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  • 151.
    Björklund, Geir
    et al.
    Council Nutr & Environm Med, Mo I Rana, Norway.
    Lindh, Ulf
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Aaseth, Jan
    Innlandet Hosp Trust, Res Dept, Brumunddal, Norway;Inland Norway Univ Appl Sci, Elverum, Norway.
    Mutter, Joachim
    Environm Med, Constance, Germany;Paracelsus Clin Ronc, Castaneda, Switzerland.
    Chirumbolo, Salvatore
    Univ Verona, Dept Neurosci Biomed & Movement Sci, Verona, Italy.
    Mercury in dental amalgams: A great concern for clinical toxicology in developing countries?2019In: Journal of Trace Elements in Medicine and Biology, ISSN 0946-672X, E-ISSN 1878-3252, Vol. 51, p. 9-11Article in journal (Other academic)
  • 152.
    Björkman, Matilda
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Enhancing Cryptosporidium spp. Detection and Typing in Water Samples: A Pilot Study2024Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    Cryptosporidium spp. is an intracellular parasite that can cause cryptosporidiosis, a disease involving diarrhea and pain. Immunocompromised patients are more likely to suffer from complications and severe dehydration, and there is no medication with proven clinical efficacy for treatment. Cryptosporidium outbreaks are commonly caused by contaminated water. At the Swedish Veterinary Agency (SVA), a method to detect Cryptosporidium spp. in stool samples through Magnetic Capture Hybridization (MCH) followed by qPCR has been developed. The aim of this study was to test the MCH-PCR method for detecting Cryptosporidium in water samples as well. At the Swedish Food Agency (SLV), Cryptosporidium is detected in water by filtration through a cartridge filter, followed by immunomagnetic separation and microscopic analysis. By combining the method used at SLV with the method used at SVA, MCH-PCR was performed directly on the filtration eluate. The preliminary results showed that the SVA method can be used to detect Cryptosporidium in water, and that a combination of the filtration and MCH-PCR yield similar results as to when MCH-PCR is performed alone. The results are promising but much work is needed to establish a robust and standardized method. For future studies, the method has to be performed on several water types, the sensitivity of the analysis has to be determined and improved, and the probes used may need revision.

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    Enhancing Cryptosporidium spp. Detection and Typing in Water Samples: A Pilot Study
  • 153.
    Björlin Svozil, Magnus
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Det riktade yrkesfiskets påverkan på torskens livshistoria längs Sveriges kust2022Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [sv]

    Sammandrag

    Enligt Förenta nationernas livsmedel och agrikulturorganisation (FAO) är 51% av världens fiskbestånd fullt exploaterade och 17% överexploaterade. Denna andelen har ökat kraftigt de senaste hundra åren och en art som varit hårt drabbad av detta är den populära matfisken torsk (Gadus morhua). Havet runt svenska kusten har tidigare ett av världens mest produktiva torskbestånd, men har de två senaste decennierna minskat drastiskt pga. överfisket. Den intressanta frågan blir då hur torsken påverkats av detta hårt riktade fisket? Den här sammanfattningsartikeln diskuteras först om livshistorieteorin, om torsken och hur fisket på Grand banks utanför Kanada fick hela beståndet att kollapsa. Där efter kommer mera ingående om hur det fisket kan ha påverkat torskens evolution och livshistoria.

    Torskens fenotypiska variation har minskat under det senaste århundradet. Tillväxten har gått ner pga. av denna anledningen. Regimskiften i ekosystemet, som klimat eller föda, har inte påverkat lika mycket som yrkesfisket. Konkurrensen mellan torskens och yrkesfisket efter samma bytesdjur har en inverkan på torsken genom direkta och fördröjda effekter. Skyddade marina områden kan ha gynnsamma effekter på torskbeståndet genom Allee-effekter som en hårt fiskad population kan besitta, som hämmar tillväxten.

    Slutligen en diskussion om hur hållbart fiske med en jämförelse mellan aktiva och passiva redskap. Sedan om hur dagens fiske i svenska vatten ser ut och en analys av de nya fiskereglerna för år 2022 i delar av Östersjön. Till sist en kort diskussion om skyddade marina områden kan gynna torskbestånden runt Sveriges kuster.

    Sammanfattningsvis behöver fisket efter torsk runt Sveriges kuster moderniseras och bedriva ett fiske som tar hänsyn till torskens livshistoria.

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  • 154.
    Björnström, Emil
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Hur starka är växter mot kyla2024Other (Other (popular science, discussion, etc.))
  • 155.
    Björnström, Emil
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Procedure for testing freezing tolerance in Arabidopsis thaliana2024Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
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  • 156.
    Björnör, Saga
    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.
    Investigating the unknown CdiA-CT-2 toxin used by E. coli D12 to outcompete other bacteria2024Independent thesis Advanced level (degree of Master (Two Years)), 30 credits / 45 HE creditsStudent thesis
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  • 157.
    Bleichner, Lukas
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Eriksson, David
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Magnell, Alva
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Petersson, Josefine
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    van Bruggen, Ragna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Self-cleaving tag systems: The future of protein purification2024Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
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  • 158.
    Blockert, Dylan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre. Uppsala University.
    Histological analysis of the amygdala and para-subthalamic nucleus2023Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    The para-subthalamic nucleus (PSTN) and amygdala are two brain regions of central focus in recent neurobiology. The PSTN is a hypothalamic brain region that acts as a relay point for sensory signals towards regions that use learned behaviour and experiences to integrate the bottom-up sensory information. One region that the PSTN sends sensory information to is the amygdala, which uses certain emotive responses to form higher cognitive function and to produce new learned behaviour. Due to the PSTN acting as the middle man of sensory integration, it connects interoception and emotion within the brain. The amygdala contains several different nuclei which can be distinguished using different molecular markers. The aim of this study is to distinguish between spatio-molecular subpopulations or anatomically identified subnuclei in the amygdala and PSTN by analysing Tac1-Cre driven GFP expression in those areas. This was tested using immunohistochemistry techniques on Cre/loxP crossed mice. Tac1 is a gene that encodes for preprotachykinin-A, which can be transformed into several other neuropeptides. The results found that Tac1-Cre driven GFP expression was especially visible and dense in the dorsal anterior amygdala and medial posterior amygdala. Scattered expression was observed in the lateral region of the amygdala. Lack of expression was further observed in the lateral and basolateral amygdalar nuclei. Tac1-Cre driven GFP positive cells were also seen in and around the PSTN. These results showed a strong expression in the central amygdalar nucleus  and some areas of the medial amygdalar nucleus, as well as throughout the extent of the PSTN. 

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  • 159.
    Blomberg, Louise
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Characterization and contribution of Plavaka elements in the genome of Lactarius deliciosus (Milk-cap mushrooms).2023Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
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  • 160.
    Blomgren, Eric
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal Ecology. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Avian malaria in collared flycatchers: fitness consequences and a relation to a secondary sexual character2011Independent thesis Advanced level (degree of Master (One Year)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    All organisms have limited amounts of energy, time and nutrients to spend during their lifetime and this gives rise to trade-offs in life histories. It has been shown that increased reproductive effort can reduce parasite resistance and specific immune response in birds. This suggest that there is a trade-off between spending energy on immune system and reproductive effort. Within birds there are several suitable blood parasites that can be used as model organisms for the study of parasite - host interactions, of which 3 genera of protozoan haemosporidians which one could call malaria parasites. Since a few years back it is possible to detect and investigate with high accuracy and speed whether individual organisms are infected with blood parasites or not. Still, there is not sufficient knowledge about how avian malaria parasites affect their host's fitness. In this study I investigated how reproductive success of collared flycatchers is affected by the presence of malaria and if a certain secondary sexual character is correlated to infection. I also used old biometrical data to see if there is a correlation between size as nestling and malaria infection as old.

    I found that females infected with avian malaria have a lower reproductive success, and that adult males infected with malaria have on average less white on their 3rd tertial feather than non-infected ones. I also show that infected individuals were smaller as 12 day nestlings than non-infected individuals.

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  • 161.
    Blomlöf, Alexander
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Unge, Alvin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Byström, Petter
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Lindberg, Erika
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Fries, Torbjörn
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Immunological Cross-Reactivity: Construction of a Workflow That Enables Cross-Reactivity Predictions2022Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    Cross-reactivity occurs when an antibody binds to the epitope of a protein that is not the targeted antigen. This is problematic in the analysis of immunoassay diagnostics. Detecting a protein incorrectly might cause issues such as incorrect mapping of metabolic conditions for research or diagnosis. In this study, articles have been collected within two main fields. The first of which is focused on bioinformatic tools to predict cross-reactivity risk and the second field investigates how single substitutions affect the antibody-antigen binding. The results from the collected articles were analyzed with the aim of providing as much information surrounding the topic as possible, to gain a further understanding of how protein similarities impact cross-reactivity. FASTA alignments proved to be efficient in classifying cross-reactive proteins based on sequence similarity. Moreover, epitope analysis, using PD tool or Cross-React, can provide an even more precise subset of proteins with risk of causing cross-reactivity. Individual residues of the epitopes of the subset can then be analyzed. Specific residue’s physicochemical properties such as hydrophobicity, polarity, size and charge have proven to be relevant for the binding affinity, with charge having the largest impact. The position of an amino acid has also shown great importance. More centrally located amino acids within the epitope contribute more to paratope affinity than those on the outer positions. However, a conclusive classifier based on specific residues within epitopes is difficult to implement in cross-reactivity analysis. A workflow of the different prediction steps has been constructed into a workflow that may be implemented as an automated pipeline in the future. 

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  • 162.
    Blomqvist, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology.
    Development of a cell killing adenovirus with a novel cytotoxic transgene2023Independent thesis Advanced level (degree of Master (Two Years)), 30 credits / 45 HE creditsStudent thesis
    Abstract [en]

    Cancer is among the most common causes of human deaths globally. Because of limitations and adverse effects of conventional cancer treatments, the need for new treatments is imminent. A rapidly expanding field in cancer therapy is cancer immunotherapy, which aims to, in one way or another, aid the patient’s own immune system in its battle against the tumor cells. A type of cancer immunotherapy is oncolytic virotherapy which utilizes viruses that either have a natural inclination to infect and replicate inside tumor cells or have been engineered to specially replicate in tumor cells causing oncolysis. An example of an oncolytic virus is the Lokon Oncolytic Adenovirus (LOAd). This virus specifically replicates inside cancer cells and is based on adenovirus serotype 5 but with a serotype 35 fiber, causing it to infect via the cluster of differentiation 46 receptor, which is ubiquitously expressed on somatic and tumor cells. A notable virus with the LOAd backbone, that is being evaluated in several clinical trials, is LOAd703, which is armed with the immunostimulatory transgenes 4-1BB ligand and a trimerized cluster of differentiation 40 ligands.

    In this project, I describe the development and evaluation of Ad703+, a cell killing adenovirus carrying the transgenes of LOAd703 as well as a novel cytotoxic transgene that never has been used in oncolytic virotherapy previously. This virus was developed using the AdEasy system, which is a replication-deficient virus platform based on adenovirus serotype 5. This virus enters cells using the human coxsackie and adenovirus receptor, which is homologous to the murine equivalent. 

    The ability to express the immunostimulatory transgenes and the cell killing ability of Ad703+ was evaluated in two different human cell lines, HEK293 which allows the replication of Ad703+, and the lung cancer model A549. Ad703+ was shown to express the immunostimulatory transgenes in both of the cell lines, but in a replication-dependent manner. Ad703+ was also shown to exhibit cell killing ability in a replication-independent manner on par with other oncolytic viruses. 

    The ability of Ad703+ to trigger cell death in a replication-independent manner opens up for the possible application in pre-clinical in vivo studies using mice due to its theoretical ability to infect murine cells and simulate viral oncolysis. 

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  • 163.
    Blomster, Klaus
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    HOW AYAHUASCA-CEREMONIES CHANGE PERCEPTIONS OF NATURAL VALUES IN PARTICIPANTS: THE LINKS TO NATURE AND THE ROLE OF SHAMANIC RITUALS2021Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    The South American psychedelic brew ayahuasca has seen a surge of popularity among western users in the past decade, both in the Amazon and in the Western World. This has caused interest in the field of psychiatric research, as some psychedelics have been approved in some countries for clinical trials in treating mental illnesses. The traditional use of psychedelics, however, has its roots in shamanism and indigenous cultures.

    The shamanic ritual contains many complex elements that are often overlooked by researchers. Most important is the intimate connection to nature and the differences in the human-nature relationship between western and indigenous societies, where westerners generally see themselves as separate from nature, while indigenous people see themselves as one with nature. Participants in ayahuasca ceremonies report not only an increased connection to nature, but a shift in human-nature relationships which becomes much closer to that of the indigenous view.

    There are also economics and political issues regarding the use of ayahuasca, as the internationalization of this practice has led to controversy regarding commercialization and its effect on cultural landscape in the Amazon. Integrating ayahuasca into the western world and decolonizing psychedelic science thus requires an integration of these two widely different perspectives.

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  • 164.
    Bogstedt, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Predicting and classifying atrial fibrillation from ECG recordings using machine learning2023Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Atrial fibrillation is one of the most common types of heart arrhythmias, which can cause irregular, weak and fast atrial contractions up to 600 beats per minute. Atrial fibrillation has increased prevalence with age and is associated with increased risks of ischemia, as blood clots can form due to the weak contractions. During prolonged periods of atrial fibrillation, the atria can undergo a process called atrial remodelling. This causes electrophysiological and structural changes to the atria such as increased atrial size and changes to calcium ion densities. These changes themselves promotes the initiation and propagation of atrial fibrillation, which makes early detection crucial.

    Fortunately, atrial fibrillation can be detected on an electrocardiogram. Electrocardiograms measures the electrical activity of the heart during its cardiac cycle. This includes the initiation of the action potential, the depolarization of the atria and ventricles and their repolarization. On the electrocardiogram recording, these are seen as peaks and valleys, where each peak and valley can be traced back to one of these events. This means that during atrial fibrillation, the weak, irregular and fast atrial contractions can all be detected and measured.

    The aim of this project was to develop a machine learning model that could predict onset of atrial fibrillation, and that could classify ongoing atrial fibrillation. This was achieved by training one multiclass classification machine learning model using XGBoost, and three binary classification machine learning models using ROSETTA, on electrocardiogram recordings of people with and without atrial fibrillation. XGBoost is a tree boosting system which uses tree-like structures to classify data, while ROSETTA is a rule-based classification model which creates rules in an IF and THEN format to make decisions. The recordings were labelled according to three different classes: no atrial fibrillation, atrial fibrillation or preceding atrial fibrillation.

    The XGBoost model had a prediction accuracy of 99.3%, outperforming the three ROSETTA models and other atrial fibrillation classification and prediction models found. The ROSETTA models had high accuracies on the learning set, however, the predictions were subpar, indicating faulty settings for this type of data.

    The results in this project indicate that the models created can be used to accurately classify and predict onset of and ongoing atrial fibrillation, serving as a tool for early detection and verification of diagnosis.

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  • 165.
    Bohlin, Matilda
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    DEHP - från mjukgörare till hormonstörande2014Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
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    Arbetet
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    Populärvetenskaplig sammanfattning
  • 166.
    Bolinder, Kristina
    et al.
    Stockholm Univ, Dept Ecol Environm & Plant Sci, SE-10691 Stockholm, Sweden..
    Humphreys, Aelys M.
    Stockholm Univ, Dept Ecol Environm & Plant Sci, SE-10691 Stockholm, Sweden.;Royal Bot Gardens, Comparat Plant & Fungal Biol, Richmond TW9 3AB, Surrey, England..
    Ehrlen, Johan
    Stockholm Univ, Dept Ecol Environm & Plant Sci, SE-10691 Stockholm, Sweden..
    Alexandersson, Ronny
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Ickert-Bond, Stefanie M.
    Univ Alaska Fairbanks, Dept Biol & Wildlife, 907 Yukon Dr,POB 756960, Fairbanks, AK 99775 USA.;Univ Alaska Fairbanks, Inst Arctic Biol, 907 Yukon Dr,POB 756960, Fairbanks, AK 99775 USA.;Arizona State Univ, Sch Life Sci, POB 874501, Tempe, AZ 85287 USA..
    Rydin, Catarina
    Stockholm Univ, Dept Ecol Environm & Plant Sci, SE-10691 Stockholm, Sweden..
    From near extinction to diversification by means of ashift in pollination mechanism in the gymnosperm relict Ephedra (Ephedraceae, Gnetales)2016In: Botanical journal of the Linnean Society, ISSN 0024-4074, E-ISSN 1095-8339, Vol. 180, no 4, p. 461-477Article in journal (Refereed)
    Abstract [en]

    Pollination in gymnosperms is usually accomplished by means of wind, but some groups are insect-pollinated. We show that wind and insect pollination occur in the morphologically uniform genus Ephedra (Gnetales). Based on field experiments over several years, we demonstrate distinct differences between two Ephedra species that grow in sympatry in Greece in pollen dispersal and clump formation, insect visitations and embryo formation when insects are denied access to cones. Ephedra distachya, nested in the core clade of Ephedra, is anemophilous, which is probably the prevailing state in Ephedra. Ephedra foeminea, sister to the remaining species of the genus, is entomophilous and pollinated by a range of diurnal and nocturnal insects. The generalist entomophilous system of E.foeminea, with distinct but infrequent insect visitations, is in many respects similar to that reported for Gnetum and Welwitschia and appears ancestral in Gnetales. The Ephedra lineage is well documented already from the Early Cretaceous, but the diversity declined dramatically during the Late Cretaceous, possibly to near extinction around the Cretaceous-Palaeogene boundary. The clade imbalance between insect- and wind-pollinated lineages is larger than expected by chance and the shift in pollination mode may explain why Ephedra escaped extinction and began to diversify again.

  • 167.
    Boman, Jesper
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Genome size and phenotypic plasticity in the seed beetle, Callosobruchus maculatus2017Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    It has long been evident that genome size is not an accurate measure of organismal complexity. This paradox was “solved” with the discovery of nonfunctional and selfish DNA in the 1970s. However, emerging from this explanation was an enigma of complexity. Neither neutral nor adaptive models can account for all genome size variation across the tree of life. An organism with intraspecific variation is needed to investigate the functional role of genome size differences. Here I use different populations of the seed beetle, Callosobruchus maculatus, with a known intraspecific genome size variation of ~4%. It has previously been shown that a larger genome is associated with higher scores in fitness-related traits for this species. In this study, genome size is regressed with phenotypic plasticity along three different environmental gradients. Genome size did not correlate with plasticity in mass and development time along environmental gradients of temperature and host types. However, the results show that larger genomes are consistent with higher canalization of fitness under different food regimes. This further supports the idea that natural selection acts on genome size variation in this species. 

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  • 168.
    Boqvist, Natalie
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Är ett framtida vaccin mot Alzheimers sjukdom möjligt?2014Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    Alzheimer’s disease is an insidious neurodegenerative dementia disease that primarily affects elderly and is characterized by the formation of amyloid plaques and neurofibrillary tangles in the brain. The most common symptoms are dementia, cognitive problems, delusions, and aggressiveness. Alzheimer’s occurs in two forms, presenile and senile Alzheimer’s disease. The complete mechanism behind Alzheimer’s is still unknown but two proteins, beta-amyloid and tau, are considered to be behind the cause of Alzheimer’s. A third protein involved that was found through genetic analysis is apolipoprotein E. Today, Alzheimer’s is a growing problem as the world’s population is getting older. A complex of problems exists as the symptomatic treatment available against Alzheimer’s is considered to be insufficient; a cure is therefore aimed at. Immunotherapy is a cure that hopes can be offered, this in the form of an active or a passive vaccine effective against beta-amyloid. Research to find such a vaccine is therefore under progress right now. AN-1792 (active vaccine), CAD106 (active vaccine), Bapineuzumab (passive vaccine), and Solanezumab (passive vaccine) are four vaccines that have been developed and tested on humans. In the vaccine studies that have been done setbacks have been encountered but also successes have been made. AN-1792 is the vaccine proved to be effective but with severe side effects while CAD106 is the vaccine proved to be less effective but safer. Both Bapineuzumab and Solanezumab showed to be ineffective. Since several of the produced vaccines have been active against amyloid plaques scientists believes that a future vaccine against Alzheimer’s disease is possible to make. 

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  • 169.
    Borenstein, Mirjam
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Effects of per- and polyfluoroalkyl substances on transgenerational epigenetic inheritance2023Independent thesis Advanced level (degree of Master (Two Years)), 30 credits / 45 HE creditsStudent thesis
    Abstract [en]

    Endocrine-disrupting chemicals (EDCs) are abundant in aquatic environments today. Organisms are exposed constantly, and these chemicals interfere with the hormone system in various ways, disrupting functions such as development and reproduction. Per- and polyfluorinated alkyl substances (PFAS) are a class of EDCs that are highly persistent and stable. They have been used for many years thus large amounts are today found in ground water and in tissue of organisms. Due to their physiochemical properties a phase-out has been ongoing for the past 23 years. Aside from effects of direct exposure PFAS have been shown to cause multigenerational effects. The most common PFAS is Perfluooctanesulfonic acid (PFOS), and much like other PFAS, it has been shown to cause a range of adverse effects in fish; direct, multi- and transgenerational. In this study we examined transgenerational effects in an F2 generation of zebrafish (Danio rerio) where the F0 generation was exposed to PFOS and one of its replacement chemicals, Perfluorobutanesulfonic acid (PFBS), at two different concentrations relevant to natural environments (0.2 och 2 μg/ L). We aimed to investigate potential epigenetic marks and their involvement in transgenerational effects on phenotype in the unexposed F2 generation. Two approaches were taken. First, targeted epigenetic analyses were performed in selected regions in relevant target genes using Bisulfite Pyrosequencing. Levels of 5-methylcytosine (5mC) in regulatory regions were analyzed to look for significant differences. The other part of this project was the development and optimization of a pipeline for whole-genome sequencing using Oxford nanopore Technology (ONT). This technology allows for untargeted analysis of many different epigenetic marks rather than just one. Results from the targeted analysis showed significantly lower methylation level in the gene tubb5 in F2 samples where F0 was exposed to 0.2 μg/ L of PFOS, compared to the controls. This gene is generally expressed in the brain, nervous system and spinal cord, making these results of interest for further study. The pipeline development was successful, and we managed to identify potential methods yielding the highest possible amount of material for analysis. 

  • 170.
    Boström, Fredrik
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Single-cycle kinetics for QCM biosensors for high throughput nanoparticle characterization application2016Independent thesis Advanced level (professional degree), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Characterizing nanoparticles to be able to understand how they functions in the body is important for development of drugs. Furthermore with increasing number of nanoparticle product the nanotoxicity of nanoparticles is important to understand. This report is a part of the EU-project Nanoclassifier which purpose is to “develop a cost effective, high throughput screening platform for characterization of the bionanointerface and its cell-binding partners”. Single-cycle kinetic was used to determine the number of binding epitopes on polystyrene nanoparticle with transferrin corona. The number of available epitopes describes how active the Nanoparticle will be in the body. For this purpose Single-cycle kinetic methodology was successfully used on nanoparticles. Single-cycle kinetic methodology has great potential to become the standard method for high throughput nanoparticle epitope characterization.

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  • 171.
    Bountis, Stavros
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Effects of a phthalate mixture on Wnt/β-catenin signaling, apoptosis and metabolic rate in zebrafish embryos2020Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    One of the most common plasticizers used in the production of plastic are phthalates. These chemicals have been associated with many adverse effects including developmental and reproductive anomalies. Early developmental processes targeted by chemicals can have long-lasting effects on individuals. The focus of this study was on investigating the effects of a phthalate monoester mixture on two evolutionarily conserved processes, Wnt/β-catenin signaling and apoptosis, both of which play an important role during development. Focus was also given on the mixture’s effect in metabolic rate. The phthalate mixture used is part of mixture G, a mixture which additionally contains triclosan and three perfluoroalkyl acids. The components of Mixture G were identified in a Swedish pregnancy cohort (SELMA) and were inversely associated with birth weight. The experiments were conducted in zebrafish embryos. Wnt signaling was analyzed in a transgenic zebrafish line, which had the EGFP gene linked to β-catenin regulated promoters, by measuring the fluorescence in the caudal fin. Apoptosis was analyzed through the acridine orange assay and metabolic rate through the transformation of resazurin to resorufin in presence of NADH/NADPH. The results showed a downregulation of Wnt signaling in zebrafish at two days post-fertilization (2 dpf), at a water concentration 100 times higher than the geometric mean serum concentration (100x hsc) of the mothers in the SELMA cohort. An upregulation of apoptosis was found at 1 dpf, at 60x hsc and 100x hsc. An effect on metabolic rate was observed at 100x hsc at 5 dpf. The results indicate that phthalates can disrupt Wnt signaling, induce apoptosis and influence metabolic rate, which along with the various reproductive effects they can induce warrants cause for concern not only for zebrafish embryos but for human fetuses as well.

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  • 172.
    Braesch-Andersen, Ken
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Temperature dependence in human Rhinovirus infection of human MRC-52019Independent thesis Advanced level (professional degree), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Temperature has been known to be an important factor for in vitro studies where human cell cultures are infected with HRV (human Rhinovirus). The mechanisms behind the temperature effect on the struggle between virulence and cellular defense, are still largely unknown and may be a crucial part in finding a treatment to the common cold. In this study we focused on a few cellular key elements in this struggle and observed behavior changes in regards to the pre-infection growth temperature and the temperature during the viral infection.

    Past studies have focused mainly on the temperature post inoculation, but here we also wanted to correlate virulence to the growth temperatures preceding the viral infection. We found that the growth temperature of the cell did indeed affect its response to the HRV. If the cells had been growing in an optimal body temperature of 37°C before getting virally infected at 33°C, the viability of the cells did decrease in comparison to cells that had been growing in 33°C from before the viral infection.

    We could also observe a significant temperature dependence regarding IL-8 release upon HRV inoculation. HRV strive to block induction of inflammatory cytokines such as interferons and IL-1. It may be that impaired IL-8 release at lower temperatures will prevent important danger signals alerting the immune system when cytokine signaling is otherwise hampered by viral intervention.

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  • 173.
    Brandt Korall, Elin
    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.
    Headfirst into shallow water - Wetland restoration and its contribution to the Habitats Directive2024Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Located in the borderland between aquatic and terrestrial environments, the wetlands cover a wide spectrum of habitats and enable living standards for a great variety of organisms. Although important habitats, a great extent of the original wetlands have disappeared in Europe and Sweden due to anthropogenic disturbances. In recent decades, there has been a significant increase in efforts to restore wetlands due to their popularity as a climate mitigation tool and their suggested multifunctional benefits. However, little is known about what kind of wetlands that have been restored in Sweden. Is it merely amphibian dams or is it fens and bogs? In this thesis, I have investigated whether the projects within LONA (The Local Nature Conservation Program) had contributed to reaching the aims of the Habitats Directive (79/409/EEC). My results showed that eleven (20 %) of the LONA projects from 2021-2022 contributed to favorable conservation status for five of the wetland habitat types listed in the Habitats Directive. In particular, there were positive impacts on Transition mires and quaking bogs (7140), and Bog woodland (91D0) from the hydrological restoration of peatlands. Although a major part of the projects rather resulted in novel ecosystems. A potential future challenge lies therefore in finding ways to increase the contribution to the Habitats Directive through the utilization of LONA funding. However, considering that LONA has unrelated aims and that other funding sources are better suited for this purpose, it is arguable whether this is the most suitable way forward. Hence, I propose adopting a landscape view that considers different funding sources and an integration of the expected ecosystem services in the national database with restored and created wetlands. With this approach, we can determine which wetland types to prioritize on a basin scale and identify the gaps where restoration of high-biodiversity wetlands is absent. Wetland restoration is a crucial aspect of conservation efforts, but if we are to reach the aimed functions, it requires careful planning, effective management, and long-term funding for future management.

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    Headfirst into shallow water_Masters thesis
  • 174.
    Brechlin, Birte Hildegard Elisabeth
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Bridges for the wolverine (Gulo gulo): Spatial and non-spatial population genetic analysis in STRUCTURE and BAPS and implications for decision makers2015Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    The conservation of large predators is among the most challenging tasks facing conservation biologists and the protection of the wolverine (Gulo gulo) is no exception. Studying and monitoring these vastly roaming carnivores is only possible due to the collective effort from the Norwegian Nature and Swedish Environmental protection agencies and the group for Monitoring of Large Carnivores at Uppsala University. Wolverines are as so many large predators beloved from the ones and hatefully persecuted from the others. After facing a dramatic bottleneck in the 1970s, the wolverines have been given protective status in Norway and Sweden and could increase their numbers again until licensed hunting was allowed in 1993. Today legal and illegal hunting as well as other anthropogenic factors work against that trend. To observe population trends genetic monitoring of the wolverine has been pursued over a number of years. Data has been collected in Norway and Sweden from sampling of tissue, hair and faeces. This study explores SNP data from tissue samples in the statistical programs R and STRUCTURE for analysing multi-locus genotype data to investigate population structure and the program BAPS for spatial genetic clustering. All analyses agreed on the clustering of the wolverine population into two distinct populations. In Scandinavia there are, besides the Sarek area in northern Sweden, very little truly wild and undisturbed territories left. Human impact plays a well-known, but little studied role in mammal population analyses. Conclusively, the spatial clustering results are projected onto maps displaying anthropogenic development. It shows that the fast growing human population and consecutive urban development around Trondheim in Norway might cause a major obstacle to gene flow between the populations south and north of that belt of urbanization. In order to allow gene flow and thus saving the genetic variety and long-term survival of the Scandinavian wolverine population, the investigation and construction of Wildlife crossings or incorporating other measures to include wildlife into our ever changing landscapes is called into focus for decision makers in city and road development.

  • 175.
    Breimark, Linda
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Investigating the use of isotope-labeled standards as calibrants in label-free quantification2018Independent thesis Advanced level (professional degree), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    The ability to accurately identify and quantify proteins in complexsamples is of great importance in the field of proteomics. Using massspectrometry, samples can be analysed and quantified either by theincorporation of a labelled standard of known concentration, or bylabel free quantification. Label free quantification has manybenefits, including time, cost, and ease of use, but is not asaccurate as the use of isotope label standards. In this project, thepossibility of increasing accuracy in quantification results from LFQusing a set of isotope labelled standards, QPrESTs, is investigated.The standards were produced by metabolic incorporation of heavyLysine and Arginine during expression inE. coli. They were then qualitycontrolled using SDS-PAGE for purity analysis, and LC-MS/MS forquantification and confirmation of MW. Human cell lysate samplesspiked with a set of 21 QPrEST standards were analysed by LC-MS/MSand quantified by QPrEST-H/L intensity ratios and intensity basedLFQ. In the LFQ protein quantification indices obtained from MaxQuantwere combined with BCA results, or with calibration curves obtainedfrom spiked in QPrEST standards. The LFQ results that best matchedthose obtained from QPrEST-H/L were those that used the calibrationcurves for quantification, which were found in a ~3-fold range, witha correlation coefficient varying from 0.67 to 1. Assuming thatQPrEST-H/L is the most accurate quantification method used, thisindicates that the use of QPrEST standards as calibrants can bebeneficial when it comes to increasing the accuracy in LFQ.

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  • 176.
    Bringeland, Nathalie
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience, Functional Pharmacology. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    DNA methylation correlation networks in overweight and normal-weight adolescents reveal differential coordination2013Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Multiple health issues are associated with obesity and numerous factors are causative of the disease. The role of genetic factors is well established, as is the knowledge that dietary and sedentary behavior promotes weight gain. Although there is strong suspicion towards the role of epigenetics as a driving force toward disease, this field remains l in the context of obesity. DNA methylation correlation networks were profiled from blood samples of 69 adolescents of two distinct weight-classes; obese (n=35) and normal-weight (n=34). The network analysis revealed major differences in the organization of the networks where the network of the obese had less modularity compared to normal-weight. This is manifested by more and smaller clusters in the obese, pertaining to genes of related functions and pathways, than the network of the normal-weight. Consequently, this suggests that biological pathways have a lower order of coordination between each other in means of DNA methylation in obese than normal-weight. Analysis of highly connected genes, hubs, in the two networks suggests that the difference in coordination between biological pathways may be derived by changes of the methylation pattern of these hubs; highly connected genes in one network had an intriguingly low connectivity in the other. In conclusion, the results suggest differential regulation of transcription through changes in the coordination of DNA methylation in overweight and normal weighted individuals. The findings of this study are a major step towards understanding the role of DNA methylation in obesity and provide potential biomarkers for diagnosing and predicting obesity.

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    MastetThesisNathalieBringeland
  • 177.
    Broberg, John
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Development of novel multiplexed systems for in situ PLA2011Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    The in situ proximity ligation assay (in situ PLA) is an immunoassay that enables directvisualisation of single protein targets or protein interactions in cell or tissue samples. This project revolves around designing and introducing several novel multiplexable components tobe used in conjunction with Olink Bioscience's Duolink product line. In this report, a novel in silico approach to DNA oligomer interaction design is presented. Using this in silico method, a multiplexed system of DNA oligomers has been designed andevaluated using in situ PLA and fluorescence microscopy.

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    Development of novel multiplexed systems for in situ PLA
  • 178.
    Brobäck, David
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Preventing the spread of the invasive plant Lupinus polyphyllus.2015Independent thesis Advanced level (degree of Master (Two Years)), 30 credits / 45 HE creditsStudent thesis
    Abstract [en]

    Invasive species are an increasing problem worldwide, threatening indigenous communities and species. Many human-made environments promote introductions of alien species and one such habitat is road verges. The invasive plant Lupinus polyphyllus is benefiting from these habitats and is today widespread along road verges in many parts of Sweden. However, it has been shown to be a problematic species, as it supresses native plants. Many of these plants originate from semi-natural grasslands, but have found a refuge in road verges. The Swedish Transport Administration has tried to control L. polyphyllus, but it is unclear to what extent it is possible. To manage an invasive species, it is often preferable to prevent further extension by limiting its dispersal, which can be done by reducing seed production. To find out how to prevent L. polyphyllus from spreading, I investigated how resprouting capacity and seed production was affected by cutting of L. polyphyllus at different times throughout the season, and at different heights. Plants in all plots resprouted after being cut, but resprouted leaf stalks grew taller in the plants cut early at the flowering stage, compared to the later cutting treatments. These were also the only ones producing new flowers and fruits, perhaps due to stored resources in roots or the fact that they were cut before the summer solstice. Plants cut higher above the ground produced more flowers and fruits and produced taller leaf stalks and might have used photosynthesizing aboveground parts to acquire resources for regeneration. Fruits were produced but not ripe before the mid-summer cutting. These seeds were still able to germinate after maturing on cut plants. However, they were more mould-infected than seeds maturing on non-cut plants. Seeds from cut plants were also lighter. Thus, seeds produced by the mid-summer cutting might disperse and germinate but may perhaps suffer from lower survival due to more frequent mould infections. The late-cut plants had already produced mature seeds, and thus, were probably able to disperse. Also, the later cutting treatments produced more seeds over the entire season. This indicates that to hinder dispersal by limiting seed production, it is best to cut Lupinus polyphyllus as early as possible, in the flowering stage, when seeds are not produced and to cut them entirely to the ground.

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    Masteruppsats_David Brobäck
  • 179.
    Broman, Elias
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Observation of methanogenesis and potential iron-dependent anaerobic oxidation of methane in old lake sediments, a study of two boreal forest lakes.2013Independent thesis Advanced level (degree of Master (Two Years)), 30 credits / 45 HE creditsStudent thesis
    Abstract [en]

    Organic and inorganic carbon can enter inland waters in different ways, and often a considerable amount of this carbon is coming from terrestrial input. Once this terrestrial carbon enters a lake, the carbon may be degraded, mineralized or eventually buried in the sediment. Below the oxic zone of the sediment carbon may be used by archaea to produce methane (CH4). The CH4 can then diffuse up in the sediment and escape to the bottom waters, or the CH4 can be oxidized by bacteria using oxygen as an oxidant. There is also an anoxic process to oxidize CH4 (anaerobic oxidation of methane: AOM), using sulfate (SO4) and by recent findings also ferric iron (Fe(III)) as electron acceptors. In this study the main questions of interest were if CH4 is produced in deep (i.e. old) lake sediments and if CH4 is oxidized anaerobically using Fe(III). Two Swedish boreal forest lakes were studied, sediment profiles of CH4 were conducted in the field (down to 60 cm). Collected sediments were sliced anoxically at different depths and then analyzed for ferrous iron (Fe(II)), Fe(III) and SO4. Sediment from different depths was also incubated anoxic in order to test if CH4 production depends on sediment age. The results show that methanogenic activity occurs by degrading old carbon in deep boreal forest lake sediments, and that a certain part of this might then be oxidized anaerobically. However, all cores exposed a general trend of increasing CH4 concentrations with sediment depth, indicating that CH4 production in old sediment layers is greater than AOM. AOM could therefore only act as a partial sink for CH4 in anoxic deep sediments.

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  • 180.
    Brugnone, Nicolò
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Targeting a new potential autophagy-related protein in Arabidopsis using CRISPR/Cas92024Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
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  • 181.
    Brunell, Stina
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Pettersson Gradin, Elis
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Englöf, Victor
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Wigertz, Lovisa
    Persson, Embla
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Maglio, Josephine
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Decoding Hormone Interactions: Investigating Health Status Using Hormone Signatures in Blood2023Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    Hormones are integral molecules in the human body, controlling most body systems and maintaining homeostasis in the body. They function as signal molecules for communication between cells, and are often secreted by one tissue with another as target. Protein hormones make up the majority of the hormones in the body, are mostly transported in the bloodstream, and bind to receptors on the cell surface since they can not diffuse through cell membranes. Hormones and their associated proteins are linked to many diseases, and could therefore have a lot of potential as biomarkers. With the use of the company Olink’s Proximity Extension Assay (PEA) technology the concentrations of human proteins in blood can be measured. These proteins can be combined into different sets, called panels, to measure biomarkers related to specific diseases or conditions. This project aimed to identify the protein hormones of the human body, and investigate their associated proteins and the pathways and potential diseases they were related to. Suggestions of new panels based on disease areas that were found to be particularly related to protein hormones were also to be put forward. Databases such as UniProt, Reactome, String, Signor, Olink Insight, and the Human Protein Atlas were used to investigate protein hormones and their associated proteins. The result of the research was compiled into three different panels: the overall Protein Hormone panel, the Wellness panel, and the Diabetes panel. These panels were based on the disease areas commonly found associated with protein hormones, and that were deemed to be of interest to Olink and to the research community. The research also resulted in a table detailing all found protein hormones with additional info on pathways and diseases, normal concentrations of the proteins in blood or plasma, and the associations between the hormones and other proteins. The financial viability and marketability of the suggested panels were also investigated in a business case. It was determined that the development of the new panels had potential to be of significant importance to research efforts, healthcare providers, and individual patients. While there are some risks associated with developing and marketing new products, it was concluded that the economical potential of the panels make them an opportunity worth considering for Olink.

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  • 182.
    Bublys, Kasparas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Diet variability in Eurasian perch (Perca fluviatilis) as a response to environmental variables along a latitudinal gradient2018Independent thesis Advanced level (degree of Master (Two Years)), 30 credits / 45 HE creditsStudent thesis
    Abstract [en]

    Climate change is expected to have a profound impact on freshwater fish communities, especially at higher latitudes. In this study I investigated potential effects of climate change on the niche structure of Eurasian perch (Perca fluviatilis) by looking at their diet across a latitudinal gradient and at varying light climate. Dietary niche width of Eurasian perch did not differ significantly between boreal and temperate latitudes. Additionally, no significant difference in the prevalence of specialist individuals was found along the latitudinal gradient and water transparency levels. Habitat was the main factor that significantly affected niche width and level of specialization with both being significantly higher in the littoral habitat. Taken together my results suggest that climate change might indirectly affect niche patterns by altering fish densities through changes in productivity resulting in niche and specialization variation among habitats.

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  • 183.
    Buinovskaja, Greta
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Identifying structural variants from plant short-read sequencing data2022Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
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    Master_Thesis_Greta_Buinovskaja
  • 184.
    Bulterijs, Sven
    et al.
    Univ Ghent, Fac Sci, B-9000 Ghent, Belgium.;Heales Vzw, Brussels, Belgium..
    Hull, RaphaellaS.
    Univ Oxford, Dept Biochem, Oxford OX1 3QU, England.;Biogerontol Res Fdn, London, England..
    Björk, Victor C. E.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre. Heales Vzw, Brussels, Belgium.
    Roy, Avi G.
    Heales Vzw, Brussels, Belgium.;Biogerontol Res Fdn, London, England.;Univ Buckingham, Sch Sci, Inst Translat Med, Buckingham, Bucks, England..
    It is time to classify biological aging as a disease2015In: Frontiers in Genetics, E-ISSN 1664-8021, Vol. 6, article id 205Article in journal (Other academic)
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    FULLTEXT01
  • 185.
    Bundsen, Andreas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Artificial selection for large and small relative brain size in guppies (Poecilia reticulata) results in differences in cognitive ability2012Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    Vertebrate brain size is remarkably variable at all taxonomic levels. Brains of mammals forexample, range from 0.1 gram in small bats (Chiroptera) to about 8-9 kilos in Sperm whales(Physeter macrocephalus). But what does this variation in size really mean? The link between brainsize and cognition is debated due to, for instance the difficulties of comparing cognitive ability indifferent species. A large number of comparative studies continue to provide information aboutcorrelations found both within and between species. The relative size of the brain is an example of apopular measurement that correlates with cognitive ability. But to date, no experimental studieshave yielded any proof causality between relative brain size and cognitive ability. Here I usedguppies selected for either large or small relative brain size to investigate differences in cognitiveperformance of a quantity discrimination task. The results from this experiment provideexperimental evidence that relative brain size is important for cognitive ability, and that a differencein cognitive ability could be obtained already after two generations of selection experiments onrelative brain size in a vertebrate.

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    Artificial selection for large and small relative brain size in guppies (Poecilia reticulata) results in differences in cognitive ability
  • 186.
    Bundsen, Andreas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Impact of sustainable forest management through FSC-certified logging on bird communities in Berau District, east Kalimantan, Indonesia2014Independent thesis Advanced level (degree of Master (Two Years)), 30 credits / 45 HE creditsStudent thesis
  • 187.
    Buonfrate, Chiara
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Determining chemical stress effects in Phytoplankton cells2021Independent thesis Advanced level (degree of Master (Two Years)), 30 credits / 45 HE creditsStudent thesis
    Abstract [en]

    Phytoplankton, photosynthetic unicellular organisms, play a fundamental role in aquatic food webs and half of the world’s primary production is sustained by these organisms.Diatoms are a particular abundant and biodiverse group, responsible for approximately 40% of global primary production and one-fifth of the photosynthesis on Earth. Therefore, understanding diatom’s response to stress in a constantly changing environment, strongly influenced by humans, is crucial. This project explored effects of chemical stress on diatoms; the focus was inhibition of growth after stress exposure. Stressors aimed to be explored were reactive oxidative species, and anthropogenic introduced chemicals, as herbicides and heavy metals. Bulk approaches were performed. Three different chemicals were tested using a bulk method with a microplate reader, and absorbance values were used as a measure of growth and growth inhibition. Similar to previous studies high doses of chemicals showed to inhibit at least partially growth. However, a bulk approach ignores the phenotypic heterogeneity and existence of resilient subpopulations among populations single cells. Therefore, in this project a single cell method, consisting in a hydrogel microfluidics device, was tested, and implemented. Despite difficulties encountered during the testing of this new methods, results obtained corroborates the goal of using hydrogel device for single cell studies on chemical exposure and it could be potentially useful for future applications. 

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  • 188.
    Bylander Camitz, Kalle
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Cehlin, Emelie
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Högberg, Gustav
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Lock, Emma
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Meyer, Emil
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Söderberg, Nora
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Bioproduction in Need of Change: An investigation of the needs and bottlenecks of the biomanufacturing industry2023Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    This report was conducted at the request of Testa Center to compile the essential requirements and challenges faced by the biomanufacturing industry. The gathered information will serve as a guide for Testa Center's future objectives in accelerating technological advancements in bioproduction. Based on insights provided by 14 companies involved in various stages of biological production, a comprehensive conclusion was reached.

    A bioproduction process was defined to encompass cell optimization, creation of starter cell cultures, cell cultivation/fermentation in bioreactors, product harvest, clarification, capture, and polishing, with the latter three stages focused on purification. The companies were contacted through surveys and personal interviews, which were tailored to suit each interviewee while aligning with the survey questions. Data obtained was subsequently categorized, highlighting the areas in need of significant development, where frequency of mentioned bottlenecks within each category determined its level of importance.

    According to the companies, the three most critical areas requiring attention were purification, continuous processing, and single-use technologies. Consequently, these areas were given thorough consideration during the analysis of individual company responses. However, all bottlenecks raised by company representatives were included, along with relevant background information to ensure a comprehensive understanding of each issue. The remaining areas of need, in descending order of significance, were classified as "miscellaneous" (bottlenecks not assignable to a specific area), "scalability", "cooperation and communication", "cell optimization and gene-editing", "other material and equipment issues", "high costs", "screening and assaying", "harvest", "bioreactors", and "virtual modeling". The expressed needs varied depending on each company's unique biological production process.

    By addressing these identified challenges and focusing on the crucial areas, Testa Center can effectively contribute to the acceleration of technological advancements in bioproduction.

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  • 189.
    Bylund, Jonatan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Physiology and Environmental Toxicology. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Cre-driven reporter gene analysis of parvalbumin and vesicular glutamate transporter 2 in the mouse brain and their internal distribution within subthalamic areas2022Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
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  • 190.
    Bălan, Mirela
    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.
    Integrative bioinformatic analysis of SARs-CoV-2 data2021Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
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  • 191.
    Camargo Romera, Paula
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Computational prediction of cell-cell interactions in the brain-tumour microenvironment2023Independent thesis Advanced level (degree of Master (Two Years)), 30 credits / 45 HE creditsStudent thesis
    Abstract [en]

    Glioblastoma is the fastest-growing, and the most common malignant brain tumour in adults. It is normally treated with surgery and radio- or chemotherapy, but the approximate life expectancy is of 15 months with a high probability of cancer recurring. Therefore, there is a need for decreasing its severity. Bulk and single-cell RNA sequencing allow the identification of cellular states in tumours affected by cell-intrinsic and extrinsic factors. Four different cellular states have been identified in glioblastoma: neural progenitor-like, oligodendrocyte progenitor-like, astrocyte-like, and mesenchymal-like. As glioblastoma is an immunosuppressive tumour, it can alter the immune system and increase the tumour's immune escaping by segregating immunosuppressive factors or interacting with the brain microenvironment.Two datasets were used in this study to explore if the localization of the tumour in the brain microenvironment and the tendency of glioblastomas to activate microglial cells are due to particular ligand-receptor interactions. Data quality control was applied to both datasets and SingleCellSignalR and CellphoneDB packages were used to predict the possible interactions. A total of seven experiments were designed for this study. The first dataset, GBmap, allowed us to do a comparison between tumour cells and microglia, tumour cells and other cell types in the brain, and the four cellular states of glioblastoma with microglia and macrophages. Next, healthy microglia from GBmap was used to compare with the tumour bulk data from the second dataset, HGCC. The bootstrap technique was performed to compare bulk data vs single-cell data, and a comparison between tumour cells and microglia or other cell types was analysed.Results showed specific and shared interactions between cell types or cellular states, revealing the different localization of the tumour cells depends on the expressed ligand-receptor pairs. Also, a total of four patterns of interactions were found in the 50 samples to have a different tendency to activate microglial cells, which are promising results to further explore drugs to interfere with or how these interactions are related to patient survival. Furthermore, even if glioblastoma is a heterogenous disease, more interactions were predicted with microglial/macrophage cells without a uniform pattern between patients, and therefore, this study is a starting point upon which further in vitro studies would be needed to study the predicted interactions as potential targets to stop the progression of this type of cancer.

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  • 192.
    Cao, Shuowen
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    The expression and regulatory functions of Ms1 RNA in Mycobacterium marinum2021Independent thesis Advanced level (degree of Master (Two Years)), 30 credits / 45 HE creditsStudent thesis
    Abstract [en]

    Ms1 RNA (Mycobacterium smegmatis small RNA 1) is a recently characterized small non-coding RNA. It appears in some Mycobacterium species and exhibits a stress-related expression pattern. Despite its essential regulatory function, there is still much to learn about the expression, functions, and structure. Here we quantify the Ms1 RNA expression levels in different growth phases using the model system Mycobacterium marinum (Mmar) and show that the high Ms1 RNA level in the stationary phase is due to high expression level rather than accumulation. The data also suggest that the aceA gene is downregulated by Ms1 RNA in the exponential phase and upregulated in the stationary phase while the alkB_2 gene is upregulated by Ms1 RNA in all phases. Furthermore, we identify Ms1 RNA functional regions by overexpressing the mutant Ms1 RNA genes and then observing the downstream regulatory effects. As a result, all 3 mutations changed the general expression patterns or the regulations of the aceA or alkB_2 gene, which indicates that the 3 regions (29~41, 81~103, and 259~295 bases) are potential Ms1 RNA functional regions. It was also attempted to compensate for the knock-out of the genomic Ms1 RNA gene by a vector-carried Ms1 RNA under the control of a Tet inducible promoter but not a single colony was obtained. Apart from that, we also generated large amounts of Ms1 RNA by T7 in vitro expression which can be used for structure probing.

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  • 193.
    Cao Sánchez, Julia
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    What's going on under the Baltic?: Investigating the effect of abiotic and biotic factors on zoobenthos abundance patterns in the southern Baltic Sea2023Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Benthic macrofauna in the Baltic Sea are subjected to many pressures, both natural and anthropogenic, thus understanding what factors affect species abundance and distribution is an essential first step for aiding in their conservation. Species distributions are a result of both the environment and biotic filters acting on the ability of species to disperse, also influenced by the biogeographical history and stochastic processes. However, most studies on Baltic zoobenthos communities have focused on the effect of environmental variables, while the role that biotic interactions might play has not been given as much attention. Joint Species Distribution Modelling allows a more integrative approach to understand the effects of both of these factors in driving species distributions. In this study, data on abundance of benthic macrofauna communities in the southern Baltic Sea were analysed in this framework using a latent variable model with the gllvm package in R. The results of the model indicated that salinity and depth are the environmental covariates that most importantly affect zoobenthos abundances, although all covariates analysed have a significant effect. Therefore, abiotic factors seem to have a strong influence in zoobenthos abundances, probably due to the extreme environmental conditions that characterize the Baltic Sea. The analysis of the residual correlations of the model indicated the existence of multiple correlations between species. However, actual interactions are hard to infer as correlations could be induced by other covariates not included in the model. In addition, the low abundance and richness of organisms in the Baltic probably reduce the strength of interspecific interactions, as comeptition for food and space will be less intense and likely more conspicuous at a more local scale than the one covered in the study. Nevertheless, some strong negative correlations were found for the bivalve Macoma balthica and the invasive polychate Marenzelleria sp, which could be indicating competition of these species with the ones they co-occur with.

    The full text will be freely available from 2025-07-31 15:51
  • 194.
    Capuccini, Marco
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmaceutical Biosciences. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Structure-Based Virtual Screening in Spark2015Independent thesis Advanced level (degree of Master (Two Years)), 30 credits / 45 HE creditsStudent thesis
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  • 195.
    Cardoso, Lourenço
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Development of reporter plasmids to study the role of the E6E7-coding region on the regulation of HPV16 early gene expression2023Independent thesis Advanced level (degree of Master (Two Years)), 60 credits / 90 HE creditsStudent thesis
    Abstract [en]

    The human papilloma virus, or HPV, is the second most common sexually transmitted pathogen in the world, as well as the main cause of cervical cancer, though it has also started to be increasingly associated with colon and throat cancer over the years. There are many HPV types, of which, HPV16 causes infections that show the highest risk of turning into cancer. HPV16, like other HPV types that may progress into cancer, depends on a tightly regulated expression of the early genes to regulate infection. Proteins expressed by early genes like E1 and E2 regulate the expression of other early genes and make the DNA polymerase more readily available for viral replication, while E6 and E7 more directly associate with the development of cancer, maintaining a constant state of division and blocking apoptosis. As such, the E6E7 CDS is of particular interest to understanding the processes behind tumorigenesis from HPV infections. In high-risk HPV types, like HPV16, the expression of these genes is regulated by post-transcriptional changes, in processes like alternative splicing, the process by which different sections of a pre-mRNA may be spliced out to express different products. Vaccination for HPV16, and other types, is available and very effective, but post-exposure therapy for this virus has not been developed. However, by understanding the specific mechanisms behind HPV early gene regulation, it may be possible to identify therapy targets. The HPV genome has different genetic elements that interact to regulate expression, like splice sites or splicing enhancers and silencers. As such, in this project, we attempted to construct, characterize and study reporter plasmids containing different sections of the E6E7-coding region, to better understand how this region individually regulates the expression of HPV16’s early genes, in hopes of developing a strong tool to study this virus.

  • 196.
    Carl, Damell
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Collateral sensitivity towards gentamicin in ciprofloxacin resistant Escherichia coli2024Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    The full text will be freely available from 2025-01-11 16:54
  • 197.
    Carlson, Matilda
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Hansen, Alma
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Levin, Tyra
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Rick, Moa
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Tallqvist, Frida
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Tiefensee, Malin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Streamlining the manufacturing of biotherapeutics: SPPS vs. Recombinant protein production2021Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    In this paper we have researched two methods for peptide synthesis; solid phase peptide synthesis (SPPS) and recombinant protein production, hereafter called recombinant production. The goal was to create a decision support that can be of use when choosing a production method for a given peptide. Additionally, we wanted to find a way to tell if a given sequence might be difficult to synthesize with SPPS, and in those cases recommend recombinant production as an alternative. To accomplish this, we have investigated general problems that may occur for the two methods as well as amino acid and sequence specific issues. We have also researched if there are any known solutions to avoid these problems, and by evaluating the gravity and frequency of the problems, with these solutions in mind, the decision support was created.

    A description of each considered issue is given, but the amount of each amino acid and the sequence of the amino acids in the peptide also needs to be considered when choosing the method. For 15 out of the 20 individual amino acids we have recommended the use of SPPS. For the remaining five, three are dependent on the placement within the sequence and in two cases we recommend considering recombinant production. We believe we have created a decision support that fulfills its purpose and can be of use when choosing the production method for future biotherapeutics.

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  • 198.
    Carlsson, Jennifer
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Elevated IgG4 is associated with higher risk for cholangitis, cirrhosis, ERCP and liver-transplantation among patients with primary sclerosing cholangitis2022Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Primary sclerosing cholangitis (PSC) is a rare inflammatory chronic liver disease that causes damage to the intra- and or extrahepatic bile ducts leading to cholestasis. As the disease proceeds the development of cirrhosis and eventually liver failure occurs. This study aims to determine the role of IgG subclasses in the prognosis of PSC and its outcome. A retrospective analysis was performed of 183 patients followed at the Department of Upper Abdominal Diseases at the Karolinska University Hospital. Factors that were analysed were sex, age at PSC diagnosis, total IgG values, IgG subclasses values and events of autoimmune hepatitis (AIH), inflammatory bowel disease (IBD), colectomy, cirrhosis, cholangitis, endoscopic retrograde cholangiopancreatography (ERCP), liver transplantation and cholangiocarcinoma. This study showed that high IgG4 levels were associated with a higher incidence of cirrhosis, liver transplantation, cholangitis and ERCP, while low IgG4 levels were associated with a prior IBD diagnosis. In conclusion, elevated IgG4 levels were associated with a higher occurrence of cirrhosis, cholangitis, ERCP and liver transplantation. It seems that IgG4 could be of importance for outcome prediction in PSC.

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  • 199.
    Carlsson Tysk, Sofia
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Elofsson, Hampus
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Frisk, Kamilla
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Lillkull, Caroline
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Lundmark, Kristoffer
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    MCShane, Ellen
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Nervsjukdomar - Nästa stora satsning: Kartläggning av forskningsanslag i Sverige inomnaturvetenskap, medicin och life science2014Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    The aim with this project was to investigate how research grants in Sweden are distributed inthe selected fields; natural science, medicine and life science. Our client Olink producesdetection kits for biomarkers and our goal with this study was to give an indication of apossible new market area for their products. Three foundations were included in the study;VINNOVA, Vetenskapsrådet (Swedish Research Council) and Stiftelsen för strategiskforskning (Swedish foundation for strategic research). Nearly a thousand research grantswere analysed which included a total of 4,92 billion Swedish kronor. Seven selecteduniversities were contacted; Chalmers tekniska högskola, Karolinska Institutet, Kungligatekniska högskolan, Linköpings universitet, Lunds universitetet, Sverigeslantbruksuniversitet, Uppsala universitet. The aim was to get an indication if any specificuniversity invested in a research of significant interest. The analysis of the foundationscombined with the analysis of the universities internal funding distribution gave theconclusion that a possible future market area for Olink Bioscience is the field of neurologicaldisorders.

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  • 200.
    Cayón, David
    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.
    Different anti-predator defenses induced by roach and signal crayfish in the invader zebra mussel2010Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
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