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Insights into the diversity of the endophytic community in potatoes and factors affecting this diversity
No full textPlant-microbiome interactions have become a critical focus in sustainable agricultural management due to their significant impact on plant health and growth. The role of the plant microbiome in promoting plant vitality is well established. Using results from controlled greenhouse experiments, this thesis investigates the influence of environmental and host-related factors on the diversity of endophytes. Our study provides new insights for breeders seeking to incorporate microbiome-related traits into breeding programmes. This thesis starts by highlighting the concept of holobiont and emphasises the importance of plant-microbe interactions in Chapter 1. Chapter 2 provides a concise review of the strategies that have recently been employed to fully leverage the plant-microbiome interaction in agricultural practices. To delve deeper into the effect of biotic and abiotic conditions on the plant endophytic diversity, Chapter 3 highlights the significant role of soil in determining the composition of bacterial and fungal endophytes. This chapter further emphasises the stronger role of cultivars in shaping the fungal endophytes in potatoes.Chapter 4 of this thesis offers a deeper insight into plant microbiome interaction by studying the recruitment of endophytes from the rhizosphere. Source tracking analysis using FEAST package explains the discrepancies in the recruitment pattern of bacterial and fungal communities. Chapter 5 reveals that the soil microbiome inoculation effect is not limited to the rhizosphere but extends up to the endophytic compartment of the plant. Chapter 6 emphasises the importance of considering the local soil microbiome before applying microbiome-based strategies
Lifelines of young people with a history in residential care:A qualitative investigation from a complex systems perspective
No full textCare for youngsters in residential settings is often disorder focused rather than based on a holistic understanding of their unique developmental histories. In this study, we used a lifeline drawing method, inspired by complex systems theory, to map the life histories and broader developmental contexts of young people with residential living experience. Lifelines of wellbeing were analyzed for distinct dynamic patterns to arrive at a process explanation of how person-environment interactions shape the onset and maintenance of psychological suffering and recovery. Lifeline interviews were conducted with seven adolescents with residential living experience. Each lifeline was segmented and coded for the functioning of the person and their environment. We then sought for dynamic patterns that were repeated within and across cases. The overall line shape showed that youth experienced the majority of their lives as hardship and that their psychological problems worsened over time. While idiosyncratic in content, we found general dynamics (patterns of stability, fluctuations, and diverse change patterns) that could be linked to distinct developmental mechanisms. Fluctuating patterns pointed towards periods of instability (or crisis), during which youth appeared more sensitive to external stressors, and which typically marked the start of recovery. Whereas the worsening of youths’ problems typically occurred fast, recovery was a much slower process which required an autonomy-supported living environment, psychological interventions, and/or changes in youths’ school or living environment. We call for an interaction-based approach to diagnosis and care, in which psychological suffering is understood in the light of a person's history and developmental context.</p
Biochemical insights into Energy Coupling Factor (ECF) transporters and exploration of the inhibitory potential of novel binders
No full textABC transporters, ubiquitous across life, utilize ATP hydrolysis to translocate diverse substrates across membranes via conserved cytoplasmic nucleotide-binding domains. Their Type III subclass (energy coupling factor transporters, ECF transporters), exclusive to prokaryotes, employs distinct micronutrient uptake mechanisms. This thesis investigates ECF transporters' structure, mechanism, and potential as novel antimicrobial targets.PdxU2, the substrate binding domain for microbial vitamin B6 uptake in ECF transporters, was cloned from a deep sea hyperthermophilic archaeon Pyrococcus abyssi and purified using detergent to main stability. A low-resolution structure (4.6 Å) was obtained, but ligand binding remained unresolved.Mechanistic studies performed with ECF-PanT and ECF-FolT2 from Lactobacillus delbrueckii which transport vitamin B5 and B9 and reconstituted in proteoliposomes, showed that the transporters require ATP hydrolysis, and are not very sensitive to pH but have significant thermal sensitivity, indicating substantial conformational rearrangements during catalysis.ECF transporters are exclusive to prokaryotes, including pathogens, and are a hitherto underexplored drug target. A systematic structure-activity relationship (SAR) study of ECF inhibitors identified key inhibition determinants. We confirmed our inhibitors' antimicrobial activity against the human pathogen S. pneumoniae and demonstrated effectiveness correlates with ECF transporter expression, establishing them as novel druggable targets against antimicrobial resistance.Nanobodies (Nbs), featuring monomeric architecture and high-affinity specificity, are powerful structural tools. We generated nanobodies against ECF-PanT. Biochemical validation confirmed binding, and proteoliposome uptake assays demonstrated Nb inhibition of ATP-dependent transport. Two Nbs exhibited nanomolar affinity for ECF-FolT2. Cryo-EM structures of Nb-ECF-FolT2 in detergent micelles revealed Nb binding sites on nucleotide binding domain (EcfA), and the complexes were found in the apo-conformation
Looking through the neutral hydrogen glasses:the hidden population and clustering of gas-rich dwarf galaxies
No full textDwarf galaxies, defined as having at least ten times less stellar mass than our Milky Way, are the most abundant galaxy population in the Universe. Nevertheless, their observed properties often deviate from theoretical expectations, making them one of the least well understood classes of galaxies. This PhD thesis explores the diversity and clustering of dwarf galaxies using observations of an emission line of neutral hydrogen (HI) present in their interstellar gas. Unlike traditional optical surveys that rely on starlight, HI can be detected even in optically faint and diffuse galaxies, allowing dwarf galaxies to be identified regardless of their stellar distributions.This work shows that HI-detected dwarf galaxies are systematically larger for their stellar mass than those found in optical surveys and that ultra-diffuse galaxies—large but extremely faint systems—naturally emerge as part of the normal dwarf galaxy population, indicating that optical observations miss a significant fraction of the dwarf galaxy population. The thesis also demonstrates that interactions between dwarf galaxies are more common than previously indicated by optical studies and can significantly influence their star formation activity. In addition, this work reveals a faint stellar counterpart to a previously identified HI source thought to be a candidate dark galaxy, showing that some apparently starless systems may instead be distant or extremely faint dwarfs. Overall, this thesis highlights how observing galaxies through their gas provides a more complete picture of the low-mass Universe and helps refine models of galaxy evolution on the smallest mass scales
Should all polymyalgia rheumatica be referred to rheumatology? A call for unified stratified specialist care of the GCA-PMR spectrum
No full textEngineering <i>Escherichia coli</i> for the production of saturated archaeal lipids
No full textArchaeal membrane phospholipids have a different chemical composition than the phospholipids found in bacteria and eukaryotes. Typically, in archaea, phospholipids consist of saturated isoprenoid chains that are ether-bonded to glycerol 1-phosphate whereas in bacteria and eukaryotes, the main phospholipids are fatty acyl chains ester-bonded to glycerol 3-phosphate. This distinct chemical structure of phospholipids is believed to play a crucial role in enabling archaea to survive extreme environments and energy-limited conditions. Escherichia coli has previously been engineered to synthesize archaeal phospholipids next to its endogenous bacterial phospholipids. Cells equipped with these mixed heterochiral membranes were found to be viable with some improvement in robustness. However, a complete biosynthetic pathway for the production of substantial amounts of saturated archaeal lipids has not yet been realized in E. coli. Here, we engineered E. coli for the production of saturated archaeal phospholipids by introducing next to the geranylgeranyl reductase (GGR) and ferredoxin (Fd) from Methanosarcina acetivorans, the pyruvate-ferredoxin oxidoreductase (PFOR) from E. coli to allow for an efficient reduction of Fd. This resulted in a strain where approximately 75 % of the produced archaeal lipids are partially or completely saturated. Importantly, E. coli cells containing this mixed heterochiral membrane showed improved resistance to both heat and cold shock as compared to native E. coli strain. This E. coli strain with saturated archaeal phospholipids can serve as a valuable model for further engineering to incorporate different types of more complex archaeal membrane lipids.</p
Turning EU Consumer Law Against Itself? Taking Stock of the EU's Sustainable Consumption Strategy
No full textThe escalating ecological impact of private consumption has generated growing momentum among policymakers to promote sustainable consumption. This article critically assesses the EU’s strategy for sustainable consumption within the broader political economy of the Union. Grounded in the information paradigm, the EU’s primary approach has been to empower ethical individual choice to drive market change, though the recent emergence of by-design regulatory measures signals a positive move towards making sustainable consumption the market default. Yet these measures remain modest in scope and riddled with inconsistencies. At its core, this reflects the enduring neoliberal capture of the EU’s sustainable consumption agenda, which recasts sustainability from a collective public good into a private commodity to shop for. As a result, prospects for a fundamental transformation of consumption in the EU remain remote. The article argues that taking planetary boundaries seriously requires a more radical reorientation of EU consumer law – one that turns it against its own consumerist bias
Ecological Momentary Assessment for Assessing Affect Patterns Associated With Depression in Cancer Survivors in Primary Care:A Pilot Study
No full textINTRODUCTION: Depressive symptoms are common in cancer survivors. Recognizing depression can be complicated due to recall bias or oncological treatment-related symptoms including cognitive problems, which in turn may undermine the reliability of self-report questionnaires.AIM: To explore the feasibility and patient satisfaction of smartphone-based Ecological Momentary Assessment (EMA) in primary care cancer survivors.METHODS: Patients > 18 years, curatively treated for cancer within the past two years, regardless whether they experienced depressive symptoms, were selected based on the GPs' health records. EMA questionnaires were sent three times daily for 6 weeks, covering positive and negative affect, along with related experiences. Patients received weekly EMA feedback reports. After the EMA period, they completed an evaluation questionnaire and participated in a follow-up phone call to discuss their EMA experiences.RESULTS: Patient recruitment achieved a reach of 17.0% who were invited for participation (158/931), of whom 33/158 agreed to participate yielding a response rate of 20.9%. Patients found the EMA questions clear and study participation easy with a completion rate of 67% among those who started. However, 64% felt the frequency of EMA prompts was excessive, with 52% considering the 6-week duration appropriate and 48% feeling it was too long. During phone call evaluations, patients reported becoming inattentive with filling out the EMA's. Weekly reports were viewed as relevant and provided valuable insights into levels and changes in their mood.CONCLUSION: The relatively low reach and response rate do not entirely support the feasibility and acceptability of a 6-week EMA in cancer survivors in primary care without depressive symptoms. EMA was, however, completed by a majority among those who started and was regarded as a user-friendly tool that offered valuable insights to individuals. It could potentially benefit cancer survivors or other patients who do experience depressive symptoms in primary care.</p
Real-Time Pathways of Hierarchical Self-Assembly in Artificial Light-Harvesting Nanotubes
No full textNature has perfected the art of self-assembly, in which disordered individual components spontaneously organize to form ordered structures. A prime example is the light-harvesting antennae (chlorosomes) in green sulfur bacteria, which absorb sunlight and efficiently transport energy for photosynthesis. This thesis investigates how individual dye molecules (labeled C8S3) spontaneously organize into double-walled cylindrical nanostructures upon the addition of water, structures reminiscent of chlorosomes in green sulfur bacteria.The thesis begins by investigating how outer nanotube reforms after selective dissolution, and extends these insights to the complete self-assembly process. The thesis concludes by exploring how guest molecules influence self-assembly dynamics and the resulting double-walled structure. We employ a microfluidic system in which reagents are mixed, establishing precise timing: the mixer marks "time zero," and as the sample flows downstream, self-assembly proceeds spatially. By sampling at different flow-cell positions, we capture snapshots of assembly at known time intervals, enabling real-time observation. We combine optical spectroscopy and electron/optical microscopy to reveal the whole picture. The former infers the underlying molecular structure by studying how molecules absorb and emit light, while the latter visualizes physical features such as diameter and length. Together, these methods reveal both the molecular-level details and the macroscopic organization during self-assembly.The results establish a general framework for real-time monitoring of self-assembly. This understanding of how molecules cooperatively build complex architectures from the bottom up provides fundamental insights into self-organizing systems. Such knowledge has broad implications for nanotechnology, materials science, and our understanding of how nature constructs sophisticated molecular systems
Thiophenol-Based Designer Enzymes
No full textNew synthetic building blocks for creating artificial (metallo)enzymesChemical reactions drive many essential processes, but often proceed too slowly to be practical. Catalysts speed up these reactions, and enzymes, which are proteins that act as biocatalysts, do this with great precision and under sustainable conditions. However, their scope is limited because they are built from only twenty natural building blocks. Artificial enzymes overcome this limitation by adding new synthetic building blocks that do not exist in nature.The PhD research of Mathijs Veen focuses on a special class of such building blocks: thiophenols. These small sulfur-containing groups have useful catalytic properties, but can be difficult to use in synthetic chemistry, partly because of their instability. By incorporating them into proteins, their reactivity can be combined with the selectivity of enzymes.Veen first explored how thiophenols can be incorporated into proteins with genetic methods. He then showed that the presence and position of the thiophenol within the protein strongly influences both activity and selectivity in model reactions. The work also demonstrates that thiophenols can anchor metals, such as gold, at precise locations in a protein. This enabled the creation of stable artificial metalloenzymes capable of performing complex reactions, including stereoselective transformations, which had not been achieved before with gold catalysis inside an enzyme