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  • 1.
    Abrikossov, Alexei
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Computer simulations: Orientation of Lysozyme in vacuum under the influence of an electric field2011Independent thesis Advanced level (professional degree), 20 credits / 30 HE creditsStudent thesis
    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.

  • 2.
    Afewerki, Isaias
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Genflödet från genetiskt modifierade grödor till vilda populationer2014Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    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. 

  • 3.
    Agnas, Axel Jönses Bernard
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Non-Independent Mate Choice in Female Humans (Homo sapiens): Progression to the Field 2016Independent thesis Advanced level (degree of Master (Two Years)), 30 credits / 45 HE creditsStudent thesis
    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. 

  • 4.
    Ahlström, Anna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Testing the specificity of the pBAD arabinose reporter2017Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    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.

    The full text will be freely available from 2018-06-30 15:30
  • 5.
    Ahlström, Christoffer
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Aho, Milja
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Edblom, Johan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Gehlin Björnberg, Gabriella
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Petersson, Nina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Sör, Lennart
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Felsökning och förbättringar kring identifiering och kvantifiering av norovirus i livsmedel och vattenprover2015Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
  • 6.
    Ahlström, Christoffer
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Industrial Engineering & Management. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Röjås, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Industrial Engineering & Management.
    Framtida konsumtion på befintliga och nya handelsplatser: En plats- och konsumentundersökning för obemannade självservicebutiker2017Independent thesis Advanced level (professional degree), 20 credits / 30 HE creditsStudent thesis
    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.

  • 7.
    Akula, Srinivas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Analysis of the isotype specificity of three platypus immunoglobulin Fc receptors2012Independent thesis Advanced level (degree of Master (Two Years)), 30 credits / 45 HE creditsStudent thesis
    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.   

  • 8.
    Al Jewari, Caesar
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Examining the Root of the Eukaryotic Tree of Life2017Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    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.

  • 9. Alam, Md. Maksudul
    et al.
    Sharmin, Sazia
    Nabi, Zinnatun
    Mondal, Shakhinur Islam
    Islam, Md. Shahidul
    Bin Nayeem, Sarmah
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Shoyaib, Muhammad
    Khan, Haseena
    A Putative Leucine-Rich Repeat Receptor-Like Kinase of Jute Involved in Stress Response2010In: Plant Molecular Biology Reporter, ISSN 0735-9640, E-ISSN 1572-9818, Vol. 28, no 3, p. 394-402Article in journal (Refereed)
    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.

  • 10.
    Alcalde, Joaquín
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    The effects of endocrine disruptor cocktails on bleak (Alburnus alburnus) behavior, growth, and morphology2014Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
  • 11.
    Alexiou, Athanasios
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Sets of Genes Predict Survival of Glioblastoma Patients2016Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
  • 12.
    Alexis, Laura
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Alftrén, Ida
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Elvmarker, Josefin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Mach, Klara-Maria
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Nyman, Rebecca
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    DETEKTERA MERA!: - En studie av LigandTracer® och andra vanliga detektionstekniker för interaktion inom antikroppsutveckling2013Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    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.

  • 13. Ali, N.
    et al.
    Junaid, M.
    Ahmad, D.
    urRahman, M.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Katzenmeier, G.
    Antibacterial and antifungal activity of solvent extracts from Plumeria obtusa Linn2014In: Tropical Biomedicine, ISSN 0127-5720, Vol. 31, no 4, p. 607-615Article in journal (Refereed)
    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.

  • 14.
    Allbrand, Carin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    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 credits / 15 HE creditsStudent thesis
  • 15.
    Altgård, Sofia
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Berggren, Sofia
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Björklund, Viktor
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Lundsten, Sara
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Olafsson, Thorsteinn
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Pettersson, Lovisa
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    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 credits / 15 HE creditsStudent thesis
    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.

  • 16.
    Al-walai, Somar
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience.
    Characterization of solutecarrier SLC38A62012Student paper other, 10 credits / 15 HE creditsStudent thesis
    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.

  • 17.
    Amalia, Clausson
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Hormonet leptin och dess funktioner2014Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
  • 18.
    Amanda, Folkö
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    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 credits / 15 HE creditsStudent thesis
  • 19.
    Ament Velásquez, Sandra Lorena
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Genomic insights into the reproductive biology of Icmadophilaceae species (lichenized ascomycetes)2014Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    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.

  • 20.
    Amnesten, Josefine
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Ekologiska effekter vid återintroduktion av visent i södra Sveriges lövskog2014Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    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.

  • 21. Anderson, Bruce
    et al.
    Alexandersson, Ronny
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Johnson, Steven D
    Evolution and coexistence of pollination ecotypes in an African Gladiolus (Iridaceae)2010In: Evolution, ISSN 0014-3820, E-ISSN 1558-5646, Vol. 64, no 4, p. 960-972Article in journal (Refereed)
    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.

  • 22.
    Anderson, Jenna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Prevalence and phylogeny of Borrelia burgdorferi s.l.-infected ticks in central and southern Sweden2010Student paper other, 10 credits / 15 HE creditsStudent thesis
  • 23.
    Andersson, Hilda
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Appelgren, Sofia
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Boström, Anna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Norlander, Siri
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Stam, Emma
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Stiernborg, Miranda
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Snabba mikrofluidiska test möjliggör specialanpassad sjukvård: Utveckling av två designförslag med fokus på material, struktur och pump2016Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    Two designs were developed for a fast antibiotic susceptibility test (AST) based on a microfluidicsystem by Gradientech AB. Antibiotic resistance is a big and growing global problem. Fasterdiagnostic tests are needed to improve the diagnostics of bacterial infections and enablespecialized antibiotic therapy. Linear gradients of antibiotics in the microfluidic system in thisproject enables faster detection of antibiotic susceptibility compared to ASTs used today inhealth care. The aim of this project has been to adapt the test developed by Gradientech AB fora clinical market. The main focus has been on materials, pumping systems and structure of theAST. The two designs are based on requirements of a reliable and cheap test that is easy to useand minimizes the biohazard. The first design uses a chip-based peristaltic pump and the otherdesign is a three-layer structure with a diaphragm pump. The two designs consists of both arigid plastic material and an elastic material. When this test becomes available to the clinicalmarket it will improve the care of patients with bacterial blood infections and reduce healthcarecosts. It will also reduce the use of broad-spectrum treatment of antibiotics and help counteractincreased global antibiotic resistance.

  • 24.
    Andersson, Karin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Mosquito repellency of essential oils derived from Lao plants2010Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    Essential oils or extracts obtained from four plant species growing in Laos were tested foranti-mosquito activity in the field. Solutions of alcohol or acetone containing differentconcentrations of essential oil; 5, 10 or 19 v/v %, were prepared and tested. Mosquitoes werecollected by human baits wearing oil impregnated mosquito nets around their shanks. Thenumber of attracted mosquitoes was compared to the number attracted to positive andnegative controls, i.e., human baits wearing nets impregnated with 19 % N,N-diethyl-metatoluamide (DEET, NN-diethyl-methyl-benzamide) or untreated nets, respectively. A one wayANOVA analysis was conducted on the log-transformed total number of mosquitoes collectedusing each treatment. The statistical analysis showed that significantly fewer mosquitoes wereattracted to the treatment harbouring 19 % oil of Scutellaria angustifolia than to the negativecontrol. No significant decrease in attracted mosquitoes could be detected for the treatmentscontaining oil from the plant Litsea cubeba. However, a tendency of repellency was indicated. Therefore, an investigation running over a longer period of time is desired for Litsea cubeba. No conclusions could be drawn for the remaining two species; Tagetes patula and Citrussinensis.

  • 25.
    Andersson, Klara
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Gustafsson, Wiktor
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Lindeberg, Fredrik
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Luckey, Tobias
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Ramström, Elin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Count Your Microbial Enemies Faster: Recommending the Best Bioburden Test for High-Fat Parenteral Nutrition2017Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
  • 26.
    Andersson, Pontus
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Edenståhl, Selma
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Eriksson, Elin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Hävermark, Tora
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Nielsen, Jonas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Pihlblad, Alma
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Framtidens expressionssystem för svåruttryckta proteiner: Utvärdering av tolv expressionssystem2018Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    Today, recombinant expression of proteins is used for a variety of purposes. One of these is the production of allergens, which are vital components in allergy diagnostics. However, traditional expression systems such as ​Escherichia coli​ and ​Pichia pastoris​ might not have the capacity to express all proteins of interest. Thermo Fisher, which is a leading producer of allergy tests, has requested an evaluation of different microorganisms and their capacity for heterologous protein expression in order to expand their existing toolbox of expression systems. This summary was made through a literature study, where twelve organisms were evaluated. Six eukaryotic and six prokaryotic expression systems are compared based on their ability to properly glycosylate protein, need for specific culture conditions, safety, protease activity, duration, protein yield and protein solubility. The prokaryotic systems – Corynebacterium glutamicum​ , ​Lactococcus lactis​ , ​Pseudomonas fluorescens​ , Pseudoalteromonas haloplanktis​ , ​Ralstonia eutropha​ and ​Streptomyces lividans​ – are characterized by being easy to cultivate, operating in different temperature ranges and providing relatively high yields of recombinant protein. The eukaryotic systems – ​Aspergillus fungi, the green algae ​Chlamydomonas reinhardtii​ , the yeast ​Hansenula polymorpha​ , the parasite ​Leishmania tarentolae​ , the moss ​Physcomitrella patens​ and suspension-based plant cells – all have very different morphology and properties. In comparison with the prokaryotic systems, it can be concluded that they are generally better at folding and providing the correct glycosylation patterns for mammalian and plant proteins. However, they require more time and effort to establish a competent cell line. Furthermore, the resulting protein yield is usually less than for the prokaryotic systems. The conclusion can be drawn that no expression system is perfect. The solution is a toolbox, containing various expression systems and vector systems, providing the basis for successful expression of all kinds of complex proteins. Based on the evaluation of expression systems in this review, such toolbox can be obtained.

  • 27.
    Andersson Schönn, Mikael
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Borg, Malin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Bunpuckdee, Benja
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Gioeli, Erik
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Holdar, Karl
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Odlingsmedium: Att ersätta fetalt kalvserum med ett kemiskt definierat substitut2014Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [sv]

    SammanfattningProjektgrupp 14-X5 avser med denna rapport att ge avdelningen Bioreagens på Thermo Fisher Scientific ett underlag för att på sikt kunna byta ut fetalt kalvserum (FCS) mot ett kemiskt definierat suplement vid odling av mushybridomceller för produktion av monoklonala antikroppar. Thermo Fisher Scientific är ett världsomspännande bioteknikföretag som utvecklar blodtestsystem som stöd för klinisk diagnos och uppföljning av allergier, astma och autoimmuna sjukdomar.

    Fetalt kalvserum är en tillsats i många odlingsmedier som ofta är nödvändig för att cellerna ska växa. Det finns dock många problem med FCS. Det är en biprodukt av köttindustrin och produceras på ett etiskt tveksamt sätt, variation mellan olika batcher förekommer och då det är en animalisk produkt finns en risk för kontamination av bland annat bakterier, virus och prioner. Av dessa anledningar vill man byta ut FCS mot ett kemiskt definierat, serumfritt supplement. Vi har utrett vilka ämnen eller grupper av ämnen som har störst potential att vara bra substitut för FCS, samt rangordnat dessa. Genom våra artikelstudier har vi kommit fram till att man kan dela in alternativen i tre grupper: lipider, tillväxtfaktorer och små biomolekyler. Bland lipiderna är det linol- och oljesyra som i flera artiklar har visats ha god effekt på både celltillväxt och antikroppsproduktion. Kolesterol har även visats ha positiva effekter. Tillväxtfaktorerna som har valts är epidermal growth factor (EGF), fibroblast growth factor (FGF), interleukin-2 (IL-2) och interleukin-6 (IL-6). Dessa har främst en positiv effekt på cellernas antikroppsproduktion. Bland de små biomolekyler som har valts ut finns en mängd olika ämnen som på olika sätt kan bidra till att skapa en bra miljö för hybridomceller i ett serumfritt medium.

    För att få en klarare bild av de olika förslagen har de jämförts. Vi menar att de ämnen som är komponenter i det basala mediet Ham F-12 bör prioriteras då det används som standard vid odling av en bred grupp av celltyper. Denna grupp inkluderar linolsyra, putrescin, tymidin, hypoxantin samt liponsyra. Därefter anser vi att återstående lipider (oljesyra och kolesterol) ska prioriteras då de har visats kunna öka både hybridomcellers tillväxt och antikroppsproduktion i ett serumfritt medium. Tillväxtfaktorer, som främst ökar antikroppsproduktionen hos cellerna  och i vissa fall även deras livslängd placerar vi på tredje plats i vår rangordning. Övriga ämnen i gruppen “Små biomolekyler” (paraaminobensoesyra och glutation) prioriterar vi sist då de inte är komponenter i Ham F-12 och de inte explicit visats påverka celltillväxten ellerantikroppsproduktionen, men har identifierats i det serumfria mediet IBL media III.

  • 28.
    Andersson, Staffan
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Physics Didactics.
    Andersson Chronholm, Jannika
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Physics Didactics.
    Jakobsson, Tobias
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Larsson, Johan
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Physics Didactics.
    Sjöström, Håkan
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, Solid Earth Geology.
    Koyi, Hemin
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, Solid Earth Geology.
    Eriksson, Anders
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Materials Chemistry, Structural Chemistry.
    Elmgren, Maja
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry.
    Rangordningsövningar i naturvetenskap2011Book (Other academic)
  • 29.
    Andersson, Staffan
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Physics Didactics.
    Andersson Chronholm, Jannika
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Physical Chemistry. Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Physics Didactics.
    Larsson, Johan
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Physics Didactics.
    Elmgren, Maja
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Physical Chemistry.
    Jacobsson, Tobias
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Jämföra och rangordna: studentaktiv undervisning2012In: Universitetspedagogisk utveckling och kvalitet: i praktiken!, 2012Conference paper (Other academic)
  • 30.
    Andersson Svärd, Agnes
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Peripheral blood cell HLA class II gene expression in children at genetic risk for type 1 diabetes and coeliac disease2015Independent thesis Advanced level (professional degree), 20 credits / 30 HE creditsStudent thesis
  • 31.
    Andersson Svärd, Agnes
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Lundgren, Christian
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Lindfors, Viktor
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Hunde, Sara
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Hellsten, Sandra
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Mul, Sebastiaan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Snabbtest för utredning av anafylaxi2012Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
  • 32. Andres, Sonke
    et al.
    Skoglund, Anna
    Nilsson, Christina
    Krabbe, Margareta
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Björkholm, Britta
    Engstrand, Lars
    Type I Restriction-Modification Loci Reveal High Allelic Diversity in Clinical Helicobacter pylori Isolates2010In: Helicobacter, ISSN 1083-4389, E-ISSN 1523-5378, Vol. 15, no 2, p. 114-125Article in journal (Refereed)
    Abstract [en]

    Background: A remarkable variety of restriction-modification (R-M) systems is found in Helicobacter pylori. Since they encompass a large portion of the strain-specific H. pylori genes and therefore contribute to genetic variability, they are suggested to have an impact on disease outcome. Type I R-M systems comprise three different subunits and are the most complex of the three types of R-M systems. Aims: We investigated the genetic diversity and distribution of type I R-M systems in clinical isolates of H. pylori. Material and methods: Sixty-one H. pylori isolates from a Swedish hospital based case-control study and 6 H. pylori isolates of a Swedish population-based study were analyzed using polymerase chain reaction for the presence of the three R-M systems' subunits. Representative gene variants were sequenced. Results: Although the hsdM and hsdR genes appeared conserved in our clinical H. pylori isolates, the sequences of the hsdS loci were highly variable. Despite their sequence diversity, the genes per se were present at high frequencies. We identified a number of novel allelic hsdS variants, which are distinct from corresponding hsdS loci in the sequenced H. pylori strains 26695, J99 and HPAG1. In analyses of paired H. pylori isolates, obtained from the same individuals with a 4-year interval, we observed genetic modifications of hsdS genes in patients with atrophic gastric mucosa. Discussion: We propose that the genetic variability of hsdS genes in a bacterial population will give rise to new specificities of these enzymes, which might lead to adaptation to an ever-changing gastric environment.

  • 33.
    Anlind, Alice
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Improvments and evaluation of data processing in LC-MS metabolomics: for application in in vitro systems pharmacology2017Independent thesis Advanced level (professional degree), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    The resistance of established medicines is rapidly increasing while the rate of

    discovery of new drugs and treatments have not increases during the last decades

    (Spiro et al. 2008). Systems pharmacology can be used to find new combinations or

    concentrations of established drugs to find new treatments faster (Borisy et al. 2003).

    A recent study aimed to use high resolution Liquid chromatography–mass

    spectrometry (LC-MS) for in vitro systems pharmacology, but encountered problems

    with unwanted variability and batch effects(Herman et al. 2017). This thesis builds on

    this work by improving the pipeline and comparing alternative methods and evaluating

    used methods. The evaluation of methods indicated that the data quality was often

    not improved substantially by complex methods and pipelines. Instead simpler

    methods such as binning for feature extraction performed best. In-fact many of the

    preprocessing method commonly used proved to have negative or neglect-able effects

    on resulting data quality. Finally the recently introduced Optimal Orthonormal System

    for Discriminant Analysis (OOS-DA) for batch removal was found to be a good

    alternative to the more complex Combat method.

  • 34.
    Anlind, Nils
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Eriksson, Alexandra
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Gromova, Arina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Hong, Marcus
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Ljungström, Sara
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Markstedt, Olof
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Marknadsanalys av proteinstandarder för kvantitativ masspektrometri2015Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [sv]

    QPrEST är en ny intern standard för absolut kvantifiering av proteiner utvecklat av företaget Atlas Antibodies AB. I en marknad där det redan finns etablerade standarder kan det vara svårt att konkurrera ut de nuvarande produkterna. Därför har denna rapport gjorts vilken består av en marknadsanalys av nuvarande standarder, statistisk undersökning av publicerade artiklar inom absolut kvantitativ proteomik samt en global kundundersökning med 35 svarande. Resultaten har legat till grund för förbättringsförslag till Atlas Antibodies AB för bättre marknadsföring och lansering av sin nya produkt, QPrEST. Slutsatsen från denna rapport är att Atlas Antibodies AB måste nischa in sin produkt till kvantifiering av ett målprotein då det är där standarden presterar bäst.

  • 35.
    Annala, Elina
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Brink, Matilda
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Ekdahl, Simon
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Iggström, Sofia
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Mejáre, Felicia
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Spetsare, Ebba
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Peptider som läkemedel - en marknads- och trendanalys2017Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [sv]

    Rapporten syftar till att ge en overskådlig bild av den aktuella peptidbaseradelläkemedelsmarknaden. Från en i rapporten definierad marknad har primärdata kring etablerade företag på marknaden, samt peptidbaserade läkemedel till försäjning på marknaden, sammanställts. Rapporten finner att onkologiska- och metaboliska sjukdomar är överrepresenterade i statistiken, vilket även stöds av rapporter från tredje part. Utforskandet av samarbeten mellan företag och akademi, företag och företag, och andra samarbetsformer presenteras också. En tydlig trend i dessa undersökningar tyder på att kontraktsbaserade samarbeten mellan organisationer, där forskning och produktion görs av ett externt företag som ett annat företag använder sig av, är på uppgång. Detta sänker kostnader för framställningen av nya läkemedel, och effektiviserar denna process. Trender inom forskningen talar också för att folkhälsosjukdomar i västvärlden ar trendsättande för läkemedelsföretagens inriktningar. Rapporten baseras på primärt insamlad statistik som verifieras genom rapporter från tredje part, fallstudier för att exemplifiera generaliseringar gjorda av andra källor, samt reflektioner kring vad denna information utrönar i för slutsats.

  • 36.
    Anyango, Stephen Omondi Otieno
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre. Uppsala University.
    VisuNet: Visualizing Networks of feature interactions in rule-based classifiers2016Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
  • 37.
    Arnroth, Cornelia
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Chumpitaz Chavez, Gabriel
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    von Euler, Edvin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Hedar, David
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Lindbäck, Klara
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Stenerlöv, Oskar
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Optimering av en aerob biorening med avseende på minimering av filament2018Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    Deficiencies in biotreatment due to uncontrolled growth of filamentous microorganisms is a problem for wastewater plants worldwide. The project was assigned with the task of reducing the growth of filamentous bacteria at the paper mill SCA Munksund.

    12 bacteria and 1 fungi species were presented to the project as problematic due to their filamentous properties. Operating parameters affecting filamentous growth was examined and presented. The information gathered showed that a decrease in filamentous growth for 5 especially problematic bacteria could possibly be achieved by raising the DO, increasing the concentration of nutrients and decreasing the sludge age. Other parameters affecting the growth of filamentous bacteria, such as pH, temperature and F/M were found to be too diverse among the examined species.

    Alternative solutions not focused on finding optimal operating parameters was also investigated. Promising results were treatment using a feast-famine approach, installation of an anaerobic selector and ozonation of return sludge.

    A statistical analysis was also performed on operating data. Methods used were Principal component analysis, Clustering and Logistic regression. These were used as a proof of concept rather than providing meaningful data for an operating window.

  • 38.
    Arvidsson, Staffan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Automating model building in ligand-based predictive drug discovery using the Spark framework2015Independent thesis Advanced level (professional degree), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Automation of model building enables new predictive models to be generated in a faster, easier and more straightforward way once new data is available to predict on. Automation can also reduce the demand for tedious bookkeeping that is generally needed in manual workflows (e.g. intermediate files needed to be passed between steps in a workflow). The applicability of the Spark framework related to the creation of pipelines for predictive drug discovery was here evaluated and resulted in the implementation of two pipelines that serves as a proof of concept. Spark is considered to provide good means of creating pipelines for pharmaceutical purposes and its high level approach to distributed computing reduces the effort put on the developer compared to a regular HPC implementation. 

  • 39.
    Arvidsson, Staffan
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Berglund, Tomas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Ehrenborg, Anna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Ghiassi Tari, Parisa
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Ledent, Sofie
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Nordstedt, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Nya dispenseringstekniker för feromoner: För ett hållbart jordbruk2012Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [sv]

    Projektets mål har varit att utveckla nya alternativa dispenseringstekniker för insektsferomoner som bekämpar skadeinsekter på fruktodlingar. Resultatet av projektet har gett tre teoretiskt möjliga förslag. Det första förslaget är en polymerbaserad feromondispensering som inte är baserad på någon nuvarande teknik. Förslaget är uppdelat i två koncept, antingen en polymer i gelform eller en gjuten polymer. Polymererna som ges i förslaget är biologiskt nedbrytbara och har egenskaper som inte finns i produkter på marknaden idag. Det andra förslaget grundar sig på vaxbaserad feromondispensering som är en nuvarande teknik. En vaxmassa blandas tillsammans med en specifik feromonlösing och appliceras direkt på ett bladverk eller i fällor. Genom att ha en definierad form på dispensrarna erhålls en bättre kontroll på utsöndring av feromon. Det tredje förslaget är en sprejbaserad feromondispensering även den grundas på nuvarande tekniker. Idén är att en sprejbehållare med tillhörande feromonlösning kan fjärrstyras genom att kopplas till ett kontrollsystem. Fördelen med tekniken är att en större kontroll över dispenseringen på fruktodlingsfältet kan uppnås utifrån information från en väderstation eller annan källa. Kontrollsystemet kan ställas in för att rätt mängd feromon skall släppas ut i olika väderförhållande.

  • 40.
    Asklöf, Anna
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Fermér, Elin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Zillén, Linnea
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Berglund, Emelinda
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Jonsson, Sony
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Lundberg, Lovisa
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Identifiering av biomarkörer och matchning av dessa mot Atlas Antibodies produktportfölj2017Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
  • 41.
    Assefa, Aster
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Single cell analysis of attached microbes in sediment and biofilm2017Independent thesis Advanced level (degree of Master (Two Years)), 30 credits / 45 HE creditsStudent thesis
  • 42.
    Attwood, Misty
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    The gene repertoire and functional characterization of membrane bound proteins: with focus on three- and four-transmembrane regions2015Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
  • 43.
    Augusto, Rafael
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Assortative reproduction in a seed beetle?2016Independent thesis Advanced level (degree of Master (Two Years)), 30 credits / 45 HE creditsStudent thesis
    Abstract [en]

    How genetic variation for fitness is maintained is still debated in evolutionary biology. Sexually antagonistic (SA) selection, favouring alternative alleles in males and females, has been proposed to be one mechanism capable of maintaining genetic variation for fitness. However the conditions under which SA polymorphisms are maintained are still thought to be somewhat restrictive. Several models have explored potential mechanisms that may help maintain genetic variation at SA loci. One such mechanism is assortative mating by fitness, where individuals with similar fitness mate more frequently than expected by random chance. This study explores if there is such assortative reproduction for fitness in a population of Callosobruchus maculatus seed beetles, which could explain the large amounts of SA genetic variance for fitness exhibited by this population. However, on the contrary, results show that there is evidence of disassortative reproduction for fitness in this population. 

  • 44.
    Aydin, Zeynep
    et al.
    Institutionen för biologi och miljövetenskap, Göteborgs universitet, Department of Biology, Faculty of Sciences, University of Dicle.
    Ertekin, Alaattin Selcuk
    Department of Biology, Faculty of Sciences, University of Dicle.
    Långström, Elisabeth
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Oxelman, Bengt
    Institutionen för biologi och miljövetenskap, Göteborgs universitet.
    A new section of Silene (Caryophyllaceae) including a new species from South Anatolia, Turkey2014In: Phytotaxa, ISSN 1179-3155, E-ISSN 1179-3163, Vol. 178, no 2, p. 98-112Article in journal (Refereed)
    Abstract [en]

    Silene section Cryptoneurae (Caryophyllaceae) and S. ertekinii from Western Antalya, Turkey, are described as new taxa onthe basis of morphological and molecular investigations. Nuclear ITS and chloroplast rps16 DNA sequences clearly supportthe recognition of the new section. Inclusiveness and characterization of the new section is discussed and described, and akey for the included species is provided. Diagnostic characters of the new species S. ertekinii are given and its relation to theother species of the section is discussed.

  • 45.
    Bagge, Joakim
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Hedman, Erik
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Smedsrud, Sabina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Svärdström, Cornelia
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Söderberg, Elisabeth
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Valdez, Fernando
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Utveckling av metodik för påvisning och typning av Listeria i livsmedelskedjan2017Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
  • 46.
    Baho, Didier
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Resistance and resilience of microbial communities - temporal and spatial insurance against perturbations2010Independent thesis Advanced level (degree of Master (One Year)), 30 credits / 45 HE creditsStudent thesis
    Abstract [en]

    Bacterial communities are fundamental components of many processes occurring in aquatic ecosystems, since through microbial activities substantial amount of matter and energy is transferred from a pool of DOC to higher trophic levels. Previous studies highlighted the beneficial effects of diversity on ecosystem functioning, however studies on the resistance and resilience in microbial communities are scarce. Similarly, studies focusing on factors that might improve resistance or resilience of communities such as the influence of refuges are equally missing, although an understanding of the underlying mechanisms could be very useful in the field of conservation management. In this study, chemostat cultures were used to investigate the influence of a spatial and a temporal refuge on bacterioplankton communities’ resistance and resilience measured in terms of functioning and community composition after applying a salinity pulse disturbance. Respiration rate and substrate utilization were used to estimate bacterial functioning while community composition was determined by using T-RFLP. The perturbation was found to affect bacterial functioning and community composition. Moreover our findings indicate that the resistance and resilience measured in terms of bacterial functioning and community composition were significantly influenced by the provision of refuges.  

  • 47.
    Balck, Marianne
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Phthalates in preschool dust: the relation between phthalates and parameters in the preschool environment2015Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Children are constantly exposed to many chemicals via the products they come in contactwith in their everyday life. One chemical group is phthalates, the most commonly usedplasticisers in the world. Phthalates are used mainly in PVC plastic products like floors, toys,food containers and wallpaper but they are also used in rubber, glue, paint, cables etc. Sincethese chemicals are weakly chemically bound to the PVC they can leak and migrate to the air,food, water and skin. Children are exposed to phthalates mainly through food, but because ofthe hand to mouth behaviour they are also exposed via dust inhalation and dust ingestion.About ten years ago regulations of the most toxic phthalates in toys and child care productswere implemented in the EU and from February 2015 it is a general prohibition for the use ofDEHP (diethylhexyl phthalate), DnBP (di-n-butyl phthalate), DiBP (diisobutyl phthalate) andBBzP (butyl benzyl phthalate). DiNP (diisononyl phthalate) is a relatively new phthalate andit has replaced DEHP to some extent in floors and toys. In phthalate free products DINCH(1,2-cyclohexane dicarboxylic acid diisononyl ester) is one of the plasticizer replacingphthalates. The banned phthalates have been shown to cause adverse effects on reproductionand recent research also investigates links between phthalate exposure and asthma and allergysymptoms in children. More experimental animal studies are needed to further investigate theasthma and allergy correlation.

    In the present project dust samples were collected from 30 preschool indoor environments inthe Stockholm city area to evaluate the levels of the six substances mentioned and thephthalate DEP (diethyl phthalate). The main aim of this thesis project was to search forrelations and links between the phthalate concentrations in dust and parameters from theindoor environment in preschools. Studied parameters are e.g. construction year, floor type,cleaning routines and quantity of toys and furniture made of plastic or foam. The project wascommissioned by the Swedish EPA and performed at the Institute of Environmental Medicine(IMM) at Karolinska Institutet.

    A negative relation was found between dust phthalate (DEHP and DnBP) concentrationand construction year. Also rooms with old PVC floors had higher concentrations of DEHPand DnBP in dust than rooms with new PVC floors. There was also a trend that dust frompreschools with PVC floors had higher DiNP concentration than dust from preschools withother floor types. The preschools that used foam mattresses for resting had higher DiNPconcentrations than those with no foam mattresses. Most preschools had new foammattresses, which could indicate a more common use of DiNP in new mattresses or mattress2covers compared to old mattresses that contains more DEHP. The four Waldorf preschoolsthat participated had lower DiNP dust concentrations than the other preschools, which wasexpected since Waldorf orientation includes using as little plastic material as possible. Norelation was found between the phthalate dust concentrations and the quantity of toys made ofsoft plastic in the sampled area.

    Many preschools had made a plastic inventory where they removed old and soft plastic toysand material. Also many preschools recently replaced old foam mattresses used for resting.This could be due to the big chemical focus in the media and authorities and the brochuresthat have been sent out the last couple of years about what preschool can do to decrease thechemical exposure of children. This interest and awareness seen in the preschools waspositive and hopefully the trend spreads to more preschools. Since children spend a big part oftheir time at preschools it is an important mission for society and the government to decreasethe exposure to hazardous chemicals there. Hopefully what has been done so far is just thebeginning.

  • 48.
    Balck, Marianne
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Utgör användning av p-piller ett hot mot livskraftiga grodpopulationer?: Etinylöstradiols och levonorgestrels effekter hos arterna Xenopus leavis, Xenopus tropicalis och Rana temporaria2013Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [sv]

    En eskalerande minskning hos grodpopulationer och grodarter har skett världen över sedan 1980. Minskningen har påverkats av flera faktorer, bland annat utsläpp av endokrina ämnen till vattendrag. Endokrina ämnen är naturliga och syntetiska hormoner och kemikalier som stör människors och djurs hormonsystem. Syntetiska hormoner finns i p-piller och andra preventivmedel och hormonerna släpps ut i vattendrag via urinen. Det har visats att grodor påverkas av de syntetiska hormonerna etinylestradiol och levonorgestrel som finns i p-piller. Den här litteraturstudien syftar till att undersöka vilka effekter de två hormonerna har på modellarterna Xenopus laevis och Xenopus trolpicalis och på svenska grodarter såsom Rana temporaria. Effekterna är främst förändrad könskvot, med honor i majoritet, samt minskad fertilitet. Fertiliteten försämras genom missbildade könsorgan, genom att äggen mognar långsammare och honor kan bli sterila med avsaknad av äggledare. Hormonexponering kan leda till försenad metamorfos och det kan bli en högre mortalitet hos juvenila grodor. Även hormonuttryck kopplade till reproduktion och fertilitet kan påverkas av hormonexponering. Dock behövs mer forskning, särskilt i fält då mestadels experimentella studier gjorts hittills i laboratorier. Hormonutsläpp är en bidragande faktor till att sex av Sveriges åtta grodarter är rödlistade och i världen handlar det om tusentals arter. Även den så kallade cocktail effekten, det vill säga de effekter flera olika ämnen skapar tillsammans, bör undersökas närmare.

  • 49.
    BALTEKIN, ÖZDEN
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Experimental Evolution of Persister Fractions in Escherichia coli2014Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
  • 50.
    Barkenäs, Emelie
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Automation of a solid-phase proximity ligation assay for biodefense applications2013Independent thesis Advanced level (professional degree), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    The extent of devastation caused by a biological warfare attack is highly correlated to the time from release to detection. As a step towards lowering the detection time the international project TWOBIAS was launched. Here, the main goal is to develop an automated, specific and sensitive combined detection and identification instrument capable of identifying a biological threat within an hour. The identification unit is comprised of a sample preparation module, an amplification module and a detection module and utilizes a proximity ligation assay in combination with circle-to-circle amplification in order to detect a biological threat. This thesis describes the automation of the sample preparation steps of the assay and the integration with the downstream units. The functionality of the sample preparation module was verified by subjecting it to biological samples in a laboratory and at a real-life location. The results showed that the sample preparation module was capable of preparing a sample collected in a complex environment with the same results as a sample prepared in a laboratory. 

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