6,707 research outputs found

    Pollution-induced community tolerance in freshwater biofilms – from molecular mechanisms to loss of community functions

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    Exposure to herbicides poses a threat to aquatic biofilms by affecting their community structure, physiology and function. These changes render biofilms to become more tolerant, but on the downside community tolerance has ecologic costs. A concept that addresses induced community tolerance to a pollutant (PICT) was introduced by Blanck and Wängberg (1988). The basic principle of the concept is that microbial communities undergo pollution-induced succession when exposed to a pollutant over a long period of time, which changes communities structurally and functionally and enhancing tolerance to the pollutant exposure. However, the mechanisms of tolerance and the ecologic consequences were hardly studied up to date. This thesis addresses the structural and functional changes in biofilm communities and applies modern molecular methods to unravel molecular tolerance mechanisms. Two different freshwater biofilm communities were cultivated for a period of five weeks, with one of the communities being contaminated with 4 μg L-1 diuron. Subsequently, the communities were characterized for structural and functional differences, especially focusing on their crucial role of photosynthesis. The community structure of the autotrophs was assessed using HPLC-based pigment analysis and their functional alterations were investigated using Imaging-PAM fluorometry to study photosynthesis and community oxygen profiling to determine net primary production. Then, the molecular fingerprints of the communities were measured with meta-transcriptomics (RNA-Seq) and GC-based community metabolomics approaches and analyzed with respect to changes in their molecular functions. The communities were acute exposed to diuron for one hour in a dose-response design, to reveal a potential PICT and uncover related adaptation to diuron exposure. The combination of apical and molecular methods in a dose-response design enabled the linkage of functional effects of diuron exposure and underlying molecular mechanisms based on a sensitivity analysis. Chronic exposure to diuron impaired freshwater biofilms in their biomass accrual. The contaminated communities particularly lost autotrophic biomass, reflected by the decrease in specific chlorophyll a content. This loss was associated with a change in the molecular fingerprint of the communities, which substantiates structural and physiological changes. The decline in autotrophic biomass could be due to a primary loss of sensitive autotrophic organisms caused by the selection of better adapted species in the course of chronic exposure. Related to this hypothesis, an increase in diuron tolerance has been detected in the contaminated communities and molecular mechanisms facilitating tolerance have been found. It was shown that genes of the photosystem, reductive-pentose phosphate cycle and arginine metabolism were differentially expressed among the communities and that an increased amount of potential antioxidant degradation products was found in the contaminated communities. This led to the hypothesis that contaminated communities may have adapted to oxidative stress, making them less sensitive to diuron exposure. Moreover, the photosynthetic light harvesting complex was altered and the photoprotective xanthophyll cycle was increased in the contaminated communities. Despite these adaptation strategies, the loss of autotrophic biomass has been shown to impair primary production. This impairment persisted even under repeated short-term exposure, so that the tolerance mechanisms cannot safeguard primary production as a key function in aquatic systems.:1. The effect of chemicals on organisms and their functions .............................. 1 1.1 Welcome to the anthropocene .......................................................................... 1 1.2 From cellular stress responses to ecosystem resilience ................................... 3 1.2.1 The individual pursuit for homeostasis ....................................................... 3 1.2.2 Stability from diversity ................................................................................. 5 1.3 Community ecotoxicology - a step forward in monitoring the effects of chemical pollution? ................................................................................................................. 6 1.4 Functional ecotoxicological assessment of microbial communities ................... 9 1.5 Molecular tools – the key to a mechanistic understanding of stressor effects from a functional perspective in microbial communities? ...................................... 12 2. Aims and Hypothesis ......................................................................................... 14 2.1 Research question .......................................................................................... 14 2.2 Hypothesis and outline .................................................................................... 15 2.3 Experimental approach & concept .................................................................. 16 2.3.1 Aquatic freshwater biofilms as model community ..................................... 16 2.3.2 Diuron as model herbicide ........................................................................ 17 2.3.3 Experimental design ................................................................................. 18 3. Structural and physiological changes in microbial communities after chronic exposure - PICT and altered functional capacity ................................................. 21 3.1 Introduction ..................................................................................................... 21 3.2 Methods .......................................................................................................... 23 3.2.1 Biofilm cultivation ...................................................................................... 23 3.2.2 Dry weight and autotrophic index ............................................................. 23 3.2.4 Pigment analysis of periphyton ................................................................. 23 3.2.4.1 In-vivo pigment analysis for community characterization ....................... 24 3.2.4.2 In-vivo pigment analysis based on Imaging-PAM fluorometry ............... 24 3.2.4.3 In-vivo pigment fluorescence for tolerance detection ............................. 26 3.2.4.4 Ex-vivo pigment analysis by high-pressure liquid-chromatography ....... 27 3.2.5 Community oxygen metabolism measurements ....................................... 28 3.3 Results and discussion ................................................................................... 29 3.3.1 Comparison of the structural community parameters ............................... 29 3.3.2 Photosynthetic activity and primary production of the communities after selection phase ................................................................................................. 33 3.3.3 Acquisition of photosynthetic tolerance .................................................... 34 3.3.4 Primary production at exposure conditions ............................................... 36 3.3.5 Tolerance detection in primary production ................................................ 37 3.4 Summary and Conclusion ........................................................................... 40 4. Community gene expression analysis by meta-transcriptomics ................... 41 4.1 Introduction to meta-transcriptomics ............................................................... 41 4.2. Methods ......................................................................................................... 43 4.2.1 Sampling and RNA extraction................................................................... 43 4.2.2 RNA sequencing analysis ......................................................................... 44 4.2.3 Data assembly and processing................................................................. 45 4.2.4 Prioritization of contigs and annotation ..................................................... 47 4.2.5 Sensitivity analysis of biological processes .............................................. 48 4.3 Results and discussion ................................................................................... 48 4.3.1 Characterization of the meta-transcriptomic fingerprints .......................... 49 4.3.2 Insights into community stress response mechanisms using trend analysis (DRomic’s) ......................................................................................................... 51 4.3.3 Response pattern in the isoform PS genes .............................................. 63 4.5 Summary and conclusion ................................................................................ 65 5. Community metabolome analysis ..................................................................... 66 5.1 Introduction to community metabolomics ........................................................ 66 5.2 Methods .......................................................................................................... 68 5.2.1 Sampling, metabolite extraction and derivatisation................................... 68 5.2.2 GC-TOF-MS analysis ............................................................................... 69 5.2.3 Data processing and statistical analysis ................................................... 69 5.3 Results and discussion ................................................................................... 70 5.3.1 Characterization of the metabolic fingerprints .......................................... 70 5.3.2 Difference in the metabolic fingerprints .................................................... 71 5.3.3 Differential metabolic responses of the communities to short-term exposure of diuron ............................................................................................................ 73 5.4 Summary and conclusion ................................................................................ 78 6. Synthesis ............................................................................................................. 79 6.1 Approaches and challenges for linking molecular data to functional measurements ...................................................................................................... 79 6.2 Methods .......................................................................................................... 83 6.2.1 Summary on the data ............................................................................... 83 6.2.2 Aggregation of molecular data to index values (TELI and MELI) .............. 83 6.2.3 Functional annotation of contigs and metabolites using KEGG ................ 83 6.3 Results and discussion ................................................................................... 85 6.3.1 Results of aggregation techniques ........................................................... 85 6.3.2 Sensitivity analysis of the different molecular approaches and endpoints 86 6.3.3 Mechanistic view of the molecular stress responses based on KEGG functions ............................................................................................................ 89 6.4 Consolidation of the results – holistic interpretation and discussion ............... 93 6.4.1 Adaptation to chronic diuron exposure - from molecular changes to community effects.............................................................................................. 93 6.4.2 Assessment of the ecological costs of Pollution-induced community tolerance based on primary production ............................................................. 94 6.5 Outlook ............................................................................................................ 9

    Signals and Images in Sea Technologies

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    Life below water is the 14th Sustainable Development Goal (SDG) envisaged by the United Nations and is aimed at conserving and sustainably using the oceans, seas, and marine resources for sustainable development. It is not difficult to argue that signals and image technologies may play an essential role in achieving the foreseen targets linked to SDG 14. Besides increasing the general knowledge of ocean health by means of data analysis, methodologies based on signal and image processing can be helpful in environmental monitoring, in protecting and restoring ecosystems, in finding new sensor technologies for green routing and eco-friendly ships, in providing tools for implementing best practices for sustainable fishing, as well as in defining frameworks and intelligent systems for enforcing sea law and making the sea a safer and more secure place. Imaging is also a key element for the exploration of the underwater world for various scopes, ranging from the predictive maintenance of sub-sea pipelines and other infrastructure projects, to the discovery, documentation, and protection of sunken cultural heritage. The scope of this Special Issue encompasses investigations into techniques and ICT approaches and, in particular, the study and application of signal- and image-based methods and, in turn, exploration of the advantages of their application in the previously mentioned areas

    The Multifaceted Nature of Food and Nutrition Insecurity around the World and Foodservice Business

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    The international concept of food security is a situation where all people have physical, social, and economic access at all times to sufficient, safe, and nutritious food that meets their dietary needs and food preferences for an active and healthy life. All four parameters (availability, access, utilization, and stability) should therefore be measured to determine food security status.Taking into account these premises, this book aims to present original research articles and reviews concerning the following: Agriculture and food security; Agri-tourism and its potential to assist with food security; Business–science cooperation to advance food security; Competing demands and tradeoffs for land and water resources; Consumer behavior, nutritional security and food assistance programs; Food and health; Global and local analyses of food security and its drivers; Global governance and food security; Infectious and non-infectious diseases and food security; Reducing food loss and waste; Reducing risks to food production and distribution from climate change; Supply chains and food security; Technological breakthroughs to help feed the globe; Tourism food security relationship; Urbanization, food value chains, and the sustainable, secure sourcing of food; Food and service quality at food catering establishments; Consumer behavior at foodservice operations (restaurants, cafés, hotels)

    Annals [...].

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    Pedometrics: innovation in tropics; Legacy data: how turn it useful?; Advances in soil sensing; Pedometric guidelines to systematic soil surveys.Evento online. Coordenado por: Waldir de Carvalho Junior, Helena Saraiva Koenow Pinheiro, Ricardo SimĂŁo Diniz Dalmolin

    Fiabilité de l’underfill et estimation de la durée de vie d’assemblages microélectroniques

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    Abstract : In order to protect the interconnections in flip-chip packages, an underfill material layer is used to fill the volumes and provide mechanical support between the silicon chip and the substrate. Due to the chip corner geometry and the mismatch of coefficient of thermal expansion (CTE), the underfill suffers from a stress concentration at the chip corners when the temperature is lower than the curing temperature. This stress concentration leads to subsequent mechanical failures in flip-chip packages, such as chip-underfill interfacial delamination and underfill cracking. Local stresses and strains are the most important parameters for understanding the mechanism of underfill failures. As a result, the industry currently relies on the finite element method (FEM) to calculate the stress components, but the FEM may not be accurate enough compared to the actual stresses in underfill. FEM simulations require a careful consideration of important geometrical details and material properties. This thesis proposes a modeling approach that can accurately estimate the underfill delamination areas and crack trajectories, with the following three objectives. The first objective was to develop an experimental technique capable of measuring underfill deformations around the chip corner region. This technique combined confocal microscopy and the digital image correlation (DIC) method to enable tri-dimensional strain measurements at different temperatures, and was named the confocal-DIC technique. This techique was first validated by a theoretical analysis on thermal strains. In a test component similar to a flip-chip package, the strain distribution obtained by the FEM model was in good agreement with the results measured by the confocal-DIC technique, with relative errors less than 20% at chip corners. Then, the second objective was to measure the strain near a crack in underfills. Artificial cracks with lengths of 160 μm and 640 μm were fabricated from the chip corner along the 45° diagonal direction. The confocal-DIC-measured maximum hoop strains and first principal strains were located at the crack front area for both the 160 μm and 640 μm cracks. A crack model was developed using the extended finite element method (XFEM), and the strain distribution in the simulation had the same trend as the experimental results. The distribution of hoop strains were in good agreement with the measured values, when the model element size was smaller than 22 μm to capture the strong strain gradient near the crack tip. The third objective was to propose a modeling approach for underfill delamination and cracking with the effects of manufacturing variables. A deep thermal cycling test was performed on 13 test cells to obtain the reference chip-underfill delamination areas and crack profiles. An artificial neural network (ANN) was trained to relate the effects of manufacturing variables and the number of cycles to first delamination of each cell. The predicted numbers of cycles for all 6 cells in the test dataset were located in the intervals of experimental observations. The growth of delamination was carried out on FEM by evaluating the strain energy amplitude at the interface elements between the chip and underfill. For 5 out of 6 cells in validation, the delamination growth model was consistent with the experimental observations. The cracks in bulk underfill were modelled by XFEM without predefined paths. The directions of edge cracks were in good agreement with the experimental observations, with an error of less than 2.5°. This approach met the goal of the thesis of estimating the underfill initial delamination, areas of delamination and crack paths in actual industrial flip-chip assemblies.Afin de protéger les interconnexions dans les assemblages, une couche de matériau d’underfill est utilisée pour remplir le volume et fournir un support mécanique entre la puce de silicium et le substrat. En raison de la géométrie du coin de puce et de l’écart du coefficient de dilatation thermique (CTE), l’underfill souffre d’une concentration de contraintes dans les coins lorsque la température est inférieure à la température de cuisson. Cette concentration de contraintes conduit à des défaillances mécaniques dans les encapsulations de flip-chip, telles que la délamination interfaciale puce-underfill et la fissuration d’underfill. Les contraintes et déformations locales sont les paramètres les plus importants pour comprendre le mécanisme des ruptures de l’underfill. En conséquent, l’industrie utilise actuellement la méthode des éléments finis (EF) pour calculer les composantes de la contrainte, qui ne sont pas assez précises par rapport aux contraintes actuelles dans l’underfill. Ces simulations nécessitent un examen minutieux de détails géométriques importants et des propriétés des matériaux. Cette thèse vise à proposer une approche de modélisation permettant d’estimer avec précision les zones de délamination et les trajectoires des fissures dans l’underfill, avec les trois objectifs suivants. Le premier objectif est de mettre au point une technique expérimentale capable de mesurer la déformation de l’underfill dans la région du coin de puce. Cette technique, combine la microscopie confocale et la méthode de corrélation des images numériques (DIC) pour permettre des mesures tridimensionnelles des déformations à différentes températures, et a été nommée le technique confocale-DIC. Cette technique a d’abord été validée par une analyse théorique en déformation thermique. Dans un échantillon similaire à un flip-chip, la distribution de la déformation obtenues par le modèle EF était en bon accord avec les résultats de la technique confocal-DIC, avec des erreurs relatives inférieures à 20% au coin de puce. Ensuite, le second objectif est de mesurer la déformation autour d’une fissure dans l’underfill. Des fissures artificielles d’une longueuer de 160 μm et 640 μm ont été fabriquées dans l’underfill vers la direction diagonale de 45°. Les déformations circonférentielles maximales et principale maximale étaient situées aux pointes des fissures correspondantes. Un modèle de fissure a été développé en utilisant la méthode des éléments finis étendue (XFEM), et la distribution des contraintes dans la simuation a montré la même tendance que les résultats expérimentaux. La distribution des déformations circonférentielles maximales était en bon accord avec les valeurs mesurées lorsque la taille des éléments était plus petite que 22 μm, assez petit pour capturer le grand gradient de déformation près de la pointe de fissure. Le troisième objectif était d’apporter une approche de modélisation de la délamination et de la fissuration de l’underfill avec les effets des variables de fabrication. Un test de cyclage thermique a d’abord été effectué sur 13 cellules pour obtenir les zones délaminées entre la puce et l’underfill, et les profils de fissures dans l’underfill, comme référence. Un réseau neuronal artificiel (ANN) a été formé pour établir une liaison entre les effets des variables de fabrication et le nombre de cycles à la délamination pour chaque cellule. Les nombres de cycles prédits pour les 6 cellules de l’ensemble de test étaient situés dans les intervalles d’observations expérimentaux. La croissance de la délamination a été réalisée par l’EF en évaluant l’énergie de la déformation au niveau des éléments interfaciaux entre la puce et l’underfill. Pour 5 des 6 cellules de la validation, le modèle de croissance du délaminage était conforme aux observations expérimentales. Les fissures dans l’underfill ont été modélisées par XFEM sans chemins prédéfinis. Les directions des fissures de bord étaient en bon accord avec les observations expérimentales, avec une erreur inférieure à 2,5°. Cette approche a répondu à la problématique qui consiste à estimer l’initiation des délamination, les zones de délamination et les trajectoires de fissures dans l’underfill pour des flip-chips industriels

    Full stack development toward a trapped ion logical qubit

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    Quantum error correction is a key step toward the construction of a large-scale quantum computer, by preventing small infidelities in quantum gates from accumulating over the course of an algorithm. Detecting and correcting errors is achieved by using multiple physical qubits to form a smaller number of robust logical qubits. The physical implementation of a logical qubit requires multiple qubits, on which high fidelity gates can be performed. The project aims to realize a logical qubit based on ions confined on a microfabricated surface trap. Each physical qubit will be a microwave dressed state qubit based on 171Yb+ ions. Gates are intended to be realized through RF and microwave radiation in combination with magnetic field gradients. The project vertically integrates software down to hardware compilation layers in order to deliver, in the near future, a fully functional small device demonstrator. This thesis presents novel results on multiple layers of a full stack quantum computer model. On the hardware level a robust quantum gate is studied and ion displacement over the X-junction geometry is demonstrated. The experimental organization is optimized through automation and compressed waveform data transmission. A new quantum assembly language purely dedicated to trapped ion quantum computers is introduced. The demonstrator is aimed at testing implementation of quantum error correction codes while preparing for larger scale iterations.Open Acces

    Optical coherence tomography methods using 2-D detector arrays

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    Optical coherence tomography (OCT) is a non-invasive, non-contact optical technique that allows cross-section imaging of biological tissues with high spatial resolution, high sensitivity and high dynamic range. Standard OCT uses a focused beam to illuminate a point on the target and detects the signal using a single photodetector. To acquire transverse information, transversal scanning of the illumination point is required. Alternatively, multiple OCT channels can be operated in parallel simultaneously; parallel OCT signals are recorded by a two-dimensional (2D) detector array. This approach is known as Parallel-detection OCT. In this thesis, methods, experiments and results using three parallel OCT techniques, including full -field (time-domain) OCT (FF-OCT), full-field swept-source OCT (FF-SS-OCT) and line-field Fourier-domain OCT (LF-FD-OCT), are presented. Several 2D digital cameras of different formats have been used and evaluated in the experiments of different methods. With the LF-FD-OCT method, photography equipment, such as flashtubes and commercial DSLR cameras have been equipped and tested for OCT imaging. The techniques used in FF-OCT and FF-SS-OCT are employed in a novel wavefront sensing technique, which combines OCT methods with a Shack-Hartmann wavefront sensor (SH-WFS). This combination technique is demonstrated capable of measuring depth-resolved wavefront aberrations, which has the potential to extend the applications of SH-WFS in wavefront-guided biomedical imaging techniques

    Novel strategies for the modulation and investigation of memories in the hippocampus

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    Disruptions of the memory systems in the brain are linked to the manifestation of many neuropsychiatric diseases such as Alzheimer’s disease, depression, and post-traumatic stress disorder. The limited efficacy of current treatments necessities the development of more effective therapies. Neuromodulation has proven effective in a variety of neurological diseases and could be an attractive solution for memory disorders. However, the application of neuromodulation requires a more detailed understanding of the network dynamics associated with memory formation and recall. In this work, we applied a combination of optical and computational tools in the development of a novel strategy for the modulation of memories, and have expanded its application for interrogation of the hippocampal circuitry underlying memory processing in mice. First, we developed a closed-loop optogenetic stimulation platform to activate neurons implicated in memory processing (engram neurons) with a high temporal resolution. We applied this platform to modulate the activity of engram neurons and assess memory processing with respect to synchronous network activity. The results of our investigation support the proposal that encoding new information and recalling stored memories occur during distinct epochs of hippocampal network-wide oscillations. Having established the high efficacy of the modulation of engram neurons’ activity in a closed-loop fashion, we sought to combine it with two-photon imaging to enable high spatial resolution interrogation of hippocampal circuitry. We developed a behavioral apparatus for head-fixed engram modulation and the assessment of memory recall in immobile animals. Moreover, through the optimization of dual color two-photon imaging, we improved the ability to monitor activity of neurons in the subfields of the hippocampus with cellular specificity. The platform created here will be applied to investigate the effects of engram reactivation on downstream projections targets with high spatial and cell subtype specificity. Following these lines of investigations will enhance our understanding of memory modulation and could lead to novel neuromodulation treatments for neurological disorders associated with memory malfunctioning

    Episodic outflow feedback in low-mass star formation

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    Protostellar outflows are a ubiquitous signpost of star formation. Even the youngest and most embedded sources launch outflows that entrain ambient core material, significantly altering the whole accretion phase of protostars. Thereby outflows reduce the star formation efficiency and determine the finial stellar mass. By extracting angular momentum outflows allow the stars to accrete mass from their surrounding accretion discs. In the case of low-mass star formation, outflows are considered to be the most important feedback mechanism. Observations of long chains of outflow bullets show that outflow feedback is episodic rather than continuous. How episodic outflow feedback impacts the evolution and outcome of star formation is still not fully understood. This thesis contains three publications addressing the impact of episodic outflow feedback on the star formation process and the fossil information carried by the outflows. Using an episodic, sub-grid outflow model in a total of 111 numerical smoothed particle hydrodynamics simulations are performed to follow the star formation process through the early stages. These simulations contain a resolution and parameter study showing that episodic outflow feedback is highly self-regulating. Episodic protostellar outflows entrain about ten times their initially ejected mass, thereby approximately halving the star formation efficiency, resulting in a shifted stellar initial mass function. Protostellar outflows affect how the stars accrete by promoting disc accretion over radial accretion. The promoted disc accretion enhances the fraction of equal-mass twin binaries to a fraction in good agreement with observations. Simulations without outflow feedback form more stars and higher-order multiple systems, which predominantly break apart into binary systems. Outflow feedback enhances the stability of higher-order multiple systems such that the resulting multiplicity statistics are in good agreement with observations. Since the accretion of gas and the launching of outflows are highly connected, protostellar outflows carry fossil records of the launching protostar's accretion history. Hubble wedges in position-velocity diagrams correspond to episodically ejected outflow bullets that have not yet interacted with the cavity wall. Using the kinematic information carried by the outflow and especially by the bullets, it is possible to estimate stellar accretion rates. Dynamical ages of outflows and individual bullets give an estimate of the protostellar age and a history of outburst events. The outflow opening angle and activity help to differentiate between evolutionary stages. This information combined allows a reconstruction of the launching protostars accretion history. Episodic outflows significantly shape the evolution and morphology of the star formation process and should therefore be considered when studying star formation
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