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  • 1.
    Abaurre, María del Carmen
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning. Department of Medical Biochemistry and Biophysics, Karolinska Institutet.
    Transcriptional states of human oligodendroglia during development2021Independent thesis Advanced level (degree of Master (Two Years)), 30 poäng / 45 hpOppgave
    Abstract [en]

    Differentiation of oligodendroglia lineage cells in humans still remains largely unclear. Oligodendrocyte progenitor cells (OPCs) are known to participate in remyelination processes by proliferating, migrating to the area of the lesion and then differentiating into oligodendrocytes (OLs), which can myelinate the affected axons again. This has sparked an interest in OPCs, since cell transplant could be a potential form of therapy for demyelinating diseases such as multiple sclerosis. However, that is not the only relevant aspect about them. OPCs have been shown to present heterogeneous populations with different functions, such as participating in immunological processes or responses to injury.

    Single cell technologies have become a powerful tool for the identification of unknown functions in OPCs and the characterization of the evolution of the oligodendroglia lineage. In this project, we analysed single-nuclei data of human foetal brain samples. For most of the steps of this pipeline, we used the Scanpy toolbox. In order to mitigate batch effects in our data, the Harmony algorithm was used for the correction. The Harmony-corrected principal components still retained part of the bias by batch. Leiden graph-based clustering resulted in a total of 19 clusters, 14 of which we were able to successfully annotate. Annotation was performed in combination of differential expression analysis and literature markers from public datasets. We obtained a single OPC cluster in our data, but marker genes expression suggests not all cells within this cluster are equally mature. Instead, some of them seem to be closer to commitment to an OL fate. This hypothesis would have to be confirmed by lineage inference analysis, which we could not include in this study. Finally, validation of our annotation with label transfer gave mixed results depending on the dataset used. This step was performed in Seurat. A possible explanation of these results could be sensitivity to differences between plate-based and droplet-based technologies for library preparation before sequencing. OPCs were successfully transferred regardless of the dataset used, so we can be certain of their identity.

  • 2.
    Abbu, Tom
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Effect of long-term exposure to oxazepam on whole-body cortisol concentration in stickleback2018Independent thesis Basic level (degree of Bachelor), 10 poäng / 15 hpOppgave
    Abstract [en]

    Pharmaceuticals are common contaminants in aquatic ecosystems. Pharmaceutical residues in aquatic systems have gained increased interest the last decades and are now recognized as a major threat to aquatic ecosystems around the globe. Benzodiazepines (BZDs) are a class of psychiatric pharmaceuticals classified as anxiolytics, i.e. pharmaceuticals used to treat anxiety disorders. A study reports that dilute concentrations of the BZD oxazepam influences fish behavior, which potentially can damage ecosystems. The objective of this study was to investigate the effect of a 7-day exposure to the benzodiazepine oxazepam (1 or 100 ug/L tank water) on whole-body cortisol concentration in three-spined stickleback (Gasterosteus aculeatus). Cortisol concentrations were measured using RIA (Radioimmunoassay). Our results show that the highest oxazepam concentration (100 μg/L) we tested displayed a significantly reduced cortisol concentrations compared to controls when analyzed separately. But when fish were exposed to the lower concentration of oxazepam (1 μg/L), an effect on cortisol levels was not shown. After all, our results show that oxazepam have no effect on cortisol levels and therefore will not influence the behavior of three-spined stickleback regarding cortisol. Our result contradicts several earlier studies and it is imperative to do further studies regarding this manner using other protocols. The complexity of how benzodiazepines affect aquatic life and ecosystems remains largely unknown and environmental predictions are difficult to make. However, it is necessary to study how pharmaceuticals potentially can affect aquatic life because of its alarming effects.

    Fulltekst (pdf)
    Effect of long-term exposure to oxazepam on whole-body cortisol concentration in stickleback
  • 3.
    Abdelaziz, Nouha
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi.
    The role of RNA-binding protein FUBL-1 in epigenetic inheritance in C. elegans2022Independent thesis Advanced level (degree of Master (Two Years)), 30 poäng / 45 hpOppgave
    Fulltekst (pdf)
    fulltext
  • 4.
    Abdul Rahman, Zozek
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi.
    Expression of FLAG-tagged argonautes in Dictyostelium discoideum2022Independent thesis Advanced level (degree of Master (Two Years)), 20 poäng / 30 hpOppgave
    Abstract [en]

    Argonautes are conserved RNA-binding proteins that can regulate gene expression post transcriptionally through a process known as RNA interference (RNAi). This is done through the use of small RNAs, e.g. sRNAs that act as a guide for the argonautes, allowing for sequence-specific binding to the target site. This interaction has been studied in many organisms, one of which is the model organism Dictyostelium discoideum. D. discoideum is an amoeba that has been used extensively in genetic experiments due to its unique lifestyle, and ease of use. Being a eukaryotic, unicellular organism, it proves to be a great tool for the study of regulatory systems in eukaryotes, allowing us to study this argonaute-sRNA interaction in detail. By analysing which RNAs bind to the argonautes, we can better understand which genes these proteins regulate and what role RNAi has in the organisms as a whole. 

    In this study, I investigate three of the five argonautes found in D. discoideum, namely agnA, agnC and agnE. By transforming FLAG-tagged versions of these genes into the amoeba, I successfully express two of these modified proteins in D. discoideum and verified expression by using antibodies designed specifically to recognise the FLAG-tags. This opens up the possibility for the characterisation of the argonaute proteins to better understand their role and function in the regulation of genes. 

    Fulltekst (pdf)
    fulltext
  • 5.
    Abrikossov, Alexei
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Computer simulations: Orientation of Lysozyme in vacuum under the influence of an electric field2011Independent thesis Advanced level (professional degree), 20 poäng / 30 hpOppgave
    Abstract [en]

    The possibility to orient a protein in space using an external electrical field was studied bymeans of molecular dynamics simulations. To model the possible conditions of an electrospray ionization (ESI) the protein Lysozyme in vacuum was considered under the influence ofdifferent field strengths. The simulations showed three distinct patterns: (1) the protein wasdenaturated when exposed to too strong electrical fields, above 1.5 V/nm; (2) the proteinoriented without being denaturated at field strengths between 0.5 V/nm and 1.5 V/nm (3) theprotein did not orient and did not denaturate if the strength of the field became to low, below0.5 V/nm. Our simulations show that the orientation of the protein in the fields correspondingto the second pattern takes place within time intervals from about 100 ps at 1.5 V/nm to about1 ns at 0.5 V/nm. We therefore predict, that there exists a window of field strengths, which issuitable for orientation of proteins in experimental studies without affecting their structure.The orientation of proteins potentially increases the amount of information that can beobtained from experiments such as single particle imaging. This study will therefore bebeneficial for the development of such modern techniques.

    Fulltekst (pdf)
    FULLTEXT01
  • 6.
    Abu Jaish, Ahmad
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Comparison of post-thaw sperm viability, kinematic parameters and chromatin structure after cryopreservation of raw semen and semen prepared by gradient centrifugation2023Independent thesis Advanced level (degree of Master (Two Years)), 10 poäng / 15 hpOppgave
    Fulltekst (pdf)
    fulltext
  • 7.
    af Geijerstam, Lukas
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Magnusson, Andreas
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Nordström, Ida
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Westerberg, Samuel
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Zingmark Lien, Max
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    The Use of Surface Plasmon Resonance 2014-2024: A Review2024Independent thesis Basic level (degree of Bachelor), 10 poäng / 15 hpOppgave
    Abstract [en]

    Surface plasmon resonance (SPR) is a label-free, versatile and highly sensitive method for studying molecular interactions in real time. It is widely used by industry and academia alike in fields ranging from Alzheimer’s disease research to detection of heavy metals. In this review, studies published during the last 10 years using Biacore or other SPR instruments were compiled and compared. Trends were also identified in the field. Amine coupling was found to be the most common ligand strategy for proteins, and most SPR research related to the field of medicine. Furthermore, three main purposes of an SPR experiment were identified: To determine the affinity between a pair of molecules, kinetics between a pair of molecules or to detect a certain molecule in a solution. The results presented are often related to these three purposes, and are most often presented and evaluated in terms of kinetic, affinity and sensitivity constants. SPR can be used for studying a broad range of molecular interactions, and an overview was obtained by dividing up the field into different parts based on molecular interactions and SPR methods. The study of molecular interactions using SPR was divided into protein-protein interactions (PPIs), antibody-antigen, protein-biomolecule interactions, interactions between proteins and small molecules, and non-conventional SPR methods. Non-conventional SPR methods include localized surface plasmon resonance (LSPR) and SPR imaging (SPRi), which are both based on the same optical sensing principles as SPR. 

    Fulltekst (pdf)
    The Use of Surface Plasmon Resonance 2014-2024: A Review
  • 8.
    af Klercker, Anna
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    The impact of the ribosomal 16S rRNA modifications on the antibiotic susceptibility and fitness in Escherichia coli  2024Independent thesis Basic level (degree of Bachelor), 10 poäng / 15 hpOppgave
    Abstract [en]

    The rRNA molecules which make up the two subunits of the Escherichia coli ribosome are extensively post-transcriptionally modified. The specific purpose of each modification is still unknown. It is proposed that they provide a structure for the ribosomal assembly, which would indicate that they are essential. However, previous literature in this area using E. coli shows that when the modification enzymes are removed individually the effects on growth fitness and antibiotic sensitivity are limited. This makes their role in ribosomal assembly unclear. The effect of removing multiple ribosomal modification enzymes is largely unexplored. The position of many of the modifications are found in clusters, usually in the catalytic domains of the ribosome, which are often targeted by antibiotics, indicating that removing the modification enzymes could affect antibiotic sensitivity. Most of the previous studies on strains with these modification enzymes removed were performed with traditional lambda-red that leaves behind FRT scars, which can cause unwanted spontaneous excisions via recombination between the FRT scars. Here, DIRex lambda-red was used to create clean deletions, which does not produce FRT scars and therefore, allows for more reliable analysis of the ribosomal modification enzymes’ role. The results show that there is a fitness cost and change in antibiotic sensitivity due to multiple of the deletions of the ribosomal modification enzymes. For some of the modifications, this is true when that particular site alone is left unmodified, while for other positions, these effects are only observed when multiple sites are modified simultaneously. For example, the methyltransferase RsmG knockout has a big effect on streptomycin resistance but no fitness cost, while the methyltransferase RsmA and RsmF knockouts causes a fitness cost in combination and causes tetracycline and gentamycin resistance respectively. This indicates that the ribosomal modifications significantly affect the interaction with antibiotics and fitness, and therefore, have a significant part in ribosomal function. 

    Fulltekst tilgjengelig fra 2025-06-12 00:00
  • 9.
    Afewerki, Isaias
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Genflödet från genetiskt modifierade grödor till vilda populationer2014Independent thesis Basic level (degree of Bachelor), 10 poäng / 15 hpOppgave
    Abstract [sv]

    Tillämpningen av genetiskt modifierade (GM) grödor har varit utbredd över hela världen och har ökat markant sedan den första GM-grödan blev tillgänglig för kommersiellt bruk 1996. Sedan starten har det tillkommit mycket forskning kring risken för spridning av transgener från grödor till vilda populationer. För att en transgen ska kunna etableras i en vild population så måste tidiga generationer av hybrider överleva för att kunna återkorsas upprepade gånger med den vilda arten, det gör att det genetiska materialet från grödan succesivt reduceras i varje generation tills det att transgenen är det enda DNA från grödan kvar hos avkomman. För att denna process ska vara stabil krävs det en stark selektion för transgenen. Det här sättet för en gen att etableras i en population kallas för introgression och tros ha spelat en stor roll i växternas evolution. Hos vete så har man observerat introgression i ett tidigt skede med det besläktade ogräset bockvete där man även observerade en ökande fertilitet i efterföljande generationer. Hos odlad majs har man lyckats visa att majs kunnat anpassa sig till kallare klimat i nya habitat genom introgression från inhemska besläktade arter. Tecken på hybridisering och introgression har observerats hos flera grödor där selektionen har visat sig vara en av de viktigaste faktorerna för en nyintroducerad transgens fortlevnad inom en population. Migration mellan två populationer av besläktade arter, i form av pollen och fröspridning, påverkar kraftigt utsträckningen av hybridisering medan migration mellan subpopulationer inom en metapopulation påverkar effektiviteten av introgression. Om en transgen ger en förhöjd fitness till en sådan grad att hybrider framgångsrikt kan konkurrera med andra individer och reproducera sig så leder det till en spridning av genen. Trangenens interaktion med miljön påverkar också plantans fitness. En gen för insektresistens kommer att ge en ökad fitness när insektspopulationerna är stora, om insektspopulationen reduceras kraftigt så kommer genen stå för en onödig kostnad och utsättas för en negativ selektion. Den selektion som råder på åkern är anpassad för att möta våra behov av hög kvalitativ produktion av livsmedel och råvaror medan den naturliga selektionen väljer de individer som är bäst anpassade att överleva i den miljön. Sannolikheten för fixering av en transgen, skapad för att möta våra behov, in en vild population är låg, men den risken kräver ändå en noggrann utvärdering där man ser till de olika faktorerna i varje enskilt fall. 

    Fulltekst (pdf)
    Genflödet från genetiskt modifierade grödor till vilda populationer (Afewerki, 2014)
  • 10.
    Agnadóttir, Védís Mist Eyju
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Investigating the expression and function of RNA-binding protein FUBL-1 in C. elegans2023Independent thesis Advanced level (degree of Master (Two Years)), 40 poäng / 60 hpOppgave
    Abstract [en]

    RNA interference (RNAi) is an important mechanism of gene silencing in Caenorhabditis elegans, in which short RNAs direct sequence-specific silencing of gene expression mediated by Argonaute proteins. RNAi in C. elegans can be sorted into exogenous RNAi, where the short RNAs originate from foreign RNA sequences, and endogenous RNAi, where the short RNAs originate from RNA sequences in the genome. One endogenous RNAi pathway is the ERGO-1 pathway, which is active in the germline and in embryos. Mutants deficient in the ERGO-1 pathway show an increased response to exogenous RNAi, which is thought to be due to competition between exogenous and endogenous silencing pathways. 

    FUBL-1 is an RNA-binding protein found in C. elegans, which has three predicted functional isoforms: isoforms a, b and c. Prior research by the Hinas group has indicated that FUBL-1 may play a role in the ERGO-1 pathway of RNAi. FUBL-1 deletion mutants show an increased response to exogenous RNAi similar to ERGO-1 mutants, and also an upregulation of ERGO-1 target genes. They have also found that FUBL-1 is broadly expressed in somatic tissues, but germline expression has not been confirmed. The function of the three different isoforms has not yet been examined.

    The aim of this study was to further investigate the function of FUBL-1 by assessing the function of the different isoforms through RT-qPCR of C. elegans with mutations affecting the different isoforms, to use immunofluorescence staining to see whether FUBL-1 is expressed in the germline, and to identify FUBL-1 RNA targets through CLIP-seq. Preliminary RT-qPCR results indicated that the upregulation of ERGO-1 targets is less in isoform mutants than in FUBL-1 deletion mutants, indicating partial redundancy of the isoforms. Immunofluorescence staining showed that FUBL-1 is expressed in the germline nuclei. Growth protocols have been optimized and crosslinking has been performed on worms, but the full CLIP-seq protocol has not been performed yet.

    Fulltekst (pdf)
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  • 11.
    Agnas, Axel Jönses Bernard
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Non-Independent Mate Choice in Female Humans (Homo sapiens): Progression to the Field 2016Independent thesis Advanced level (degree of Master (Two Years)), 30 poäng / 45 hpOppgave
    Abstract [en]

    There is much evidence that mate-choice decisions made by humans are affected by social/contextual information. Women seem to rate men portrayed in a relationship as more desirable than the same men when portrayed as single. Laboratory studies have found evidence suggesting that human mate choice, as in other species, is dependent on the mate choice decisions made by same-sex rivals. Even though non-independent mate choice is an established and well-studied area of mate choice, very few field studies have been performed. This project aims to test whether women’s evaluation of potential mates desirability is dependent/non-independent of same-sex rivals giving the potential mates sexual interest. This is the first field study performed in a modern human’s natural habitat aiming to test for non- independent mate choice in humans.

    No desirability enhancement effect was found. The possibilities that earlier studies have found an effect that is only present in laboratory environments or have measured effects other than non-independent mate choice are discussed. I find differences in experimental design to be the most likely reason why the present study failed to detect the effect found in previous studies. This field study, the first of its sort, has generated important knowledge for future experimenters, where the most important conclusion is that major limitations in humans ability to register and remember there surrounding should be taken in consideration when designing any field study investigating human mate choice. 

    Fulltekst (pdf)
    fulltext
  • 12.
    Agongo, Hassanat
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Characterization of DNA Methylation in Giardia intestinalis2021Independent thesis Advanced level (degree of Master (Two Years)), 40 poäng / 60 hpOppgave
    Abstract [en]

    Abstract

    G. intestinalis is an intestinal protozoan parasite that causes 180 million symptomatic diarrheacases (giardiasis) and more than 0.5 billion asymptomatic infections per year. Symptomaticinfections are usually treated with metronidazole (Flagyl). However, resistance is emerging, andan alternative treatment is required. The mechanism to which the parasite causes the disease is notunderstood and, neither is the regulation of encystation (a process where trophozoites differentiateto cyst) However, preliminary data suggest that an epigenetic mechanism is involved. DNAmethylation is an important epigenetic regulator in many organisms, but it is not known if theDNA is methylated in Giardia. The main goal of this project was to characterize DNA methylationin G. intestinalis and, if it exists, study if it is linked to cell differentiation and use it as a target fordrug treatment. We found out using the dot blot technique complemented withimmunofluorescence assays, that 6mA and 5mC DNA methylation exists on the genomic DNA ofthe assemblage A G. intestinalis isolate WB. 6mA methylation was also found on RNA. However,no major differences were detected between trophozoites and cysts. Assemblage B Giardia isolates(GS and H3) also have methylated genomic DNA, but we detected lower levels of methylation. Abioinformatic search was performed in the G. intestinalis WB genome in an attempt to identifyDNA methylases. Expression levels through-out the life cycle, sequence similarities and structuralmodelling using iTASSER identified six putative DNA methylases in the WB genome. The sixDNA methylases were over-expressed in Giardia, three were lethal and three localized to thenucleus. 5-azacytidine and 5-aza-2’-deoxycytidine nucleoside analog drugs prevent methylationand are incorporated into RNA and DNA, respectively. We tested these two drugs on Giardiatrophozoites, and both have effects on the trophozoite stage (IC50 1.46±0.46 μM for 5-aza-2’-deoxycytidine and 111±24 μM for 5-Azacytidine). The 5-aza-2’-deoxycytidine drug is actuallymore effective than metronidazole, showing that nucleoside analogs affecting DNA methylationcould be alternative drugs for treatment of giardiasis.

    Fulltekst (pdf)
    fulltext
  • 13.
    Agrillo, Caroline
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Miljötoxikologi. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    DNA methylation modifications in human mesenchymal stem cells  induced by exposure to endocrine disrupting plasticiser metabolites MBP, MEP, MBzP, MEHP and MINCH2022Independent thesis Advanced level (degree of Master (Two Years)), 80 poäng / 120 hpOppgave
    Abstract [en]

    Endocrine disrupting chemicals (EDCs) are exogenous substances which can modify the function of the endocrine system and lead to adverse health effects. Humans experience daily uncontrolled exposure to EDC mixtures. Predicting mixture effects is complicated since the chemicals may produce different effects when combined together. EDCs may produce epigenetic effects such as alterations of the DNA methylation, which could modify the expression of the gene. Previously, 14 chemicals linked to metabolism (mixture G1) were reported to induce DNA methylation changes in an in vitro model. Mixture G1 were based on a Swedish longitudinal study which had identified the chemical burden of >2300 pregnant women. This project aimed to study single chemical driver effects of five individual chemicals from mixture G1, namely the four phthalate metabolites monobutyl phthalate (MBP), monoethyl phthalate (MEP), monobenzyl pthtalate (MBzP), mono-(2-ethylhexyl) phthalate (MEHP) and the non-phthalate plasticiser Bis(7-methyloctyl) Cyclohexane-1,2-dicarboxylate (DINCH) metabolite 2-4-methyl-7-oxyoctyl-oxycarbonyl-cyclohexane carboxylic acid (MINCH). Human mesenchymal stem cells (hMSCs) were exposed to the five compounds individually at the same concentrations as in mixture G1. After exposure, DNA methylation changes in four CpG sites within PGM1, MYOF and HCFC1 genes were analysed. While som chemicals did not show statistically significant effects, one chemical showed significant effects and thus could be a potential driver. The discrepancy between the observed DNA methylation alterations in the analysed genes and the alterations in mixture G1 highlights the need for comparing mixture to single chemical effects to identify drivers within mixes and for increased understanding of mixture effects.

    Fulltekst tilgjengelig fra 2026-01-01 15:14
  • 14.
    Ahlström, Anna
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Testing the specificity of the pBAD arabinose reporter2017Independent thesis Basic level (degree of Bachelor), 10 poäng / 15 hpOppgave
    Abstract [en]

    The project highlights Salmonella enterica subspecies enterica serovar Typhimurium (S. Tm)'s ability to metabolize simple sugars released from dead commensal bacteria, by using the pBAD (araBAD promoter) system as a reporter of L-arabinose availability. Using bioinformatics and homology of conserved L-arabinose transporter genes shared in Escherichia coli K12 (E. coli) and S. Tm, we aimed to create a S. Tm mutant strain unable to obtain L-arabinose from it environment. During the projects course of time it was discovered that L-arabinose transporters are not a shared gene trait between E. coli and S. Tm, and that putative L-arabinose transporter orthologues may exists in the S. Tm genome.

    Fulltekst (pdf)
    fulltext
  • 15.
    Ahlström, Christoffer
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Aho, Milja
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Edblom, Johan
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Gehlin Björnberg, Gabriella
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Petersson, Nina
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Sör, Lennart
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Felsökning och förbättringar kring identifiering och kvantifiering av norovirus i livsmedel och vattenprover2015Independent thesis Basic level (degree of Bachelor), 10 poäng / 15 hpOppgave
    Fulltekst (pdf)
    fulltext
  • 16.
    Ahlström, Christoffer
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Tekniska sektionen, Institutionen för teknikvetenskaper, Industriell teknik. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Röjås, Martin
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Tekniska sektionen, Institutionen för teknikvetenskaper, Industriell teknik.
    Framtida konsumtion på befintliga och nya handelsplatser: En plats- och konsumentundersökning för obemannade självservicebutiker2017Independent thesis Advanced level (professional degree), 20 poäng / 30 hpOppgave
    Abstract [en]

    Our demands on services and availability increases at the same time as the society gets more urbanized and more people tends to commute. In order to facilitate the consumer, technology based self-service (TBSS) stores might survive and thrive. This thesis had a focus on finding out the general public's perception on TBSS stores and how they perceive the availability even if it is unmanned. The extended marketing mix contains people as a means of competition and we wanted to investigate whether this competitive mean could be ruled out which would mean that the extended marketing mix needs to be revised.

    In order to find out the people's perception of the TBSS concept a short enquiry were constructed containing three questions. People from Uppsala central station and four countryside towns, corresponding to two percent of the population, answered this enquiry. In order to collect data for information concerning establishment a factor rating method with five chosen factors were performed.

    From the results of the enquiry we found that the majority of the respondents have a positive attitude towards TBSS, which means that the competitive mean people are not critical when it comes to consumer perception of accessibility; conclusion from this is that the extended marketing mix needs to be revised. The products that was stated most frequently were edible goods followed by ticket and fuel services. The analysis using the factor rating method exemplifies a way for companies to compare differents places for establishment from various chosen factors.

    Fulltekst (pdf)
    fulltext
  • 17.
    Ahmedova, Sibel Ismetova
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning. Mercodia AB.
    Development of a Sandwich ELISA to Quantify the GLP-1 Analogs2022Independent thesis Advanced level (degree of Master (Two Years)), 30 poäng / 45 hpOppgave
    Abstract [en]

    Immunoassay is a technology to quantify the molecules of biological samples. Enzyme-Linked Immunosorbent Assay (ELISA) is one of the most common immunoassays that is used to analyze biological samples. Mercodia is a company that is specialized in developing immunoassays within the area of metabolic disorders such as type 2 diabetes, obesity, and cardiovascular diseases. Mercodia wanted to develop a prototype sandwich ELISA for quantitative measurement of GLP-1 analogs, especially for Exenatide due to the customer requests. Thus, Mercodia in-house antibodies are paired with anti-Exenatide commercial antibodies and initial tests are performed. Various parameters and conditions are tested. Exenatide and Lixisenatide are successfully detected several times at 10 to 1000 pg/mL concentration. However, further optimizations are required in order to be more consistent with the results and to develop a more sensitive assay.

    Fulltekst tilgjengelig fra 2032-07-29 10:41
  • 18.
    Ahopelto, Lilli
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning. Ångströmlaboratoriet.
    Microfluidic sample preparation forbacterial DNA assays2023Independent thesis Advanced level (degree of Master (Two Years)), 20 poäng / 30 hpOppgave
    Abstract [en]

    The aim of this project was to use microfluidics for diagnostics by taking a pre-existing sample preparation protocol and transferring it on-chip. By doing this the expectation was to reduce the total assay time in order to make the process of diagnostics quicker. Previous research has shown that transferring the protocol to on-chip would be possible since agarose allows for diffusion of the required chemicals and DNA fragments.

    First part of the project was to design and build a microfluidic chip that could contain bacteria encapsulated in an agarose plug. The chip was built out of PDMS, glass and 3D printed parts containing the plug in the center of the chip. 

    Second part of the project was to transfer the protocol on-chip and optimize it. Here, the bacteria inside the 55μL agarose plug were chemically lysed by connecting the chip to a peristaltic pump which allowed the chemicals to flow through the chip in a closed system. By changing parameters like total plug volume, temperature and flow rate the total assay time decreased from 4 hours to 1.5 hours. This gave a 62.5% reduction in total assay time from the original protocol.  

    In conclusion, changing the original sample preparation protocol to a microfluidic approach significantly reduced the total assay time. Results also showed that it is possible for further optimization to be done which may lead to even more reduction in time. Another possible parameter which could be further optimized was the total plug volume which had potential to be further reduced. 

  • 19.
    Akcan, Ece
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning. Department of Immunology, Genetics and Pathology.
    Characterization of a novel EPHB2 R155C mutant with respect to its proteolytic cleavage by TF/FVIIa2021Independent thesis Advanced level (degree of Master (Two Years)), 40 poäng / 60 hpOppgave
    Abstract [en]

    EPHB2, an ephrin receptor (EPH) from receptor tyrosine kinase (RTK) family, is one of the substrates for tissue factor (TF) - coagulation factor VIIa (FVIIa) complex and it is cleaved in its ectodomain. EPHB2 cleavage is important for ephrin receptor (EPH) - ephrin ligand (EFN) signaling and cell repulsion. TF has been reported to be overexpressed in different cancer types such as breast and colorectal cancer (CRC). Furthermore, EPHB2 R155C mutation, at the TF/FVIIa-mediated cleavage site, has been identified as one of the somatic mutation sites in human metastatic CRC. Therefore, the aim of the present work was to characterize the EPHB2 R155C mutation and its effect on the cleavage by TF/FVIIa on EPHB2 in context to CRC. We generated overexpression cell models for EPHB2 wild type (wt) and R155C mutant in human CRC DLD-1 cell line for in vitro compartmentalization assay analysis to demonstrate repulsion event in EPH-EFN signaling. Whereas low endogenous TF expression led to incomplete cleavage of EPHB2 wt protein, stable overexpression of TF resulted in complete cleavage. Moreover, overexpression of TF resulted in reduced compartmentalization in EPHB2 wt cells after FVIIa treatment. Transient expression of TF in EPHB2 wt and R155C cells showed no clear difference in EPHB2 cleavage. Interestingly, it was difficult to obtain similar stable overexpression level of TF in EPHB2 R155C cells compared to EPHB2 wt cells. This may lead to further research in context to the role of TF/FVIIa-mediated EPHB2 cleavage in CRC by the generation of TF overexpression cell lines using lentiviral transduction.

    Fulltekst (pdf)
    fulltext
  • 20.
    Akel, Sarah
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning. Department of Clinical Neuroscience, University of Gothenburg/Sahlgrenska University Hospital.
    Evaluating Blood Biomarker Profiles in Adults with New-onset Seizures using Machine Learning2022Independent thesis Advanced level (degree of Master (Two Years)), 30 poäng / 45 hpOppgave
    Abstract [en]

    Around 1% of the population worldwide suffer from epilepsy, a condition which is characterized by recurring seizures. The development of reliable biomarkers for both prediction and targeted treatment of seizures is critical, as they can pave the way towards personalized therapy in epilepsy. In addition, sensitive biomarkers can be utilized for the detection of epilepsy in its early stages and allow for early treatment intervention. Various types of biomarkers have been studied in relation to epilepsy, with blood markers emerging as major candidates. Blood biomarkers offer the benefit of being cost and time efficient, in addition to being less invasive to sample in contrast to cerebrospinal fluid markers. Importantly, they can enhance patient diagnosis and prognosis when supplemented with other diagnostic methods, such as EEG. In this pilot study, five blood biomarkers of brain injury are studied in epilepsy, post-stroke epilepsy and single seizure patients. The aim is to analyze whether S100B, NSE, GFAP, NfL and tau are promising indicators of epilepsy after a first seizure in adults. The results present S100B as the most promising biomarker, with potential to predict early epilepsy.

    Fulltekst (pdf)
    fulltext
  • 21.
    Akula, Srinivas
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Analysis of the isotype specificity of three platypus immunoglobulin Fc receptors2012Independent thesis Advanced level (degree of Master (Two Years)), 30 poäng / 45 hpOppgave
    Abstract [en]

    The host’s defense against diseases called immunity acts either via innate or adaptive defense mechanisms. Immunoglobulins (Ig’s) are important players in adaptive immunity. They have evolved both structurally and functionally during vertebrate evolution. The Fc region of Igs can interact with specific receptors on the surface of various immune cells; crosslinking of these Fc receptors can trigger a wide array of immune reactions. To trigger such reactions, higher mammals have five different classes of Igs (IgM, IgG, IgA, IgE and IgD) while amphibians, reptiles and birds have four (IgM, IgD, IgA and IgY).  Our recent studies have revealed that the early mammals (Platypus) have eight Ig isotypes (IgM, IgD IgO, IgG1, IgG2, IgA1, IgA2 and IgE) and at least four Fc receptors: FcRA, FcRB, FcRC and FcRD. In this study we investigated the specificity of three of these platypus Fc receptors to get a better picture of their isotype specificity.   

    Fulltekst (pdf)
    Report-srinivasakula.pdf
  • 22.
    Al Jewari, Caesar
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Examining the Root of the Eukaryotic Tree of Life2017Independent thesis Advanced level (degree of Master (Two Years)), 20 poäng / 30 hpOppgave
    Abstract [en]

    Identifying the evolutionary root of eukaryotic tree of life (eToL) is a central problem in systematic biology that has been receiving growing attention. This task has been aided by the development of advanced phylogenetic methods and the availability of large amounts of genomic data from across the tree. Recently, two studies have tried a novel approach to define the eToL root, using euBacteria (instead of the more distantly related Archaea) as the outgroup. The results of these two recent studies are partially overlapping datasets, which produce contradictory results. One study, using mixed eubacterial data (euBac), makes the case for a neozoan-excavate root, while the other study, using alpha-proteobacterial (aP) data, concluded the traditional unikont-bikont root. These two results suggest different theories of early eukaryote evolution. However, there is also evidence of substantial artefacts in these datasets and traces of horizontal gene transfer (HGT), the exchange of DNA between unrelated organisms. This project aims to re-examine the datasets of both publications (61 total protein markers). The work started with updating both datasets with solid new phylogenomic data from the supervisor lab and new publicly available data. I then used these data to systematically investigate the phylogenetic signals of the 61 protein markers across 88 taxa (68 eukaryotes and 20 Bacteria). These were first subjected to preliminary phylogenetic analyses to sort orthologues from paralogues. All orthologues were then combined into a single dataset and subjected to in depth phylogenetic analyses to evaluate the support for various hypotheses. I also investigated potential sources of artefact in the data using traditional and novel methods I devised and developed myself including computer scripts specifically written for this work. I created a pipeline for the data curation process to make it fast and efficient by automating various parts of the workflow, including concatenating the multigene dataset into a super matrix. I estimated the level of incongruence in each dataset, excluded the protein markers that have a strong phylogenetic bias, and reconstructed new datasets. I conclude that the data in hand (protein markers and taxa) contain conflicting and inconsistent phylogenetic signal and that a few proteins can have a very strong effect on the results of the analyses. However, a third possible hypothesis is clearly rejected. This suggests that there are specific artefacts in the data, favouring one or the other of the two remaining hypotheses.

  • 23.
    Alacamli, Erkin
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Developing an Advanced Method for Kinship from Ancient DNA Data2023Independent thesis Advanced level (degree of Master (Two Years)), 30 poäng / 45 hpOppgave
    Abstract [en]

     The analysis of kinship from ancient DNA (aDNA) data has the potential to provide insight into social structures of prehistoric societies. Kinship analysis is gaining popularity as optimised wet-lab methods allow for studies with sample sizes on the level of whole cemeteries. However, the specifics of ancient DNA require different methods than what would be used for modern DNA. A common way is to use the sites that are identical-bydescent (IBD), however, detecting these is often a challenging task since it is not easy to determine whether a shared locus between two individuals is inherited from the ancestor or if another factor caused the similarity. Most methods used in the field are able to identify up to 2nd or 3rd degree relatives from aDNA data but do not distinguish between different types of relationship for the same degree, for instance not being able to differentiate between parentoffspring and full sibling-sibling relationship in first degree. The aDNA kinship methods often use either of window-based or single-site approaches, however, these two approaches have not been compared formally before in terms of effectivity and efficiency. In this work, READv2 is presented as a re-implementation of a popular kinship analysis method for aDNA studies with additional features such as accepting .bed files as input, which take up less space than the previous input type, plain-text .tped files. It is shown that the new version works more efficiently in terms of runtime. However, the memory requirements seem to be increased with the new implementation. Furthermore, a window-based approach is compared with the single-site approach of READv2, as well as varying window sizes, with benchmarked simulation data which contains approximately 700 individuals with known 1st degree, 2nd degree and 3rd degree relationships. According to the comparison, the sensitivity of the method does not vary between the approaches and different window sizes for high coverages. However, the single-site approach has been shown to be the superior one by a small margin for lower coverages. In addition to these, using the variance of non-shared alleles in windows along the genome has been used to implement a method to differentiate different first-degree relationships, parent-offspring and siblings. The method is tested with an independent dataset from the 1000 Genomes Project which shows that the proposed method is able to work with different datasets with varying sets of SNPs. Nevertheless, the first-degree classification method requires further analyses to determine the stress-point where the True Positive rates for both categories start to drop. Additionally, some necessary changes and decisions are required for READv2 to be a user-friendly method that can be used by other researchers. The preliminary release of READv2, including example data as well as instructions to install the necessary packages and to run the algorithm can be found in https://github.com/GuntherLab/READv2/releases/tag/READ. 

    Fulltekst (pdf)
    fulltext
  • 24. Alam, Md. Maksudul
    et al.
    Sharmin, Sazia
    Nabi, Zinnatun
    Mondal, Shakhinur Islam
    Islam, Md. Shahidul
    Bin Nayeem, Sarmah
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Shoyaib, Muhammad
    Khan, Haseena
    A Putative Leucine-Rich Repeat Receptor-Like Kinase of Jute Involved in Stress Response2010Inngår i: Plant Molecular Biology Reporter, ISSN 0735-9640, E-ISSN 1572-9818, Vol. 28, nr 3, s. 394-402Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    A putative leucine-rich repeat receptor-like protein kinase (LRR-RLK) gene together with its 5' and 3' untranslated regions of jute (Corchorus olitorius L.) has been identified and sequenced. The gene is 3,371 bp long containing two exons and one intron. The coding sequence of the gene is 2,879 bp long encoding a peptide of 957 amino acids. The predicted protein contains several domains and motifs characteristic of a transmembrane protein kinase. It is complete with domains for an N-terminal leucine-rich repeat and a protein kinase core, an active site for serine/threonine protein kinase, an ATP binding conserved site and a transmembrane region. Expression of the gene is induced by low temperature, high salt concentration, dehydration, abscisic acid treatment, and fungal infection, suggesting the involvement of the gene in multiple stress response pathways in jute (C. olitorius L.). A possible mechanism of the role of the gene in signal transduction and environmental stress response is discussed. To date, LRR-RLK is the only jute gene which has been completely sequenced and characterized.

  • 25.
    Alam, Parvez
    et al.
    Univ Edinburgh, Inst Mat & Proc, Sch Engn, Edinburgh, Midlothian, Scotland.
    Sanka, Immanuel
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning. Univ Gadjah Mada, Fac Biol, KSK Biogama Marine Biol Study Grp, Yogyakarta, Indonesia.
    Alam, Lilja Piuli
    Int Baccalaureate Sch, Turku, Finland.
    Wijaya, Saka
    Univ Gadjah Mada, Fac Biol, Dept Trop Biol, Yogyakarta, Indonesia.
    Sintya, Erly
    Univ Edinburgh, Inst Mat & Proc, Sch Engn, Edinburgh, Midlothian, Scotland; Univ Gadjah Mada, Fac Biol, KSK Biogama Marine Biol Study Grp, Yogyakarta, Indonesia; Kings Coll London, Dept Imaging Sci, London, England; Kings Coll London, Biomed Engn Res Div, London, England.
    Handayani, Niken Satuti Nur
    Univ Gadjah Mada, Fac Biol, Lab Genet & Breeding, Yogyakarta, Indonesia.
    Rivero-Mueller, Adolfo
    Univ Turku, Turku Ctr Biotechnol, Turku, Finland; Åbo Akad Univ, Turku, Finland; Med Univ Lublin, Dept Biochem & Mol Biol, Lublin, Poland.
    The snapping shrimp dactyl plunger: a thermomechanical damage-tolerant sandwich composite2018Inngår i: Zoology (Jena), ISSN 0944-2006, E-ISSN 1873-2720, Vol. 126, s. 1-10Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The dactyl plunger of Alpheus sp. was found to be a layered composite, with mineral-rich outer and inner layers and a chitin-rich middle layer of high porosity. The chitin-rich middle layer is itself composed of several porous chitin laminae. Modelling heat conduction through the plunger cross-section revealed that the chitin-rich layer is able to insulate heat and retard its progress through the material. Heat accumulates in the plunger after a series of successive snaps and as such, its thermally resistant design can be considered most useful under the conditions of successive snapping. The plunger has a concurrent mechanical damage-tolerant design with biogenic mineral layers, viscous (chitin–mineral) interfaces, energy-dissipating porous chitin, and sidewalls composed of ordered, layered aragonite. The snapping shrimp plunger has a design that may protect it and internal soft tissues from thermomechanical damage during plunger–socket compression prior to cavitation bubble release.

  • 26.
    Al-Ani, Abdullah
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning. University of Northampton.
    Investigating the subcellular localisation and function(s) of dystrophin protein Dp71 isoforms in glioma2022Independent thesis Advanced level (degree of Master (Two Years)), 30 poäng / 45 hpOppgave
    Abstract [en]

    The Dp71 protein is the most expressed product of the DMD gene in the nervous system. Mutation in the region codes dystrophin protein (Dp71) linked to cognitive disturbances in Duchenne muscular dystrophy (DMD) patients. There is growing evidence that the gene is contributing to the development of Central Nervous System related cancers. The aim of this study is to characterise the role of the main 4 Dp71 isoforms by investigating its subcellular localisation and putative cellular functions in glioblastoma cells, the most aggressive and common type of glioma. By transfecting the four GFP-Dp71 constructs into a well characterised human glioblastoma cell line – U251-MG. Immunoblotting was used to assess Dp71 expression in human glioblastoma cell line. Moreover, we examined the subcellular localisation and the effect of Dp71 over expression on the nuclear Lamin B1, cell migration immunofluorescence, and scratch assay. A 71 kDa endogenous Dp71 was expressed in all glioblastoma cells and only GFP-Dp71a (99 kDa) isoform was overexpressed in the transfected cells. Lower Lamin B1 fluorescence intensity and abnormal nuclear shape was observed in cells overexpressing GFP-Dp71a. Furthermore, cytoplasmic and nuclear localisation of Dp71 isoform was found in both cytoplasm and nucleus, but higher in the nucleus. Overexpression of Dp71a transfected cells reduced the cell migration and covering the scratched tissue gaps with 5% and 6%, whilst that of the control cells were 29% and 50% at time 24 and 48 hours, respectively compared to the that at time 0. Dp71ab transfected cells showed similar cell migration to the control. We concluded that Dp71 overexpression had a clear effect on the expression of Lamin B1 and cell migration. Additionally, localisation of Dp71a was higher in the nucleus than in the cytoplasm.

    Fulltekst (pdf)
    fulltext
  • 27.
    Alcalde, Joaquín
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    The effects of endocrine disruptor cocktails on bleak (Alburnus alburnus) behavior, growth, and morphology2014Independent thesis Advanced level (degree of Master (Two Years)), 20 poäng / 30 hpOppgave
    Fulltekst (pdf)
    The effects of endocrine disruptor cocktails on bleak (Alburnus alburnus) behavior, growth, and morphology
  • 28.
    Alexiou, Athanasios
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Sets of Genes Predict Survival of Glioblastoma Patients2016Independent thesis Advanced level (degree of Master (Two Years)), 20 poäng / 30 hpOppgave
  • 29.
    Alexis, Laura
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Alftrén, Ida
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Elvmarker, Josefin
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Mach, Klara-Maria
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Nyman, Rebecca
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    DETEKTERA MERA!: - En studie av LigandTracer® och andra vanliga detektionstekniker för interaktion inom antikroppsutveckling2013Independent thesis Basic level (degree of Bachelor), 10 poäng / 15 hpOppgave
    Abstract [sv]

    Ridgeview Instruments AB är ett företag, med säte i Uppsala, som bland annat utvecklar mjukvara för detektionsanalys och detektionsinstrumenten LigandTracer®. Instrumenten detekterar cellinteraktioner i realtid och tillhandahåller information om hur interaktion mellan undersökt ligand och receptor sker. LigandTracer® används bland annat vid cancerstudier och affinitetsstudier av antikroppsinbindning till antigener på celler.

     

    LigandTracer® och teknologin bakom den har studerats för att hitta de främsta styrkorna samt utvecklingsområden i jämförelse med andra detektionstekniker. Dessa tekniker är surface plasmon resonance, BioLayer Interferometry, quartz crystal microbalance samt surface acoustic wave. Främsta styrkan hos detektion med LigandTracer® är att stor mängd data som beskriver interaktionerna erhålls. Information av denna typ är viktig för att få en helhetsbild av cellers ytprotein. Därför kan instrumenten exempelvis användas som kvalitetssäkrande steg i antikroppsprocessen. LigandTracer® kan även användas för studier av hela celler och vävnader. Utöver detta finns styrkor som minimerar det laborativa arbetet, så som tvättar i prepareringssteg. Detta gör att både tid och reagens sparas.

     

    En utvecklingsmöjlighet för LigandTracer® är egenskapen att kunna detektera fler antikroppar och cellinjer samtidigt. Då mjukvaran TraceDrawer™ är ett viktigt tillbehör för utvärderingen av detektionen, skulle utveckling med avseende på celldynamiken och receptorernas rörelsemönster kunna förbättra instrumenten ytterligare.

    Fulltekst (pdf)
    Detektera mera!
  • 30.
    Alfjorden, Anders
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Experimental Spironucleus infections in Atlantic salmon (Salmo salar): Hidden secrets of the life cycle of Spironucleus salmonicida revealed2018Independent thesis Advanced level (degree of Master (One Year)), 20 poäng / 30 hpOppgave
    Abstract [en]

    We have performed experimental infections of Atlantic salmon (Salmo salar) from the Baltic Sea region with the protozoan parasite Spironucleus salmonicida. By this infection trial we have been able to show that the life cycle may use an alternative route of transmission. Instead of the commonly used faecal-oral route, the parasites can also be excreted directly into the surrounding water from the mucous layer of the skin or from an ulcerated skin lesion. Three different stages of the infection were identified: one intestinal, one blood stage and one tissue stage. New putative life-cycle forms of S. salmonicida cells detected by ex-vivo cell-cultures. Similar cells were also observed in imprints from skin lesions sampled during the experimental infection trials. The cells differed morphologically, from normal trophozoite cells and indicate an alternative cell-cycle when exposed to salmonid host cells.

    Fulltekst (pdf)
    fulltext
  • 31.
    Alford, Liam
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning. Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för immunologi, genetik och patologi.
    Investigation of the Neddylation Pathway in Triple Negative Breast Cancer2023Independent thesis Advanced level (degree of Master (Two Years)), 40 poäng / 60 hpOppgave
    Fulltekst (pdf)
    fulltext
  • 32. Ali, N.
    et al.
    Junaid, M.
    Ahmad, D.
    urRahman, M.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Katzenmeier, G.
    Antibacterial and antifungal activity of solvent extracts from Plumeria obtusa Linn2014Inngår i: Tropical Biomedicine, ISSN 0127-5720, Vol. 31, nr 4, s. 607-615Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Extracts of Plumeria obtusa are widely used in ethnomedicine and have been investigated for a variety of biological activities; however, the antimicrobial activity of P. obtusa flowers is poorly characterized. In this study, the antimicrobial activities of different solvents (petroleum ether, ethyl acetate, chloroform, isobutanol and ethanol) extracts from flowers of P. obtusa were investigated by a disc diffusion method against Gram-positive bacteria, Gram-negative bacteria and a fungus. All extracts exhibited growth inhibition of all microorganisms at variable degrees as measured by relative zones of inhibition, however, the petroleum ether extract was ineffective against Klebsiella pneumonia and ethyl acetate and isobutanol extracts were ineffective against Pseudomonas aeruginosa. The most susceptible Gram-positive bacterium was Bacillus subtilis while the most resistant Gram-positive bacterium was Staphylococcus aureus. Erwinia carotovora was the most susceptible Gram-negative bacterium while P. aeruginosa was highly resistant among the Gram-negative bacteria. In this study, for the first time, we investigated the antimicrobial activity of several different solvent extracts from flowers of P. obtusa against a broad spectrum of human-pathogenic microorganisms. These compounds warrant further investigation by isolation and structural elucidation with the aim to find novel and affordable bioactive compounds for the treatment of infectious diseases.

  • 33.
    Al-Khafaf, Tanya
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Ancker Persson, Björn
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Cederblad, Johanna
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Häggström, Albert
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Kostines, Reneh
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Löfström, Lina
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Schleimann-Jensen, Ella
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Technology Development in the Field of Ligand Binding Assays: Comparison between ELISA and other methods2020Independent thesis Basic level (degree of Bachelor), 10 poäng / 15 hpOppgave
    Fulltekst (pdf)
    fulltext
  • 34.
    Allbrand, Carin
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Naturorienterande ämnen i skolanstidigare år: En kvalitativ studie som belyser fyra NO-lärares uppfattningar om elevers tidigare erfarenheter och kunskaper i NO.2011Independent thesis Advanced level (professional degree), 10 poäng / 15 hpOppgave
    Fulltekst (pdf)
    fulltext
  • 35.
    Altgård, Sofia
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Berggren, Sofia
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Björklund, Viktor
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Lundsten, Sara
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Olafsson, Thorsteinn
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Pettersson, Lovisa
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Ett nytt multiplext PCR-protokoll för identifiering och detektion av Shigella och enteroinvasiv E. coli (EIEC) från livsmedel2014Independent thesis Basic level (degree of Bachelor), 10 poäng / 15 hpOppgave
    Abstract [en]

    This report is the result of a project in the course Independent Projekt in Molecular Biotechnology at Uppsala University during the spring of 2014. The foremost purpose of the course is to give students the opportunity to carry through exstensive work in a project environment. This project was formed based on a comission from the biotechnology company SweTree Technologies, and the goal has been to compose a summary of the different techniques and methods that exist in the field of mass propagation of trees through the method of somatic embryogenesis.

    The project group has obtained information about the area mainly throgh reading patents, trying to find key components and bottlenecks in other companies’ somatic embryogenesis technologies. This paper is divided into different sections, containing the patents of the automation of different steps in the process. This is to make it easier for readers to find information about the area they are interested in, as well as to illustrate the main parts of the process as percieved by the project group.

    Currently, there are several automated solutions for almost every step in the process, some of which are already in use. All the information obtained shows that the cost and labour has decreased with the development of this technology. While there is still room for significant devolopment in order to produce a complete automated process, there is no doubt that this method is becoming an ever more important asset in the area of forestry. Our hope is that this report may be a useful tool for companies or laymen to geta grasp of the field of automated mass production of trees.

    Fulltekst (pdf)
    fulltext
  • 36.
    Alva Caballero, Lucia Ximena
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    A tale of two wagtails: Incongruence between phenotypic patterns and genetic differentiation in the Yellow and Citrine Wagtails2023Independent thesis Advanced level (degree of Master (Two Years)), 20 poäng / 30 hpOppgave
    Abstract [en]

    The Yellow Wagtail complex, comprising the Western Yellow Wagtail (Motacilla flava) and the Eastern Yellow Wagtail (Motacilla tschutschensis) are broadly distributed Palearctic passerine species. This complex is remarkably polytypic, presenting 15 recognized subspecies, most of which show a distinct male head plumage pattern. Their phenotypic variation and the appearance of similar-looking phenotypes in widely separated geographical areas make this species complex and particularly interesting to study the speciation process and evolution of plumage coloration. However, while trying to clarify the taxonomy of this complex, previous studies using different molecular datasets have recovered the Citrine Wagtail (M. citreola) either as nested within the yellow wagtail complex or as a sister to the yellow wagtails. These results were puzzling as the Citrine Wagtail is sympatric with both yellow wagtail species, with many morphological differences, suggesting strong reproductive barriers. The uncertainty in previous phylogenetic reconstructions motivated this study to take a deeper look into the causes behind the incongruences between gene trees and the species tree with the goal of identifying the evolutionary relationships between the Yellow and Citrine Wagtails. I employed phylogenetic analysis using whole genome SNPs and population structure analyses and tests to detect introgression and incomplete lineage sorting (ILS). Phylogenetic reconstructions always found the Citrine Wagtail nested within the yellow wagtail complex and confirmed high heterogeneity across gene trees. Our results found introgression and ILS to be present among the Yellow and Citrine Wagtails, with a high chance of being the leading causes behind gene tree discordance in this group, making the identification of the species tree challenging. All three possible topologies were recovered across the genome. In two of them, the yellow wagtails were paraphyletic; in one, there was reciprocal monophyly between the Citrine and Yellow Wagtails. Lastly, we found M. tschutschensis plexa, a subspecies of the Eastern Yellow wagtail, as an intergrade between the Western Yellow Wagtail and the Eastern Yellow Wagtail. These results have taken us a step closer to being able to solve the relationships between Citrine Wagtail and yellow wagtails, as they have given us a deeper perspective into their evolutionary history. 

  • 37.
    Al-walai, Somar
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning. Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för neurovetenskap.
    Characterization of solutecarrier SLC38A62012Student paper other, 10 poäng / 15 hpOppgave
    Abstract [en]

    Transport across the membrane of a cell is of crucial importance for cellular functions. The solute carrier family,SLC38 is a family of membrane proteins that transports various substances through the membrane and thusperforms many physiologically important functions, for example, transport of glutamine from astrocyte toneurons in the central nervous system. In this paper, we demonstrate that one of the transporters in this familynamed SLC38A6 forms several protein complexes with a variety of proteins in the membrane and in synapticvesicles, suggesting that SLC38A6 is involved in the synaptic release of neurotransmitters in synapses. Weperformed sensitive protein interaction analysis between the protein of interest and a variety of proteinsexpressed at different sites in the neuronal cell. We showed that SLC38A6 interacts with proteins in the cellmembrane as well as in the membrane of synaptic vesicles. The current theory is that SLC38A6 interact withthese proteins when the synaptic vesicles are in close proximity with the cell membrane during the release of theneurotransmitters.

    Fulltekst (pdf)
    Report_SLC38A6_solute_carrier_Somar_Al-walai_Uppsala_University_Sweden
  • 38.
    Amalia, Clausson
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Hormonet leptin och dess funktioner2014Independent thesis Basic level (degree of Bachelor), 10 poäng / 15 hpOppgave
    Fulltekst (pdf)
    fulltext
  • 39.
    Amanda, Folkö
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    The relationship between body size and dry weight in hoverflies (Syrphidae), and their movements along an urban linear landscape element2014Independent thesis Basic level (degree of Bachelor), 10 poäng / 15 hpOppgave
    Fulltekst (pdf)
    fulltext
  • 40.
    Ament Velásquez, Sandra Lorena
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Genomic insights into the reproductive biology of Icmadophilaceae species (lichenized ascomycetes)2014Independent thesis Advanced level (degree of Master (Two Years)), 20 poäng / 30 hpOppgave
    Abstract [en]

    Sexual reproduction or its absence has significant consequences for the evolutionary potential of a species, but little is known of the molecular basis of mating systems in non-model organisms. In Fungi, an extremely diverse and ecologically important group of Eukaryotes, sexual identity is regulated by mating type (MAT) genes with specific protein domains. The MAT genes determine if a species is capable of selfing (homothallism) or not (heterothallism). Among Fungi, almost one fifth of the species establish symbiotic associations with algae or cyanobacteria, that is, they form lichens. Yet, very few studies have explored the reproductive genetics of lichenized species. In this work, I extended current research to a poorly known family of lichen-forming fungi: the Icmadophilaceae. I used Next Generation Sequencing (NGS) genomic and transcriptomic data to produce gene models of the MAT genes and its flanking regions of four representative species. I found that the putative asexual Thamnolia vermicularis and Siphula ceratites, as well as the sexual Dibaeis baeomyces have a gene configuration concordant with heterothallism, while the sexual Icmadophila ericetorum is most likely homothallic. Additionally, I applied a number of methods to detect recombination as a proxy for cryptic sex in T. vermiculars populations from the Northern Hemisphere. Like previous studies, I found no evidence of recombination and very little genetic variation, which is at odds with the recovered structure of the MAT locus. On the other hand, a preliminary exploration of the GC content of the metagenome (including all the genomes within the lichen thallus) of S. ceratites revealed that the symbiotic association involves Alphaproteobacteria, as has been described before for taxonomically unrelated lichens but never before for this species. Overall, my results offer a wealth of information for new and more advance research into the reproductive and evolutionary biology of Icmadophilaceae species, an unexplored portion of fungal biodiversity.

  • 41.
    Ammunet, Tea
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning. Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi.
    Evolution and diversification of secreted protein effectors in the order Legionellales2018Independent thesis Advanced level (degree of Master (Two Years)), 20 poäng / 30 hpOppgave
    Abstract [en]

    The evolution of a large, diverse group of intracellular bacteria was previously very difficult to study. Recent advancements in both metagenomic methods and bioinformatics has made it possible. This thesis investigates the evolution of the order Legionellales. The study concentrates on a group of proteins essential for pathogenesis and host manipulation in the order, called effector proteins. The role of effectors in host adaptation, evolutionary history and the diversification of the order were investigated using a multitude of bioinformatics methods. First, the abundance and distribution of the known effector proteins in the orderwas found to cover newly discovered clades. There was a clear distinction between the proteins present in Legionellales and the outgoup, indicating the important role of the effectors in the order. Further, the effectors with known functions found in the new clades, particularly in Berkiella, revealed potential modes of host manipulation of this group. Secondly, the evolution of the effector gene content in the order shed light on theevolution of the order, as well as on the potential evolutionary differences between Legionellaceae and Coxiellaceae. In general, most of the effectors were gained early in the last common ancestor of Legionellales and Legionellaceae, as further indication of their role in the diversification of the order. New effector genes were acquired in the Legionellaceae even up to recent speciation events, whereas Coxiellacea have lost more protein coding genes with time. These differences may be due to horizontal gene transfer in the case of gene gains in Legionellaceae and loss of selection in the case of gene losses in Coxiellaceae. Third, the early evolution of core gained effector proteins for the order was studied.Two of the eight investigated core effectors seem to have a connection to eukaryotes, the rest to other bacteria, indicating both inter-domain and within bacteria horizontal gene transfer. In particular, one effector protein with eukaryotic motif gained at the last common ancestor of Legionellales, was found in all the clades and is therefore an important evolutionary link that may have allowed Legionellales to utilize eukaryotic hosts.

    Fulltekst (pdf)
    fulltext
  • 42.
    Amnesten, Josefine
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Ekologiska effekter vid återintroduktion av visent i södra Sveriges lövskog2014Independent thesis Basic level (degree of Bachelor), 10 poäng / 15 hpOppgave
    Abstract [sv]

    Förr betades södra Sveriges skogar av megaherbivorer, varav många arter idag är utdöda. På grund av deras utdöende och mycket på grund av de senaste 200 årens förändringar och Sveriges jord- och skogsbruk, som bland annat innebär att skogsbete inte längre används i lika hög grad som förr, så breder nu barrskogarna ut sig i söder. Resultaten har blivit att de öppna lövskogar som hyser ädellövträd som ek är på väg att växa igen. Marken utsätts inte längre för samma markstörning och den skuggtåliga granen som gynnas av skogsbruket etablerar sig. Det stora gamla ädellövträden blir allt färre när deras livsmiljö försvinner och med dem försvinner en mängd evertebrater och fåglar som är beroende av träden i öppna lövskogar. När arter försvinner kan man aldrig få dem tillbaka och det kan vara arter som påverkar hela ekosystem och på lång sikt även oss människor.

    Ett alternativ för att behålla de öppna lövskogarna är att återintroducera visenter i södra Sverige. Visenter har funnits i Skandinavien, men utrotades för runt 8000 år sen. De betar gräs och örter på samma sätt som tamboskap och kan utföra den markstörning som behövs för att gynna denna biotop. I delar av Europa levde vilda visenter kvar fram till första världskrigets slut 1919 och har sedan 1950-talet återintroducerats i flera länder. Hit hör bland annat Polen, Ukraina, Ryssland, Vitryssland och Litauen. Syftet har då varit att bevara visenten som art, men framgången har varit varierande. Man har haft problem med lokalbefolkningens attityd då de förstör grödor samt att de har låg överlevnad till följd av inavel. Det krävs en del planering för att det skulle kunna bli verklighet i Sverige och man måste lokalisera tillräcklig stora områden där de inte kommer i allt för stor konflikt med lokalbefolkningen. Förutom fördelen i form naturvård kan man både öka acceptans hos befolkningen och få ekonomiska fördelar på att i framtiden använda visenten inom jakt och turism. Å andra sidan innebär själva introduktionen en kostnad och man kan behöva betala ut ersättning för förstörda åkrar. En annan nackdel är trafikfaran och rädsla för djuren. Man måste här göra en avvägning mellan kostnad och naturnytta. Redan idag läggs stora summor av skattebetalarnas pengar på att skydda och restaurera hotade naturmiljöer och kanske är visenter i förhållande till det en billig och naturlig lösning som kan sköta sig relativt bra själv.

    Fulltekst (pdf)
    fulltext
  • 43.
    Anagnostou, Evangelia
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Compounds screening for the identification of novel drug to improve the Knock in efficiency mediated by CRISPR-Cas92023Independent thesis Advanced level (degree of Master (Two Years)), 40 poäng / 60 hpOppgave
    Abstract [en]

    Genome editing is an exciting field that allows for the precise modification of an organism's DNA. One of the most advanced tools in this area is CRISPR/Cas9 (Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated protein 9), which creates a DSB (Double-strand break) at a specific location in the genome. This break can then be repaired by the cell using one of two pathways – NHEJ (nonhomologous end joining) or HDR (homology-directed repair) HDR leads to more precise repair and is used to create KI (Knock-In) modifications by introducing a homologous piece of DNA with the desired changes. However, HDR is a rare event that competes with the error prone NHEJ pathway, limiting its efficiency. HDR mainly occurs in the G2 and S phases of the cell cycle, making it a challenge to control and target. To improve KI efficiency, researchers have used strategies such as inhibiting NHEJ or activating HDR. This study focuses on identifying direct and indirect activators of HDR through a library assay screening. We established a robust method for screening compounds in HEK293 cells that relies on a plasmid-based delivery Cas9, gRNA (guide RNA), and synthetic ssDNA (single strand DNA). Out of 3,000 compounds screened, 1% showed a higher signal than the positive control, and approximately 10% presented a higher signal than untreated cells. The top 5 compounds were further validated in dose response. Our system opens new avenues for improving the efficiency of KI modifications.

  • 44. Ancker, Julia
    et al.
    Berg, Elin
    Björkman, Therese
    Malmvall, Hanna
    Abdullahi, Hanad
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Wong, Victor
    Verktyg för optimerat val av testpanelerför antibiotikasensitivitetstester2023Independent thesis Basic level (degree of Bachelor), 10 poäng / 15 hpOppgave
    Abstract [sv]

    Denna rapport beskriver ett projekt vars syfte är att underlätta valet av bakteri- estammar till testpaneler som används av Q-lineas instrument ASTar®. ASTar® är ett automatiserat instrument för snabb antibiotikasensitivitetstestning (AST). Med testpanel menas en uppsättning av bakteriestammar som används för träning av den algoritm som används av ASTar®. De huvudsakliga målen med detta projekt är att ta fram indikatorer som kan användas för att utvärdera en testpanel samt att skapa verktyg för visualisering av en testpanel. Indikatorerna återspeglar en pa- nels spridning, täckning och redundans. Spridning är hur många olika MIC-värden en testpanel innefattar för varje antibiotikum och hur utspridda de är, täckning är antalet MIC-värden som varje antibiotikum har i en testpanel och redundans är kopplat till hur unikt varje MIC-värde på panelen är. Med MIC-värden menas den minsta koncentration av antibiotika som hämmar en bakteries tillväxt. I detta projekt har indikatorer tagits fram för att kunna kvantifiera en panels spridning, täckning och redundans, och enkelt kunna jämföra olika testpaneler utifrån dessa aspekter. Ett skript compare.py har skrivits i programmeringsspråket Python för att skapa en visualisering som jämför de kvantitativa indikatorvärdena för olika paneler i relation till de högsta möjliga värdena. Ytterligare ett skript, master_vis.py har skrivits för att generera olika visualiseringar av en panel och dess täckning, sprid- ning och redundans. Sex olika grafer och två tabeller kan genereras med detta skript. Dessa visualiseringar och tabeller visar bland annat hur utspridda MIC-värdena är på en panel, hur många känsliga, intermediära och resistenta MIC-värden som finns för varje antibiotikum på en panel och hur många unika MIC-värden som finns för varje stam på panelen. Slutligen har även ett tredje skript skrivits, kallat isola- te_selection.py. Detta skript utgår från de framtagna kvantitativa indikatorerna för att välja ett specificerat antal stammar till en panel och utvecklades för att under- söka hur indikatorerna skulle kunna användas för att påverka stamvalet. Möjligen skulle en liknande implementering kunna göras i Q-lineas nuvarande stamvalsskript. Samtliga skript, visualiseringar och beräkningsmetoder som har arbetats fram i det- ta projekt är tänkta att kunna användas av Q-linea för att underlätta deras fram- tagning och utvärdering av testpaneler.

    Fulltekst (pdf)
    fulltext
  • 45. Anderson, Bruce
    et al.
    Alexandersson, Ronny
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Johnson, Steven D
    Evolution and coexistence of pollination ecotypes in an African Gladiolus (Iridaceae)2010Inngår i: Evolution, ISSN 0014-3820, E-ISSN 1558-5646, Vol. 64, nr 4, s. 960-972Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Pollinator-mediated selection has been suggested as a key driver of speciation in plants. We examined the potential role of hawkmoth pollinators in driving allopatric divergence and maintaining sympatric coexistence of morphotypes in the African iris Gladiolus longicollis. Floral tube length in this species varies from 35 mm to 130 mm across its geographic range and reflects the prevailing tongue lengths of local hawkmoth assemblages. The distribution of floral tube lengths is bimodal with two relatively discrete categories—long (about 90 mm) or short (about 50 mm)—that match the bimodal distribution of hawkmoth tongue lengths in eastern South Africa. At a contact site between these two floral morphs, we found few individuals of intermediate length, suggesting limited gene flow between morphs despite their interfertility. A difference in flowering phenology appears to be the main isolating barrier between morphs at this site. Long- and short-tubed morphs differed markedly in the chemical composition of their floral fragrance, a trait that could be used as a cue for morph-specific foraging by hawkmoths. Positive directional selection on tube length was found to occur in both morphs.

  • 46.
    Anderson, Jenna
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Prevalence and phylogeny of Borrelia burgdorferi s.l.-infected ticks in central and southern Sweden2010Student paper other, 10 poäng / 15 hpOppgave
    Fulltekst (pdf)
    FULLTEXT01
    Download (pdf)
    POPULARSUMMARY02
  • 47.
    Andersson, Alfred
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Neural networks for imputation of missing genotype data: An alternative to the classical statistical methods in bioinformatics2020Independent thesis Advanced level (professional degree), 20 poäng / 30 hpOppgave
    Abstract [en]

    In this project, two different machine learning models were tested in an attempt at imputing missing genotype data from patients on two different panels. As the integrity of the patients had to be protected, initial training was done on data simulated from the 1000 Genomes Project. The first model consisted of two convolutional variational autoencoders and the latent representations of the networks were shuffled to force the networks to find the same patterns in the two datasets. This model was unfortunately unsuccessful at imputing the missing data. The second model was based on a UNet structure and was more successful at the task of imputation. This model had one encoder for each dataset, making each encoder specialized at finding patterns in its own data. Further improvements are required in order for the model to be fully capable at imputing the missing data.

    Fulltekst (pdf)
    fulltext
  • 48.
    Andersson, Elin
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Developing a protocol for RT-qPCR of wing-tissue gene expression and investigating the dynamics of photoperiodically induced polyphenism in the water strider Gerris buenoi2023Independent thesis Advanced level (degree of Master (Two Years)), 20 poäng / 30 hpOppgave
    Abstract [en]

    Wing polyphenism in insects is a type of phenotypic plasticity where environmental factors trigger the development of a set of discrete wing morphologies. In the water strider Gerris buenoi, photoperiods are the main environmental cue that trigger wing morph determination. The genetic mechanisms connecting environmental cues and the determination of wing morph in G. buenoi are not clear. However, recent experimental work suggests that engagement of the Hippo pathway via ecdysone signalling is a promising model for further investigation. In this study, a reverse-transcription quantitative PCR (RT-qPCR) protocol was developed, aimed at elucidating this potential transduction pathway by quantifying gene expression of Fat, Dachsous, Yorkie, EcR, E75 and E74. This was done using melt curve analysis, gel electrophoresis, sequencing of RT-qPCR products and qPCR standard curves. Additionally, wing morph distribution in extreme and intermediate photoperiods were examined. Wing morph proportions were significantly different between adults emerging in the intermediate photoperiods 15.30:8.30 and 15:9 (hours light : hours dark). An effect of sex was observed, with a higher probability of males becoming long-winged compared to females. This has likely evolved as a result of a dispersal-reproduction trade-off. Taken together, this study provided insight for future investigations of periodically induced wing morph determination and its genetic mechanisms in G. buenoi that will contribute to the understanding of phenotypic plasticity.

    Fulltekst (pdf)
    fulltext
  • 49.
    Andersson, Hilda
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    A machine learning pipeline for predicting success rates in PrEST production2019Independent thesis Advanced level (professional degree), 20 poäng / 30 hpOppgave
    Abstract [en]

    Protein epitope signature tags (PrESTs) are antigens produced in Escherichia coli at Atlas Antibodies and immunized into rabbits for antibody production. This project uses machine learning models to predict success rates for production and immunization and to find features important for success. The features are generated based on the PrEST sequences using web servers, downloadable software and Pyhton scripts. An additional analysis of the effect of rabbit- and environmental features on immunization success is performed. Many different models, model architectures and a few thousand features were tried. The models reached a maximum F1 scores of about 0.55 for a target outcome divided into two classes for both production and immunization analysis. No important features could be identified with significance.

    The rabbit- and environmental analysis showed that this type of features is more important for PrEST immunization success than the PrEST-related features. F1 score rose to abut 0.6 and the environmental features ranked higher based on information gain. More data is needed to draw definitive conclusions, but this indicates that Atlas Antibodies should in the future focus on recording environmental features during production for better chances of predicting success rates.

  • 50.
    Andersson, Hilda
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Appelgren, Sofia
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Boström, Anna
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Norlander, Siri
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Stam, Emma
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Stiernborg, Miranda
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Snabba mikrofluidiska test möjliggör specialanpassad sjukvård: Utveckling av två designförslag med fokus på material, struktur och pump2016Independent thesis Basic level (degree of Bachelor), 10 poäng / 15 hpOppgave
    Abstract [sv]

    Två designförslag har utvecklats för ett snabbtest av antibiotikakänslighet baserat på ettmikrofluidiskt system av Gradientech AB. Antibiotikaresistens är ett stort och växande problem ivärlden. För att förbättra diagnostiken av bakteriella blodinfektioner krävs snabbarediagnostiska tester vilket möjliggör specialanpassad behandling. Linjära gradienter av antibiotikai det mikrofluidiska systemet möjliggör snabbare detektion av antibiotikakänslighet jämfört meddiagnostiska test som används idag. Projektet har syftat till att anpassa testet utvecklat avGradientech AB för en klinisk marknad. Fokus har varit på material, pumpsystem och strukturför snabbtestet. De två designförslagen baseras på krav på ett pålitligt och billigt test som äranvändarvänligt och som minimerar smittorisker. Det ena designförslaget använder sig av enchipbaserad peristaltisk pump och det andra förslaget är ett trelagersystem med endiafragmapump. De två förslagen består av både hårdplast och ett elastiskt material. När dettatest kommer ut på den kliniska marknaden så kommer det förbättra vården av patienter medbakteriella blodinfektioner och minska sjukvårdskostnader. Testet kommer även minskabehovet av behandling med bredspektrumantibiotika och därmed hjälpa till att stoppa spridningav antibiotikaresistens.

    Fulltekst (pdf)
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