In this work we report a new mechanism for ageing, where passive aggregation and stochastic segregation of protein aggregates can switch cells from a non-ageing to an ageing state. This switch is activated by the increase in the total amount of protein aggregates. We established a damage reporter system by labeling Hsp104, a chaperone which binds protein aggregates, with GFP. By observing that the accumulation of Hsp104 labeled aggregates correlated with the majority of cell death in the population, and that cells which are born with a high level of aggregates are more likely to die, we validated protein aggregation as being an ageing factor in S. pombe. To identify the mechanism of damage segregation, we monitored nucleation, fusion and partition of aggregates at division. We established that aggregates are present in the cytoplasm fraction which is not occupied by vacuoles and lipid vesicles, and that they are not actively transported by the cytoskeleton. Protein aggregates were not distributed in a biased manner at division. Their position in the cytoplasm dictates to which cell they will be partitioned at division, as confirmed by studies using an asymmetrically dividing mutant, pom1Δ, in which the larger cells inherited more aggregates. This shows that aggregate segregation in S.pombe is a stochastic process. Stochastic distribution contributes to a constant dilution of damage and the maintenance of a non-ageing division, where the total levels of damage in the individuals are on average maintained constant. Together with Steven Lade and Thilo Gross, from the MPI-PKS, we designed a model in which passive aggregation and stochastic segregation reproduced our experimental results. Surprisingly, when cells are exposed to heat stress and the total levels of protein aggregates increase, aggregates are unequally segregated, i.e., ageing is turned on. The switch in segregation results from increased fusion due to a higher number of aggregates, which generates large single aggregates, which are retained by one of the cells at division. Our model reproduced the heat stress condition, showing that fusion is an essential parameter to generate clean cells quickly after the levels of damage increase. Fission yeast cells can therefore switch between non-ageing and ageing like division depending on the total amount of damage at birth. To clarify if other cellular components could be ageing factors in S. pombe, we tested if the inheritance of the old cell wall at the cell pole was associated with an increase in division time, similarly to what occurs in E. coli. We also tested if the inheritance of the new centrosome-analog, the SPB, which is segregated to the ageing mother cell in S. cerevisiae, resulted in an increase in division time. We did not find evidence for ageing associated with these structures. Finally we determined that the feature of slow division was not a transmissible trait, i.e., daughters of slow diving cells divided faster than their mothers. Another ageing hallmark, the cumulative increase in division time with the total number of divisions before death, was not present in S.pombe. Our combined results from damage segregation and pedigree analysis show that stochastic segregation of damage is a viable strategy to avoid ageing. Passive aggregation in the presence of a high number of aggregates can switch on ageing, representing an alternative to active segregation mechanisms and to the existence of pre-defined ageing lineages, as shown for other organisms. Finally, our results show that ageing is not ubiquous to life, and that it can be a facultative strategy to cope with stress.

Le traitement antiplaquettaire à l’aspirine (ASA) est moins efficace chez certains patients coronariens, ce qui augmente leur risque de développer une thrombose. Des taux sanguins élevés de médiateurs thrombo-inflammatoires, tels que le sCD40L, peuvent expliquer de telles variabilités. Nous avons émis l’hypothèse que, en présence de taux élevés de sCD40L, l’efficacité de l’ASA peut être réduite. Ainsi, nous avons viser à déterminer les effets de l’ASA sur la signalisation et l’agrégation des plaquettes en présence de sCD40L. Les effets de l'ASA sur les plaquettes humaines traitées par le sCD40L, en réponse à des concentrations sub-optimales de collagène ou de thrombine, ont été évalués sur l'agrégation, la sécrétion de thromboxane A2 (TxA2) et la phosphorylation de la p38- « Mitogen-activated protein kinase » (MAPK), le facteur nucléaire-κB (NF-κB), la kinase activée par le TGF-β 1 (TAK-1) et la chaîne légère de la myosine (MLC). Le sCD40L a significativement augmenté la sécrétion de TxA2 dans les plaquettes, en réponse à des doses sub-optimales de collagène et de thrombine, ce qui a été inversé par l'ASA. L'ASA n'a pas inhibé la phosphorylation de p38-MAPK, NF-KB, TAK-1, que ce soit avec une stimulation par le sCD40L seul ou en présence des agonistes plaquettaires. Cependant, Le sCD40L a potentialisé l'agrégation plaquettaire, un effet complètement inversé et partiellement réduit par l'ASA en réponse au collagène et à la thrombine, respectivement. Les effets de l'ASA sur les plaquettes traitées par le sCD40L et stimulées par le collagène étaient liés à l'inhibition du changement de forme des plaquettes et la phosphorylation de la MLC. L'ASA n'affecte pas la signalisation du sCD40L dans les plaquettes, mais empêche son effet sur la sécrétion de TXA2 et l'agrégation plaquettaire en réponse au collagène, via un mécanisme impliquant l'inhibition de la MLC. Le ciblage de l'axe sCD40L dans les plaquettes peut avoir un potentiel thérapeutique chez les patients, présentant des taux élevés de sCD40L, qui ne répondent pas ou moins à l'ASA. / Antiplatelet therapy with Aspirin (ASA) is less efficient in some coronary patients, which increases their risk of developing thrombosis. Elevated blood levels of thrombo-inflammatory mediators, like sCD40L, may explain such variabilities. We hypothesized that in the presence of elevated levels of sCD40L, the efficacy of ASA may be reduced. Accordingly, this study was designed to determine the effects of ASA on sCD40L signalling and aggregation of platelets. The effects of ASA on sCD40L-treated human platelets, in response to suboptimal concentrations of collagen or thrombin, were assessed on aggregation, thromboxane A2 (TxA2) secretion, and phosphorylation of p38-MAPK, NF-κB, TGF-β-activated kinase 1 (TAK-1), and myosin light chain (MLC). sCD40L significantly elevated TxA2 secretion in platelets, in response to suboptimal doses of collagen and thrombin, which was reversed by ASA. ASA did not inhibit phosphorylation of p38-MAPK, NF-κB, TAK-1, either with sCD40L stimulation alone or with platelet agonists. However, sCD40L potentiated platelet aggregation, an effect completely reversed and partially reduced by ASA in response to collagen and thrombin, respectively. The effects of ASA in sCD40L-treated platelets with collagen were related to inhibition of platelet shape change and MLC phosphorylation. ASA does not affect platelet sCD40L signalling, but prevents its effect on TXA2 secretion and platelet aggregation in response to collagen, via a mechanism implying inhibition of MLC. Targeting sCD40L axis in platelets may have therapeutic potential in patients with elevated levels of sCD40L that are none or less responding to ASA.

9 ABSTRACT For proper function proteins should have a native conformation. If their conformation is impaired due to environmental stress or genetic mutation, proteins become prone to aggregation. There exist various types of protein aggregates. Stable non-membraneous inclusions can form which can serve for clearance of aberrant proteins from place where they can interfere with essential cellular processes. Another type of aggregates can serve as transient deposits of proteins thus protecting them from stress conditions. Stress granules (SG) are a such example of transient granules. Their formation is induced by heat shock for example. SGs contain mRNA, components of translation machinery, and other proteins. One of these proteins is Mmi1, small highly conserved protein with unknown function. Association of Mmi1 with stress granules and partial co-localization with chaperon Cdc48 and proteasom indicates Mmi1 can mediate heat stress damaged protein degradation. We have uncovered that yeast prion protein Sup35 is a component of stress granules as well. With regard to its aggregation capability there existed an assumption that prion domain of Sup35 could serve as scaffold for SG assembly. However as we show deletion of prion domain of Sup35 protein does not affect stress granules formation dynamics. Yeast...

α-Synuclein (AS) is a small intrinsically disordered protein expressed in neurons and abundantly present in synapses where it is involved in regulation of synaptic vesicle-mediated protein trafficking. Misfolding of AS into amyloid fibrils is a key process in progression of Parkinson's disease (PD), the second most common neurodegenerative disorder which has no cure to date. Inhibition of AS aggregation and blocking of cell-to-cell spreading of AS fibrils is a promising strategy for PD treatment. However, rational design of inhibitors of this type remains complicated due to the lack of thorough knowledge about the mechanisms of aggregation. Therefore, the aim of this thesis was to gain deeper knowledge about AS aggregation and to apply it for developing inhibitors of AS fibrillization. In my work on the mechanisms of AS aggregation, I first determined that the concentration of AS that enables the fibril growth is an order of magnitude lower than the concentration of AS required for initial fibril formation from monomers. I explored fibril disaggregation at AS concentrations below its Kd value, and characterized AS aggregation at low micromolar concentrations. I then investigated how different modifications of AS C-terminus (namely, extensions of various sizes and charges) affect fibril growth and...

Generalization of LOD2 building models using the aggregation method Abstract The thesis proposes and implements a method of 3D building models aggregation. The procedure achieves global optima by the means of mathematic optimization. Buildings are aggregated according to similarity characteristics typical for LOD2, e. g. roof type. Aggregation process is driven by minimalization of volume changes and of the aggregate count. The optimization problem was implemented as a Python script with optional parameters to meet custom demands of a wide range of users. Input data models of buildings are created by the method of procedural modelling. Its outcome is further restructured into form of continuous blocks. Finally, the visualization procedure is designed and implemented to illustrate the results of optimized aggregation of 3D building models. Keywords: 3D GIS, generalization, aggregation, mathematical optimization, procedural modelling

3D city models have been widely used in different applications such as urban planning, traffic control, disaster management etc. Effective visualisation of 3D city models in various scales is one of the pivotal techniques to implement these applications. In this thesis, a framework is proposed to visualise the 3D city models both online and offline using City Geography Makeup Language (CityGML) and Extensible 3D (X3D) to represent and present the models. Then, generalisation methods are studied and tailored to create 3D city scenes in multi-scale dynamically. Finally, the quality of generalised 3D city models is evaluated by measuring the visual similarity from the original models.   In the proposed visualisation framework, 3D city models are stored in CityGML format which supports both geometric and semantic information. These CityGML files are parsed to create 3D scenes and be visualised with existing 3D standard. Because the input and output in the framework are all standardised, it is possible to integrate city models from different sources and visualise them through the different viewers.   Considering the complexity of the city objects, generalisation methods are studied to simplify the city models and increase the visualisation efficiency. In this thesis, the aggregation and typification methods are improved to simplify the 3D city models.   Multiple representation data structures are required to store the generalisation information for dynamic visualisation. One of these is the CityTree, a novel structure to represent building group, which is tested for building aggregation. Meanwhile, Minimum Spanning Tree (MST) is employed to detect the linear building group structures in the city models and they are typified with different strategies. According to the experiments results, by using the CityTree, the generalised 3D city model creation time is reduced by more than 50%.   Different generalisation strategies lead to different outcomes. It is important to evaluate the quality of the generalised models. In this thesis a new evaluation method is proposed: visual features of the 3D city models are represented by Attributed Relation Graph (ARG) and their similarity distances are calculated with Nested Earth Mover’s Distance (NEMD) algorithm. The calculation results and user survey show that the ARG and NEMD methods can reflect the visual similarity between generalised city models and the original ones. / QC 20100923 / ViSuCity Project

<p>In insect pest management, the plant volatiles and pheromones associated with host-plant location can be used to manipulate insect pest behavior by attracting or “pulling” insects from a valuable resource. Conversely, deterrents can be used to prevent behaviors or “push” insects away from a resource. If combined, attractants and deterrents can have powerful synergistic effects that promote greater response than the individual components. This dissertation explores the use of attractants and deterrents of the specialist herbivore and challenging agricultural pest, the striped cucumber beetle, <em>Acalymma vittatum</em>, to ultimately develop a push-pull management system. </p> <p><br></p> <p>In first chapter, we examine the combination of two striped cucumber beetle attractants in attract-and-kill mass trapping: live striped cucumber beetles as a proxy for aggregation pheromone, and cucurbit floral volatiles. In the second chapter, we examine natural products—essential oils, pawpaw extract, squash bugs, and kaolin clay—as a means for repelling or deterring beetles from cucurbit crops. Lastly, we combine the findings of previous chapters as way of using both attractive and deterrents to further modify striped cucumber beetle behavior and to observe potential synergies in removing these pests from cucurbit crops. In this, we use the aggregation pheromone and floral lures in attract-and-kill trapping with the deterrent kaolin. </p> <p><br></p> <p>We found that while aggregation pheromones and floral lures were useful in trapping striped cucumber beetles, floral lures may potentially distract pollinators. Striped cucumber beetle response to floral lures varied across the season and were most attractive in the late growing season, when plants were in bloom. The tested natural products did not successfully prevent beetles from colonizing plants, but instead deterred the specialist herbivore from feeding. While the attractant and deterrent did not have a synergistic effect, they remained complementary in that aggregation pheromones were useful in reducing pest populations, while kaolin clay deterred feeding. Thus, pest management systems should be flexible in timing and type of management used, and should look toward other metrics, such as feeding damage, rather than population density thresholds to measure management success. </p>

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Highly corrosion-resistant alloys are used in sensitive environments such as the human body and food environments. However, even tiny amounts of released metals from these surfaces could potentially cause adverse effects. It is hence important to study the biointerface between corrosion-resistant alloys and protein-rich environments. This licentiate thesis focused on the metal release processes for stainless steels and cobalt-chromium-molybdenum (CoCrMo) alloys in different protein-rich environments. It aimed at investigating the effect of protein displacement (Vroman effect), gamma irradiation, and friction on the metal release processes. Trace metal analysis was the main tool, combined with other solution analytical tools, electrochemical methods, and surface sensitive techniques. The effect of gamma irradiation, of relevance for cancer radiotherapy, on metal release from CoCrMo and stainless steel 316L was investigated in Paper I. The effect was minor, however the released amount of metals increased after irradiation causing an enhanced surface passivation effect. Whether the displacement of surface proteins (Vroman effect) was playing a role on the metal release and corrosion processes of stainless steels 316L and 303, and of CoCrMo, was investigated in Papers II and III. A Vroman effect influencing the metal release could be observed for stainless steel 316L, but not for CoCrMo and stainless steel grade 303. However, the displacement of the smaller protein bovine serum albumin (BSA) from the surface by the larger protein fibrinogen (Fbn) was observed for both stainless steel grades. The Vroman effect also caused a higher corrosion susceptibility of stainless steel 303, probably due to a thicker layer or patches of adsorbed Fbn. Most probably, protein aggregation and precipitation caused an underestimation of the extent of metal release, especially in the case of CoCrMo. Protein aggregation and precipitation were significantly observed in all studies, especially for solutions with high protein concentrations (Papers II-IV). The effect of friction, by using different setups (stirring with physical contact and sliding in a pin-on-disk machine), on metal release from stainless steel 316L and CoCrMo was investigated in Papers II and IV. Friction induced an increased extent of metal release, increased protein aggregation and precipitation, and enhanced metal precipitation. A combined friction and complexation effect was observed for stainless steel 316L, resulting in an etching effect and relatively high amounts of released metals. Due to enhanced precipitation effects and the experimental setup, it is recommended to strongly consider protein aggregation and metal precipitation events in systems where this could be expected and where friction is present. Otherwise, there is a risk to strongly underestimate the extent of metal release in these protein-rich environments. / <p>QC 2020-09-28</p>

The Paşalar fauna includes 56 mammalian species of European. Asian, African and North American origin. Evidence provided on the stage-of-evolution of the primates Sivapithecus darwini and cf. Kenyapithecus, the rodent Turkomys pasalarensis, insectivores, carnivores, rhinos, suids and ruminants suggests that Paşalar is correlative with the Late Langhian marine stage and European Mammal Neogene Zone 6., circa 15 Ma (million years ago). A review of the Paşalar fauna's biogeographic history suggests that it was aggregated by a succession of pulsed intercontinental geographic extensions tied to global sea-level lowering events during the earlier half of the Miocene.