Sclerotinia sclerotiorum, a fungal pathogen of over 400 plant species has been estimated to cost UK based farmers approximately £20 million per year during severe outbreak (Oerke and Dehne 2004). S. sclerotiorum disease incidence is difficult to predict as outbreaks are often sporadic. Ascospores released from the fruiting bodies or apothecia can be dispersed for tens of kilometres. This makes disease control problematic and with no S. sclerotiorum resistant varieties available, growers are forced to spray fungicides up to three times per flowering season in anticipation of the arrival of this devastating disease. This thesis reports the development of the first infield S. sclerotiorum biosensor which aims to enable rapid detection of airborne ascospores, promoting a more accurate disease risk assessment and fungicide spraying regime. The sensor is designed to detect the presence of oxalic acid, the main pathogenicity factor secreted during early S. sclerotiorum ascospore germination. Upon electrochemical detection of this analyte in the biosensor, a binary output is relayed to farmer to warm him of a disease risk. This project focused on the development of a nutrient matrix which was designed to be contained within the biosensor. The role of this matrix was to promote the growth of captured airborne S. sclerotiorum ascospores and induce high levels of oxalic acid secretion. The use of the designed biological matrix to promote oxalic acid production was tested during three field trials in S. sclerotiorum artificially inoculated fields. This thesis describes the use of contemporary pathogenomics technologies to further investigate candidate genes involved in pathogenicity alongside the secretion of oxalic acid. A pre-described bioinformatics pipeline was used to predict the S. sclerotiorum secretome to identify potential effector proteins as well as explore proteins which are unique to S. sclerotiorum to be used as other novel targets for detection. GFP tagged constructs were designed to investigate the expression of the putative targets for S. sclerotiorum detection. The transcriptomes of wild type and oxalic acid deficient S. sclerotiorum strains during infection as well as during a saprotrophic stage were investigated. This study provided expression support for not only some of the unannotated genes identified in the putative secretome, but some candidate genes speculated to be involved in infection.

Background: Oesophagogastric cancers generally present late in life with advanced disease and carry a poor prognosis. Few patients receive curative treatment. Polo-like Kinase 1 (PLK1) is a mitotic kinase with regulatory functions at the G2/M cell cycle phase transition. In mammalian cells, PLK1 phosphorylates and activates FOXM1, a forkhead transcription factor at the G2/M cell cycle phase transition. FOXM1 then promotes transcription of multiple gene products, including PLK1 and CCNB1, which then act individually or in complexes to further phosphorylate FOXM1 generating a positive feedback loop driving the cell into M phase. Aims: We aimed to assess the expression of PLK1 and FOXM1 in oesophageal and gastric cancer patients. Secondly we aimed to investigate the expression and inter- relationship of PLK1 and FOXM1 in oesophageal cell lines during the cell cycle. Results: FOXM1 and PLK1 are expressed in oesophageal cell lines and demonstrate cross-regulatory interactions. Inhibition of PLK1 leads to the decreased expression of FOXM1 and it’s target gene in oesophageal cell lines. FOXM1 and PLK1 are also concomitantly overexpressed in a large proportion of oesophageal and gastric carcinoma’s at both the protein and mRNA level. Other FOXM1 target genes including, CCBN1, AURKB and CKS1 are co-expressed in a similar manner. In a homogenous cohort of patients who underwent surgery, the expression of PLK1 and AURKB was prognostic for overall survival. Conclusions: This study has demonstrated that FOXM1 and a number of target genes including PLK1 are coordinately expressed in a proportion of oesophageal and gastric carcinomas. This suggests that chemotherapeutic treatments that target this pathway may be of clinical utility.

A degradação da qualidade de água no Brasil é um problema sério que afeta grande parte dos rios e lagos. O objetivo desse trabalho é discutir quais mecanismos podem ser usados para a melhora da qualidade das águas tendo em vista a garantia dos seus usos. A legislação brasileira prevê que o sistema de gestão de recursos hídricos deve definir os usos pretendidos para as águas das bacias hidrográficas. Nos casos em que a qualidade das águas precisa ser melhorada para garantir os usos pretendidos, o sistema de gestão de recursos hídricos deve estabelecer etapas progressivas, em que, para cada etapa, são definidas metas de qualidade de água específicas. Utilizando como exemplo o sistema de gestão de qualidade de água de diferentes países, essa dissertação analisa o sistema brasileiro, a definição de metas e a sua relação com o sistema de gestão de recursos hídricos, conforme as definições previstas na Resolução CONAMA 357/05, e identifica os desafios e estratégias para superá-los. Também demonstra que, para que haja mudanças efetivas no cenário de qualidade das águas, será necessário para o país um planejamento estratégico, com prioridades definidas de acordo com as especificidades locais, os investimentos necessários e os aspectos econômicos, enfatizando-se o planejamento e o controle dos serviços de saneamento. / Water quality degradation is a serious problem that affects large extensions of rivers and lakes. The purpose of this thesis is to discuss which mechanism can be used to improve water quality in order to guarantee designated uses. The Brazilian water law establishes that the water resource management system must define the designated uses for the watershed. In cases where water quality must be improved to guarantee such uses, the water resource management system establishes a step-by-step system in which, for each step, specific water quality targets are defined. Using as an example the water quality management system of different countries, this thesis analyses the Brazilian system, the target definitions and its relations with the water resource management system, as defined by CONAMA Resolution 357/05, and identifies the challenges and the strategic seams to surpass them. It also demonstrates that, in order to get an effective change in the water quality scenario, it will be necessary for the country to work on strategic planning, with priorities based not only on specific local characteristics, but also on financial needs and economical aspects, with special emphasis on regulation and control of wastewater systems.

The diploma thesis deals with selected risks of soft targets, which may have a negative impact on the safety and security of these objects. In the current, we can find an explanation of the concept of soft targets, the terrorism that affects them and possible ways of protecting those targets. In our own solution we find an evaluation of the vulnerability of soft targets, possible countermeasures and risks arising from these measures.

<p>c-Myc is one of the most important oncogenes. G-quadruplex DNA secondary structure formed in the proximal promoter region of c-Myc functions as a transcription silencer and is targetable by small molecules. Therefore, the c-Myc promoter G-quadruplex (MycG4) is an attractive anticancer drug target. Protein recognition of MycG4 is essential for its transcriptional regulating. Nucleolin was discovered as a major MycG4 binding protein in 2009. It shows a remarkably higher binding affinity for MycG4 over its known substrate NRE_RNA and overexpression of nucleolin represses the activity of the c-Myc promoter. However, little is known about its molecular recognition of MycG4. Here, we use X-ray crystallography combined with other biochemical and biophysical methods to understand how nucleolin recognizes MycG4. Nucleolin is a 77 kD protein with a modular organization. The four RNA-binding domains (RBD) of nucleolin are the minimal domains for high affinity binding with MycG4. We show that nucleolin prefers the c-Myc parallel G-quadruplex with a 6-nt central loop (Myc161) that is the thermodynamically favored conformation. Using a custom G4 DNA microarray, we optimized the MycG4 sequence with over 10-fold increased binding affinity to nucleolin. Fabs are widely used tools to facilitate crystallization and we have discovered Fabs that specifically bind the nucleolin-MycG4 complex using a phage display screening. This approach enabled us to obtain crystals of the nucleolin-MycG4-Fab ternary complex diffracted at 2.6 Å and we determined the crystal structure. In the structure, the parallel MycG4 is very well-defined with two K⁺ between the three G-treads. The central 6-nt loop residue protrude from the G4-core and extensively recognized by the nucleolin. Only RBD1 and RBD2 of nucleolin are seen in the crystal structures and interact extensively with the 6-nt central loop and 5′-flanking of MycG4. The binding surface and area of the globular MycG4 by nucleolin is much more extensive than NRE_RNA and involves an extra binding site. Fab binds to both RBD1 and 3′-end of MycG4 to stabilize the complex. The well-defined partial RBD2-3 linker and a cavity close to the 1-nt T19 loop suggest that the missing RBD3 likely binds the 3^rd loop of MycG4. This structure is the first MycG4-protein complex structure. It will help understand MycG4 and nucleolin interactions and the development of MycG4 targeted cancer therapeutics. This structure also provides novel insights into how proteins recognize the globular G-quadruplexes, highlighting the potential of G-quadruplexes as a platform for multivalent interactions such as with multiple tandem RBDs.</p>

京都大学 / 新制・論文博士 / 博士(医学) / 乙第13534号 / 論医博第2274号 / 新制||医||1065(附属図書館) / 京都大学大学院医学研究科医学専攻 / (主査)教授 滝田 順子, 教授 伊藤 貴浩, 教授 江藤 浩之 / 学位規則第4条第2項該当 / Doctor of Medical Science / Kyoto University / DFAM

Tracking multiple targets with uncertain target dynamics is a difficult problem, especially with nonlinear state and/or measurement equations. Random finite set theory provides a rigorous foundation to multitarget tracking problems. It provides a framework to represent the full multitarget posterior in contrast to other conventional approaches. However, the computational complexity of performing multitarget recursion grows exponentially with the number of targets. The Probability Hypothesis Density (PHD) filter, which only propagates the first moment of the multitarget posterior, requires much less computational complexity. This thesis addresses some of the essential issues related to practical multitarget tracking problems such as tracking target maneuvers, stealthy targets, multitarget tracking in a distributed framework. With maneuvering targets, detecting and tracking the changes in the target motion model also becomes important and an effective solution for this problem using multiple-model based PHD filter is proposed. The proposed filter has the advantage over the other methods in that it can track a timevarying number of targets in nonlinear/ non-Gaussian systems. Recent developments in stealthy military aircraft and cruise missiles have emphasized the need to t rack low SNR targets. The conventional approach of thresholding the measurements throws away potential information and thus results in poor performance in tracking dim targets. The problem becomes even more complicated when multiple dim targets are present in the surveillance region. A PHD filter based recursive track-before-detect approach is proposed in this thesis to track multiple dim targets in a computationally efficient way. This thesis also investigates multiple target tracking using a network of sensors. Generally, sensor networks have limited energy, communication capability and computational power. The crucial consideration is what information needs to be transmitted over the network in order to perform online estimation of the current state of the monitored system, whilst attempting to minimize communication overhead. Finally, a novel continuous approximation approach for nonlinear/ non-Gaussian Bayesian tracking system based on spline interpolation is presented. The resulting filter has the advantages over the widely-known discrete particle based approximation approach in that it does not suffer from degeneracy problems and retains accurate density over the state space. The filter is general enough to be applicable to nonlinear/non-Gaussian system and the density could even be multi-modal. / Thesis / Candidate in Philosophy

<p> Oxetan-2-ones (β-lactones) represent important synthetic targets because they are versatile synthetic intermediates and are present in a wide variety of pharmacologically relevant natural products. Using several reported methods, a homologous series of racemic C4-monosubstituted and trans-1 ,2-disubstituted β-lactones was prepared for investigation as potential inhibitors of yeast 3-hydroxy- 3-methylglutaryl-Coenzyme A (HMG-CoA) synthase. However, no general method were then available for the preparation of the corresponding cis-1 ,2- disubstituted β-lactones. </p> <p> Using the mercury (II) promoted Masamune lactonization of β-hydroxy thiopyridyl ester 3-7, cis-3-methyl-4-decyloxetan-2-one (3-1) was prepared in high yield. The requisite syn thiol ester was prepared starting from undecanal: (1) in one step using a titanium {IV) promoted Mukaiyama aldol condensation with silyl ketene acetal 1-28; and (2) in three steps using a titanium (IV) promoted Evans-type aldol condensation with N-propionyl thiazolidinethione 4-24, followed by conversion of the thiazolidinethione aldol adduct to thiol ester 3-7 through the corresponding free acid. Substituting N-propionyl thiazolidinethione 4-24 for chiral N-acetyl and N-propionyl thiazolidinethiones 4-26 and 5-16, respectively, the Evans-type aldol condensations with undecanal proceeded with excellent diastereoselectivity (> 90 %de); this is necessary for the preparation of optically active cis-1 ,2-disubstituted and C4-monosubstituted β-lactones. </p> <p> A tandem-Evans aldol-lactonization (TEAL) reaction was developed using the lithium enolates of N-acetyl (5-16) and N-propionyl thiazolidinethione 4-24. Thus far, trisubstituted spiro β-lactones 6-17 and 6-19, and C4-disubstituted spiro β-lactone 6-22, have been successfully prepared in one-pot. </p> <p> In addition to using aldol condensations to prepare the carbon skeleton for C4-monosubstituted β-lactones, a Claisen-type condensation on a glycoluril template was attempted; the advantage of this route was the potential use of well developed asymmetric reductions of the product β-keto carboxylic acid derivative to introduce optical activity in an enantioselective preparation of C4- monosubstituted β-lactones. Unfortunately, using glycoluril 7-11, racemic 4- nonyloxetan-2-one (2-7v) was produced in poor yield because of difficulties encountered removing the aldol adduct-like β-hydroxy carboxylic acid derivative from the template. </p> / Thesis / Doctor of Philosophy (PhD)

Chlorpyrifos (CPF) is one of the most widely used organophosphorus insecticides (OPs). The developmental exposure to low levels of CPF results in the inhibition of the endocannabinoid metabolizing enzyme fatty acid amide hydrolase (FAAH) and in altered emotional behavior (increased social play) without affecting the acetylcholinesterase, the canonical target of OPs. However, the molecular mechanisms responsible for this increased social play are not known. In this study, male rat pups were exposed orally to either corn oil, 0.75 mg/kg CPF, or 0.02 mg/kg PF-04457845 (PF; a specific inhibitor of FAAH) daily from postnatal day 10 (PND10) - PND16. This dosage of CPF does not alter brain cholinergic activity but inhibits FAAH. Once these rats reached adolescence (PND38), they were divided into two cohorts and each cohort contained all treatments. One cohort underwent social behavior testing and the other cohort remained naïve to behavioral testing. Following testing, the amygdala was collected from each cohort and protein expression was determined using a labelree shotgun proteomic approach. The obtained differentially expressed proteins from the different cohorts were analyzed by DAVID and Ingenuity Pathway Analysis software. Comparison of control non-behavior and control behavior rats suggests that social play altered the systems involved in the regulation of reward such as the opioid, dopaminergic, and serotonergic systems. These data also suggest that synaptic levels of GABA and glutamate increased during play. Comparison of non-behavior control and treated rats suggests that FAAH inhibition resulting from developmental exposure to CPF and PF persistently affects glutamatergic and GABAergic signaling. These data also suggest that there is a similar pattern of protein expression between CPF and PF. Comparison of the data from the behavioral groups of rats suggests that alterations in glutamatergic and GABAergic signaling and improper activation of opioid signaling could be responsible for the increased social play behavior. These alterations in the neurotransmitter signaling were observed in both CPF and PF treated rats. Overall, the results suggest that FAAH inhibition by either CPF or PF leads to alterations in opioid, glutamatergic, and GABAergic signaling that could be responsible for increased levels of social play.

No description available.