Wetenschappen

Doctoraten 2024

Woon een doctoraat bij of raadpleeg de voorbije verdedigingen

Study of the skin microbiome and the potential of topical probiotics for atopic dermatitis - Lize Delanghe (05/03/2024)

Lize Delanghe

  • 05/03/2024
  • 17.00 uur
  • Locatie: Campus Drie Eiken, O.01
  • Online Doctoraatsverdediging
  • Promotoren: Sarah Lebeer, Ingmar Claes & Julie Leysen
  • Departement Bio-ingenieurswetenschappen


Abstract

The human skin microbiome is an open ecosystem that is influenced by external and personal factors and forms a key barrier against pathogens and other foreign substances. Different inflammatory skin conditions, such as atopic dermatitis (AD), are associated with a disturbed skin microbiome. The etiology of AD is complex, with roles for genetics, the immune system, environmental factors, and the skin microbiome, with a key role for Staphylococcus aureus as a skin pathogen. A high need for alternative treatments for AD has sparked the interest in probiotic interventions. This PhD thesis aimed to achieve in-depth insights into the relation between the skin microbiome and AD and to contribute to the development of a new probiotic product for AD. To develop microbiome-based treatments, we should first thoroughly understand the healthy skin microbiome. For this, we collected skin samples from the inner elbow of healthy volunteers and identified the core bacterial community. Age showed the be the major driver defining the skin microbiome composition and longitudinal stability. In addition, significant associations were found between specific skin taxa and season, hygiene, supplements, and the number of household member. Next, we compared the skin microbiome of our healthy cohort with AD patients. Here, we showed that S. aureus did not appear to have a prominent role in mild AD. We also assessed other taxa associated with mild AD and identified six skin species with an increased and 15 genera with a decreased abundance. To elucidate the potential of lactobacilli-based probiotics, we performed an exploratory study investigating the application of three lactobacilli strains on mild AD skin. The lactobacilli showed a good engraftment in the skin niche and the formulated creams reduced erythema and itch on the patients skin. These results already showed that probiotics have a high potential for AD, but there exists a large variety in strain-specific modes of action wherefore a careful selection of the most effective strains is important. Therefore, we selected 76 bacterial isolates and based on in vitro characterization of these strains, with the focus on safety, applicability and functional activity, we could finally select seven probiotic strains.

In conclusion, this work contributed to the microbiome research field and the development of new and effective treatments for AD by gaining insights into the skin microbiome in health and disease. In addition, we could select seven strains showing high promising modes of action, next to good safety and growth conditions.

Methodological Advances in Studying Postnatal Locomotor Development - Falk Mielke (01/03/2024)

Falk Mielke

  • 01/03/2024
  • 16.00 uur
  • Locatie: Campus Drie Eiken, O.04
  • Promotoren: Peter Aerts & Chris Van Ginneken
  • Departement Biologie


Abstract

One crucial characteristic which sets animals apart from most other forms of life is the capability of quick locomotion.

Yet moving around does not always come easy: some animals are better at it than others, and common research tools in the field of locomotor biomechanics occasionally fail to quantify subtle differences.

For example, during early development, variability in locomotor patterns is high, faults and instabilities are common, but maturation is quick, which is a challenging context for comparative biomechanics.

In this project, I set out to expand our methodological capabilities for developmental, comparative biomechanics.

The thesis covers kinematics (how animals move) and kinetics (why they move). Based on the observation that locomotor patterns are often repetitive, and applying probabilistic, predictive models which incorporate variability, I spotlight the most fragile of newborn animals: those who are born with particularly low weight.

My primary model system are piglets, where low birth weight is common due to increasing litter sizes in commercial breeding.

The applied methods (Fourier analysis, probabilistic statistics) are exapted from other fields, thus not novel, but rarely applied to quantitative biomechanics to date.

I also highlight limitations and quantify commonly accepted inaccuracies of existing inverse dynamic methods. The case of piglet locomotion can demonstrate how the exapted tools enable unprecedented detail in the analysis of locomotor biomechanics.

In particular, I can confirm that low birth weight piglets are fully capable of normal locomotion, and I precisely quantify how their development is halted shortly after birth.

This provides some important constraints for the evaluation of coping strategies in commercial farming.

Besides, the methodological advances which I present in detail enable a whole new set of research questions for different contexts, within the field of locomotor biomechanics and beyond.

Electrochemical sensing strategies for multiple illicit drugs - Jonas Schram (23/02/2024)

Jonas Schram

  • 23/02/2024
  • 16.00 uur
  • Locatie: Campus Drie Eiken, O.4
  • Online Doctoraatsverdediging
  • Promotoren: Karolien De Wael & Marc Parrilla Pons
  • Departement Bio-ingenieurswetenschappen


Abstract

Today, illicit drugs are omnipresent in society. Clandestine markets are growing faster than ever before, record amounts of cocaine are seized in seaports and airports, while the associated violence is spiralling out of control. In addition, drug monitoring centres worldwide are warning for the increasing complexity of the drug markets, as the traditionally popular drugs are joined by countless new synthetic variants, while medical drugs are also increasingly being abused. In order to provide services confronted with illicit drug samples (police, customs, forensic scientists, first responders, …) with important information on the identity of an unknown sample, suitable analytical tests are required. While these exist for laboratory environments, on-site applicable tests are important to accelerate the decision-making process. Electrochemical sensors have all the advantages required for such on-site tests: they are fast, portable, easy-to-use and reliable. Furthermore, they are not influenced by colours, which are frequently added to drug samples to deceive the existing tests.

Previous work has mainly focussed on the detection of a single drug per analysis. However, many drugs could be encountered due to the diversity of the drug markets. Therefore, this project developed electrochemical strategies for the detection of multiple drugs simultaneously. First, the electrochemical behaviour of the individual drugs was studied in different measuring conditions (assessing the influence of pH, concentration and temperature). Then, all findings and strategies were combined to detect multiple targets simultaneously. An electrochemical sensor was developed for the four most popular drugs at music festivals: cocaine, MDMA, amphetamine and ketamine. This sensor generates a so-called ‘superfingerprint’ of the sample, which is then automatically interpreted by a developed algorithm in order to produce a straightforward output.

Finally, a pill analysis sensor was developed in the context of drug checking services, where a consumer can anonymously have a sample chemically analysed to obtain information on the composition, dose and potentially harmful additives. The sensor achieved an outstanding accuracy in identifying the main component and provided the option to quantify, as well as an indication on the presence of other substances in the sample. The project’s findings demonstrate the potential for electrochemistry in illicit drug detection and provide a basis for the development of new sensors, targeting other drug combinations.

An Advanced EPR Investigation of Copper Complexes in Catalysis - Fardokht Rezayi (22/02/2024)

Fardokth Rezayi

  • 22/02/2024
  • 16.00 uur
  • Locatie: Campus Drie Eiken, O.01
  • Online Doctoraatsverdediging​
  • Inkomend dubbeldoctoraat Cardiff University - Universiteit Antwerpen
  • Promotoren:  Sabine Van Doorslaer & Damien Murphy
  • Departement Chemie


Abstract

Cu(II) coordination chemistry is of significant importance due to copper's widespread applications, particularly in chemical catalysis. This thesis explores the molecular structure, electronic properties, and variable coordination geometry of trigonal bipyramidal complexes of Cu(II) with tripodal ligands, more specifically different tripodal tetraamines. While square planar and square pyramidal Cu(II) complexes are commonly studied, less attention is given to trigonal bipyramidal Cu(II) centres. A variety of Electron Paramagnetic Resonance (EPR) techniques is used as a unique analytical tool to probe Cu(II) complex chemistry.

While the counter ions had only a negligible effect on coordination through outer sphere interactions, the effect of the type of tetraamine, pH and their concentration was significant, revealing subtle and strong variations in the coordination chemistry upon change of these conditions and thus emphasizing the importance of understanding the solution-based structures when aiming for specific applications.

The performance of different trigonal bipyramidal Cu(II)-tetraamine complexes for the selective oxidation of glycerol was further explored. The interest in glycerol oxidation is growing, since glycerol is a valuable bio-renewable compound formed during biomass conversion. Through a combination of different techniques, the catalytic behaviour could be fit to the faith of the Cu(II) complex during reaction. Attempts were made to heterogenise the Cu(II) complexes into Y zeolites in order to allow easy removal of the catalyst from the reaction mixture after glycerol oxidation. Though the correlation between Cu(II)-complex encapsulation, Si:Al ratio, and proton count in the zeolitic structure was identified, the heterogeneous material proved unsuitable for glycerol oxidation. Nevertheless, it holds promise for exploring alternative catalytic reactions.

Coastal enhanced olivine weathering for climate change mitigation: investigating the CO2 sequestration potential and ecotoxicological risks - Gunter Flipkens (19/02/2024)

Gunter Flipkens


Abstract

Drastic greenhouse gas emission reductions and gigaton-scale atmospheric carbon dioxide (CO2) removal are needed to keep global warming below 2°C. Silicate rock weathering has regulated climate on earth over geological time scales. Coastal enhanced silicate weathering (CESW) aims to accelerate this process by distributing gigatons of finely ground olivine-rich rock in dynamic coastal environments. Olivine is a proposed candidate mineral due to its abundance, relatively fast weathering rate, and theoretically high CO2 sequestration potential. However, the in situ CO2 sequestration potential remains uncertain and olivine’s high nickel (Ni) and chromium (Cr) content could be of potential ecological concern. This thesis aimed to advance our understanding of olivine dissolution and CO2 sequestration kinetics under the influence of hydrodynamics and assess potential ecotoxicological effects of CESW.

First, we investigated the effect of continuous grain-grain collisions on olivine weathering rates in seawater. Physical agitation enhanced olivine dissolution by 8 to 19 times compared to stagnant conditions, likely due to advective pore water flushing. Therefore, olivine should be supplied in coastal areas with sufficiently high bed shear stress and pore water exchange rates. Subsequently, a flume experiment was conducted to investigate the effect of current on olivine dissolution in permeable sediment. Olivine dissolution was more than one order of magnitude lower than expected, for reasons that could not be identified, highlighting the need for studies under environmentally realistic conditions.

Next, a first assessment of the safe olivine deployment scale was made based on existing marine Ni and Cr environmental quality standards. Results indicated that 0.059 to 1.4 kg of olivine per m2 of seabed could be supplied without posing metal toxicity risks for benthic biota. Changes in sediment physicochemical properties may also lead to avoidance of olivine rich sediments by marine organisms. Short choice experiments with the gastropod Littorina littorea and amphipod Gammarus locusta indicated avoidance of pure olivine but tolerance to environmentally relevant olivine concentrations of 30% w/w and lower. Metal bioaccumulation and chronic olivine toxicity testing with Gammarus locusta further revealed concentration and grain size dependent effects, with adverse reproductive outcomes at olivine concentrations of 10% w/w and higher. These findings underscore the necessity for additional olivine toxicity data to derive accurate, site-specific olivine application guidelines. Overall, our work provides novel insights into the stimulating effect of hydrodynamics on olivine reactivity and shows possible trace metal-related adverse ecological impacts of CESW.

Advanced Electron Tomography to Investigate the Growth and Stability of Complex Metal Nanoparticles - Mikhail Mychinko (12/02/2024)

Mikhail Mychinko


Abstract

During the past decades, metallic nanoparticles (NPs) have attracted great attention in materials science due to their specific optical properties based on surface plasmon resonances. Because of these phenomena, plasmonic NPs (or nanoplasmonics) are very promising for application in biosensing, photocatalysts, medicine, data storage, solar energy conversion, etc. Currently, colloidal synthesis techniques enable scientists to routinely produce mono and bimetallic NPs of various shapes, sizes, composition, and elemental distribution, with superior properties for plasmonic applications. Two primary directions for further advancing nanoplasmonic-based technologies include synthesizing novel morphologies, such as highly asymmetric chiral NPs, and gaining deeper insights into the factors affecting the stability of produced nanoplasmonics. With the increasing complexity of nanoplasmonics’ morphologies and higher stability requirements, there is a pressing need for thorough investigations into their 3D structures and their evolution under different conditions, with high resolution. Electron tomography (ET) emerges as an ideal tool to retrieve shape and element-sensitive information about individual nanoparticles in 3D, achieving resolution down to the atomic level. Moreover, ET techniques can be combined with in situ holders, enabling detailed studies of processes mimicking real applications of nanoplasmonic-based devices. The first part of this defense will focus on structural and morphological characterization of chiral Au NPs, promising for spectroscopy techniques based on the differential absorption of left- and right-handed circularly polarized light. Specifically, I will discuss the primary strategies for wet-colloidal growth of the various types of intrinsically chiral Au NPs. Advanced ET methods will be demonstrated as powerful tools for characterizing the final helical morphologies of the produced Au NPs and for studying the chiral growth mechanisms by examining intermediate structures obtained during chiral growth.

The second part will focus on the stability under heating of various Au@Ag core-shell NPs. Operating in real conditions, such as elevated temperatures, may cause particle reshaping and redistribution of metals between the core and shell, gradually altering nanoplasmonics properties. Hence, a thorough understanding of the influence of size, shape, and defects on these processes is crucial for further developments. I will show how recently developed techniques, combining fast ET with in-situ heating holders, have allowed me to evaluate the influence of various parameters (size, shape, defect structure) on heat-induced elemental redistribution in Au@Ag core-shell nanoparticles qualitatively and quantitatively. Additionally, I will discuss the prospects of high-resolution ET for visualizing the diffusion of individual atoms within complex nanostructures.

The potential for upward range expansion of alien plant species in cold-climate mountains in a warming world - Jan Clavel (05/02/2024)

Jan Clavel

  • 05/02/2024
  • 14.00 uur
  • Locatie: Campus Drie Eiken, Q0.02
  • Promotoren: Ivan Nijs, Erik Verbruggen & Jonas Lembrechts
  • Departement Biologie


Abstract

Non-native species invasions are one of the most impactful drivers of biodiversity and ecosystem services loss worldwide and their occurrence is increasing rapidly as a consequence of ever-growing anthropogenic activities. One aspect of plant species invasion, which is only recently being recognized as a significant determinant of invasion success, is the symbiosis between plants and mycorrhizal fungi. Here, I focus on anthropogenic disturbance in mountain ecosystems and its impact on plant communities and mycorrhizal fungi to answer how these communities are impacted by said disturbance and whether non-native plants can benefit from these altered conditions. Therefore, I used three different approaches: 1) repeated surveys of plants and arbuscular mycorrhizal fungi along disturbed roadsides in the mountains of Norway, 2) combining a global plant dataset from along mountain roads with a database associating plants with their mycorrhizal types, and 3) an in-situ seed addition experiment measuring non-native plant success and changes in fungal community following different types of disturbance treatments. Through these methods, I assessed the effects of anthropogenic disturbance on mycorrhizal symbiosis and non-native plant species at multiple scales and resolutions.

I found that road disturbance has a globally consistent effect on mycorrhizal types in mountain systems: plants associated with arbuscular mycorrhizal (AM) fungi were more abundant following disturbance, and vegetation associated with ectomycorrhizal- or ericoid-mycorrhizal fungi was conversely less abundant. In the Norwegian regional study, AM fungi were similarly more abundant and diverse in the roots of plant communities affected by roadside disturbance. Experimental results found that physical disturbance and nutrient addition facilitate non-native plant success, have negative effects on EcM fungi and positive effects on fungal pathogens.

Our results show that anthropogenic disturbance has an effect on mycorrhizal fungi and in turn impacts the distribution of plant species in disturbed mountain systems. The resulting shift in mycorrhizal fungi towards AM can facilitate non-native plant success through disruption of the native fungal communities, especially so in high elevation and cold climate regions which are naturally less dominated by AM plants. I believe that these conclusions highlight the role of mycorrhizal symbiosis in understanding plant invasions trajectories and in turn emphasize the importance of closely monitoring sources of anthropogenic disturbance in mountain systems in order to prevent future establishment of non-native plants.

Search for longlived Heavy Neutral Leptons using a displaced jet tagger in the CMS experiment - Haifa Rejeb Sfar (29/01/2024)

Haifa Rejeb Sfar

  • 29/01/2024
  • 14.00 uur
  • Locatie: Campus Groenenborger, T.105
  • Online Doctoraatsverdediging
  • Promotoren: Albert De Roeck & Nick Van Remortel
  • Departement Fysica


Abstract

This thesis presents a search for long-lived heavy neutral leptons (HNLs) using proton-proton collision events, with a focus on the νMSM model for HNL production. The νMSM model is a theoretical framework that extends the Standard Model of particle physics to include right-handed neutrinos and provides a possible explanation for the observed neutrino masses and mixing angles. We have analyzed a data sample containing two leptons (electron or muon) and jets, with an integrated luminosity of 138 fb1 collected from 2016 to 2018, which corresponds to the full RunII dataset, and have developed a novel jet tagger based on a deep neural network to identify displaced jets from the HNL decay.

To estimate the contribution from background processes, we used an ABCD method, which is a data-driven technique that relies on the correlation between two independent variables to separate signal and background events. We applied this method to the data in sideband regions and determined the expected background in the signal region. No excess in data over the expected background is observed. Limits on the HNL production cross section are derived as a function of the HNL mass and the three coupling strengths (VlN ) to each lepton generation (l).

Our results provide the best limit on the coupling strength for pure muon coupling scenarios, excluding values of |VμN |2 > 5(4) × 107 for Dirac (Majorana) HNLs with a mass of 10 GeV at 95% CL. This has important implications for the viability of the νMSM model and other theoretical models that propose the existence of HNLs. Our methodology, including the use of the jet tagger and the ABCD method, can be applied to future searches for HNLs at higher energies and luminosities.

However, our study has limitations, such as the assumption of a specific HNL production mechanism and the use of simplified background models. Future research could focus on improving the sensitivity of the jet tagger, exploring alternative HNL production scenarios, developing more sophisticated background estimation techniques, and combining the results from existing HNL searches to improve the sensitivity and coverage of the parameter space.


Applications of Photoredox Chemistry for the Generation of Valuable Products - Tong Zhang (26/01/2024)

Tong Zhang

  • 26/01/2024
  • 15.00 uur
  • Locatie: Campus Groenenborger, V.008
  • Promotoren: Shoubhik Das & Bert Maes
  • Departement Chemie


Abstract

Due to the climate change, pollutions, energy shortage and other interrelated global crises, there is always an increasing demand for the development of environmentally friendly processes in the chemical industries. In the last two decades, the field of photochemistry has emerged as a potent methodology across diverse domains, enabling the synthesis of numerous intricate compounds through environmentally sustainable means. This thesis elucidates four distinct methodologies concerning the generation of valuable products across diverse domains through the utilization of photoredox and photochemical reactions. The thesis is divided into five chapters:

• Chapter 1: An overview and introductory exposition of the fundamental principles and concepts pertaining to photochemistry are provided.

• Chapter 2: We have enhanced the generation of hydrogen peroxide by introducing an aryl amino group in polymeric carbon nitrides via visible light-mediated photocatalysis. In addition to increasing the efficiency of photocatalytic system, the description of the whole reactive scenario for the polymeric carbon nitrides has been depicted by combining diverse characteristic methods and theoretical calculations. Futhermore, the possible active catalytic sites are identified with the aid of 15N and 19F solid state NMR without using any expensive labeling reagent.

• Chapter 3: We have developed a unique methodology for the generation of α-amino radicals under the irradiation of visible light under a metal-free condition. This strategy is induced by π–π stacking and ion-pairing interactions and facilitated the synthesis of functionalized amines through three-component coupling reactions.

• Chapter 4: We have designed an efficient method for the red light-mediated sulfonyltrifluoromethylation of olefins which provide remarkable regioselectivity. This reaction system has been thoughtfully designed, and excellent substrate compatibility and functional group tolerance exhibits the industrial potential, thus validating the significance of this strategy.

• Chapter 5: We have developed a metal-free photocatalytic system for the transformation of biomass into formic acid. Compared to previous strategies, our method can work efficiently at room temperature and atmospheric pressure. Notably, real biomass and even daily-life-based-materials such as waste papers and oak cork stoppers of wine bottles are also smoothly converted to formic acid.

Elucidating the molecular mechanisms underlying grassland species in response to more persistent precipitation regimes - Lin Zi (22/01/2024)

Lin Zi

  • 22/01/2024
  • 09.00 uur
  • Locatie: Campus Drie Eiken, Q.002
  • Promotoren: Han Asard, Hamada Abd Elgawad & Kris Laukens
  • Departement Biologie


Abstract

One aspect of climate change is the increased persistence of precipitation regimes (PRs), characterized by alternated longer dry and wet periods. While the ecological impacts of singular extreme events like drought and flood have been extensively studied, the immediate and legacy effects of the evolving more persistent PR, particularly at the molecular level in plants, remain underexplored.

This doctoral thesis aims to bridge this knowledge gap by conducting a large-scale outdoor experiment, applying a range of PR from short to long dry/wet cycles to grassland mesocosms. Ecometabolomics analysis revealed that the metabolome of a relatively sensitive species, Centaurea jacea, shifted under mild PR (10-day dry/wet cycle), while the metabolome of other less sensitive species changed only from a 20-day PR onwards. Accumulation of amino acids, lignin, and decreased non-structural sugar levels are universal responses across several species to increasing PR extremity, while changes in other metabolite classes are exhibited in a more species-specific manner. The sensitive species are less capable of inducing sufficient changes in important molecules such as lignin and phenylalanine, which may partly explain its sensitivity in PR responses.

Beyond immediate effects, my research found that previous exposure to more persistent PR resulted in acclimated grassland communities in the following year. These communities showed increased aboveground productivity and structural sugar content, reduced molecular stress responses and reduced diversity. Furthermore, soil inoculum from more persistent PR promoted the upregulation of several pathways, such as hormone synthesis (e.g., jasmonic acid, abscisic acid, salicylic acid, ethylene), oxidative stress, cell wall modification (e.g., lignin deposition, callose synthesis, cell wall thickening, pectin metabolic process), and chitin catabolic processes, which may provide potential beneficial effects for plants.

In conclusion, this thesis demonstrates that more persistent PR induces significant changes in plant biochemical and transcriptional levels. While these changes may enhance the acclimation of grassland species, they may also decrease nutritive value, potentially altering their role in the feeding of organisms. Species or individuals unable to induce sufficient protective changes may be excluded from the community, leading to a loss of diversity in the ecosystem.

Improved X-ray CT reconstruction techniques with non-linear imaging models - Nathanaël Six (18/01/2024)

Nathanaël Six

  • 18/01/2024
  • 16.00 uur
  • Locatie: Campus Drie Eiken, S1
  • Promotoren: Jan Sijbers & Jan De Beenhouwer
  • Departement Fysica


Abstract

X-ray computed tomography (CT) is a powerful and non-invasive technique to visualise the internal structure of an object from a set of X-ray radiographs. Reconstruction algorithms are used to map projection data to a 3D volume. A model of the X-ray acquisition process is used by reconstruction algorithms and the algorithms require a large number of projections to function well. However, in certain applications, the number of projections has to be limited, to reduce total delivered dose, lower acquisition time or because of geometrical constraints. Furthermore, the most commonly used algorithms have a simple linear forward model for X-ray attenuation that does not model the real acquisition accurately. Finally, conventional reconstruction algorithms in CT are not efficient with respect to computation time. In this thesis, we will develop improved reconstruction algorithms for CT by investigating more accurate non-linear forward models, and different numerical optimisation approaches for these models.


Exploring the potential and molecular mechanisms of beneficial lactic acid bacteria in respiratory mucosal disorders - Eline Cauwenberghs (16/01/2024)

Eline Cauwenberghs

  • 16/01/2024
  • 17.00 uur
  • Locatie: Campus Drie Eiken, Q0.02
  • Promotoren: Sarah Lebeer & Kim van Hoorenbeeck
  • Departement Bio-ingenieurswetenschappen


Abstract

For several decades, it was widely believed that the healthy respiratory tract was sterile. However, advancements in next-generation sequencing techniques have enabled us to unveil the microbial communities residing within the respiratory tract, both in health and disease. However, there is a lack of in-depth functional insights into these communities to design innovative microbiome therapies for the respiratory tract. Nevertheless, such therapies show great promise as they can act via multifactorial mechanism of action improving respiratory health. Specifically for people with cystic fibrosis (CF), microbiome therapies could complement current treatments by preventing chronic colonization of pathogens at early age and by enhancing the effectiveness of therapies such as antibiotics and modulators through creation of a more stable microbial ecosystem. This PhD thesis aimed to expand the knowledge on the microbial communities within various respiratory tract niches and explore the potential of microbiome therapies as a preventive or complementary treatment strategy for CF. First, we studied the salivary microbiome of 246 women using 16S rRNA amplicon sequencing to investigate whether we could detect bacterial biomarkers linked with respiratory disease. We found that the salivary microbiome was highly preserved among healthy women and lifestyle and host-related parameters had only subtle effects on specific taxa. For the detection of bacterial biomarkers linked with respiratory disease, more targeted sampling methods and insights at a lower taxonomic level were needed. Therefore, we next performed shallow metagenomic shotgun sequencing on respiratory tract samples, including nasopharyngeal, oropharyngeal and sputum samples. The host DNA depletion step was found to reduce the presence of Gram-negative taxa, which play an important role in the human airways. Taken this bias into account, we could show the potential of shallow shotgun sequencing in a clinical setting by identifying important CF pathogens at species level in oropharyngeal and sputum samples providing valuable information about the patient’s disease status. Lastly, we aimed to evaluate the potential of probiotics for CF. Lacticaseibacillus casei AMBR2 demonstrated important adaptation and multifactorial probiotic characteristics in vitro with a focus on CF pathogenesis. Moreover, we identified four putative bacteriocin gene clusters in the genome of AMBR2 of which one exhibited high activity against Gram-negative pathogens.

This work combined microbiome research (16S rRNA amplicon and shallow metagenomic shotgun sequencing) with functional studies to achieve the research goals. It has enriched the understanding regarding microbe-microbe and microbe-host interactions in the context of CF, paving the way for future therapeutic applications.


Fluctuations in multicomponent quantum fluids - Lennart Fernandes (10/01/2024)

Lennart Fernandes

  • 10/01/2024
  • 16.00 uur
  • Locatie: CST, Promotiezaal van de Grauwzusters, Lange Sint-Annastraat 7, 2000 Antwerpen
  • Online Doctoraatsverdediging
  • Promotoren: Michiel Wouters & Jacques Tempere
  • Departement Fysica


Abstract

In this thesis the behaviour of quantum fluids out of equilibrium is studied. These are ultracold gases in which quantum mechanical effects - usually only visible at the atomic scale - determine the macroscopic properties. The work is composed of several related projects, in which the central role of quantum fluctuations is highlighted.

In the Gaussian theory for quantum systems, fluctuations are approximated as corrections to a classical description of the fluid. A central contribution of this work is the development and application of a new approach that enables this established method to describe quantum states with large, nonlinear fluctuations. Inspired by the study of open quantum systems, we do this by introducing a virtual environment, which continuously measures the system to suppress the growth of quantum fluctuations. This method is successfully applied to the dynamics of a spinor fluid, in which restrictions on the interactions between atoms lead to the formation of a non-equilibrium state with a high degree of quantum entanglement.

Finally, the acquired knowledge on spinor fluids is used for their application as a platform for analog gravity. We introduce Hawking radiation emitted by black holes, show that the underlying mechanism is a general property of quantum fields in a flowing background, and apply this analogy to spin waves in a spinor gas.