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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.
    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.

  • 3.
    Aho, Milja
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing.
    Optimisation of Ad-hoc analysis of an OLAP cube using SparkSQL2017Independent thesis Advanced level (professional degree), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    An Online Analytical Processing (OLAP) cube is a way to represent a multidimensional database. The multidimensional database often uses a star schema and populates it with the data from a relational database. The purpose of using an OLAP cube is usually to find valuable insights in the data like trends or unexpected data and is therefore often used within Business intelligence (BI). Mondrian is a tool that handles OLAP cubes that uses the query language MultiDimensional eXpressions (MDX) and translates it to SQL queries. Apache Kylin is an engine that can be used with Apache Hadoop to create and query OLAP cubes with an SQL interface. This thesis investigates whether the engine Apache Spark running on a Hadoop cluster is suitable for analysing OLAP cubes and what performance that can be expected. The Star Schema Benchmark (SSB) has been used to provide Ad-Hoc queries and to create a large database containing over 1.2 billion rows. This database was created in a cluster in the Omicron office consisting of five worker nodes and one master node. Queries were then sent to the database using Mondrian integrated into the BI platform Pentaho. Amazon Web Services (AWS) has also been used to create clusters with 3, 6 and 15 slaves to see how the performance scales. Creating a cube in Apache Kylin on the Omicron cluster was also tried, but was not possible due to the cluster running out of memory. The results show that it took between 8.2 to 11.9 minutes to run the MDX queries on the Omicron cluster. On both the Omicron cluster and the AWS cluster, the SQL queries ran faster than the MDX queries. The AWS cluster ran the queries faster than the Omicron cluster, even though fewer nodes were used. It was also noted that the AWS cluster did not scale linearly, neither for the MDX nor the SQL queries.

  • 4.
    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.

  • 5.
    Andersson, Annsofie
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmaceutical Biosciences.
    Pharmaceutical knowledge retrieval through reasoning of ChEMBL RDF2011Independent thesis Advanced level (degree of Master (Two Years)), 30 credits / 45 HE creditsStudent thesis
  • 6.
    Andersson, Hilda
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    A machine learning pipeline for predicting success rates in PrEST production2019Independent thesis Advanced level (professional degree), 20 credits / 30 HE creditsStudent thesis
    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.

  • 7.
    Andersson Schönn, Mikael
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Molecular Biomimetics.
    Promoter regulation: designing cells for biotechnological applications2016Independent thesis Advanced level (professional degree), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    The filamentous cyanobacteria Nostoc punctiforme ATCC 29133 is a model species fordevelopment of sustainable production methods of numerous compounds. One of its uniquefeatures is the anaerobic environment of the strains nitrogen fixing heterocyst cells. To be ableto properly utilize this environment, more knowledge regarding what regulates cell specificexpression is required. In this study, three motifs of the NsiR I promoter of Anabaena sp.PCC 7120 was studied in this system utilizing YFP-fluorescence as a reporter to determinetheir impact on spatial expression pattern. Investigations were performed on immobilizedcells with the use of confocal microscopy and results point towards sigma factor regulation.

  • 8.
    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.

  • 9.
    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
  • 10.
    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.

  • 11. Annala, Katja
    Characterization of promoter regions for design of a cell specific promoter2017Independent thesis Advanced level (professional degree), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Global warming is one of the modern world’s biggest problems and renewable fuels

    are needed to meet this challenge. Biohydrogen is one alternative of a renewable fuel

    and can be produced from genetically modified cyanobacteria. Although the

    production is not yet efficient enough to compete with fossil fuels on a commercial

    level, it has potential. By gaining knowledge regarding pathways and regulatory

    mechanisms in cyanobacteria, genetic tools can be built and further enhance the

    production of biohydrogen. A synthetic promoter, which is active only in hydrogen

    producing cells, heterocysts, is an example of a wanted genetic tool. Such a promoter

    would make it possible to overexpress proteins essential for hydrogen production in

    heterocysts and thereby increase the production of hydrogen. In this study, several

    promoters have been designed and compared quantitatively on both transcriptional

    and translational levels. The promoters were compared regarding their heterocyst

    specific expression and their strength. By comparison of the designed promoters, all

    with different contents, the essential promoter regions have been identified and two

    well characterized and heterocyst specific promoter have been proposed.

  • 12.
    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. 

  • 13.
    Bagge, Joakim
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Farmakognosi.
    Chromatography of Therapeutic Peptides - Contrasting SFC and HPLC2019Independent thesis Advanced level (professional degree), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    This work is a comparison of a well-established and a novel, "green" and efficient technique to separate peptides of pharmaceutical interest. An attempt is made to derive the chromatographic retention behaviour from these techniques to a number of property descriptors derived from the linear sequence of amino acids. A set of therapeutic peptides were carefully chosen to be experimentally evaluated using in silico-based descriptor calculations. A principle component analysis was performed to assess the distribution of calculated descriptors for including peptides with variable properties. A diluent optimization study was also included to find the optimal diluent for peptides with minimal diluent effects and peak splitting phenomena. The results showed that the solvents tert-butanol and methanol performed best between 20-30 and 50 volumetric percent water as additive in SFC and HPLC, respectively. These diluents were then used for the peptides within the set to evaluate the retention and selectivity in HPLC and SFC. SFC performed well in terms of resolving power. Inparticular, SFC was able to separate Leuprolide and Triptorelin while HPLC was not. A comparison was also made in between the two stationary phases CN and XT, where a global selectivity was shown to be higher for CN.

    This work does also assess a novel method for determining solubility of analytes in supercritical fluid. The method was evaluated using the pharmaceutical compounds caffeine and aspirin and then used to determine solubility of Leu-Enkephalin in 20% (v/v%) methanol. The solubility of caffeine was determined to be 0.45 mg ml-1 in pure SF-CO2 under 140 bar pressure and 3.9 mg ml-1 for aspirin in 2.4% methanol. Both values correlated well with measurements from four acknowledged papers within this field. Leu-Enkephalin was found to have a solubility of 1.90 mg ml-1 using a solvent corresponding to the initial phase condition of the gradient used for peptide analysis in SFC. Further experimental work is required before the method can be implemented as a useful tool in preparative chromatography, however the results presented here show the compatibility of assessing biomolecules in both pure SF-CO2 and mixed with modifier. The possibility to determine solubility with additional modifier infers an important step of including and evaluating these compounds creating a solid support to subsequent large scale separation.

  • 14.
    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. 

  • 15.
    Basu, Alex
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Relation between hydrogen production and photosynthesis in the green algae Chlamydomonas reinhardtii2015Independent thesis Advanced level (professional degree), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    The modernized world is over-consuming low-cost energy sources that strongly contributes to pollution and environmental stress. As a consequence, the interest for environmentally friendly alternatives has increased immensely. One such alternative is the use of solar energy and water as a raw material to produce biohydrogen through the process of photosynthetic water splitting. In this work, the relation between H2-production and photosynthesis in the green algae Chlamydomonas reinhardtii was studied with respect to three main aspects: the establishment of prolonged H2-production, the involvement of PSII in H2-production and the electron pathways associated with PSII during H2-production. For the first time, this work reveals that PSII plays a crucial role throughout the H2-producing phase in sulfur deprived C. reinhardtii. It further reveals that a wave-like fluorescence decay kinetic, before only seen in cyanobacteria, is observable during the H2-producing phase in sulfur deprived C. reinhardtii, reflecting the presence of cyclic electron flows also in green algae. 

  • 16. Benevides, Kristina
    Exploring tangles in the Epigenome: Genome-wide Analysis of G-quadruplexes in mouse embryonic stem cells (mESC)2019Independent thesis Advanced level (professional degree), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    G-quadruplexes (G4s) are four-stranded, non-canonical secondary DNA structures which have been shown to readily form in G-rich sequences in vitro. G4 formation can affect chromatin architecture and has been implicated in promoting genomic instability, and linked to biological processes such as transcription, replication and telomere maintenance. In this project, ChIP-seq data derived with G4-specific antibodies from mouse embryonic stem cells (mESC) are analysed and integrated with different histone 3 (H3) modification data sets.The analysis method follows a standard ChIP-seq data analysis workflow, which includes steps such as calculation of quality metrics, peak calling and downstream analyses. The results show enrichment of G-rich motifs and prevalence of G4s in functional regions such as promoter-TSSs and 5'UTRs. In addition, there is some evidence of a potential association with oncogene promoter regions and location of G4s, which would support previous findings. Furthermore, the results indicate a possible correlation between loss of histone modifications H3 lysine 4 trimethylation (H3K4me3) and H3 lysine 27 acetylation (H3K27ac), and G4 occurence. G4s have become increasingly popular to study in recent times and may harbour potential to be targeted for cancer therapy.

    The full text will be freely available from 2021-08-01 08:15
  • 17.
    Berggren, Sofia
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Validation and characterisation of a micro-protein in Campylobacter jejuni2017Independent thesis Advanced level (professional degree), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    The Epsilonproteobacterium Campylobacter jejuni is a major foodborne pathogen in humans mainly causing gastroenteritis, and is connected to several secondary autoimmune diseases. A large part of the small genome of C. jejuni is still to be characterized, with many hypothetical proteins present. Micro-proteins - those that are < 50 amino acids and encoded by a small open-reading frame (micro-ORF) - are an understudied class of proteins that have been shown to be involved in vital processes in the cell, such as cell division, modulation of enzymatic activities, and stress responses. So far, few examples of micro-proteins are known in pathogenic bacteria, and fewer are known that affect virulence. In this study, we provide first evidence that the conserved micro-ORF Cj0878 of C. jejuni is translated by showing that a GFP translational fusion to the ORF is translated, and that Cj0878 mRNA and protein levels are affected by the absence of iron in minimal media. With in silico analysis we found that Cj0878 is likely a highly basic protein and may have an amphipathic nature. We also show that a predicted base-pairing interaction between Cj0878 mRNA and the sRNA CJnc170 likely has a regulatory consequence, by showing that CJnc170 mutant strains have different levels of the Cj0878 translational fusion protein. To summarise this study provides the first validation and characterisation of a micro-protein in the important pathogen C. jejuni, and provides the basis for future studies on the function of the protein.

  • 18.
    Bergman, Ebba
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution.
    Haplotype Inference as a caseof Maximum Satisfiability: A strategy for identifying multi-individualinversion points in computational phasing2017Independent thesis Advanced level (professional degree), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Phasing genotypes from sequence data is an important step betweendata gathering and downstream analysis in population genetics,disease studies, and multiple other fields. This determination ofthe sequences of markers corresponding to the individualchromosomes can be done on data where the markers are in lowdensity across the chromosome, such as from single nucleotidepolymorphism (SNP) microarrays, or on data with a higher localdensity of markers like in next generation sequencing (NGS). Thesorted markers may then be used for many different analyses anddata processing such as linkage analysis, or inference of missinggenotypes in the process of imputation

    cnF2freq is a haplotype phasing program that uses an uncommonapproach allowing it to divide big groups of related individualsinto smaller ones. It sets an initial haplotype phase and theniteratively changes it using estimations from Hidden MarkovModels. If a marker is judged to have been placed in the wronghaplotype, a switch needs to be made so that it belongs to thecorrect phase. The objective of this project was to go fromallowing only one individual within a group to be switched in aniteration to allowing multiple switches that are dependent on eachother.

    The result of this project is a theoretical solution for allowingmultiple dependent switches in cnF2freq, and an implementedsolution using the max-SAT solver toulbar2.

  • 19.
    Björkesten, Johan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Development and evaluation of procedures and reagents for extraction of proteins from dried blood spots for analysis using Proseek2014Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    A method for extraction of proteins from dried blood spots (DBS) for analysis using Proseek is developed and evaluated. DBS, as sample format, possesses a number of desirable advantages over for example plasma samples. These advantages include for example minimal patient invasiveness, sampling simplicity and non regulated sample transportation. Highly reproducible quantitative detection of 92 proteins is demonstrated from a 1.2 mm in diameter DBS disk. The DBS inter spot analysis precision (7% coefficient of variance) is comparable to plasma inter assay precision (6% coefficient of variance). Coefficient of variance is the ratio between standard deviation to mean value for the analysed replicates. Proseek analysis of DBS could possibly reveal a unique opportunity to examine health related issues in extremely premature infants hopefully resulting in increased survival rates in the future.

  • 20.
    Björklund, Viktor
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    ProQ-dependent phenotypes in Escherichia coli and Salmonella Typhimurium2017Independent thesis Advanced level (professional degree), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    RNA-binding proteins (RBPs) regulate gene expression at the posttranscriptional

    level by interacting with mRNAs and sRNAs. Recently,

    ProQ has been discovered to be a global RBP with extensive RNA

    targets in

    Escherichia coli and Salmonella enterica. However, many

    aspects of the function of ProQ, including mechanisms of RNA-binding,

    regulated pathways, and ProQ-dependent phenotypes are yet to be

    understood. In this study, it is shown that ProQ can affect both persister

    cell

    􀀀formation and motility. A proQ deletion reduces the number of

    persister cells independent of both SOS-response and the persisterrelated

    type I toxin/antitoxin system

    tisB/istR-1. Furthermore, ProQ

    overexpression also reduces persister cell formation, indicating an

    intricate regulation by ProQ on persister-related pathways. Finally,

    it is confirmed that deletion of

    proQ leads to down-regulation of

    motility-related genes.

  • 21.
    Borg, Malin
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Investigation of the regulation of the rhs locus in Salmonella enterica serovar Typhimurium2016Independent thesis Advanced level (professional degree), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    The rearrangement hotspot (rhs) loci were discovered over thirty years ago, but it was only

    recently that the Rhs proteins were found to have the capacity to mediate Contact-Dependent

    growth Inhibition (CDI) of related bacterial species. However, the regulation of the rhs loci

    has been poorly understood. In this study the regulation of the rhs locus in the pathogen

    Salmonella enterica serovar Typhimurium (S.tm.) was investigated in infection-relevant

    conditions. A set of plasmid transcriptional fusions of different rhs promoters to YFP was

    used to analyse the activities of the promoters in wild type and in S.tm. regulatory mutants. An

    internal rhs transcript was shown to be expressed and at different levels within the bacterial

    population. Furthermore, it was found to be regulated by the virulence factors RpoS and HilD.

  • 22.
    Boström, Fredrik
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Single-cycle kinetics for QCM biosensors for high throughput nanoparticle characterization application2016Independent thesis Advanced level (professional degree), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

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

  • 23.
    Braesch-Andersen, Ken
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Temperature dependence in human Rhinovirus infection of human MRC-52019Independent thesis Advanced level (professional degree), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

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

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

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

  • 24.
    Breimark, Linda
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Investigating the use of isotope-labeled standards as calibrants in label-free quantification2018Independent thesis Advanced level (professional degree), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

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

  • 25.
    Bringeland, Nathalie
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience, Functional Pharmacology. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    DNA methylation correlation networks in overweight and normal-weight adolescents reveal differential coordination2013Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

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

  • 26.
    Broström, Oscar
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Development of a single-molecule tracking assay for the lac repressor in Escherichia coli2019Independent thesis Advanced level (professional degree), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Gene regulation by transcription factors are one of the key processes that are important to sustain all kinds of life. In the prokaryote Escherichia coli this has shown to especially crucial. The operator sequence to which these transcription factors bind to are very small in comparison to the whole genome of E. coli, thus the question becomes how these proteins can find these sequences quickly. One particularly well-studied transcription factor in this regard is the lac repressor. It has been shown that this transcription factors finds its operators faster than the limit of three dimensional diffusion. The leading model for how the repressor does that is facilitated diffusion and this model has gained more experimental evidence, particularly using single-molecule fluorescence microscopy.

    This study aimed at measuring the unspecific binding time between the lac repressor and DNA in vivo, but in the end the project evolved to trying to establish a single-molecule tracking assay of the repressor in vivo. In this study a mutant of the repressor was expressed and purified, labelled with a synthetic fluorophore, electroporated into E. coli and tracking was performed under a microscope. One of the three types of experiments were partially analysed with an image analysis software. Unfortunately, analysis was not completed for all experiments which made it difficult to compare the results. In the end the data was compared by eye while also using the results from image analysis. With slight optimism it can be concluded that the assay worked, but it needs more development.

  • 27.
    Carlsson, Mattias
    Uppsala University.
    Optimering och validering av realtids-PCR assay för detektion av verocytotoxin-producerande E. coli (VTEC)2011Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Pathogenic E. coli such as VTEC can cause serious diseases to humans. A detection method for VTEC based on realtime-PCR has been developed by EU-RL VTEC (European Union Reference Laboratory VTEC) and the National Food Administration. In this master thesis I have optimized and validated a part of the method which detects serotypes of VTEC. During optimization the primer concentration, probe concentration and annealing temperature were evaluated for a more sensitive detection. Validation showed that the PCR-reaction is both effective and sensitive (LOD100). Validation of the whole method did not give any significant results due to the fact the sensitivity (LOD50) could not be determined.    

  • 28.
    Celma, Gunta
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Nanocellulose hydrogels for topical wound-care applications: a study on human skin interactions2017Independent thesis Advanced level (professional degree), 20 credits / 30 HE creditsStudent thesis
  • 29.
    Dahlberg, Gunnar
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Implementation and evaluation of a text extraction tool for adverse drug reaction information2010Independent thesis Advanced level (degree of Master (One Year)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Background: Initial review of potential safety issues related to the use of medicines involves reading and searching existing medical literature sources for known associations of drug and adverse drug reactions (ADRs), so that they can be excluded from further analysis. The task is labor demanding and time consuming.

    Objective: To develop a text extraction tool to automatically identify ADR information from medical adverse effects texts. Evaluate the performance of the tool’s underlying text extraction algorithm and identify what parts of the algorithm contributed to the performance.

    Method: A text extraction tool was implemented on the .NET platform with functionality for preprocessing text (removal of stop words, Porter stemming and use of synonyms) and matching medical terms using permutations of words and spelling variations (Soundex, Levenshtein distance and Longest common subsequence distance). Its performance was evaluated on both manually extracted medical terms (semi-structuredtexts) from summary of product characteristics (SPC) texts and unstructured adverse effects texts from Martindale (i.e. a medical reference for information about drugs andmedicines) using the WHO-ART and MedDRA medical term dictionaries.

    Results: For the SPC data set, a verbatim match identified 72% of the SPC terms. The text extraction tool correctly matched 87% of the SPC terms while producing one false positive match using removal of stop words, Porter stemming, synonyms and permutations. The use of the full MedDRA hierarchy contributed the most to performance. Sophisticated text algorithms together contributed roughly equally to the performance. Phonetic codes (i.e. Soundex) is evidently inferior to string distance measures (i.e. Levenshtein distance and Longest common subsequence distance) for fuzzy matching in our implementation. The string distance measures increased the number of matched SPC terms, but at the expense of generating false positive matches. Results from Martindaleshow that 90% of the identified medical terms were correct. The majority of false positive matches were caused by extracting medical terms not describing ADRs.

    Conclusion: Sophisticated text extraction can considerably improve the identification of ADR information from adverse effects texts compared to a verbatim extraction.

  • 30.
    Dahlberg, Jenny
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Development of a triplex real-time PCR method for detection of Chlamydia pneumoniae, Chlamydia psittaci and Mycoplasma pneumoniae2016Independent thesis Advanced level (professional degree), 20 credits / 30 HE creditsStudent thesis
  • 31.
    Dey, Bonoshree
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Evaluation of peptide-receptor radionuclide therapy in breast cancer and neuroblastoma, in combination with the radio-sensitizing drug VIP-1162018Independent thesis Advanced level (professional degree), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Cancer being one of the leading causes of death globally, raises an international fight to defeat and finally conquer cancer. It represents more than 200 different diseases that individually have varying symptoms and treatments. The p53-pathway is of great interest as it has shown to be crucial in the formation of cancerous cells. One method is to use peptide-receptor radionuclide therapy to target somatostatin receptors that are overexpressed on cancer cells. The somatostatin-receptor analogue DOTATATE is a peptide that targets these receptors. In this project, the radionuclide (177Lu) is attached to DOTATATE to achieve a localized radiation effect targeting only the tumour cells and not surrounding tissue. In combination with the radiation-sensitizing drug VIP-116, the effect is supposedly enhanced. The findings of this project conclude the specific targeting of 177Lu-DOTATATE and the potential of VIP-116 to act as a radiosensitizer. The combination of both components works more efficiently on some cell lines than others, which emphasizes the need for tailored cancer therapies. 

    The full text will be freely available from 2021-09-25 00:00
  • 32.
    Dyrhage, Karl
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Bioinformatic Analysis of Genomic and Proteomic Data from Gemmata2016Independent thesis Advanced level (professional degree), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Members of the bacterial phylum Planctomycetes have been claimed to have a

    compartmentalised cell plan, with cell walls lacking peptidoglycan despite being free-living.

    These theories have been challenged in recent years, and the nature of the planctomycete cell

    structure is currently under debate. Yet it remains clear that the planctomycete membranes

    have unique properties, and are thus likely localisations of evolutional innovation. In this

    study, proteomes and genomes of four planctomycete species from the Gemmata/Tuwongella

    clade were investigated with the aim to find candidate genes for functional characterisation.

    Analysis based on full genome sequencing and mass spectrometry revealed 21 proteins unique

    to the Gemmata/Tuwongella clade that were present in the proteomes of all four species. The

    gene coding for one of these was found to be organised in an operon, containing an additional

    four clade-specific genes, likely related to type II secretion. A planctomycete-specific cell

    surface signal peptide previously not seen in Gemmata was identified in all four species, with

    proteins found to have the motif indicating that their cell surface has a strong negative charge.

    Lastly, the study has revealed evidence suggesting that the planctomycetes have a traditional

    gram-negative cell wall, contradicting the previously proposed proteinaceous cell wall model.

  • 33.
    Edblom, Johan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Exploration of big data and machine learning in retail2017Independent thesis Advanced level (professional degree), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    During the last couple of years, there has been an immense increase

    in data generation. This new data era has been referred to as the big

    data paradigm. More and more business areas are today realizing the

    power of capturing more data, and by this hope to reveal hidden

    patterns and gain new insights of their business. ICA is one of the

    largest retail business in Sweden, and saw the potential of utilizing

    the big data technologies to take the next step in digitalisation.

    The objective of this thesis is to investigate the role of these

    techniques in combination with machine learning algorithms and

    highlights advantages and possible limitations. Two use cases were

    implemented and tested which reveals possible application areas and

    important aspects to consider.

  • 34. Elfman, Sara
    et al.
    Abubeker, Ismail
    Sjöberg, Erik
    Utterbäck, Marie
    Petterson, Rickard
    Borg, Emma
    Bioreaktorodling av gran2013Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
  • 35.
    Elison Kalman, Grim
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Structural Biology.
    Purification, functional characterization and crystallization of the PerR peroxide sensor from Saccharopolyspora erythraea2019Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    This report summarizes the work on the cloning, expression, and purification of PerR, a metal sensing regulator from Saccharopolyspora erythraea and the subsequent characterization using small angle X-ray scattering and other biochemical methods. The report aims to provide an insight into prokaryotic metal homeostasis, provide a better understanding of how PerR works and provide valuable information for the continued work on the crystallization of PerR.

  • 36.
    Elofsson, Hampus
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Immunoassay engineering: An explorative comparison of detection chemestries and surfaces for protein microarrays2016Independent thesis Advanced level (professional degree), 20 credits / 30 HE creditsStudent thesis
  • 37.
    Erik, Gioeli
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Biochemistry.
    Utbytesoptimering inom läkemedelsproduktion: Identifiering av kassationsorsaker inom AstraZenecas packningsprocess i Gärtuna2017Independent thesis Advanced level (professional degree), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    The project aimed to deliver recommendations of how to optimize the yield of thepackaging process of tablets and capsules within AstraZeneca's facility in Gärtuna(Södertälje), Sweden. The project scope included nine packaging lines of blisterproducts with highly similar process steps. The crucial part of the puzzle was toidentify cassation sources within these production lines, which was achieved by thecombined methology of qualitative interviews, quantitative surveys and statisticalprocess control applied to logged production data.The following cassation sources were identified:- Cassation as a side effect of start-up controls within an order- Safety cassation of tablets when the blister machine stops- In many cases, the safety cassation also occours when the cartoner stops- A cut-in-half tablet causing cassation of multiple tablets in the rejection steps- Leftover product on the packaging line when the order is finished- Target conflict between high productivity of the production line and high yield withinthe order- Difficulty optimizing machines settings for small order sizes, leading to higher stopfrequency and therefore more safety cassation of tablets, as well as a higher risk thattablets are sorted out in control stepsWhich led to these recommendations:- Optimizing the yield as a target value for process optimization- Log the yield for all the process steps within the packaging line- Consider the possibility of reintroducing rejected blisters containing approvedtablets- Clear prioritization of the target conflict between high productivity and high yield- Analyze if there are any time-consuming steps conflicting with high yield within theprocess of closing an order which are not required to be performed at that particularprocess stepAs well as future work:- Get to the bottom of the correlation between low yield and small order sizes- Investigate further which materials are prone to cause machine stops within thecartoner- Dig deeper into the problem of cut-in-half tablets existing pre-packaging-process

  • 38.
    Eriksson, Alexandra
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    The internationalization of new technology within an organization with unclear ownership2017Independent thesis Advanced level (professional degree), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    This master thesis was done at Uppsala Clinical Research Center (UCR). UCR have recently developed the technical platform QReg 5 for managing quality registries. UCR have been in contact with several international organizations interested in collaborating with UCR because of their expertise within quality registries as well as their technical competence. UCR have a complicated owner structure as well as organizational structure, as they are owned by Uppsala University and Uppsala County Council. The purpose of this master thesis was to present how QReg 5 could be commercialized under UCR's preconditions. In order for the internationalization plans to be successful, it was shown that the shared ownership of UCR needs to become clearer. By taking advantage of the possibilities with the new development section at UCR, the management of the contacts will be more efficient. Potential competitors for UCR are registry centers that have created their own technical solutions, large software companies, Life Science related organizations (e.g. hospitals), the organizations that UCR license QReg 5 to, as well as software companies creating electronic medical records. The most interesting customer segment for UCR are organizations with technical competences, which are placed in countries were quality registries are not yet in use. 

  • 39.
    Eriksson, Hanna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre. Uppsala universitet.
    Implementation of thiamine pyrophosphate (TPP) riboswitches as synthetic biosensors and regulatory tools in cyanobacteria2018Independent thesis Advanced level (professional degree), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    The natural occurrence of the non-mevalonate (also called MEP after the compound methyl-erythriol phosphate) pathway in the model cyanobacterium Synechocystis sp. PCC 6803 allows for biosynthesis of various high-value terpenoid compounds. An important co-factor of this pathway is thiamine pyrophosphate (TPP), coenzyme to the 1- deoxy-D-xylulose-5-phosphate synthase (DXS) reaction in the initial step of the MEP pathway. Concurrently, TPP biosynthesis derives partially from 1-deoxy-D-xylulose phosphate, the product of DXS. This makes TPP a potentially significant measure of MEP pathway activity, and thus terpenoid productivity. The implementation of a molecular biosensor for TPP could be a promising approach towards on-line assessment and feedback regulation of MEP pathway activity and this application is therefore investigated in this work. Riboswitches have been suggested as versatile RNA-based tools for biotechnological applications in bacteria, including various cyanobacterial species. However, TPP-responsive riboswitches have not been addressed in cyanobacteria thus far. This project therefore aims at the evaluation and implementation of TPP-responsive riboswitches in Synechocystis, using a yellow fluorescent reporter protein as quantitative readout of translational regulation. Native putative OFF-switches from two cyanobacterial species are investigated along with one synthetic ON-switch, originally based on the native riboswitch from E. coli. The induction effects are assessed on both RNA and protein level for both TPP and its precursor thiamine. The synthetic riboswitch is found to be effective in Synechocystis and is further examined for its dynamic range. Several protocols for fluorescence and transcript level experiments are developed. Several continuation experiments are suggested, including further investigation of the cyanobacterial OFF-switches.

  • 40.
    Eriksson Röhnisch, Kajsa
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Purification and Technical Application of a Serine Protease Inhibitor from Solanum tuberosum2016Independent thesis Advanced level (professional degree), 20 credits / 30 HE creditsStudent thesis
  • 41.
    Flinkfeldt, Linnea
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    High throughput pipeline for rapid antibiotic susceptibility testing and ID of bacteria from blood cultures2019Independent thesis Advanced level (professional degree), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Rapid and accurate species identification and antibiotic susceptibility testing are of great importance for patients with sepsis and to stop over- and misuse of antibiotics contributing to antibiotic resistance. QuickMIC™ is a rapid antibiotic susceptibility testig system based on a microfluidic technology solution developed by Gradientech that measure MICs on bacteria from positive blood culture bottles. By combining QuickMIC™ with a rapid system for detection and identification, the time to detection, identification and antibiotic susceptibiolity testing could be shortened with days compared to pipelines used today which could mean the difference of life and death for patients. The T2Bacteria® panel and T2Dx® instrument developed by T2 biosystems is an FDA-cleared test for rapid detection and identification of bacteria from whole blood based on magnetic molecular resonance technology. The time to result of the T2Dx® instrument is 3-4 hours and the time to result for QuickMIC™ is 2-4 hours. In this project, the possibilities and benefits of such a pipeline have been studied by comparison to a pipeline typically used today. Time, accuracy and practical aspects have been investigated during the project and the results are promising for future further studies.

  • 42.
    Fogelström, Anna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    DNA barcoding of freshwater fishes in Matang, Malaysia2015Independent thesis Advanced level (professional degree), 20 credits / 30 HE creditsStudent thesis
  • 43.
    Frisk, Christoffer