions, K (R2 = 0.82), Ca (R2 = 0.90) and Mg (R2 = 0.98) over Nemarioc-AL phytonematicide exhibited positive quadratic relations, whereas Fe (R2 = 0.91) and Zn (R2 = 0.79) over the product exhibited negative quadratic relations. In contrast, K (R2 = 0.60), Ca (R2 = 0.68) and Zn (R2 = 0.95) over Nemafric-BL phytonematicide exhibited positive quadratic relation, whereas Mg and Fe over the product did not have significant relationships. Under greenhouse conditions, MCSP values for Nemarioc-AL and Nemafric-BL phytonematicides on Swiss chard were 3.03 and 2.36%, whereas overall sensitivity (∑k) values of the crop to the product were 3 and 0 units, respectively. In contrast, MCSP values of Nemarioc-AL and Nemafric-BL phytonematicides on Swiss chard under microplot conditions was successfully established at 3.71 and 3.33%, whereas the ∑k values were 2 and 1 units, respectively. Under field conditions, at 64 days after initiating the treatments, the nemarioc-group phytonematicides had highly significant effects on eggs in roots and reproductive potential (RP), contributing 79 and 77% in total treatment variation (TTV) of the respective variables. In contrast, the nemafric-group phytonematicides had highly significant effects on eggs in roots and RP, contributing 67 and 76% in TTV of the respective variables. Under field conditions, all plant growth variables were not significantly affected by the treatments. The nemarioc-group phytonematicides had significant effects on K and Mg in leaf tissues of Swiss chard, contributing nemafric-group phytonematicides had significant effects on Mg, contributing 62% in TTV of the variable. In conclusion, the products could be used on Swiss chard for managing population densities of Meloidogyne species. However, due to the sensitivity of Swiss chard to the products, it would be necessary to use the derived MCSP values to determine the application intervals of the products on the test cultigen / National Research Foundation (NRF) Agricultural Research Council (ARC)

Les fluoroalcènes sont employés pour préparer des mimes de peptides. Malgré de nombreuses études réalisées dans ce domaine, la préparation d'analogues de peptides comportant une proline modifiée en position C-terminale a été très peu explorée. Ce travail de thèse est consacré à la synthèse de pyrrolidine comportant un motif fluorovinylique. La préparation de sulfones fluorées comportant un cycle pyrrolidine a été réalisée, par réaction d'aza-Michael intramoléculaire. Ce réactif permet la formation de pyrrolines par réaction de Julia modifiée, là où la réaction de Horner-Wadworth-Emmons échoue. Cette étude a été étendue à la préparation de pipéridines fluorées. Cette méthode a été appliquée avec succès à la préparation de précurseurs de peptides Pro-Ψ[CF=CH]-Xaa, peu étudiés dans la littérature. / Fluoroalkenes are used to prepare peptide mimics. In spite of numerous studies carried out in this field, the preparation of peptide analogs comprising a modified proline in the C-terminal position has been very little explored. This thesis is devoted to the synthesis of pyrrolidine with a fluorovinyl unit. The preparation of fluorinated sulfones containing a pyrrolidine ring was carried out by reaction of intramolecular aza-Michael. This reagent allows the formation of pyrrolines by modified Julia reaction, where the Horner-Wadworth-Emmons reaction fails. This study was extended to the preparation of fluorinated piperidines. This method has been successfully applied to the preparation of pro-Ψ peptide precursors [CF = CH] -Xaa, which are poorly studied in the literature.

Thesis (M.Sc. Agriculture (Horticulture)) -- University of Limpopo, 2019 / Cucurbitacin-containing phytonematicides and a variety of unidentified soil microbes in suppressive soils (Biomuti) had been consistent in suppression of population densities of root-knot (Meloidogyne spp.) nematodes on various crops. However, information on suppressive effects of cucurbitacin-containing phytonematicides and Biomuti on citrus growth and suppression of the citrus nematode (Tylenchulus semipenetrans) had not been documented. The objective of this study therefore, was to determine the interactive effects of Nemarioc-AL and Nemafric-BL phytonematicides and Biomuti on growth and nutrient elements in leaf tissues of Poncirus trifoliata rootstock seedlings under greenhouse and field conditions. Uniform six-month-old citrus rootstock seedlings [Du Roi Nursery (Portion 21, Junction Farm, Letsitele)] were transplanted in 4 L plastic bags filled with growing mixture comprising steam-pasteurised (300°C for 1 h) loam and compost (cattle manure, chicken manure, sawdust, grass, woodchips and effective microorganisms) at 4:1 (v/v) ratio and placed on greenhouse benches. A 2 × 2 × 2 factorial experiment with the first, second and third factors being Nemarioc-AL phytonematicide (A) and Nemafric-BL phytonematicide (B) and Biomuti (M), were arranged in randomized complete block design, with 10 blocks. The treatment combinations were A0B0M0, A1B0M0, A0B1M0, A0B0M1, A1B1M0, A1B0M1, A0B1M1 and A1B1M1, with 1 and 0 signifying with and without the indicated factor. Treatments were applied at 3% dilution for each product as substitute to irrigation at a 17-day application interval. Under greenhouse conditions, seedlings were irrigated every other day with 300 ml chlorine-free tap water. Under field conditions, the study was executed using similar procedures to those in the greenhouse trial, except that the citrus seedlings were transplanted directly into the soil of a prepared field and seedlings were irrigated using drip irrigation for 2 h every xxi other day. At 64 days after transplanting, plant growth variables were measured and foliar nutrient elements were quantified using the Inductively Coupled Plasma Optical Emission Spectrometry (ICPE-9000). Data were subjected to analysis of variance using SAS software. Significant second and first order interactions were further expressed using the three-way and two-way tables, respectively. At 64 days after the treatments, under greenhouse conditions Nemarioc-AL × Nemafric-BL × Biomuti interaction was not significant (P ≤ 0.05) on plant variables of seedling rootstocks in both experiments. In contrast, the Nemarioc-AL × Biomuti interaction was highly significant (P ≤ 0.01) on stem diameter, contributing 52% in TTV of the variable in Experiment 1 (Table 3.1), whereas in Experiment 2 the interaction was highly significant on dry shoot mass, contributing 33% in TTV of the variable (Table 3.2). Relative to untreated control, the two-way matrix showed that the Nemarioc-AL × Biomuti interaction, Nemarioc-AL phytonematicide and Biomuti each increased stem diameter by 1%, 12% and 5%, respectively (Table 3.3). Relative to untreated control, the two-way matrix table showed that Nemarioc-AL × Biomuti interaction increased dry shoot mass by 10%, whereas Nemarioc-AL phytonematicide and Biomuti each increased dry shoot mass by 23% and 17%, respectively (Table 3.4). Nemarioc-AL × Nemafric-BL × Biomuti interaction was not significant (P ≤ 0.05) for all plant growth variables in both experiments. However, Nemarioc-AL × Nemafric-BL interaction was significant for leaf number and stem diameter contributing 45% and 29% in TTV of the respective variables in Experiment 2 (Table 4.1). Relative to untreated control, two way matrix table showed that the Nemarioc-AL × Nemafric-BL interaction and Nemafric-BL phytonematicides each increased stem diameter by 8% and 11% respectively, whereas Nemarioc-AL phytonematicides reduced stem diameter by 2% (Table 4.2). Also using two-way matrix table showed that Nemarioc-AL and Nemafric xxii BL phytonematicides each increased leaf number by 1% and 7% respectively, whereas the Nemarioc-AL × Nemafric-BL interaction increased leaf number by 6% (Table 4.2). Nemafric-BL × Biomuti interaction was significant for stem diameter contributing 29% in TTV of the respective variable in Experiment 2 (Table 4.1). Using two-way matrix table showed that Nemafric-BL × Biomuti interaction and Nemafric-BL phytonematicide each increased stem diameter by 7%, whereas Biomuti alone reduced stem diameter by 6% (Table 4.3). Under greenhouse conditions, the second order Nemarioc-AL × Nemafric-BL × Biomuti interaction was highly significant for foliar Mg, contributing 5% in TTV of the variable in Experiment 1 (Table 3.4). Relative to untreated control, the three-way matrix table showed that the three factors, Nemafric BL phytonematicide and Biomuti each reduced Mg by 33%, 35% and 53%, respectively, whereas Nemarioc-AL phytonematicide increased Mg by 12% (Table 3.5). Nemarioc-AL × Biomuti interaction was highly significant for foliar Mg, contributing 9% in TTV of the variable in Experiment 1 (Table 3.4). Relative to untreated control, the two-way matrix table showed that the Nemarioc-AL × Biomuti interaction and Nemafric-BL phytonematicide reduced Mg by 42% and 12%, respectively, whereas Nemarioc-AL phytonematicide alone increased Mg by 14% (Table 3.6). Nemarioc-AL × Biomuti interaction was highly significant for foliar Ca and Mg, contributing 59 and 4% in TTV of the respective variables in Experiment 1 (Table 3.4). Also using two-way matrix table showed that Nemarioc-AL phytonematicide and Biomuti separately reduced Ca by 12% and 22% respectively, whereas the Nemarioc-AL × Biomuti interaction increased Ca by 1% (Table 3.7). Relative to untreated control, the Nemarioc-AL × Biomuti interaction, Nemarioc-AL phytonematicide and Biomuti reduced foliar Mg by 26%, 21% and 33%, respectively (Table 3.7). Nemafric-BL × Biomuti interaction was highly significant for foliar Mg and P, contributing 50 and 21% xxiii in Experiment 1, whereas in Experiment 2 the interaction was significant for foliar Ca and Mg, contributing 41% and 38% in TTV of the respective variables (Table 3.4). Relative to untreated control, the two-way matrix table showed that Nemafric-BL phytonematicide and Biomuti individually reduced Mg by 60% and 51%, respectively, whereas the Nemafric-BL × Biomuti interaction reduced Mg by 38% (Table 3.8). Also, in the two-way matrix table the Nemafric-BL × Biomuti interaction and Nemafric-BL phytonematicide each reduced Mg by 13% and 2%, respectively, whereas Biomuti alone increased P by 17% (Table 3.8). Relative to untreated control, Nemafric-BL phytonematicide and Biomuti reduced Ca by 29% and 18%, respectively, whereas Nemafric-BL × Biomuti interaction reduced Ca by 14% (Table 3.9). Using two-way matrix table showed that Nemafric-BL phytonematicide and Biomuti separately reduced Mg by 21%, whereas the Nemafric-BL × Biomuti interaction reduced Mg by 16% (Table 3.9). Interaction of Nemarioc-AL × Nemafric-BL × Biomuti had no significant effect on K, Na and Zn in both experiments. Under field conditions, the second order Nemarioc-AL × Nemafric-BL × Biomuti interaction was not significant for all the nutrient elements in Experiment 1. Nemarioc-AL × Biomuti was significant for Ca, K and highly significant for Mg and P, contributing 31, 8, 23 and 19% in TTV of the respective variables in Experiment 1 (Table 4.4). Relative to untreated control, two-way matrix table showed that Nemarioc-AL phytonematicide and Biomuti each increased Ca by 15% and 26% repectiviely, whereas the Nemarioc-AL × Biomuti increased Ca by 17% (Table 4.5). Interaction of Nemarioc-AL × Biomuti, Nemarioc-AL phytonematicide and Biomuti each reduced Mg by 48%, 70% and 37% (Table 4.5). Also using two-way matrix table showed that Nemarioc-AL phytonematicide and Biomuti each increased P by 4% and 5% respectively, whereas the Nemarioc-AL × Biomuti interaction increased P by 50% (Table 4.5). Realative to untreated control, xxiv Biomuti and Nemarioc-AL phytonematicide each reduced K by 10% and 5% respectively, whereas the Nemarioc-AL × Nemafric-BL interaction reduced K by 38% (Table 4.7). Nemafric-BL × Biomuti interaction was highly significant for Mg and Zn, contributing 11% and 29% in TTV of the respective variables in Experiment 1 (Table 4.4). Relative to untreated control, two-way matrix table showed that Nemarioc-AL phytonematicide and Biomuti separately increased Mg by 1% and 19% respectiviely, whereas the Nemafric-BL × Biomuti interaction reduced Mg by 43% (Table 4.6). Nemafric-BL × Biomuti interaction, Nemafric-BL phytonematicide and Biomuti each reduced Zn by 35%, 31% and 64% (Table 4.6). Using three-way matrix table showed that the Nemarioc-AL × Nemafric-BL × Biomuti, Nemarioc-AL × Nemafric-BL, Nemarioc-AL × Biomuti and Nemafric-BL × Biomuti interactions each increased Ca by 44%, 18%,10% and 24% (Table 4.8). Further the matrix showed that Nemarioc-AL, Nemafric-BL phytonematicides and Biomuti each increased Ca by 25%, 31% and 23% (Table 4.8). Under both greenhouse and field conditions, although second and first order interactions were not consistent of various variables, results demonstrated that the three products interacted significantly for various products. In conclusion, the study suggested that these innovative products could be used in combination with Biomuti to stimulate plant growth but had antagonistic effects on accumulation of nutrient elements in P. trifoliata rootstock seedlings, suggesting that the products should be applied separately. / Agricultural Research Council-Universities Collaboration Centre and the National Research Foundation (NRF)

EN This Ph.D. thesis focuses on the heme containing gas sensor proteins. These proteins are predominantly present in bacteria, in which play an important role in processes like, sporulation, antibiotic resistance and so on. Heme containing sensor proteins composed of two domains. First one is a globin domain, which contains the heme molecule. Interaction of heme with gas molecule acts as a signal for the activation/inactivation of the second functional domain. Part of this thesis is formed by a review, which summarized the current knowledge about heme containing sensor proteins. In the next part of this thesis we focused on three representatives from the group of oxygen sensor proteins - histidine kinase AfGcHK, diguanylate cyclase YddV and phosphodiesterase EcDOS. The main aim of this thesis was to solve the mechanism of interdomain/intraprotein signal transduction in two oxygen sensor proteins with globin fold of their sensor domain (AfGcHK, YddV). For this purpose, we used the kinetic analysis of their functional domain activity and the methods of structural biology. We also studied the mechanism of interprotein signal transduction in AfGcHK and its cognate partner RR protein. It was also tested, how the presence of sodium disulfide affects the functional properties of oxygen sensor proteins...

The influence of basicity, heat treatment as well as different oxygen partial pressures on the phase relationships in the CaO-MgO-SiO2-Cr2O3 slags was studied with a view to control the precipitation of Cr-spinel in the slag phase. The equilibrium phases in CaO-MgO-SiO2-Cr2O3 slag system in the range on 1673-1873 K have been investigated under low oxygen partial pressure as well as in as air atmosphere. In low oxygen partial pressure experiments, a suitable mixture of CO and CO2 was used to control the oxygen partial pressure. The oxygen partial pressure was kept at 10-4 Pa. The Cr2O3 and MgO contents in the slag were fixed to be 6 and 8wt% respectively. The basicity (CaO/ SiO2) of the slag was varied in the range 1.0-2.0. Gas/slag equilibrium technique was adopted to synthesize the slag at a suitable temperature above the liquidus point. One heat treatment procedure is that the samples were heated to and soaked at 1873 K for 24h in order to achieve the equilibrium state and subsequently quenched in water. The other is that the samples were heated to and soaked at 1873 K for 24h, then slow cooled to 1673 K and soaked at this temperature for additional 24h in order to achieve the equilibrium state at lower temperature before quenching in water. The chromium distribution and phase compositions in the quenched slag were studied using scanning electron microscopy (SEM), energy dispersive spectroscopy (EDS) and X-ray diffraction techniques (XRD). FACTsage software was used for the phase equilibrium calculations. The experimental results obtained from the present work are compared with the calculation results from FACTsage software as well as with results from samples directly quenched after soaking at 1873K. It is found that the spinel formation at 1873 K in air atmosphere is favored in the slag basicity range of 1.0 to 1.6. The size of spinel crystals increased drastically after slow cooling followed by annealing compared to samples being quenched after soaking at 1873 K. The amount of foreign elements dissolved in the spinel phase, and matrix phases decreased after slow cooling followed by annealing at lower temperature, resulting in purer phases with less defects. It was found that the amount of foreign elements in the spinel phase, and other phases decreased after soaking at very low PO2. The size of the spinel crystals was found to be larger in samples with low basicity. Spinel phase precipitation has improved in the samples with higher basicities compared to the results obtained in air. / QC 20111208

A ninhydrin-positive, phosphorus-negative lipid from Paracoccus denitrificans ATCC 13543 has been isolated and purified by mild alkaline methanolysis followed by silicic acid column chromatography and preparative thin-layer chromatography. The lipid was identified as an ornithine-containing lipid. The major ester-linked fatty acid was cis vaccenic acid. Major amide-linked fatty acids were 3-OH-20:1 and 3-OH-18:0. Ornithine-containing lipid was a major lipid component of P. denitrificans. Phospholipids made up about 57% and ornithine-containing lipid about 14% of the weight of the total lipid of the organism. The ratios of lipid ornithine: lipid phosphorus were 0.23, 0.65 and 0.58 in cytoplasmic membrane, outer membrane, and an NaCl extract, which is thought to represent chiefly outer membrane, respectively. Thus ornithine-containing lipid appears to be present in larger amounts in outer membrane than cytoplasmic membrane. No substantial variations in lipid ornithine levels were noted in stationary phase versus exposnential phase organisms, organisms grown in complex medium versus organisms grown in minimal medium with and without amino acid supplements, or in organisms grown in low phosphate-containing medium.

京都大学 / 新制・課程博士 / 博士(工学) / 甲第23432号 / 工博第4887号 / 新制||工||1764(附属図書館) / 京都大学大学院工学研究科合成・生物化学専攻 / (主査)教授 杉野目 道紀, 教授 村上 正浩, 教授 大江 浩一 / 学位規則第4条第1項該当 / Doctor of Philosophy (Engineering) / Kyoto University / DFAM

Indiana University-Purdue University Indianapolis (IUPUI) / Cyclobutane pyrimidine dimers (CPD) are the predominant DNA lesions formed upon exposure of this biopolymer to sunlight. Given the potentially dire biological consequences of DNA lesions, there is a need to fully characterize their behavior, with an eye towards understanding their complete reactivity and as a possible means to detect and quantify their presence in the genome. The work described in this dissertation describes studies of the alkaline reactivity of CPD lesions generated within dinucleotide & polynucleotide strands. It was found that CPD-TpT is generally inert under alkaline conditions at room temperature, which is in agreement with earlier studies on alkaline hydrolysis of CPD-thymine and CPD-thymidine. However, a re-evaluation of the same reaction in the presence of 18O labelled water demonstrated that, similar to other UV-induced DNA lesions containing a saturated pyrimidine ring, CPD undergoes a water addition at the C4=O group of the nucleobase leading to the formation of a hemiaminal intermediate. This intermediate, however, does not lead to hydrolysis products and completely reverts to starting material under those same conditions. Moreover, the two C4=O groups present on 3′ and 5′-thymines in a CPD molecule show different chemical reactivities, with the 3′ C4=O group having greater affinity towards water addition as compared to the one on 5′ end, a fact reflected in different rates of exchange with the incoming nucleophile leading to the hemiaminal intermediate. The 18O labelling reaction was also investigated in CPD lesions generated within oligonucleotides to probe the cause of asymmetry between the 3′ vs 5′ C4=O groups; ultimately, it was determined that the asymmetric reactivity observed to occur between the two C4=O groups was an intrinsic property of the CPD molecule and did not arise as a result of asymmetry in a dinucleotide setting. In addition to the above studies, during the course of the investigation of the nucleophilic reactivity of CPD, a chemical reaction was observed leading to what appeared to be the rapid and total chemical reversal of CPD lesions to the original TpT (thymine-thymine dinucleotide)! This “repair” reaction occurred when CPD reacted with hydrazine, and appears facilitated by an inert atmosphere under which it rapidly proceeds to completion at room temperature.