Les cellules eukaryotes sont compartimentées par des structures intracellulaires nommées organites. On peut citer le réticulum endoplasmique, l'appareil de Golgi, le réseau endosomal et lyzosomal. Ces structures délimitées par des membranes cellulaires sont hautement dynamiques, structures dont les composants s'échangent sans cesse entre les différents compartiments. Malgré cette dynamique, les structures qui composent les réseaux d'organites sont très stables et robustes, de sorte que l'on peut décrire un état stationnaire pour ces systèmes hors équilibre et auto-organisés. Bien qu'ils soient robustes en conditions physiologiques, ces compartiments peuvent subir des modification de structures en condition pathologiques ou sous l'effet de traitements pharmacologiques. L'auto-organisation de systèmes à l'équilibre et relativement bien compris par le biais de diagrammes de phases, où l'on peut représenter lesdites phases en fonctions de paramètres physiques, tels que la concentration, ou les interaction entre les différents composants. La situation est bien moins prédictible pour des systèmes hors équilibre. C'est là donc une question scientifique intéressante que de comprendre les mécanismes contraignant l'organisation intracellulaire, où transports actifs et modification biochimiques des composant, tout deux consommant de l'énergie, sont en compétition avec des phénomènes passifs telle que la diffusion. Nous étudions, aussi bien numériquement qu'analytiquement, des modèles d'auto-organisation et de transport, dans des systèmes où un nombre réduit de composants s'organisent par le biais de réaction stochastiques, en des structures de grandes tailles. La question principale que nous posons est de comprendre comment les dynamiques d'échanges entre compartiments (par le biais de vésiculations et de fusion) jouent de concert avec les cinétiques de maturation des composants d'organites, permettent la mise en place d'un réseau robuste. A cette fin, nous nous focalisons sur un organite type, multi-compartiments, doté d'une dynamique riche de transport et de maturation de ses composants : l'appareil de Golgi. Nous décrivons et analysons l'état stationnaire de ces systèmes, en des termes de tailles et de pureté des compartiments le composant - sont ils gros ou petit, triés dans leur composition ou mixés. De cet état stationnaire émerge spontanément un transport de vésicules entre les compartiments, dont la directionnalité est intimement liée à l'état stationnaire. Ce transport est antérograde dans les régimes triés, rétrograde dans les régimes mixés. Des interactions locales, entre les compartiments et ce qu'ils renferment (protéines dont le nom générique est cargo), suffisent à biaiser ces dynamiques de transport. Cela impacte à la fois le temps de résidence des cargos, mais aussi leur localisation dans le système. La capacité de cet organite à trier ces cargos dépend cependant grandement de l'état stationnaire précédemment décrit. / Eukaryotic cells are highly compartmentalized into intracellular organelles, such as the endoplasmic reticulum, the Golgi apparatus, endosomes and lysosomes. These are dynamical structures bounded by lipid membranes, within which components undergo biochemical modification by enzymes, and between which components are constantly being exchanged. Despite their highly dynamical nature, their spatial organization is fairly well conserved over time, so that they could be seen as stationary states of a highly non-equilibrium, and multi-component system. On the other hand, this organization has been observed to be totally disorganized in pathologies or drug treatments. Self-organization in equilibrium systems is fairly well understood by means of phase diagrams where the occurrence of different phases (dispersed, condensed, phase separated) depends on physical parameters (concentrations, interaction energy between components). The situation is much less clear for non-equilibrium systems. It is therefore an exciting challenge to reach a quantitative understanding of the mechanisms dictating the intra-cellular organization, where active transport and biochemical modification by energy-consuming enzymes compete with purely passive phenomena such as diffusion. We design and study, both analytically and numerically, simple models of self-organization and transport in systems where a limited number of components may self-organize into larger structures by means of stochastic reactions. Our main fundamental question is to determine how the interplay between the dynamics of inter-organelle exchange (by means of vesicle secretion, transport and fusion) and the kinetics of biochemical maturation within organelles may yield a precise and robust organelle network. To this end we focus on one "stereotype" organelle, that is already multi-compartments and with a very rich dynamics of vesiculation, fusion and maturation: the Golgi Apparatus. We describe and understand the steady-state organization of such systems, in term of compartments' size and purity - how big and well sorted are the different compartments. From this steady-state, a vesicular transport spontaneously emerges, whose directionality is linked to the steady-state organization. It is anterograde in a pure regime, and retrograde in a mixed configuration. Local interaction between components being transported, and membranes are sufficient to bias those transport. This both change the kinetics of transport in the system, and thus their location in the compartments. How efficient the system is in sorting these elements, strongly relies on the steady-state organization and the vesicular transport.

When integrating sustainability, companies are often overlooking the changes needed in their organisational culture. This hinders organisations’ core business to efficiently embed sustainability and dooms corporate sustainability initiatives to be superficial. A possible solution is for organisations to develop a sustainability- oriented organisational culture that engages employees with the sustainability change and that develops a leadership supportive of the engagement of their employees. As a result, this thesis aims at exploring how organisations can change their organisational culture in order to fully integrate sustainability by engaging employees and managers. Specifically, it studies how employee engagement can contribute to transforming organizational cultures to fully embed sustainability. Additionally, this paper analyses how managers can support employee engagement with sustainability. The thesis conducts a literature review to set the theoretical foundations; it further resorts to semi-structured interviews and document analysis conducted in a Swedish public company, which has begun to integrate sustainability into its culture. The study finds that organisations’ cultures are being changed at the artifact levels and, partially, at the values and beliefs level of their cultures. Additionally, the thesis establishes that organisations are failing to create the conditions for employee engagement. It finally shows that leadership in companies is not efficiently supporting the engagement of employees to integrate sustainability into their culture.

Climate change and exotic plant invasions are significant anthropogenic threats to desert community structure and resilience . In the Mojave Desert, the invasive grass red brome (Bromusrubens L) is increasing fire frequency and extent in response to climatic factors. The resilience of this ecosystem will be affected by how plant and animal communities respond to fire. To better understand these dynamics, we studied the environmental factors underlying changes in invasive grass fire regimes in the Mojave Desert and its structural and functional effects on plant and animal communities. Following fire, reestablishment of native vegetation can be preempted by repeated burning associated with the abundant exotic grass red brome. Red brome density is correlated with various climate and landscape variables, but to establish causality, we experimentally assessed germination and growth of red brome. Red brome responded positively to fall precipitation, finer-textured soils, fertile-islands soils, and soils from burned landscapes. Red brome germination is maximized in wet fall periods when adequate water and optimal temperatures overlap . To evaluate landscape responses of pre- and post-fire plant communities and the potential for repeated burning we analyzed vegetation greenness (NDVI) data from 1985-2011 in response to temperature and precipitation. Landscape analysis indicated that the dominance of exotic grasses increases on post-fire landscapes. Following wet fall and winter seasons, high red brome productivity increases fire potential. Without mitigation, the establishment of an invasive-plant-driven fire regime is likely and may drive state transitions from arid shrublands to arid annual grasslands. Potential revegetation of post-fire landscapes will depend at least in part upon the physiological response of surviving vegetation to post-fire landscapes. Plant physiological responses to post-fire landscapes were generally neutral or positive, suggesting that revegetation of post-fire landscapes is not precluded by resource loss associated with fire and may even be enhanced by post-fire conditions. This will likely translate to increased reproductive potential of surviving plants. Alterations to small mammal populations will likely play a role in the reestablishment of vegetation (both native and exotics) as small mammals have strong top-down effects in arid ecosystems. Diversity and species richness responded negatively to burned landscapes as Merriam's kangaroo rat (Dipodomys merriami) increased in abundance while other species practically disappeared from burned landscapes. Merriam's kangaroo rat affects propagule sources through direct consumption, and seed dispersal. Increases in abundance and dominance of Merriam's kangaroo rat will likely alter plant recruitment.

This study aims to investigate how the choice of media form, i.e. printed format, audiobook or reading and audio combined, affect the ability of ESL students to achieve comprehension, and how different ways of asking questions can affect their comprehension ability. Lastly, the study aims to investigate the relationship between comprehension and students’ proficiency levels in their L2. To answer this question, 155 students were recruited and divided into three groups and assigned one type of media form. The quantitative data was collected through an online comprehension test and analysed. The results showed a significant difference between the media forms and revealed that printed reading was superior. However, a printed and audio combination was the most time efficient way for students to achieve comprehension, which indicates that the inclusion of audio does not impede student learning. Previous research in the same field shows that the results are inconclusive, but shares one common conclusion, that students enjoy the audio format. As a result, the educational system should make every effort to media choices for students to choose their preferred media, and more research in the field needs to be done, as students enjoyment leads to increased learning.

No description available.

Tree series transformations computed by bottom-up and top-down tree series transducers are called bottom-up and top-down tree series transformations, respectively. (Functional) compositions of such transformations are investigated. It turns out that the class of bottomup tree series transformations over a commutative and complete semiring is closed under left-composition with linear bottom-up tree series transformations and right-composition with boolean deterministic bottom-up tree series transformations. Moreover, it is shown that the class of top-down tree series transformations over a commutative and complete semiring is closed under right-composition with linear, nondeleting top-down tree series transformations. Finally, the composition of a boolean, deterministic, total top-down tree series transformation with a linear top-down tree series transformation is shown to be a top-down tree series transformation.

Despite tremendous advances in mass spectrometry instrumentation and mass spectrometry-based methodologies, global protein profiling of organellar, cellular, tissue and body fluid proteomes in different organisms remains a challenging task due to the complexity of the samples and the wide dynamic range of protein concentrations. In addition, large amounts of produced data make result exploitation difficult. To overcome these issues, further advances in sample preparation, mass spectrometry instrumentation as well as data processing and data analysis are required. The presented study focuses as first on the improvement of the proteolytic digestion of proteins in in-gel based proteomic approach (Gel-LCMS). To this end commonly used bovine trypsin (BT) was modified with oligosaccharides in order to overcome its main disadvantages, such as weak thermostability and fast autolysis at basic pH. Glycosylated trypsin derivates maintained their cleavage specifity and showed better thermostability, autolysis resistance and less autolytic background than unmodified BT. In line with the “accelerated digestion protocol” (ADP) previously established in our laboratory modified enzymes were tested in in-gel digestion of proteins. Kinetics of in-gel digestion was studied by MALDI TOF mass spectrometry using 18O-labeled peptides as internal standards as well as by label-free quantification approach, which utilizes intensities of peptide ions detected by nanoLC-MS/MS. In the performed kinetic study the effect of temperature, enzyme concentration and digestion time on the yield of digestion products was characterized. The obtained results showed that in-gel digestion of proteins by glycosylated trypsin conjugates was less efficient compared to the conventional digestion (CD) and achieved maximal 50 to 70% of CD yield, suggesting that the attached sugar molecules limit free diffusion of the modified trypsins into the polyacrylamide gel pores. Nevertheless, these thermostable and autolysis resistant enzymes can be regarded as promising candidates for gel-free shotgun approach. To address the reliability issue of proteomic data I further focused on protein identifications with borderline statistical confidence produced by database searching. These hits are typically produced by matching a few marginal quality MS/MS spectra to database peptide sequences and represent a significant bottleneck in proteomics. A method was developed for rapid validation of borderline hits, which takes advantage of the independent interpretation of the acquired tandem mass spectra by de novo sequencing software PepNovo followed by mass-spectrometry driven BLAST (MS BLAST) sequence similarity searching that utilize all partially accurate, degenerate and redundant proposed peptide sequences. It was demonstrated that a combination of MASCOT software, de novo sequencing software PepNovo and MS BLAST, bundled by a simple scripted interface, enabled rapid and efficient validation of a large number of borderline hits, produced by matching of one or two MS/MS spectra with marginal statistical significance.

No description available.

<p>Nanotechnology has experienced a tremendous rise in the last decade. The synthesis of nanomaterials of defined structure and controlled properties is one of the most challenging part. Solution processing bottom-up fabrication techniques enables the facile synthesis of low dimension and ordered structures with low cost through the self-assembly of basic building blocks. Biotemplating has become an emerging field in which natural biomolecular objects are utilized for creating functional, hierarchical, controlled patterned structures with nanometric precision. It is a capital effective, eco-friendly and energy-efficient synthetic process. Viral biotemplating has shown great potential in electronics, environmental and biomedical devices. In recent years, in-planta produced Tobacco Mosaic Virus (TMV) and its variants have been used to produce metal nanorods and nanowires of monodisperse structures under mild conditions without the use of harsh chemical treatments although there remains much to be understood. Mass production of biotemplate, programming of viral particles of desired functionalities, manipulation for biomineralized metal materials of good quality have not been sufficiently studied to allow for directed synthesis. The fundamental studies on platform development for viral biotemplate production, design of viral proteins carrying engineered properties, and the hydrothermal synthesis of biotemplated metal nanomaterials, which create great uniformity and high coverage are of interest in this dissertation. Three experimental studies are outlined.<br></p><p><br></p><p>A novel virus biotemplate, Barley stripe mosaic virus (BSMV) virus-like particle is designed and engineered through genetic engineering. By fusing the Origin of Assembly from TMV to the transcript encoding BSMV capsid protein, the self-assembly of BSMV-VLP nanorod from microbial-based protein expression system was achieved for the first time. An alternate platform for viral particle production has been developed. Optimization of VLP expression, purification and processing conditions are performed. This developed alternative E. coli production platforms offer unique opportunities for genetic engineering and faster protein expression; therefore, the development of our system enables rapid design-build-test cycles for the engineering and production of BSMV-VLPs with desired properties. Results in this project shows the power of genetic engineering and serves as a springboard for genetic engineering of the VLPs.<br></p><p><br></p><p>Programming on BSMV-VLP is further used to decouple the VLP assembly into governing internal molecular interactions. To drive the nucleic acid free helical BSMV-VLP rod assembly and further increase the stability of capsid proteins, an identification of Caspar Carboxylate cluster in BSMV is performed. Various carboxylate residues were selected through protein crystal structure and examined systematically through experimental work. By introducing mutations on selected residues, the intersubunit carboxylate interaction of the proteins was significantly altered, resulting in an in vivo production of nucleic-acid free BSMV-VLP assembly for the first time. The change in interactions leads to increased stability of the modified VLP, enabling the formation of longer nanorods with lengths over one micrometer. Moreover, both wild-type and mutated BSMV-VLPs were shown to have great structural stability across a wide range of pHs. Overall, we exhibit experimental identification to systematically probe the key carboxylate interactions to increase the stability of proteins and drive RNA-free BSMV-VLP assembly. This project greatly expands the potential usefulness of the engineered BSMV-VLP biotemplates for a wide variety of applications.<br></p><p><br></p><p>Finally, to demonstrate the versatile uses of BSMV-VLP in biotemplating, the new biotemplate was utilized to expand understandings on the directed synthesis of metal nanostructures. By using the hydrothermal synthesis, VLPs were successfully utilized to synthesize monometallic palladium nanorods with a wide range of length scales. The VLP-mediated nanorods are more uniformly and fully-covered than the ones synthesized with in planta-produced BSMV virion. Besides, the synthesis shows an effective control over the metal nanorod diameter. The capability of BSMV-VLP was readily expanded from the synthesis of monometallic nanorods to bimetallic hybrid. In the absence of an exogenous reducing agent, mineralization of platinum, gold and copper was successfully demonstrated on the VLP. It is attributed to lower reduction barrier introduced by already-deposited palladium nanoparticles which serve as nucleation sites for subsequent metal reduction. The formation of bimetallic complexes was further supported by STEM, EDS and XPS analysis evidenced the presences of multiple metals. Overall, BSMV-VLP-mediated biotemplating using the hydrothermal synthesis has been confirmed to be a promising and feasible approach to create organic-inorganic complex nanocomposite.<br></p><p><br></p><p>Lastly, to move toward an application, the synthesized Pd nanorods coated with full coverage and great uniformity of nanoparticles were utilized as an exciting hydrogen sensing material. The developed hydrogen sensing system using a quartz crystal microbalance shows a fast response toward hydrogen as well as the ability of hydrogen detection and quantification of the adsorption capacity. This study serves as an entry point and opens up enormous possibility for next-generation of Pd-virus hybrid hydrogen sensors.<br></p><p><br></p><p>Taken together, this dissertation has demonstrated the engineering and production of a novel BSMV virus-like particle bacterial system. This alternative platform and developed parameter space for VLP production is genetically tractable and requires significantly shorter processing duration for large-scale and mass production. The BSMV-VLP biotemplated metal nanomaterials present great qualities and controllable dimensions. This approach has explored the synthetic palette and opened up enormous possibilities in the bottom-up nanofabrication of versatile and tunable organic-inorganic nanoscaled complex and would facilitate future engineering industrial applications.<br></p>

The aim of this study was to find out how Utbildningsverket’s (UR) pedagogical material, belonging to two miniseries aimed at upper secondary school, use top-down- and bottom-up strategies to teach listening comprehension. For this purpose, a case study method was used where the materials worked as the case to be studied. Furthermore, the approaches that were used for this study were based on taxonomies established by previous research: First, a taxonomy of strategies for listening comprehension illustrated by Graham and Santos (2015). Secondly, a taxonomy relating to listening types, illustrated by Field (2009). With these taxonomies and the English 5 syllabus, the materials were studied as a qualitative case study. The results show that the two criteria in the English 5 syllabus, which relate to strategies, are addressed within the teacher’s guide of both miniseries. Moreover, My English Mistakes and The Great Debate, both implicitly instruct students to use various strategies. The results also show that the top-down strategies are overrepresented in frequency but less varied in listening type variation. However, the strategies that are instructed are not explained or motivated in the materials.