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  • 1151.
    Wärn, Caroline
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Deviating time-to-onset in predictive models: detecting new adverse effects from medicines2015Independent thesis Advanced level (professional degree), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Identifying previously unknown adverse drug reactions becomes more important as the number of drugs and the extent of their use increases. The aim of this Master’s thesis project was to evaluate the performance of a novel approach for highlighting potential adverse drug reactions, also known as signal detection. The approach was based on deviating time-to-onset patterns and was implemented as a two-sample Kolmogorov-Smirnov test for non-vaccine data in the safety report database, VigiBase. The method was outperformed by both disproportionality analysis and the multivariate predictive model vigiRank. Performance estimates indicate that deviating time-to-onset patterns is not a suitable approach for signal detection for non-vaccine data in VigiBase.

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  • 1152.
    Xie, Hao
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Metabolic engineering for optimizing isobutanol production in Synechocystis PCC 68032018Independent thesis Advanced level (degree of Master (Two Years)), 30 credits / 45 HE creditsStudent thesis
    Abstract [en]

    The diminishing of fossil fuels and growing concerns towards climate change have intensified biofuel production from renewable resources. Recently, progresses are made in microbial production of biofuels. Among various biofuels, isobutanol is gaining an increasing attention due to its high energy content and suitable chemical and physical properties, enabling it to be a suitable substitution of fossil fuel. In this study, instead of using heterotrophic microorganisms, we performed metabolic engineering of Synechocystis PCC 6803 (Synechocystis) for isobutanol production under autotrophic condition. After introduced 2-keto acid pathway, Synechocystis is able to produce isobutanol when provided with water, carbon dioxide and solar energy. When cultivated in an optimal condition (50 μmol photons m-1s-2 and adjusted pH to 7-8 with HCl), the engineered strain pEEK2-ST was able to produce 425 mg L-1 in-flask isobutanol titer and 911 mg L-1 cumulative isobutanol titer, respectively, in 46 days. There should be bottlenecks existing in 2-keto acid pathway based on the similar isobutanol production of strain pEEK2-ST with and without pyruvate addition. However, the attempt to identify potential bottlenecks of upstream genes by overexpressing ST and one of the three upstream genes failed, instead what we conclude is that the isobutanol production is tightly correlated to Kivd (ST) expression level. Thus, more strategies will be employed for identifying bottlenecks successfully and further improvement of isobutanol production in the future. In conclusion, this study demonstrates the importance of cultivation condition on isobutanol production in Synechocystis.

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  • 1153.
    Xie, Zexian
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Role of arrestin beta-1 genetic mutation on insulin-producing beta-cell viability2022Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
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  • 1154.
    Xiong, Ye
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre. Molecular Ecology and Evolution Lab , Lund University.
    Early dietary effects of arachidonic acid on gene expression linked to  immune response and metabolism in rural and urban Great Tit (Parus Major) nestlings2017Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    This study was conducted to test the silver spoon hypothesis that earlylife nutritional conditions impact development, performance and fitness of the birdsgreat tit (Parus major) nestlings. We investigated whether fatty acid affects immunityand metabolism during the altricial period by examining the expressions of geneTLR4 (immunity related) and COX 2 (metabolism related) against a dietarymanipulation on great tit nestlings in urban vs. rural environments. The resultssuggested that arachidonic acid had no significant effect on TLR4 expression, but atendency to induce immune response, regardless of urban or rural conditions. Thestrength of immune response was however negatively correlated with laying date. Theurban great tit nestlings had a higher COX 2 gene expression than rural ones, andarachidonic acid suppressed COX 2.Thus no strong support to the hypothesis was found for the studied great titpopulations. It showed, however, i) there is a tendency of increasing immune responsewith extra fatty acid in the diet, and ii) arachidonic acid suppress metabolism. Fattyacid involved in a multiple physiological processes and this complex need to beelaborated in future studies.

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  • 1155.
    Xu, Hui
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Is CD23 a pattern recognition receptor?2012Independent thesis Advanced level (degree of Master (Two Years)), 30 credits / 45 HE creditsStudent thesis
  • 1156.
    Xu, Wenbo
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Cut-and-paste transposable elements in the arbuscular mycorrhizal fungi Claroideoglomus claroideum2019Independent thesis Advanced level (degree of Master (Two Years)), 80 credits / 120 HE creditsStudent thesis
    Abstract [en]

    Arbuscular mycorrhizal (AM) fungi are important symbionts to most of the terrestrial plants. Recent genome sequencing projects revealed that many AM fungi have repetitive genetic elements in their genomes and among these repetitive genetic elements, cut-and-paste DNA transposable elements were very prevalent. For example, in Rhizophagus irregularis, up to 21% of the genome assembly content was associated with cut-and-paste DNA transposable elements. In Diversispora epigaea, up to 23% of the genome content can also be attributed to cut-and-paste DNA transposable elements. While cut-and-paste DNA transposable elements are very abundant in AM fungi, detailed studies on these repetitive elements have been lacking. In this study, we revealed the diversity of cut-and-paste DNA transposable elements in Claroideoglomus claroideum and identified many potentially autonomous transposable elements in the genome assembly of C. claroideum. The evolutionary relationship between the DNA transposons we identified and the established sequences in public databases were also investigated.

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  • 1157. YanHui, Fan
    et al.
    Qi, Shi
    JinFeng, Chen
    WenJuan, Wang
    HongXia, Pang
    JiaoWei, Tang
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    ShiHeng, Tao
    The rates and patterns of insertions, deletions and substitutions in mouse and rat inferred from introns2008In: Chinese Science Bulletin, ISSN 1001-6538, E-ISSN 1861-9541, Vol. 53, no 18, p. 2813-2819Article in journal (Refereed)
    Abstract [en]

    The rates and patterns of InDel (insertions and deletions) and substitution in rodent (mouse and rat) have been studied. The result reveals that deletions occur more frequently than insertions, and single nucleotide insertion and deletion are the most frequent in both mouse and rat. The frequencies of both deletions and insertions decrease rapidly with increasing InDels length, and the size distributions of both insertions and deletions can be described well by power-law. There are more AT-->G than GC-->AT substitutions in the introns of rat. However, there are more GC-->AT than AT-->GC substitutions in the introns in mouse. The deletion bias found in introns in mouse and rat supports the prediction that intron insertions are more deleterious than deletions because of reduced transcription and splicing efficiency. The patterns of substitution suggest that both composition and GC content are not equilibrium in the introns in rodents.

  • 1158.
    Yoshida, Emiko
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre. Uppsala University / Science for Life Laboratory.
    Occurrence, timing, and phylogeny of Candidatus Arthromitus spp. in non-human infants2024Independent thesis Advanced level (degree of Master (Two Years)), 30 credits / 45 HE creditsStudent thesis
    Abstract [en]

    Symbiont intestinal microbiomes contribute to host immunity, but may also contribute to autoimmune diseases. Segmented filamentous bacteria (SFB), designated Candidatus Arthromitus, are one of the key players in the gut microbiome. They have a unique cell cycle and are thought to play a role in immune establishment in infancy. 

    This research explored the feasibility of non-human primate infants as animal models for elucidating SFB function by analyzing previously published 16S rRNA gene sequencing data with the Divisive Amplicon Denoising Algorithm 2 (DADA2) algorithm and statistical methods. 

    Consequently, non-human primate infants as animal models for SFB investigation were seen as a potential option. However, the study also brought up questions about the species-specificity and transmission modes of SFB, thus additional research is needed.

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  • 1159.
    Yu, Hui
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Fidelity of protein synthesis using sequence reconstructed ancient Elongation Factor Tu2021Independent thesis Advanced level (degree of Master (Two Years)), 30 credits / 45 HE creditsStudent thesis
    Abstract [en]

    To maintain a healthy growth rate of living cells, protein synthesis must take place accurately and efficiently. Translation, the core step decoding the genetic information, governs both fidelity and efficiency. For keeping a low error level, translation mainly relies on the codon-anticodon basepairing of mRNA and tRNA, which is known as ‘initial selection’. Apart from that, nature also evolved proofreading to reduce errors in protein synthesis. The current study focuses on initial selection of the correct tRNA. 

    EF-Tu, Elongation Factor Thermo-unstable, is an essential housekeeping GTPase factor responsible for transferring aa-tRNA to the ribosome. EF-Tu contributes to accuracy of initial selection although the exact mechanism is unknown. Here we have characterized and compared two sequence reconstructed ancestral EF-Tus, which are 1.3 and 3.3 billion years old respectively. Using dipeptide formation assay, we obtained the Michaelis-Menten parameters for Leu-tRNALeu on a near-cognate codon. Comparing the specificity parameter kcat/KM for the near-cognate vs. cognate we determine the accuracy of tRNA selection. My results show lower efficiency but higher accuracy using ancestral EF-Tus supporting the theory of trade-off between efficiency and accuracy. We envisage that during evolution EF-Tu sacrifices some accuracy to achieve higher efficiency as seen with modern EF-Tus.  My results demonstrate that EF-Tu can coordinate both the fidelity and the efficiency of translation.

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  • 1160.
    Yuan, Xiao
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Visual Information and Interaction.
    Graph neural networks for spatial gene expression analysis of the developing human heart2020Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Single-cell RNA sequencing and in situ sequencing were combined in a recent study of the developing human heart to explore the transcriptional landscape at three developmental stages. However, the method used in the study to create the spatial cellular maps has some limitations. It relies on image segmentation of the nuclei and cell types defined in advance by single-cell sequencing. In this study, we applied a new unsupervised approach based on graph neural networks on the in situ sequencing data of the human heart to find spatial gene expression patterns and detect novel cell and sub-cell types.

    In this thesis, we first introduce some relevant background knowledge about the sequencing techniques that generate our data, machine learning in single-cell analysis, and deep learning on graphs. We have explored several graph neural network models and algorithms to learn embeddings for spatial gene expression. Dimensionality reduction and cluster analysis were performed on the embeddings for visualization and identification of biologically functional domains. Based on the cluster gene expression profiles, locations of the clusters in the heart sections, and comparison with cell types defined in the previous study, the results of our experiments demonstrate that graph neural networks can learn meaningful representations of spatial gene expression in the human heart. We hope further validations of our clustering results could give new insights into cell development and differentiation processes of the human heart.

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  • 1161.
    Yuting, Fan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Identify Astroglia Markers to Indicate theDevelopemental Neurotoxicity Induced by Paracetamol and Radiation2023Independent thesis Advanced level (degree of Master (Two Years)), 30 credits / 45 HE creditsStudent thesis
    Abstract [en]

    The brain is one of the most essential organs in our body. During the development of children, brain development is the crucial part. Astrocyte, as a homeostasis-maintaining glial cell, is very common and performs many functions in the brain. Astrocytes have been proven to have adaptive plasticity, contributing to learning and memory. The astrogliosis defense process conducted by astrocytes when brain injuries happen minimizes harmful effects. In this study, seven markers for both neurons and astrocytes were optimized and analyzed to research the process of astrogliosis and reveal the interactions between the relevant gene expression level and astrocyte histology from the usage of paracetamol and radiation during the brain development stages. Although the clinical doses of paracetamol and radiation during these periods are considered harmless, recent studies suggest that early contact with the medicine and radiation will have further consequences, especially in behavior. This study aims to identify astrocytic genes that have connections to neurotoxicity, using qPCR and immunohistochemistry to analyze the presence of the markers and if there is any relationship, a specific figure-based cell detection method is set up to become a possible disease prediction. This experimental study shows that the combined use of paracetamol and radiation could increase oxidative stress, and cells in the developing brain would enhance cellular defense against oxidative stress by upregulating Nrf 2 or the ratio of Nrf2/Keap1. And there was the loss of astrocytes in the hippocampus when receiving the toxin, which was also shown in the Jagged 1 upregulation and more Hes 5 gene expression in the same brain area. Paracetamol is the most common medicine for dealing with pain or fever. No matter the patient's age, finding the best ways to minimize the risk of developmental neurotoxicological effects is essential. The results of this study better explain the possible neurobiological impacts of ionizing radiation combined with relevant medicine.

    The full text will be freely available from 2025-09-01 12:13
  • 1162.
    Zacharouli, Markella-Achilleia
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Characterization of immune infiltrate in early breast cancer based on a multiplex imaging method2020Independent thesis Advanced level (degree of Master (Two Years)), 30 credits / 45 HE creditsStudent thesis
    Abstract [en]

    Breast cancer is the most common type of cancer among women worldwide. Multiple studies have reported the role of tumor-immune interactions and mechanisms that the immune system uses to combat tumor cells. Therapies based on the immune response are evolving by time, but more research is required to understand and identify the patterns and relationships within the tumor microenvironment. This study aims to characterize immune cell expression patterns using a multiplex method and to investigate the way different subpopulations in breast cancer patients’ tissue samples are correlated with clinicopathological characteristics.

    The results of this study indicate that there must be an association within immune cell composition and clinicopathological characteristics (Estrogen Receptor Status (ER+/ER-), Progesterone Receptor (PR+/PR-), Grade (I,II,III), which is a way to characterize the cancer cells on how similar they look to normal ones, Menopause, Tumor size, Nodal status, HR status, HER2) but validation in larger patient population is required in order to evaluate the role of the immune infiltration as a predictive / prognostic biomarker in early breast cancer.

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  • 1163.
    Zaferani, Bahareh
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Evolution of Male Mating Success During Local Adaptation in Seed Beetles2011Independent thesis Advanced level (degree of Master (Two Years)), 30 credits / 45 HE creditsStudent thesis
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    Bahar's master thesis
  • 1164.
    Zamany Company, Ayda
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    A method for efficient synthesis of RNase A, using inteins2016Independent thesis Advanced level (professional degree), 20 credits / 30 HE creditsStudent thesis
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  • 1165.
    Zarif Saffari, Amin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Exploring the diversity of unmapped reads from human deep sequencing2012Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    currently DNA and RNA sequencing are performed as standard parts of many scientific experiments. While the majority of the reads produced in these experiments do map to the genome of the organism of interest there are a significant fraction that do not. These reads have often been viewed as uninteresting and thus discarded, sometimes explained as errors created in the sequencing process. However, there may be a real possibility that these reads actually contain genomic sequences belonging to, but not currently in the genome ofthe organism investigated, as well as information about other organisms which live and thrivein the sample material. Considering this, it is of great interest to investigate these reads to see if they contain any usable information. In this project the unmapped reads from SOLiD sequencing of blood and saliva from a twin pair were assembled. The assembled parts were thencompared to different blast databases to investigate if similar genomic regions are reported inother species. We can conclude that indeed a large fraction of the contigs found in this assemblyhave homology to bacterial genes while other contigs share similarity to genomic regions foundin apes and other species closely related to us. All in all the results show that there is more to the unmapped reads than just sequencing errors.

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  • 1166.
    Zegarra Vidarte, Paula
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    CRISPR mutagenesis in genes involved in metronidazole resistance in Giardia intestinalis.2024Independent thesis Advanced level (degree of Master (Two Years)), 30 credits / 45 HE creditsStudent thesis
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  • 1167.
    Zellmer, Ursula Ronja
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    When age makes all the difference: Methane production in sediment of contrasting Swedish lakes2020Independent thesis Advanced level (degree of Master (Two Years)), 30 credits / 45 HE creditsStudent thesis
    Abstract [en]

    Lakes are a significant source of the powerful greenhouse gas methane (CH4) globally. Methaneis produced through microbial processes in anoxic sediments. Methane emission from lakes ishighly variable in space and time. Consequently, is it difficult to predict the methane production rate and at present time it cannot be predicted from sediment characteristics. Therefore, methane production in the sediment of contrasting Swedish lakes was investigated, in order to find out if methane production rate can be related to sediment characteristics, and if a predictive model that recently was developed for Brazilian reservoirs is applicable to Swedish lakes.

    For this, sediment cores were collected from six lakes, differing in their sediment characteristics and geographical position as well as one river. The sediment cores were sliced into one centimetre thick layers. The different layers were incubated and methane production rate was measured. The sediment layers were also analysed for water content, median grain size, total nitrogen and carbon content as well as age.

    The influence of sediment age and C:N ratio as predictors for methane production were tested with a mixed linear model and a non-linear model. Both models showed that age had a significant effect on methane production rate (p < 0.001). The C:N ratio also had a statistically significant effect on methane production rate only shown with the non-linear model, however this effect was weak.

    Applying the recently published predictive model for methane production rate in Brazilian reservoir sediments to this data from the Swedish lakes, provided a good prediction of methane production rate in the nutrient-rich Swedish lakes, however it overestimated the methane production rate of the humic-rich boreal lakes and sediment older than 50 years.

    In summary, a model using age as predicting factor was developed fitting all the studied Swedish lakes. In addition, the predictive model developed in Brazilian reservoirs for the methane production rate was valid only for the studied nutrient-rich Swedish lakes and the studied oligotrophic Swedish lakes.

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  • 1168.
    Zervakis, Panagiotis-Ioannis
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Patterns of diversity of sex chromosomes and mitochondria in sub- Saharan African populations2020Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Human genetic diversity is not distributed evenly around the globe, as it decreases along the route of modern human expansion, which originated in Africa. The ancestors of Khoe-San and rainforest hunter gatherers have been linked with the roots of human history and present unmatched diversity. While the field of human evolution is in an era of whole genome sequencing, a lot of our knowledge is based on older sequencing techniques using uniparental markers (Y chromosome and mitochondria). Here we wanted to investigate ways to process and study the Y and X chromosomes and the mitochondria from high coverage whole genome sequences; compare our results to past findings; and enrich our knowledge about understudied populations of sub-Saharan hunter-gatherers. In the study, we included 179 whole genome sequences out of which 25 Khoe-San, 29 rainforest hunter gatherers and 20 rainforest hunter gatherer neighbours. To process the data, we used variations of the Genome Analysis Toolkit (GATK) Best Practices workflow for autosomes. To characterize the populations, we looked into SNP variation and haplogroup characterisation of uniparental markers. Moreover, we investigated the X-to-autosome heterozygosity ratio. Our results suggest ways to efficiently process sex chromosomes and mitochondria from whole genome sequences. Moreover, we find elevated diversity levels in sub-Saharan hunter-gatherers, compliant with past studies. Finally, the X-to-autosome heterozygosity ratio indicates higher levels for Africans with small variations between populations.

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  • 1169.
    Zetterberg, Elvira
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Andersson, Evelina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Nilsson, Alma
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Qvarnlöf, Moa
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Olivero, Corinne
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Sulyaeva, Julia
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Development of a Python Pipeline for the Analysis of Campylobacter2022Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    Statens veterinärmedicinska anstalt, SVA, is a government agency that works for better animal and human health with a primary focus on infectious animal diseases. One of their projects involves tracking the spread of Campylobacter infection in broilers and the occurrence of antimicrobial resistance in these bacteria. A pipeline was developed to contribute to making the analysis of Whole Genome Sequencing (WGS) data from Campylobacter more effective. This was done by changing the currently used pipeline’s programming language from Perl to Python and adding the possibility to run multiple analyses in parallel. With parallelization, the time for running multiple analyses was reduced compared to running them sequentially, even if it was not as fast in practice as in theory. It also did not work as well when running parallel analyses of different strains compared to identical strains. Furthermore, different attributes of the pipeline were changed or added to improve the pipeline and a database comparison was performed in order to suggest the best ones for future use. VFDB, CARD, and MEGARes were suggested as appropriate databases to use in future WGS analysis of Campylobacter. Due to a lack of resources and technical difficulties, some of the requested attributes for the pipeline could not be implemented, such as the tool Pilon and the inclusion of MLST and cgMLST analysis. Nonetheless, the pipeline is well structured, has most of the requested tools, and is easy to run. With some minor improvements, the pipeline will be a useful tool for SVA and their project.

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  • 1170.
    Zetterlind, Bobby
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Plants' belowground secrets: Integrating root exudation characteristics into the root economic space and implications for soil microbial activity2022Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
  • 1171.
    Zeynep, Özahishali
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre. Karolinska Institutet.
    Investigating YTHDC1- RNA Interactions in Mouse Brain Tissue and Cell Lines Through LACE-Sequencing2024Independent thesis Advanced level (degree of Master (Two Years)), 40 credits / 60 HE creditsStudent thesis
    The full text will be freely available from 2027-06-01 20:08
  • 1172.
    Zha, Yinghua
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Effects of diversity and dispersal on the response of bacterial community to starvation perturbation2011Independent thesis Advanced level (degree of Master (Two Years)), 80 credits / 120 HE creditsStudent thesis
    Abstract [en]

    Bacterial diversity and ecosystem functioning (BEF) relationships have received considerable attention during the last three decades and tend to be positive in most cases. However, most studies were done in closed systems and largely ignored the importance of placing local communities into the metacommunity context, in which dispersal can be a crucial factor modifying community diversity and composition and ecosystem functioning.

    The aim of this study was to investigate the effects of both diversity and dispersal on the responses of bacterial community to a starvation perturbation. To achieve this, we implemented a batch culture experiment using the dilution-to-extinction approach to create a diversity gradient of local bacterial community richness. Different dispersal rates were manipulated by transferring cells in different quantities from a regional source to the cultures, and they were then exposed to a perturbation by transferring them into water from another lake which differed in organic carbon content and quality. We evaluated the BEF relationship by measuring the bacterial community composition using t-RFLP and multiple ecosystem functions. Generally, our results demonstrated that diversity and dispersal have an interactive and positive effect on ecosystem functioning. In particular, dispersal had a stronger and more pronounced effect on ecosystem functioning when bacterial diversity was low. When evaluating the responses of bacterial community respiration, no significant difference was observed among different treatments, however, there were clear differences in substrate utilization patterns, implying that specific functions, such as decomposing certain substrates, are more sensitive to a perturbation than general functions, such as respiration. Therefore it is important to include multiple functional parameters when studying BEF relationships and, in particular, when applying our knowledge to the conservation of natural environments.

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  • 1173.
    Zhang, Jiazhuo
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Isolation and Characterization of Uncultured Freshwater Bacterioplankton from Lake Ekoln and Lake Erken through Dilution-to-Extinction Approach and Molecular Analysis Tools2012Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Not many of the abundant freshwater bacterial groups have a representative cultured isolate. In this master thesis project, some abundant bacterioplankton from two lakes (Lake Ekoln and Lake Erken) could be isolated by a dilution-to-extinction approach. Sterilized lake water which was obtained through an ultrafiltration system was used resembling a natural medium. Specific fragments of 16s rRNA of the isolates were amplified by universal bacterial primers (27f and 1492r, 341f and 805r.) for genotyping against a freshwater sequence database and RDP training set (Version 7). A total of 33 isolates from the two lakes were taxonomically classified and revealed the isolation of typical and abundant freshwater bacteria. Original bacterial community of Lake Ekoln was also analyzed by 16S rRNA clone library construction for diversity study. Phylogenetic trees were built through neighbor-joining method by Mega (Version 5) to reveal the evolutionary relationships among database entries, obtained isolates and clones. 

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    thesis report
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    popular scientific report
  • 1174.
    Zhang, Jinghan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    The invasion of Smooth cordgrass (Spartina alterniflora) in China: risk assessment using spatial modeling2012Independent thesis Advanced level (degree of Master (Two Years)), 40 credits / 60 HE creditsStudent thesis
    Abstract [en]

    Smooth cordgrass (Spartina alterniflora) is one of the harmful quarantine weeds in China. Since its first introduction in China in 1979, this alien species has spread rapidly and damaged local ecological environments. Research to predict a suitable new area is an important step for management of the species and to prevent a further spread. In this study, Spartina alterniflora’s ecological niche was modeled using the application MAXENT. Analysis was based on species’ current distribution. The investigations of this study were two-fold. First, a large-scale global investigation (outside China) was conducted to predict suitable areas in China by comparing global and Chinese records of the species. In the second set, the combined records were used to predict suitable areas in the Jiangsu Province. The model’s accuracy was evaluated by Receiver Operator Characteristic (ROC) curve. The areas under the ROC curve (AUC value) were all over 0.95, which indicated high predictive ability of this model. In the large scale prediction, Shanghai, Zhejiang, Fujian, Guangzhou, Guangxi and southern part of Wuhan, Jiangsu and Anhui were all potentially endangered by S. alterniflora invasion. On the smaller scale, the prone to invasion areas were mostly concentrated on southern part and some coastal areas of Jiangsu Province, where the precipitation and temperature were appropriate for this grass. Because of S. alterniflora has high dispersal ability and human induced history, the potential distribution areas in China are considerable and it may invade more areas, in result spreading faster in the future. To prevent further invasion and spread, an early eradication program should be adopted in the newly invaded areas. Meanwhile, the monitoring programs should also need to be applied in potential survival areas, especially in coastal harbors, airports, and tourism areas which are highly vulnerable to S. alterniflora invasion.

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    The invasion of Smooth cordgrass (Spartina alterniflora) in China - risk assessment using spatial modeling
  • 1175.
    Zhang, Yu
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    The subthalamic nucleus in health and disease2020Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    Parkinson’s disease (PD) is the second most common neurodegenerative disorder in the world. PD is caused by degeneration of the dopaminergic neurons in the substantia nigra pars compacta (SNc). Deep brain stimulation (DBS) is a surgical therapy used in PD to alleviate motor dysfunction by application of high-frequency stimulation through implanted electrodes. STN is an important target of DBS electrodes in PD treatment. However, a series of side effects have been reported upon STN-DBS treatment, and the reliability of the method could be clinically improved. To achieve this, anatomical and functional studies in mice can contribute important knowledge. There are different models to explain the internal STN organization, each of which has experimental evidence. Previous work has shown that the Vesicular glutamate transporter 2 (Vglut2) and Paired-box homeodomain transcription factor 2 (Pitx2) genes are needed for normal development and function of the STN in mice. These genes are expressed throughout the STN and their use as markers for STN neurons has enabled functional studies. To progress, more knowledge of the internal organization of the STN would be useful. Here, three antibodies representing three potential STN markers were tested using immunohistochemistry. PCR analysis was used to genotype Pitx2-Cre transgenic mice that are currently used for functional and behavioral STN studies.

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    the subthalamic nucleus in health and disease
  • 1176.
    Zhao, Xinran
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    The Effects of Mast Cell Proteases on Human Lung Cells Population2019Independent thesis Advanced level (degree of Master (Two Years)), 30 credits / 45 HE creditsStudent thesis
    Abstract [en]

    Asthma is a devastating disease characterized by airway obstruction, inflammation, and bronchial hyperreactivity. Previous studies have implicated mast cells in the pathology of asthma, yet the role and function of mast cells in the early stage of human asthma development cannot be investigated in vivo for ethical reasons. In the present study, we investigated the mast cell proteases actions on primary cell populations, including primary human lung fibroblast (HLF) and primary human small airway epithelial cells (HSAEC). Mast cell chymase caused significant morphological effects on primary HLF by degrading extracellular matrix (ECM), such as fibronectin and collagen I, and activation of pro-MMP2. Chymase also regulated the cytokine synthesis and gene expression in primary HLF after 24 h treatment. Both tryptase and chymase stimulated primary HSAEC proliferation. These results indicate that mast cell proteases can have a profound impact during asthmatic airway responses.

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  • 1177.
    Zhivkoplias, Erik
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Comparing the performance of different methods to estimate selection coefficient across parameter space using time-series genomic data2020Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Estimating selection is of key importance in evolutionary biology research. The recent price drop in sequencing and advances in NGS data analysis have opened up new avenues for novel methods that estimate selection quantitatively from time-series allele frequency data. However, it is not yet well understood which method performs best given specific model systems and experimental designs. Here, using popular quantitative metrics, we compared the performance of four prominent methods on a series of simulated data sets and on data from real biological experiments. We identified in three out of four methods the experi- mental conditions best suited for estimating selection. We also explored the limitations of these methods when estimating selection from complex patterns of allele frequency change in some relevant evolutionary scenarios. Our findings highlight the need for modification of population genomics models that are still used in inference of model parameters with the goal to develop new, more accurate methods for the quantitative estimation of selection in time-series genomic data.

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  • 1178.
    Zhou, Yan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Regulation of Aurora A activity during checkpoint recovery2012Independent thesis Advanced level (degree of Master (Two Years)), 30 credits / 45 HE creditsStudent thesis
    Abstract [en]

    Cell division requires accurate DNA replication and cells develop checkpoint mechanisms toensure the correct passage of the genetic material. Cells arrest by a checkpoint when DNAdamage is found. After the checkpoint is silenced, the cell cycle can be resumed. Polo-likekinase 1 (Plk1) and Aurora A kinase (AurA) are both important regulators for checkpointrecovery. The question how AurA is activated was studied by many researchers, but the exactmechanism stays unclear.We developed a new setup to study AurA activation during checkpoint recovery. Quantitativeimmunofluorescence of fixed cells as well as a FRET probe that monitors Plk1 activity intime-lapse filming were applied in this study as indirect readouts of Aurora A activation. Theresult suggests that a Plk1-AurA feedback loop exists during checkpoint recovery. It can alsobe concluded that the inhibition of Cdk1 reduces Plk1 and AurA activity during checkpointrecovery. We also investigated the effect of calcium interfering drugs on AurA activation butno conclusive result was obtained.

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    Yan.Zhou.report
  • 1179.
    Zhu, Xu
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    IL13R⍺2-CAR T cells for Immunotherapy of Glioblastoma2021Independent thesis Advanced level (degree of Master (Two Years)), 40 credits / 60 HE creditsStudent thesis
    Abstract [en]

    Glioblastoma is the most malignant form of gliomas and is a highly infiltrative while non-metastatic tumor of the central nervous system. Patients with glioblastoma have a poor prognosis of 15 months median survival after diagnosis. Promising results were reported in recent clinical trial regarding glioblastoma treatment with chimeric antigen receptor (CAR) T therapy. The lab has previously developed five novel scFvs targeting IL13R⍺2, a tumor-associated antigen in glioblastoma, and integrated them into the second-generation CAR. We named them, 10CAR, 27CAR, 55CAR, 75CAR and 117CAR. The ex vivo cytotoxicity and proliferation assay demonstrated that the 117CAR T construct has the best functionality, while 27CAR T construct has a poor functionality compared to the rest of the constructs. FACS analysis was performed to check the CAR expression in different constructs. 27CAR T cells showed the lowest surface CAR expression and 117CAR T cells displayed the highest out of five constructs. 27CAR T cells were also activated more without stimulation compared to other constructs. We selected out 27CAR and 117CAR T cells for the further investigation to understand the attribution of the discrepancy between 27CAR and 117CAR T cells.

     

    We observed a larger cellular size for 27CAR T cells compared to the rest constructs in flowcytometry analysis, which is usually associated with activation. IFN-γ production of all constructs without target cells stimulation were detected to examine the activation state of different constructs. We observed the highest IFN-γ production in 27CAR T cells without stimulation. These results together indicate that a potent antigen-independent activation or, in other words, tonic signaling is present in 27CAR T cell. The tonic signaling further leads to an early exhaustive phenotype of 27CAR T cells, that is not present in 117CAR T cells. Removing the endodomain of CAR rescued the antigen-independent activation and early exhaustion of 27CAR T cells.

    The surface and total CAR expression of 27CAR and 117CAR T cells were determined by flowcytometry. 27CAR T cells presented a lower expression of both surface and total CAR. A significantly lower percentage of total CAR on the surface indicates the internalization of CARs in 27CAR T cells. Removing the intracellular domain of 27CAR did not restore the surface expression of CAR. 27CAR and 117CAR differ in four CDRs of scFv, CDR1, 2,3 in the heavy chain and CDR3 in the light chain. We replaced all the amino acids differing between these two constructs with alanine in a CDR-by-CDR manner and obtained five alanine substitution constructs. We then analyzed the CAR expression in Jurkat cells, and we found that the trafficking of CAR to the surface was significantly improved by mutating the CDR2 in the heavy chain or CDR3 in the light chain. Moreover, when the two CDRs were replaced simultaneously, almost all transduced cells expressed CAR, as was the case of cells transduced with 117CAR.

     

    To summarize, the tonic signaling induced by higher tendency of clustering of 27scFv results in the antigen-independent activation and early exhaustion of 27CAR T cells. By removing the endodomain of 27CAR, we abrogated the phenomenon. Further, CDR2 in heavy and CDR3 in light chain in 27scFv are responsible for the impaired trafficking of CAR to the surface.

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  • 1180.
    Zhu, Yishu
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Evolution of body size plasticity and epigenetic inheritance of phenotypic response after sex-specific selection in a seed beetle2021Independent thesis Advanced level (degree of Master (Two Years)), 40 credits / 60 HE creditsStudent thesis
    Abstract [en]

    Phenotypic plasticity is commonly observed in nature, though little is known about the genetic architecture underlying this phenomenon. Using artificial selection lines of the seed beetle Callosobruchus maculatus, I aimed to investigate evolution of body size plasticity in the context of interplay between sex-specific selection and thermal stress, and the epigenetic inheritance of the parental phenotypic response. Contrary to my initial expectation, sexually antagonistic selection did not preserve more plasticity relative to directional selection. Rather, absolute plasticity positively changed with increasing body size after selection. Relative plasticity (per body weight) changed less and in opposite direction. This suggests high correlation of plastic body size variation with mean body size, and a partially independent genetic architecture of the relativized aspect of plasticity. Still, plasticity is sex specific and environmentally sensitive, generating possibility of some variation in sexual size dimorphism across environments. Developmental mechanism behind different temperature responses lies in diverging growth rate and developmental time. Cross- and trans-generational effects were observed, confirming that plastic response to environmental conditions can be epigenetically inherited and can potentially evolve. My results highlighted the importance of understanding the relationship between selection, phenotype, and plasticity, and showed that environmental stress could have prolonged effect through epigenetic inheritance.

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  • 1181.
    Zillén, Linnea
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Characterization of monoclonal antibodies (mAb) using high resolving analytical techniques2019Independent thesis Advanced level (professional degree), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    In monoclonal antibody (mAb) production, multiple variants are introduced. These changes will affect the final product and due to product heterogeneity it is of importance to monitor these to ensure final product quality. In this master thesis, a multi attribute monitoring method by mass spectrometry (MAM-MS) was developed and then applied on a large bioreactor sample set. The goal with this project was to develop, evaluate and apply the developed method on mAb bioreactor samples. A purification method using PreDictor MabSelectTM PrismA affinity capture followed by a digestion method was developed and optimized. Both the affinity capture and tryptic digestion methods showed to be robust and reproducible. Two LC-MS/MS methods were developed, one data dependent acquisition method for identification of post-translational modifications (PTM) and one data independent acquisition method for quantification of PTMs. Using the developed MAM-MS method, identification and quantification of modifications of interest was possible. The mAb standards used during the whole all experiments during this project indicates that the approach is robust and reproducible. The technique showed promising results, indicating that there is a possibility for future implementation of the techniqe at GEHC. Further work on the method and a deeper comparison to currently used methods are required, to ensure that the MAM-MS method can replace the classical methods that are used today for PQA analysis of mAbs.

  • 1182.
    Zou, Yimin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Optimization of super rolling circle amplification (sRCA) for detecting the cfDNA mutation in patient genomic samples2021Independent thesis Advanced level (degree of Master (Two Years)), 30 credits / 45 HE creditsStudent thesis
    Abstract [en]

    Long-chain polyunsaturated fatty acids (LC-PUFAs) are essential fatty acids to human, which is synthesized and metabolized in the liver. Altered levels of LC-PUFA has been associated with various lipids levels and risk of several diseases. The fatty acid desaturase 1 (FADS1) gene is one of the genes that encode the rate-limiting enzymes in the biosynthesis of LC-PUFAs endogenous. Genetic variation of FADS1 can regulate the synthesis of LC-PUFAs and then affect the disease risks. Haplotypes in FADS1 gene can perform as valuable biomarkers in molecular diagnostic approaches. Effective medical diagnostics technology based on the detection of biomarkers such as cell-free DNA and surface protein plays an essential role in diagnosis and disease monitoring. In recent years, rolling circle amplification (RCA) has been used for specific sequence detection in genomic samples, due to its simple procedure and high amplification efficiency. To further increase the sensitivity and specificity of FADS1 haplotypes detection in extremely low-abundance genomic samples, the super RCA (sRCA) protocol was completed and optimized in this study. The results showed more stable output and reproducibility of optimized sRCA protocol compared with a preliminary sRCA protocol. The accuracy of the optimized protocol was verified by evaluating the consistency of sRCA results with the PacBio sequencing results. SRCA has double recognition steps and the excellent amplification efficiency that effectively improve the sensitivity, fidelity and specificity of single-nucleotide polymorphism (SNP) detection. Under the optimum reaction conditions, sRCA has a significant improvement in sensitivity and specificity compared with traditional RCA, with a low detection limit of 1.3 fM and a higher product conversion rate of 42% (±13%) on average. To conclude, the optimized sRCA showed good potential to serve as a sensitive method for haplotype detection in the future.

  • 1183.
    Zu, Pengjuan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Effects of Nectar Production and Pollinator Assemblies on Mating Patterns in Orchids2011Independent thesis Advanced level (degree of Master (Two Years)), 30 credits / 45 HE creditsStudent thesis
    Abstract [en]

    Pollinator visitation patterns should affect pollination success and mating patterns in flowering species. In the orchid family, about one third of the species do not provide any reward for their pollinators. Pollination by deceit is typically associated with low fruit set but may increase the chance of cross-pollination since the pollinator should soon leave the individual plant when there is no reward in the flowers. This may be beneficial if self-fertilisation results in inbreeding depression. I studied the mating patterns of one rewarding and one deceptive orchid in two closely related genera by tracking the fate of stained pollinia. I also conducted controlled crosses to estimate inbreeding depression. The results show that the deceptive orchid Dactylorhiza lapponica has lower pollination success, but higher cross-pollination rate (ca. 90%) than the nectariferous orchid Gymnadenia conopsea (ca. 18% cross-pollination). The results further suggest that in G. conopsea, nocturnal visitors mediate higher geitonogamous pollination rate (ca. 100%) than diurnal visitors (ca. 60%). In both study species, fruits produced from cross-pollination were heavier than fruits produced from selfing. Inbreeding depression for fruit mass did not differ significantly between the two species (δ = 0.21 in D. lapponica and δ = 0.29 in G. conopsea). These data support the hypothesis that pollination by deceit can enhance cross-pollination. A literature study including several rewarding and non-rewarding orchid species indicated lower geitonogamy in the deceptive orchids, but the difference was not statistically significant. 

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    Effects of Nectar Production and Pollinator Assemblies on Mating Patterns in Orchids_Zu
  • 1184.
    Zucchetti, Paolo
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Developing a real-time assay for characterizing antibody internalization2023Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
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  • 1185.
    Ágreda López, Gabriela
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Are legacy effects important for the response of phytoplankton communities to nutrient and dissolved organic matter pulses?2023Independent thesis Advanced level (degree of Master (Two Years)), 60 credits / 90 HE creditsStudent thesis
    Abstract [en]

    Climate change predictions include increasing precipitation and runoff events that expose phytoplankton communities to colored dissolved organic matter (cDOM) and nutrient pulses of varying intensity and frequency. The consequence of different nutrient/cDOM pulse regimes on phytoplankton communities and the role of legacy effects related to the characteristics of previous exposure regimes remain largely unresolved. To investigate this, we implemented add-on bottle experiments with water collected from a mesocosm experiment conducted in Lake Erken (Sweden) with four nutrient regime treatments with varying intensity and frequency. The nutrient additions of the mesocosm experiment lasted for three weeks and were followed by a two-week recovery period. At the end of both periods, water from three mesocosm treatments was filled into microcosms and either exposed to a second single nutrient pulse or left as control. The microcosms were incubated for 8 days in the lab and changes in phytoplankton biomass and composition were analyzed to determine the legacy effect of antecedent nutrient regimes on the community response to a second nutrient addition. The results showed that past nutrient regimes created legacy effects on the community, dampening further changes in response to a second nutrient addition. However, the effects were transient, since they were not detected in the second microcosm experiment. Further, the lack of legacy effects in the second microcosm experiment suggests that the communities from the mesocosm treatments in fact recovered from the nutrient regimes they were exposed to in the two-week period. Consequently, the results of the thesis suggest that legacy effects may be important in predicting phytoplankton community response to extreme nutrient and cDOM pulses but they might be temporary.

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  • 1186.
    Ásmundsdóttir, Ragnheidur Diljá
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Effect of ascertainment bias on calculations of sex-biased admixture in Southern Africa2021Independent thesis Advanced level (degree of Master (Two Years)), 30 credits / 45 HE creditsStudent thesis
    Abstract [en]

    Southern African populations harbour great genetic diversity enhanced by  population migration to the area in the last two millennia. Africa is perhaps the least studied continent in regards to population genetics and is often underrepresented in global studies. Studying sex-biased admixture in admixed populations is a great tool to understand population demographic history as well as sex-biased admixture from past events. Various studies on sex-biased admixture in Southern Africa have shown male sex-biased admixture from the incoming Bantu-speaking populations. One study by Hollfelder (2018) shows female Bantu-speaking sex-biased admixture.

    Here I will try to determine if ascertainment bias is the cause of the unexpected results in Hollfelder (2018). I will do this by comparing the original results, genotyped using the Illumina Omni 2.5M Array, to overlapping SNPs in two different arrays, the Affymetrix Human Origin Array and the Infinium H3Africa Consortium Array. Additionally, I will use whole genome data containing same individuals and individuals from similar populations to form a hypothesis on how the sex-biased admixture should look like without ascertainment. Then extracting variants from the whole genome data to two array SNP panels, the Illumina 2.5M Array and the Infinium H3Africa Consortium Array. For both parts in my project a method by Goldberg and Rosenberg (2015) will be used to calculate female and male contribution from admixture proportions of the X-chromosome and the autosomes estimated using the software ADMIXTURE.

    The results obtained could not determine if ascertainment bias was the sole factor skewing the results. The overlap with the Affymetrix Human Origin Array showed results closest to expected results based on previous studies, suggesting that ascertainment bias likely affects the results. The results attained using the whole genome indicated that the genotype calls of individuals present in both parts of the study did not fully match and that was confirmed using a principal component analysis.

    Unfortunatly the data used and analytical limitations in this project did not yield answers to how ascertainment bias affects calculations on sex-biased admixture. The X-chromosome is difficult to work with, especially when using data from multiple publications, as there is no standard common best-practice pipeline available on how to process the data leading to different data sets having been treated differently, which possibly affects downstream analysis when combining data sets.

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  • 1187.
    Åberg, Adam
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Could Lithospermum officinale be bird dispersed?: A greenhouse experiment2015Independent thesis Advanced level (degree of Master (Two Years)), 30 credits / 45 HE creditsStudent thesis
    Abstract [en]

    Common gromwell (Lithospermum officinale) acts as a host plant for the monophagous moth Ethmia dodecea  whose larvae are completely dependent on the leaves. As conservation authorities now want to reinstate the regionally extinct moth to Mälardalen, a stable population of its host plant is a requirement. To facilitate the work of strengthening the presence of gromwell a partnership was therefore initiated between Västmanland County Board and Uppsala University. In this cooperation, I performed two studies. In the first one I examined how water and temperature affect plant germination and how nutrient levels affect early growth. In the second study I investigated whether the germination is influenced by chemical treatment (soaking in acid) and mechanical damage (seeds scratched with sandpaper) on the seeds. I worked with the hypothesis that gromwell is grazed by cows and is therefore dispersed and germinates in the spring. This should mean high water levels combined with high temperatures would produce higher germination. For the second study, it means that the germination rate should be higher in the seeds treated with the acid than in the scratched and control treatments. In the first study, so few seeds germinated that I could not draw any conclusions, but germinations appear to go faster in the combination with high nutrients high temperature and frequent watering. In the second study, the seeds scraped with sandpaper had the highest germination rate. This indicates that gromwell may be dispersed by birds, and I propose sandpaper rubbing as a method to easily increase the germination rates of L. officinale in greenhouses in order to reinforce small populations in the field. 

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  • 1188.
    Åberg Villacis, Carolina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    The role of inbreeding in female reproductive behaviour in seed beetles (Callosobruchus maculatus)2022Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
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  • 1189.
    Åhlin, Mikaela
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Mapping the binding site of the Hof1p SH3 domain in the Bnr1p FH1 domain2014Report (Other academic)
    Abstract [en]

    The unusual syndrome Wiskott-Aldrich Syndrome has been found to be linked to a mutation in a gene expressing the Wiskott-Aldrich Syndrome protein (WASp). Due to the conservation of certain mechanisms and the homologous proteins from lower to higher eukaryotes, yeast has been used to study the molecular mechanisms that underlie diseases in humans. The yeast WASp homologue, Las17p (Local Anaexthetic Sentivie 17) and the yeast homologye Vrpp of its (i.e. human WASp) partner protein known as WIP (WASp-interacting protein), have been studied with the intention to investigate the phenotypes that arise in cells deficient in Vrp1p. A protein-protein interaction is believed to occur in the absence of Vrp1p, the interaction between the SH3 domain of the yeast F-Bar protein Hof1p and the FH1 domain of the yeast formin protein Bnr1p. This interaction is thought to have pathological effects, such as inhibition of cell proliferation and other phenotypes.

    This study has been conducted in an attempt to map the binding site of Hof1p SH3 domain in the Bnr1p FH1 domain more specifically, based on previous studies suggesting that Fragment 1(755-905) of Bnr1p Full Interacting Fragment(755-1375), including the proline- rich FH1 domain, interacts with Hof1p SH3 domain in cells deficient in Vrp1p. Both Hof1p and Bnr1p are involved in the cytokinesis stagemof the yeast cell cycle. The hypothesis implies that the excessive interaction of Hof1p SH3 domain and Bnr1p FH1 domain may interrupt the cytokinesis, which thereby can lead to the growth of defects.

    There was no finding of binding site within the Bnr1p FH1 domain for the Hof1p SH3 domain during this study. This can be due to various reason as explained later. Even though, this study has cast some doubts on previously conducted studies.

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  • 1190.
    Åhlin, Mikaela
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Medicinska och farmaceutiska vetenskapsområdet, centrumbildningar mm, Ludwig Institute for Cancer Research.
    Role of MKP-2 in crosstalk between MAPK pathways2015Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Abnormalities in Mitogen Activated Protein Kinase (MAPK) signalling may affect the cells essential processes and influence the cell in acquiring traits to favour tumorigenic transformation and the progression of cancer. Deregulation of the MAPK pathways and uncontrolled crosstalk occurring in cancers may be caused by deregulation by MAP-kinase phosphatases (MKPs) that negatively regulates MAPKs by dephosphorylation. In this study, we were interested in the role of MKP-2 in MAPK-signalling pathways. MKP-2 is known to specifically dephosphorylate the MAP kinases Erk1/2, p38 and JNK. In this study, I was to elucidate key events leading to MKP-2 expression and the role of MKP-2 in regulating and balancing MAPK signaling. Also, I was to analyse the possible involvement of p53 in the deregulation of the MAPK pathways and its correlation with MKP-2 expression. In this report, I suggest a model where the Erk1/2 pathway in conjugation with p53 promote MKP-2 expression. I have also discovered a crosstalk between two different MAPK pathways, i.e between Erk1/2 and Erk5.

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  • 1191.
    Åkerman Fulford, Emma
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Organic carbon getting buried deep: A study on a subtropical reservoir and comparisonwith a chain of reservoirs.2017Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Anthropogenic emissions of greenhouse gases are widely known to have damaging effects on the world’s environment. In the search for green energy, recent studies propose that hydropower, which is considered a renewable source of energy, contribute significantly to the emissions of carbon dioxide and in particular methane gas to the atmosphere. Hydropower dams can globally act as an important carbon source, however they can bury substantial amounts of carbon and simultaneously act as net carbon sinks. The main objective of this study is to determine, with high spatial resolution, OC burial in a tropical reservoir, Camargos, Brazil, and compare data with two reservoirs downstream to see if there is any effect of multiple damming. This master’s thesis included field studies in terms of sub-bottom profiling and sediment coring. This was followed by data analysis and mapping of seismic survey data as well as lab work including organic carbon content analysis, C:N ratio and particle size calculations in order to estimate sediment characteristics. The results propose that there is significant burial of organic carbon in Camargos reservoir, of 57.7 g C m-2 yr-1 and 121.3 g C m-2 yr-1 by sub-bottom data and individual coring respectively and evidently, reservoirs further upstream tend to accumulate more sediment and have a higher rate of OC burial. More precisely, the sub-bottom data indicate a steady decrease in OC burial rates of approximately 20%, per dam following the cascade of reservoirs downstream. However, in order to rely on hydropower as a sustainable renewable source of energy to meet the demands of a world wide growing population and economy it is essential to continue studying this topic to fully understand all aspects of the carbon processes within these systems and whether they function as substantial net sinks or sources.

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  • 1192.
    Ålander, Marléne
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Uppstart av en bioreaktor för sidoströmshydrolys vid ett reningsverk: och dess inverkan på biologisk kväve- och fosforavskiljning2015Independent thesis Advanced level (professional degree), 20 credits / 30 HE creditsStudent thesis
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  • 1193.
    Ångman, Maria
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Ekologikunskaper hos blivande gymnasieelever: Skillnader i kunskapen hos sökanden till högskoleförberedande- och yrkesförberedande program2014Independent thesis Advanced level (professional degree), 10 credits / 15 HE creditsStudent thesis
    Abstract [sv]

    Syftet med denna undersökning är att ta reda på vilka kunskaper inom ekologi högstadieelever har med sig till gymnasiet. Eftersom de flesta gymnasieprogram innefattar kurser i naturkunskap eller biologi så vill jag ta reda på vad man som gymnasielärare kan förvänta sig att de nya eleverna har med sig i bagaget. Ekologi och hållbar utveckling genomsyrar stor del av samhällsdebatten idag och det är en del av skolan uppdrag att ge eleverna möjligheter till att ta ansvar för miljön som de kan påverka. För att en gymnasielärare ska kunna fortsätta utveckla sina elever är det av stor vikt att veta vilka grundkunskaper eleverna bär med sig. Detta för att läraren ska kunna förbereda sin undervisning på bästa sätt för att eleverna ska kunna tillgodogöra sig denna.

    Jag har utfört en enkätundersökning med 100 elever i årskurs 9 i närförort till en större stad. Hälften av deltagarna avsåg att välja ett högskoleförberedande program och hälften ett yrkesförberedande program. En hypotes är att eleverna som väljer högskoleförberedande respektive yrkesförberedande program i gymnasiet kan ha olika grad av studiemotivation vilket skulle kunna visa sig i eventuella skillnader mellan de två undersökningsgrupperna i den kvalitativa kunskapen de bär med sig.

    Resultaten visade att det inte var någon större skillnad i kvalitativa kunskaper mellan de två undersökningsgrupperna, men det fanns en signifikant skillnad i svarssäkerheten mellan grupperna. Ett annat resultat av studien var att eleverna har med sig godkända kunskapskrav i ämnet biologi men saknar en förståelse för materiens kretslopp.

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  • 1194.
    Åström, Miranda
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Functional studies of structural elements in toti-like virus through the development of new fluorescence-based methods2023Independent thesis Advanced level (degree of Master (Two Years)), 40 credits / 60 HE creditsStudent thesis
    Abstract [en]

    Omono River virus (OmRV), which infects Culex mosquitoes, belongs to the group of dsRNA toti-like viruses. Some members of toti-like viruses have a large negative impact on the fishing industry, which has increased the interest in understanding their propagation cycle. The structural elements of the OmRV such as the obstructed 5-fold pores and the surface crown proteins (CrPs) have been hypothesized to be of importance for viral particle replication as well as the ability of the virus to recognize and enter the host as part of the transmission cycle. In this study, a newly developed method based on fluorescence in situ hybridization (FISH) was used to observe the effect of OmRV pore mutants on viral particle genome transcription. Immobilized-metal affinity chromatography-based pull-down assays and Förster resonance energy transfer (FRET) assays were used to study the interactions between the CrPs and the viral capsid in vitro. The results show that perturbation of the obstructed pore function has a negative impact on viral propagation. One of the mutants, R925A, resulted in a reduction of viral nascent (+)ssRNA synthesis. The findings are to our knowledge the first indication that positively charged arginine residues in the pore structure might be crucial for intraparticle genome synthesis. Specific CrPs-capsid interaction could however not be detected using these in vitro methods, indicating the need for additional optimization to allow for detection of the weak and transient interactions between CrPs and capsid structure. In summary, these studies and a further development of quantitative methods will serve as starting point for and lead to a deeper understanding of the transmission cycle of the dsRNA toti-like virus family, including also the economically and societal important variants.

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    Strukturer som avslöjar virusets hemligheter
    The full text will be freely available from 2025-06-01 00:00
  • 1195.
    Åström, Miranda
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Search for the Argonaute protein that governs miRNA regulation in Dictyostelium discoideum2021Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    MicroRNAs are small non-coding RNAs that regulate gene expression through RNA interference. These small RNAs enact gene silencing by forming a RNA-inducing silencing complex together with the effector protein Argonaute. The function of the Argonautes in the social amoeba Dictyostelium discoideum is not yet fully understood. In this study, we look closer at Argonaute B by investigating if it is possible to extract the protein from the cells by the addition of a polypeptide protein tag called 3xFlag. At the same time, we also look into if Argonaute B is important for cell growth. Sequences of the 3xFlag tag with or without the Argonaute B gene (agnB) attached had previously been cloned into a vector and transformed into Dictyostelium discoideum cell. The 3xFlag::agnB sequence was confirmed in wild type and agnB knock-out strains through polymerase chain reaction. We then verified the expression of the fusion protein in the cells by western blot. The cell growth was measured by how the number of cells changed over time. The experiment suggested that Argonaute B is important for growth. Our result show that the construct 3xFlag::agnB sequenced had correctly been transformed into the strains and is highly expressed under tested conditions. We could also see that Argonaute B is an important factor in cell growth.

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  • 1196.
    Öberg, Johanna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Time prediction and process discovery of administration process2020Independent thesis Advanced level (professional degree), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Machine learning and process mining are two techniques that are becoming more and more popular among organisations for business intelligence purposes. Results from these techniques can be very useful for organisations' decision-making. The Swedish National Forensic Centre (NFC), an organisation that performs forensic analyses, is in need of a way to visualise and understand its administration process. In addition, the organisation would like to be able to predict the time analyses will take to perform. In this project, it was evaluated if machine learning and process mining could be used on NFC's administration process-related data to satisfy the organisation's needs.

    Using the process mining tool Mehrwerk Process Mining implemented in the software Qlik Sense, different process variants were discovered from the data and visualised in a comprehensible way. The process variants were easy to interpret and useful for NFC. Machine learning regression models were trained on the data to predict analysis length. Two different datasets were tried, a large dataset with few features and a smaller dataset with more features. The models were then evaluated on test datasets. The models did not predict the length of analyses in an acceptable way. A reason to this could be that the information in the data was not sufficient for this prediction. 

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  • 1197.
    Öhman, Jonas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Betingad immunpåverkan och medicinskdosreduktion: en kritisk granskning av tillämpad placebo2014Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [sv]

    Placeboeffekten; att få klinisk effekt av inaktiv behandling är ett fenomen som tilldrar sig allt större intresse. Trots att mekanismerna bakom effekten ännu är långt ifrån helt klarlagda så finns en stor mängd forskning som visar att placebobehandling på olika vis kan vara av klinisk relevans. Bland de mest imponerande demonstrationerna av placeboeffekten är de experiment som visar att s.k. klassisk betingning kan påverka immunförsvaret. Experiment har visat att detta är möjligt både hos gnagare och människor: en medicin administreras samtidigt som ett neutralt gustatoriskt stimulus i vad som kallas betingningsfasen. När denna genomförts kan associationen mellan smak och farmakologisk effekt vara så stark att samma smak, på egen hand, kan framkalla nämnd effekt. I detta arbete sammanfattas kort begrepp och forskning kring placebo i allmänhet och betingad placebo i synnerhet. Vetenskapliga belägg för betingad placebos förmåga till immunpåverkan granskas, och det mesta tyder på att sådan är möjlig i praktiken. Därefter diskuteras möjliga kliniska tillämpningar av betingad placebo i form av medicinsk dosreduktion. Avslutningsvis följer en kort genomgång av det stora kunskapsgapet mellan beläggen för denna dosreduktions kliniska relevans, och dess lämplighet inom konventionell vård.

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    Betingad immunpåverkan och medicinsk dosreduktion: en kritisk granskning av tillämpad placebo
  • 1198.
    Örjes, Elliot
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Does size matter?: A study on pollen size distribution and pollen viability in Silene latifolia and S. dioica2021Independent thesis Advanced level (degree of Master (Two Years)), 30 credits / 45 HE creditsStudent thesis
    Abstract [en]

    Pollen size dimorphism, i.e., when a plant produces more than one size of pollen, has been observed in several plant families but the underlying mechanisms have rarely been discussed. One of the hypotheses is that the smaller pollen produced by individuals with bimodal pollen size distributions are dead or non-viable. In this thesis, I use the campions Silene latifolia and S. dioica to study pollen dimorphism and pollen viability. To study the pollen dimorphism, pollen was collected from eight S. latifolia populations grown in a greenhouse and three wild S. dioica populations. The S. latifolia populations originated from France, Great Britain, Germany, Poland, Switzerland, Russia, Belgium and Romania while the S. dioica populations all came from around Uppsala. The pollen from each individual was analysed under a microscope to determine if the individual produced uni-/bimodal pollen. To test pollen viability, an in vitro germination experiment was conducted, using pollen tube length as a proxy for viability. Individuals with bimodal pollen size distributions were found in almost all populations of both species with frequencies ranging between 10 - 66%. Among the individuals with unimodal pollen size distributions, it was more common to produce larger pollen but, in some populations, there were unimodal individuals producing small pollen. The presence of individuals with different unimodal pollen size distributions as well as with bimodal pollen size distributions in the same population suggests that pollen size dimorphism might be governed by segregating alleles at one or several loci, contradicting earlier studies suggesting meiotic drive. In the viability test, the smaller pollen grew a longer tube and thus might have a higher pollen tube growth rate (PTGR) than the larger pollen. This, together with other studies showing that a high PTGR correlates with high siring success, indicates that small pollen might be highly viable. The smaller pollen may have higher pollen tube growth rate and should therefore have a higher siring success as it may be able to reach the ovules quicker and thus be more common in populations but is a rare phenotype. This might be due to large pollen being superior in other ways.

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  • 1199.
    Örnberg, Rebecca
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Arable Plant Diversity on Gotland, Sweden2023Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    Arable plant species diversity has been on a decline, with many species dependent on arable land becoming threatened. At the same time, attempts at defining the drivers of arable plant diversity have proven difficult and results are often contradictory. Much of the available data come from surveys that are small-scale and with great variability in methodology, leading to difficulties comparing them. In this study, I have used survey data from Gotland to examine how arable plant diversity is influenced by management, field size, soil texture and standing crop. I found a negative trend of diversity with increasing field size, and a suggested effect of management and soil texture on the presence of red listed arable plants. This study also evaluates the use of small datasets when examining plant diversity, and the limitations associated with it. It shows that while a small dataset cannot be analysed to the extent a more comprehensive one can, it is possible to identify trends and patterns with it, which may inform further studies.  

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    Arable Plant Diveristy on Gotland
  • 1200.
    Östberg, Alexandra
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    What is the potential to increase local biodiversity in semi-urban amenity grasslands through meadow constructions?2022Independent thesis Advanced level (degree of Master (Two Years)), 30 credits / 45 HE creditsStudent thesis
    Abstract [en]

    The loss of biodiversity worldwide and methods of prevention are hot subjects receiving increased interest in todays’ research. Meadow construction in urban areas has been the focus of recent studies to increase both local and global biodiversity. In my report, I address potential analyses to conduct in advance before practical meadow constructions in a landscape. The subject I chose to focus on for this report was a LONA-project aimed to construct meadows on contemporary amenity grasslands in a semi-urban municipality. I used vegetation data from an inventory executed in 2021. Patches were in advance classified based on conditions observed during the inventory with class 1 obtaining the highest meadow potential, class 2 obtaining mediocre potential, and class 3 weak or no potential. I analysed vegetation data on species richness, environmental indicator values, and composition. Additionally, I analysed the soil types and historical land uses in the study area to display credible soil characteristics. The order of Lepidoptera was used as a model taxon for pollinators and the red-listed Marsh fritillary (Euphydryas aurinia) was separately analysed for conservational purposes. To illustrate the landscapes’ ability to facilitate the dispersal of butterflies, connectivity analyses of varying meadow construction scenarios were executed. Results indicate higher species richness on average per patch and more indicator species in class 1, suggesting a better starting point and making quality assessments more credible in comparison to class 2. Underlaying soil type seems to some extent to influence the meadow potential by affecting vegetation composition and hence butterfly occurrence in terms of host plant distribution. I could however not draw any conclusions from the effect of historical land use on current patch classifications, and consequently meadow potential. To facilitate for E. aurinia to widen its distribution in the study area, and to avoid local extinction, further conservational efforts should focus on mimicking the conditions and current management of the powerline corridor, that currently yields high diversity of butterflies and abundance of E. aurinia, to other powerline corridors in the study area. To facilitate dispersal of butterflies and other pollinators, target meadow areas of both class 1 and class 2 patches should be constructed to avoid patch isolation, as illustrated in the connectivity analyses. Further research is needed to investigate other factors possibly affecting suitability of grasslands for meadow construction. 

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    Master thesis Alexandra
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