Publikationer från Uppsala Universitet
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Gene copy number variations in Capsella rubella(a target control approach)
No full textABSTRACT Structural variations, particularly gene copy number variations (gCNVs), play an important role in shaping genome architecture and evolutionary potential. Despite their biological significance, gCNVs remain understudied in many plant species, including Capsella rubella, a self-fertilizing member of the Brassicaceae family. In this thesis, I investigated genome-wide gCNVs in C. rubella by integrating multiple approaches to improve detection reliability. Using whole-genome resequencing data, I used the rCNV package to identify CNV candidates based on deviations in allele ratios and excess of heterozygosity. To complement this, I used ArDu, a read depth –based method, to estimate copy number across the genome. The combined application of these two tools allowed for a more robust and comprehensive identification of gene CNV. Five genes showing strong CNV signatures in both rCNV and ArDu analyses were selected for experimental validation using quantitative PCR (qPCR). While qPCR results confirmed the presence of CNVs in several genes, discrepancies between computational and experimental results highlighted important limitations, such as potential biases in read depth normalization and primer efficiency. Nonetheless, the general consistency observed in specific genes demonstrated the potential for combining bioinformatic and molecular approaches in CNV research. This study contributes valuable insight into the structural variation landscape of C. rubella and underscores the need for integrated CNV detection strategies. The results lay a foundation for future work investigating the inheritance and evolutionary impact of gCNVs, including ongoing experiments that explore segregation patterns of gene duplications across generations. Keywords: Capsella rubella, gene copy number variation, qPCR, structural variation, genome analysi
From Livelihoods to Lasting Peace? : Evaluating Employment-Based Peacebuilding in Colombia’s Conflict-Affected Regions
No full textThis study explores how employment projects with peacebuilding outcomes in Colombia incorporate theories of change and conflict sensitivity, and whether these elements influence project results. Previous research identifies employment as a pivotal peacebuilding activity, while this relation is under-explored. A more nuanced understanding of the potential of project design could assist in the development of more effective peacebuilding and humanitarian interventions. A structured coding scheme was employed to analyse three projects, focusing on four core causal theories, Opportunity, Grievance, Contact, and Competition, as well as conflict sensitivity and inclusion. The findings indicate that few projects exhibited clarity in articulating and monitoring their theories of change, and that conflict-sensitive design was applied in an inconsistent manner. Furthermore, there was a noticeable absence of meaningful inclusion of afro-descendant communities and youth. The results of the study suggest that clearer intervention logic and context-aware design may enhance peacebuilding outcomes, while also informing humanitarian action manoeuvring employment-based interventions. The necessity for more rigorous, locally grounded research to better understand the employment/peace nexus in conflict-affected settings is further emphasised
Tillgångstillväxt-anomalins förekomst på den svenska aktiemarknaden
No full textVi undersöker sambandet mellan företags tillgångstillväxt och efterföljande aktieavkastning på den svenska aktiemarknaden under perioden 2019–2024. Tidigare forskning har empiriskt identifierat ett negativt samband mellan tillväxten i totala tillgångar och framtida riskjusterad avkastning. Sambandet beskrivs som en anomali i förhållande till den effektiva marknadshypotesens svaga form. På senare tid har det däremot framkommit studier som ifrågasätter huruvida tillgångstillväxt-anomalin fortfarande förekommer på aktiemarknader globalt. Genom portföljsorteringar baserade på marknadsvärde och tillgångstillväxt utvärderas både totalavkastningen och Jensens alfa för likaviktade och värdeviktade portföljer. Studien finner inget belägg för att sambandet föreligger under den studerade perioden på den svenska aktiemarknaden. Resultaten uppvisar delvis positiva och signifikanta avkastningsspridningar för likaviktade portföljer på hela svenska marknaden, men är överlag inte tillräckligt robusta för att fastslå att tillgångstillväxt-anomalin existerar på den svenska aktiemarknaden under 2019–2024
Article The burning glass effect of water droplets triggers a high light-induced calcium response in the chloroplast stroma
No full textPlants rely on water and light for photosynthesis, but water droplets on leaves can focus light into high-intensity spots, risking photodamage. Excessive light can impair growth or induce cell death, making it essential for plants to detect and respond to light fluctuations. While Ca2+ signaling has been linked to high light (HL) acclimation, the subcellular dynamics remain unclear. Here, we investigate Ca2+ responses to HL exposure in Arabidopsis thaliana. Using a glass bead to simulate light-focusing by water droplets, a biphasic increase of Ca2+concentration was detected in the chloroplast stroma by the genetically encoded calcium indicator YC3.6 and confirmed using a newly established stroma-localized R-GECO1 (NTRC-R-GECO1). The stromal response was largely independent of light wavelength and unaffected in phot1 phot2 and cry1 cry2 mutants. Chemical inhibition of photosynthetic electron transport, microscopy-based Fv/Fm experiments, and measurement of the reactive oxygen species (ROS)-redox balance with roGFP-based reporters and Singlet Oxygen Sensor Green (SOSG) chemical dye suggested that photodamage and singlet oxygen contribute to the stromal Ca2+response. While blue and white light also triggered a Ca2+response in the cytosol and nucleus, pharmacological inhibition with cyclopiazonic acid (CPA) and loss-of-function mutants of the Ca2+trans-porters BIVALENT CATION TRANSPORTER 2 (BICAT2) and endoplasmic reticulum (ER)-type Ca2+-ATPase (ECA) suggested that the HL response depends on a Ca2+ exchange between the ER and chloroplast stroma. The response was primarily light dependent but accelerated by increasing external temperature. This study implicates a novel Ca2+-mediated acclimation mechanism to HL stress, a process of growing relevance in the context of climate change
Fermiology and Band Structure of Oxygen-Terminated Ti3C2Tx MXene
No full textThe class of two-dimensional carbides and nitrides known as MXenes exhibit remarkable electronic properties. Tailoring these properties, however, requires an in-depth understanding of the band structure and Fermi-surface topology. Surface oxidation of MXenes has previously hampered the characterization of their Fermi surface, which is crucial for understanding the topology and anisotropy in the electronic structure and, ultimately, for tailoring electronic properties. Here, we reveal the Fermi surface topology and band structure of purely oxygen-terminated Ti3C2Tx MXene achieved through rigorous thin film sample preparation and ultrahigh vacuum annealing. Polarized synchrotron radiation-based angle-resolved photoemission spectroscopy reveals electron pockets, bulk band gaps, and a Dirac-like feature in the anisotropic electronic band structure. This paves the way for a fundamental understanding of band engineering of electronic transport properties, providing insights of importance for energy storage devices, transparent conductors, and catalysis
Ion-beam channeling in a single-surface modified Si membrane
No full textThe scattering and energy distributions of ions (22Ne+ and 4He+) transmitted through a Ga implanted singlecrystal Si (00 1) membrane are studied both experimentally and with a Monte-Carlo binary collision approximation code (IMSIL). The membrane is studied in both a [001] orientation to the ion beam as well as an inverted orientation. Both the scattering and energy distributions of the transmitted particles reveal a strong dependence on the membrane orientation due to the amorphization of the Si surface. When ions well-aligned to the [001] axis first encounter the crystalline layer, they primarily travel along the axial channel before being randomly scattered by the amorphous surface layer, yielding a random scattering distribution. Alternatively, when the trajectories are initially randomized by the amorphous surface, a large fraction of the ions are directed to higher energy-loss pathways upon entering the crystal, such as planar channels and random trajectories. The resulting scattering distribution reveals the crystalline features of the sample (e.g., star pattern) but with a larger energy spread and a higher average energy loss than the former case. This work aims to extend transmitted ion beam imaging and ion energy-loss analysis in the key range to complex heterostructures with both crystalline and amorphous regions
Finding the cracks : How do frontline officials maneuver state institutions to advance Indigenous rights to land and environment?
No full textThis paper challenges the monolithic portrayal of the state as inherently 'bad' when it comes to implementation of Indigenous rights. Offering a comparative analysis of case studies from four continents we demonstrate examples of frontline state officials proactively advancing Indigenous rights to land and environment. Combining distinct literatures on institutional theory, we develop an analytical framework that sheds light on bureaucratic agency within state-Indigenous relations. The findings show how government organizations maintain a broadly colonial agenda, but that officials on the inside sometimes manage to advance decolonizing or otherwise supportive actions. We propose the concept of institutional braiding to describe this agency exerted by state officials in collaboration with Indigenous representatives when navigating co-existing normative orders. By examining the fraught institutional constraints faced by frontline actors, we contribute to debates on Indigenous-state relations and the prospects of reaching common ground in the contact zone between divergent ontologies
From Second to First Language Learning: A Close Reading of Noun Town and Its Theoretical Potential for Early Language Development
No full textThis thesis presents a close reading of the language learning game Noun Town, examining its instructional design through the lens of second language acquisition theories. Drawing primarily on Krashen’s Input Hypothesis and Swain’s Output Hypothesis, the study analyzes how the game supports language learning through contextualized, low-anxiety input and structured opportunities for meaningful output. Findings suggest that Noun Town provides rich, roughly-tuned comprehensible input (i+1) supported by visual cues and task-based interactions, while its speech-based output mechanisms encourage learners to notice gaps in their knowledge, test linguistic hypotheses, and engage in active reflection. The study also explores the game's affective design, including task goals and reward systems, in relation to Krashen’s Affective Filter Hypothesis. By mapping theoretical constructs onto actual gameplay mechanics, this research not only demonstrates the potential of Noun Town as a model for language learning game design but also highlights the broader applicability of these insights to first language acquisition. The thesis concludes by advocating for more empirically grounded studies and a more integrated application of language acquisition theory in the development of educational games
Shrinking Lung Syndrome as an Early Manifestation of Systemic Lupus Erythematosus : A Case Report With Literature Review
No full textSystemic lupus erythematosus (SLE) can involve the respiratory system through various manifestations, including the rare pulmonary complication known as shrinking lung syndrome (SLS). SLS is characterised by progressive dyspnoea, pleuritic chest pain, diaphragmatic elevation, reduced lung volumes, a restrictive pattern on pulmonary function tests, and decreased diffusing capacity for carbon monoxide. Diagnosing SLS is challenging, as it requires ruling out interstitial lung disease and significant pleural pathology. While the onset of SLS varies, it typically occurs around 4 years after SLE diagnosis. Here, we report the case of a 33-year-old woman with SLE who developed SLS as an unusual early manifestation of the disease. SLS should be considered in the differential diagnosis of respiratory symptoms in patients with suspected or confirmed SLE, even in its early stages. Early recognition and appropriate management are essential for optimising outcomes
Leveraging laser powder bed fusion to alter texture and mechanical properties of magnesium alloy WE43
No full textThe present work explored the potential of customizing the final part texture and mechanical properties of a biodegradable magnesium alloy (WE43, composition Mg-4 wt%Y-3 wt%Nd-0.5 wt%Zr) manufactured by laser beam powder bed fusion (PBF-LB). This was done by printing samples using two sets of laser scan strategies (670 and 900 rotation between consecutively scanned layers) and build directions (horizontal and vertically printed samples). Samples were characterized for density and microstructure, followed by in-depth texture analysis using both lab-based techniques and neutron diffraction measurements. The mechanical performance was evaluated through tensile testing. The findings in this work show that strong basal texture was generated in the build direction. This allowed for altering the mechanical strength of WE43, whereby horizontally built samples showed increased strength and Young's modulus under tensile loading in a direction normal to the basal texture. Laser scan strategy influences the overall texture, however with limited effect on the resulting mechanical properties for the two scan strategies under study. This study demonstrates the importance of sample design and build strategy for the resulting texture and final material properties