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  • 201.
    Hagelby Edström, Tim
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Obesogenic molecules breaching Caco-2 cells: intracellular regulation of tight junctions2016Självständigt arbete på avancerad nivå (yrkesexamen), 20 poäng / 30 hpStudentuppsats (Examensarbete)
    Abstract [en]

    Impaired function of the human intestinal epithelial barrier (IEB) might allow for

    permeability of harmful substances, such as obesogens, which induce obesity and further

    implications. Tight junction (TJ) proteins are the key component for normal functions of the

    barrier. In this master thesis, the correlation between increased TJ permeability of the IEB and

    absorption of obesogens was studied. The effect of obesogens on TJ expression was also

    investigated. Permeability tests performed on Caco-2 cell monolayers exposed to obesogens

    showed altered permeability, indicating that obesogens might have an effect on TJ protein

    expression. Furthermore, impaired monolayers showed increased permeability, which implies

    that impaired functions of IEB lead to increased absorption of obesogens.

  • 202.
    Hallander, Emelie
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Germination responses as a reproductive barrier between Silene dioica and S. latifolia2015Självständigt arbete på avancerad nivå (masterexamen), 30 poäng / 45 hpStudentuppsats (Examensarbete)
  • 203.
    Hallgren, Henrik
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Characterization of the tg(rgs4:mCherry) zebrafish line2014Självständigt arbete på avancerad nivå (masterexamen), 30 poäng / 45 hpStudentuppsats (Examensarbete)
    Abstract [en]

    Cell-to-cell communication is one of the fundamental requisites of making multicellular organisms. G protein-coupled receptors (GPCRs) are one of the most abundant receptor-types within vertebrates. They canonically mediate their signal via hetrotrimeric G proteins, and G protein signaling is regulated by regulators of G protein-signaling (RGS). One of these RGS proteins, RGS4, is preferentially expressed in the central nervous system of humans and has been strongly connected to dopaminergic signaling, along with a number of severe neuronal diseases. rgs4 is not well studied in the model organism Danio rerio, the zebrafish, with only two publications. In this project, a newly constructed transgenic line, tg(rgs4:mCherry), with the fluorophore mCherry regulated by the promoter element of rgs4 was characterized in order to investigate fidelity to endogenous rgs4 expression and the utility of the transgenic line. The mCherry expression is apparent by 48 hours post fertilization, and expression is found mainly in neuronal tissue. Cell bodies are visible only in some labeled areas, while other areas show a more diffuse signal indicative of projections. There is only one transgenically labeled area that also unambiguously expresses rgs4; the pronephric tubule. This line is therefore not particularly well suited for rgs4-specifc studies, but this does not discredit the fidelity of the construct. A transgenic line made with a site-directed technique would most likely confer the fidelity of the promoter to the expression of the fluorophore. A way of increasing the labeling resolution includes exchanging the mCherry fluorophore for one with stronger signal and a lower tendency to aggregate, e.g. eGFP. Increasing the resolution of the characterization, e.g. to the level of sub-nuclei or neuronal types, would serve to enhance the utility of the line. As it is, the tg(rgs4:mCherry) zebrafish line has limited uses, and yet it is not without them.

  • 204.
    Hammare, Annie
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Långsiktig uppföljning efter naturvårdsbränningar i Dalarna: trädmortalitet och plantföryngring2017Självständigt arbete på avancerad nivå (masterexamen), 30 poäng / 45 hpStudentuppsats (Examensarbete)
    Abstract [en]

    The County Administrative Board of Dalarna conducts controlled conservation burnings in nature reserves to increase biodiversity. The fire increases diversity in several ways by attracting fire dependent organisms, increasing the number deciduous trees, enhancing the volume of dead wood and bringing morphological diversity as fire scars on trees. After the burnings deciduous trees usually increase, but to reduce grazing from browsers (who would consume most of the deciduous biomass) fences can be used to exclude the grazers.

     

    In the first part of my study I inventoried tree status after two controlled nature conservation burnings in eastern and northern Dalarna (Trollmosseskogen and Rensjön). The aim was to increase the knowledge of fire effects on trees and to find out if the desired results were achieved on diversity. The results show that the number of tree species has increased in Trollmosseskogen. Fire damages on trees were more common in Rensjön than in Trollmosseskogen. In both nature reserves the volume of dead wood has increased successively over time which suggests that the fire gives prolonged effects on tree mortality. This shows that long-term inventories are important to do to get an overall picture on the effect on tree mortality.

     

    The second part of my study deals with Vändleberget, a nature reserve that was fenced 2005 after burning to protect particularly deciduous tree re-growth from browsers. Tree inventories and measurements were performed by placing plots both inside and outside the fenced area. Tree height and tree diversity showed a trend towards higher levels inside the fenced area, but the differences were not significant. Stem density, in total, is very high in the investigated area in Vändleberget and therefore I suggest selective logging to promote deciduous trees such as aspen (Populus tremula), ash (Fraxinus excelsior), oak (Quercus robur) and goat willow (Salix caprea). Spruce (Picea abies) and some trivial deciduous trees, especially birch (Betula spp.) can be removed. When the remaining trees are about four meters high I suggest that the fence can be taken down, as at that height the browsers can no longer harm the deciduous trees severely by eating the top of the trees or physically breaking the tree trunk. 

     

    To conclude, I found that conservation burning increases biodiversity on several levels such as number of species and morphological diversity. Fences can be used to reduce grazing which could promote tree diversity.      

  • 205.
    Hampton, Christopher
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Miljötoxikologi.
    Effects of early life exposure to flutamide on sexual development in Xenopus tropicalis2019Självständigt arbete på avancerad nivå (masterexamen), 20 poäng / 30 hpStudentuppsats (Examensarbete)
    Abstract [en]

    While endocrine disrupting chemicals have become a serious concern in human and environmental toxicology, many of the methods used for investigating developmental toxicity require long exposure periods, and thus can be technically challenging, labour intensive and expensive. For example, the current standard method, the Larval Amphibian Growth and Development Assay (LAGDA) has an exposure period of ³130 days. With the intent of developing a shorter assay for investigating amphibian developmental toxicity, the aim of this study was to characterise effects of the anti-androgenic model substance flutamide on reproductive development in the frog Xenopus tropicalis after a short 16-day post-metamorphosis exposure period using four dose groups: control (C), low (L), medium (M), and high (H) (0, 250, 500 and 1000 µg/L, nominal concentrations, n=58, 19, 39 and 36 respectively). Variations in body morphometry were used to compare C, L, M and H (for which there was no data available on sex ratios) and a random subsample of C (n=15) and H (n=15) individuals were analysed histologically for variation in germ cell maturity, gonadal cross sectional area, Müllerian Duct (MD) length and MD maturity. In addition to these endpoints, concentrations of the anti-Müllerian hormone (AMH), vitellogenin (VTG), oestradiol (E2) and testosterone (T) in the remainder of the body after dissection (normally discarded) for a subsample of C, M and H (N varying between 2 and 11 for AMH, VTG, E2 and T within the dose groups) were investigated with the objective of discovering whether these could be used as viable endpoints using commercially available ELISA kits. Due to random sampling there was an insufficient number of male H dose group individuals to allow for statistical analysis. In females, no significant differences in MD length, MD maturity and gonad size, were seen between the dose groups. No apparent differences in the proportion of mature germ cells in the testis were found, however females in the H dose group were found to have a significantly higher proportion of immature oocytes in the ovaries than C. The ELISA analysis was able to successfully detect AMH, VTG, E2 and T in all three dose groups. Some of the expected interrelationships between bodily AMH, VTG, E2 and T were observed in this study, whereas others were absent and others in direct opposition to prior research, suggesting this method shows promise but requires further study. While no conclusions cannot be drawn with regard to males from this study, effects attributable to flutamide can be detected in females during this dose period, and body homogenate ELISA shows promise for being a viable method but requires further research. 

    Publikationen är tillgänglig i fulltext från 2022-07-01 14:32
  • 206.
    Handin, Niklas
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Identification of new regulatory mechanisms that determine coagulation FXI plasma concentration2015Självständigt arbete på avancerad nivå (yrkesexamen), 20 poäng / 30 hpStudentuppsats (Examensarbete)
    Abstract [en]

    FXI is a protein in the coagulation cascade in humans proven to be involved in the propagation and stabilization of developing thrombi in previous studies. The regulatory mechanisms for FXI are not well understood. Therefore an investigation to find regulatory mechanisms for FXI was performed. A meta-analysis was conducted, consisting of six Genome-wide association studies in which the trait was FXI levels in plasma. Three genome wide significant loci were found that also were significant in a replication study, in which three cohorts not included in the discovery set were used. Functional annotation, pathway analysis and eQTL analysis of these three loci yielded three genes believed potentially responsible for the regulation of FXI. Two of these three genes were chosen for a microRNA binding prediction search. Several microRNAs were found, and one was analyzed with a luciferase reporter assay

  • 207.
    Hansson, Emma
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Physical and functional properties of chromatography media: a down-scale study2013Självständigt arbete på avancerad nivå (masterexamen), 20 poäng / 30 hpStudentuppsats (Examensarbete)
    Abstract [en]

    During down scale of column chromatography a phenomenon called wall effect appears.This supports the gel bed and gives it better flow properties. Using three different media infive different sized columns this effect was investigated regarding the physical andfunctional properties of the media. The conclusion of this study is that the effect appears incolumns below 26 mm in diameter and that the impact of the wall effect is larger the morerigid the used media is.

  • 208.
    Hansson, Jessica
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Skogsbrukets påverkan på skogslandskapet i Sverige: Vikten av artskydd och ökad hänsyn2017Självständigt arbete på avancerad nivå (masterexamen), 20 poäng / 30 hpStudentuppsats (Examensarbete)
    Abstract [sv]

    En stor andel av Sveriges hotade växt- och djurarter är beroende av skogen som livsmiljö, och har under en lång tid påverkats negativt av skogsbrukets framfart i skogslandskapet. Skogsbruksåtgärder såsom avverkning, gallring och röjning kan förstöra både livsmiljöer och påverka interaktionerna mellan populationer om miljöhänsynen är bristande, vilket kan hota den långsiktiga överlevnaden på platsen och därigenom även artens bevarandestatus. Artskyddsförordningen är det huvudsakliga regelverket i svensk lagstiftning som reglerar skyddet av växter och djur, och är en viktig del i arbetet för att upprätthålla en gynnsam bevarandestatus för arter. Syftet med mitt projekt är att analysera hur fem skogslevande nationellt hotade arter och deras livsmiljö påverkas av skogsbruket, samt hur en skogsbruksåtgärd kan genomföras på ett sådant sätt så att den inte bryter mot förbuden inom artskyddsförordningen och därmed hotar arternas bevarandestatus. Åtta fältbesök gjordes till skogsbestånd där arterna observerats, där den omgivande miljön och viktiga strukturer såsom mängd död ved, vegetationssammansättning och ljusinsläpp noterades. Specifika fallstudier för varje art och dess förekomstlokal kunde sedan konstrueras utefter den insamlade informationen för att besvara den aktuella frågeställningen. Ett hållbart skogsbruk i linje med artskyddsförordningen har framförallt visat sig innebära avsättande av större sammanhängande områden och tillämpning av hyggesfria metoder vid avverkning, men även ökad miljöhänsyn är en viktig faktor. Grunden till ett hållbart skogsbruk bygger på medvetenhet, vilket endast kan uppnås genom satsningar på utbildning inom branschen.

  • 209.
    Hansson, Malin
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Huss, Elisabeth
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Johansson, Annelie
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Petersson, Rikard
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Sundqvist, Henrik
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Widell, Lars
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Nya tillämpningar för utandningstest kopplade till Kibions diagnostikinstrument IRIS®2012Självständigt arbete på grundnivå (kandidatexamen), 10 poäng / 15 hpStudentuppsats (Examensarbete)
  • 210.
    Hansson, Malin
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Huss, Elisabeth
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Johansson, Annelie
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Petersson, Rikard
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Sundqvist, Henrik
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Widell, Lars
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Nya tillämpningar för utandningstest kopplade till Kibions diagnostikinstrument IRIS®2012Självständigt arbete på grundnivå (kandidatexamen), 10 poäng / 15 hpStudentuppsats (Examensarbete)
  • 211.
    Haughey, Caitlin
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Mesilaakso, Lauri
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Berner-Wik, Erik
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Östlund, Emma
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Ulfsparre, Jonatan
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Olin, Hampus
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Probes for ESBL: A Method for Production of Probe Targets in Antibiotic Resistant Genes2017Självständigt arbete på grundnivå (kandidatexamen), 10 poäng / 15 hpStudentuppsats (Examensarbete)
    Abstract [en]

    This project aimed to find a method for producing potential probe targets for identification of ESBL (Extended Spectrum Beta Lactamase) genes in bacteria. ESBLs are a type of enzymes responsible for antibiotic resistance in many bacteria. The result we developed was a semi-automated pipeline that utilises several Perl scripts to download gene sequences, identify sequence subgroups based on sequence similarity, find common target sequences among them and screen the target sequences against a background database. These target sequences should work with padlock probes and therefore had specific requirements regarding length and highest number of allowed mismatches. This report includes descriptions of the scripts and ideas for future improvements, as well as an ethical analysis about aspects relevant to research on antibiotic resistance.

  • 212.
    Hedén Gynnå, Arvid
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Induction kinetics of the lac operon: Studied by single molecule methods2014Självständigt arbete på avancerad nivå (yrkesexamen), 20 poäng / 30 hpStudentuppsats (Examensarbete)
    Abstract [en]

    The repression of the E. coli lac operon seems to be more efficient than the current theoretical model allows for. Specifically, it is more quiet than expected during the replication of the chromosome. I have induced cells during short periods and counted the number of protein products from the operon to determine if there is a delay in activation of transcription that could account for the discrepancy. The results are compatible with a delay of 10-20 s, but the delay could not be conclusively proven. Furthermore, it has been investigated if the mechanism behind the delay might be differential localization of the lac operon with and without induction. It is shown that the lac operon is more often located in the periphery of the cell and in the internucleoid region when induced. These might be regions where genes are higher expressed, giving a delay in expression after de-repression before the gene is transported there.

  • 213.
    Hegerl, Carla
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    The ecological effects of bushmeat hunting: comparing the mammal communities of two forests in the Udzungwa Mountains, Tanzania, with differing hunting pressures2014Självständigt arbete på avancerad nivå (masterexamen), 30 poäng / 45 hpStudentuppsats (Examensarbete)
  • 214.
    Hellner, Joakim
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Introducing quality assessment and efficient management of cellular thermal shift assay mass spectrometry data2017Självständigt arbete på avancerad nivå (yrkesexamen), 20 poäng / 30 hpStudentuppsats (Examensarbete)
    Abstract [en]

    Recent advances in molecular biology has led to the discovery of many new potential drugs. However, difficulties with in situ analysis of ligand binding prevents quick advancement in clinical trials, which stresses the need for better direct methods. A relatively new methodology, called Cellular Thermal Shift Assay (CETSA), allows for detection of ligand binding in a cells natural environment and can be used in combination with Mass Spectrometry (MS) for readout. With help from the Pelago Bioscience team, I developed a pipeline for processing of CETSA MS data and a web based system for viewing the results. The system, called CETSA Analytics, also evaluates the results relevance and helps its users to locate information efficiently. CETSA Analytics is currently being tested by Pelago Bioscience AB as a tool for experimental data distribution. 

  • 215.
    Helmersson, Erik
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Molecular identification of mosquito species: Evaluation of a rapid DNA extraction method together with DNA barcoding as a tool for identification of species2013Självständigt arbete på grundnivå (kandidatexamen), 10 poäng / 15 hpStudentuppsats (Examensarbete)
    Abstract [sv]

    När en stickmyggsart skall artbestämmas är den vanligaste metoden att använda morfologiska nycklar. I princip görs det här efter den taxonomi som Carl von Linne utvecklade på 1700-talet. Men sedan Watson och Crick presenterade sin DNA modell 1953 så har dock en ny era av molykylärt baserade metoder revolutionerat taxonomin. Förändringen består egentligen inte i hur vi klassificerar och använder taxonomin utan mer hur vi ser på den biologiska mångfalden. Morfologiska och ekologiska studier, samt studier av arters beteende, är fortfarande viktiga och komplementerar den molekylära informationen från ett genom eller från en enstaka gen. DNA barcoding är en av de lovande nya molekylära metoderna för artbestämning. Ett litet segment av en gen, på ungefär 400-1000 baspar (bp), undersöks med hjälp av polymeras-kedjereaktion (PCR) och sekvensering. Likt streckkoder i livsmedelsbutiken ger metoden ett unikt ID för varje art. Den här studien visar hur en snabb DNA-extraktionsmetod kan kombineras med DNA barcoding, för att ge en 658-bp lång DNA-sekvens, från den mitokondriella genen cytokrom c oxidas subunit 1 (COI) från olika arter av myggfamiljen Culicidae. I undersökningen ingick 15 mellankroppar eller vingar från individuella stickmyggor och av dessa kunde 11 olika barcode sekvenser utläsas. Sex av dessa stämde överrens med redan publicerade COI-sekvenser och kunde bestämmas till artnivå, varav en av sekvenserna kommer från den nyligen i Sverige funna morfologiskt artbestämda Aedes (Ochlerotatus) nigrinus. Stickmyggorna i detta arbete insamlades av privatpersoner på olika ställen i Sverige under sommaren 2012 i det nationella mygginsamlingsprojektet ”Myggjakten”. Dessa artbestämdes morfologiskt av personal på Statens veterinärmedicinska anstalt (SVA) innan de artbestämdes molekylärt. Det här arbetet belyser även vikten av att bygga upp ett referensbibliotek av barcode sekvenser för att DNA-barcoding ska kunna bli ett effektivt diagnostiskt verktyg vid studier av vektorburna zoonoser. Nationella projekt som Myggjakten kan vara mycket användbara för insamling av sådana data.

  • 216.
    Henriksson, Olle
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Växtekologi och evolution.
    Biotic interactions along a latitudinal gradient: Field study of the perennial herb Primula farinosa2019Självständigt arbete på avancerad nivå (masterexamen), 30 poäng / 45 hpStudentuppsats (Examensarbete)
    Abstract [en]

    Because climatic factors may differentially limit the distribution of plants, herbivores, and pollinators, the intensity of biotic interactions is expected to vary geographically. To determine if the intensity of biotic interactions varied along a latitudinal gradient or with population size in the perennial herb Primula farinosa, 31 populations were studied across the Swedish range of the species from latitude 56°N to 63°N. Populations were visited during flowering and fruit maturation. Intensities of grazing (proportion of plants grazed), pollination (proportion of flowers initiating fruit development), seed predation (proportion of initiated fruits consumed by seed predators), and smut infection (proportion of initiated fruit infected by smut) were recorded as well as flower production and reproductive output (number of intact mature fruits). While all tested variables varied between populations, the intensities of biotic interactions were not significantly related to latitude or population size. Number of flowers produced per plant decreased with increasing latitude, whereas the proportion of flowers developing into a mature fruit tended to be higher at the ends than in the central part of the latitudinal gradient. Grazing damage was higher and fruit set (proportion of flowers developing into intact mature fruits) lower at sites exposed to domestic grazers than at sites without domestic grazers. The results suggest that while abiotic factors limit the number of flowers a plant produce and resources decrease with increasing latitude, antagonistic biotic interactions supress seed production mainly in the central part of the geographic range in Sweden. This might be explained by edge populations escaping antagonists mainly located in the centre of the species distribution.

  • 217.
    Herbertsson, Annie
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Lundgren, Julia
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Niemi, Matilda
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Rosenius, Jennifer
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Sixtensson, Kajsa
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Westberg, Linnea
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Kartläggning av den monoklonala antikroppsmarknaden: En jämförande marknadsanalys av producenter som erbjuder utveckling av kundanpassade monoklonala antikroppar2016Självständigt arbete på grundnivå (kandidatexamen), 10 poäng / 15 hpStudentuppsats (Examensarbete)
    Abstract [sv]

    Det här kandidatarbetet baseras på en beställning från Uppsalaföretaget Olink Proteomics AB. Olink Proteomics AB önskar få tillgång till specifika monoklonala antikroppar, från ett externt företag, att använda i nya produkter. Projektgruppen har utvärderat vilka leverantörer som är de bästa strategiska valen med avseende på ledtider, kostnader, djurhållning, servicenivå, reningsmetoder, mängd, antal kloner, kvalitetskontroller och tilläggstjänster.

    Utvärderingen av företag som kan producera kundanpassade monoklonala antikroppar har skett genom informationssökning och direktkontakt med företag. Projektgruppen kom fram till att företagen Absea Biotechnology Ltd, Bio-Rad AbD Serotec Ltd, Davids Biotechnologie GmbH, GenScript USA Inc samt Innovagen AB är de fem mest lovande kandidaterna utifrån de 30 granskade. Av kandidaterna rekommenderas företaget Innovagen AB i första hand.

  • 218.
    Herman, Stephanie
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Automatic detection of protein degradation markers in mass spectrometry imaging2016Självständigt arbete på avancerad nivå (yrkesexamen), 20 poäng / 30 hpStudentuppsats (Examensarbete)
    Abstract [en]

    Today we are collecting a large amount of tissue samples to store for future studies of different health conditions, in hopes that the focus in health care will shift from treatments to early detection and prevention, by the use of biomarkers. To make sure that the storing of tissue is done in a reliable way, where the molecular profile of the samples are preserved, we first need to characterise how these changes occur. In this thesis, data from mice brains were collected using MALDI imaging mass spectrometry (IMS) and an analysis pipeline for robust MALDI IMS data handling and evaluation was implemented. The finished pipeline contains two reduction algorithms, catching images with interesting intensity features, while taking the spatial information into account, along with a robust similarity measurement, for measuring the degree of co-localisation. It also includes a clustering algorithm built upon the similarity measurement and an amino acid mass comparer, iteratively generating combinations of amino acids for further mass comparisons with mass differences between cluster members.

    Availability: The source code is available at https://github.com/stephanieherman/thesis

  • 219.
    Hilmarsson, Torfi Geir
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Photodegradation of the neurotoxicant methylmercury (MeHg) in Swedish lakes2016Självständigt arbete på avancerad nivå (masterexamen), 30 poäng / 45 hpStudentuppsats (Examensarbete)
  • 220.
    Hilow, Zeinalabedin
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    The regulatory effect of CsrA on cstA, glgCAP and flhDC in an RNase P ts mutant Escherichia coli2017Självständigt arbete på grundnivå (kandidatexamen), 10 poäng / 15 hpStudentuppsats (Examensarbete)
    Abstract [en]

    CsrA is a global post-transcriptional regulatory protein that has a great impact on many physiological pathways in a cell. It regulates central carbon metabolism, motility and biofilm formation as well as virulence, pathogenesis, quorum sensing and the oxidative stress response. However, CsrA is in turn also regulated by CsrB and CsrC sRNAs, among other factors. In this study, we explore its regulatory effect on three different genes/operons, cstA, glgCAP and flhDC. We performed beta-galactosidase assays on wild type (wt) and RNase P temperature sensitive (ts) cells to determine the dependence on RNaseP for the CsrA, CsrB and CsrC regulatory cascade on these three genes. Our results showed a clear decrease in cstA and glgCAP activity during CsrA activation, suggesting a regulatory cascade in which inhibition of RNase P leads to an inactivation of CsrB and CsrC. This in turn leads to an activation of CsrA and an inhibition of cstA and glgCAP. The effect on flhDC, however, was not as clear and needs further investigation.

  • 221.
    Hirvonen, M. Karoliina
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Assay development for in situ detection of autophagy-related protein-protein interactions for characterization of colorectal cancer2015Självständigt arbete på avancerad nivå (masterexamen), 30 poäng / 45 hpStudentuppsats (Examensarbete)
    Abstract [en]

    Every year, more than a million people are diagnosed with colorectal cancer (CRC) that develops in the large intestine. It is one of the most studied cancers in the world but still more knowledge about how this cancer develops and acts is needed in order to use more effective ways to treat CRC. Autophagy is a vital mechanism in cells that is also suggested to maintain cancer cell survival. In normal cells, it plays an important role by removing damaged cells and organelles as well as eliminating pathogens. Under metabolic stress this mechanism is induced to provide enough nutrients and energy for the cell to survive. Cancer cells are exposed to greater environmental stress than normal cells and therefore, cancer cells exhibit higher levels of autophagy suggesting it to be a crucial mechanism for their survival. Gaining a deeper understanding of this essential mechanism and its activation might provide new insights and improved treatments for the fight against colorectal cancer. In situ Proximity Ligation Assay (PLA) is a protein detection method that enables sensitive and specific detection of proteins and protein-protein interactions (PPIs) in cell lines and tissue samples. The method uses simultaneous recognition of two independent antigens on a protein or protein complex together with a rolling circle amplification (RCA) to form a rolling circle product (RCP) on top of the target. By using fluorescent oligonucleotides, RCP can be visualized and is seen as a bright spot that enables sensitive detection of the target at single-molecule resolution. The aim of this study was to develop assays to detect endogenous molecular events known to be biomarkers of autophagy in situ in order to study autophagy mechanism in CRC patient samples. We focused our research on two PPIs that were known to interact when autophagy is induced. The first investigated interaction was between microtubule-associated protein 1A/1B- light chain 3 (LC3) and sequestome-1 (SQSTM1), an interaction that occurs during autophagy initiation. The second interaction was between B-cell lymphoma 2 (Bcl-2) and Bcl-2/adenovirus E1B 19-kDa interacting protein 3 (BNIP3) that takes place during hypoxia-induced autophagy. To study whether these PPIs can be used as a detection method to monitor autophagy, we used a well- established cell model based on serum starvation and CoCl2 - an hypoxic mimetic- treatment of the intestinal cancer cell line Caco-2 in comparison to normal culture condition. According to isPLA quantification, detection of both PPIs was distinctly higher in treated cells compared to untreated cells giving promising results and suggesting that they can be potentially used as suitable assays to monitor these biomarkers of autophagy. For development of an improved protein detection method that enables the study of several PPIs simultaneously in a tissue sample (In situ Multiplexing), we conjugated directly a short oligonucleotide strand to the primary antibodies. These formed proximity probes could later be used in in situ for multiplexing. 

  • 222.
    Hjälte, Anna
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Georgsson, Elin
    Olausson, Linus
    Fichtel, Joakim
    Törnblom, Viktor
    Gamla lösningar på nya problem: Förslag på lösningsmedia för Matrix M™ adjuvans2012Självständigt arbete på grundnivå (kandidatexamen), 10 poäng / 15 hpStudentuppsats (Examensarbete)
  • 223.
    Hoffman, Ellinor
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Forced copulation hos gräsänder (Anas platyrhynchos) i Almedalen, Visby2014Självständigt arbete på grundnivå (kandidatexamen), 10 poäng / 15 hpStudentuppsats (Examensarbete)
    Abstract [en]

    In mallards (Anas platyrhynchos) a behaviour called forced copulation can be observed. Forced copulation means that one or several males chase a female, grasp her, mount her and tries to mate with her while she is putting up resistance. The study took place in the park area of Almedalen in Visby and investigated if there were any differences in frequencies regarding forced copulation on land and in water, and if there were any differences in frequencies regarding how often a male defended his mate from one or several males who were trying to subject her to forced copulation. The study also investigated if unpaired females were more often subjected to forced copulation than paired females. The results of the study showed no statistical significant differences in any of these areas.

  • 224.
    Hong, Marcus
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Screening for antibiotic combinationsagainst carbapenem-resistant Gram-negative bacteria2018Självständigt arbete på avancerad nivå (yrkesexamen), 20 poäng / 30 hpStudentuppsats (Examensarbete)
    Abstract [en]

    Carbapenem-resistant Enterobacteriaceae is a growing problem. Not only are they resistant against carbapenems but the genes that encode for carbapenemase production, are often situated amongst other resistance genes making these bacteria resistant to multiple antibiotic classes. This project aimed to screen for new antibiotic combinations with synergistic effects that could be used to combat carbapenem-resistant Enterobacteriaceae. Carbapenem-resistant E. coli and K. pneumonia was tested and the oCelloScope instrument was also evaluated for these strains combined with the antibiotics used. Four antibiotics, aztreonam, meropenem, minocycline and rifampicin were combined with polymyxin B against E. coli. Aztreonam and fosfomycin were combined with polymyxin B against K. pneumoniae. Screening experiments included time-kill experiments, time-lapse microscopy with the oCelloScope instrument and a dot test which combined the oCelloScope with viable counts at 24h. Results showed minocycline combined with polymyxin B to be the best combination with synergistic effects against 9 out of 20 E. coli strains. This was closely followed by rifampicin combined with polymyxin B with synergistic effects against 7 out of 20 E. coli. Meropenem in combination with polymyxin B resulted in synergistic effects against only 1 out of 20 E. coli. The oCelloScope instrument could not detect synergistic effects with aztreonam due to the presence of dead filamented cells, which the instrument detected as a relatively high concentration of cells, but could be determined with the dot test method showing synergistic effects against 2 out of 20 E. coli with this combination.

  • 225.
    Hulsart, Signe Gry
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Influence of Calcium Phosphate on Osteogenes is in Hydrogel with Bone Morphogenetic Protein-22010Självständigt arbete på avancerad nivå (magisterexamen), 20 poäng / 30 hpStudentuppsats (Examensarbete)
  • 226.
    Huss, Elisabeth
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Malin, Eriksson
    Sundqvist, Henrik
    IMAC - a review: The Establishment of a Small Challenger Company ina Segmented High-Technology Life Science Market2016Självständigt arbete på avancerad nivå (yrkesexamen), 20 poäng / 30 hpStudentuppsats (Examensarbete)
    Abstract [en]

    This degree project report consists of an individual study, IMAC – a review, and a study made by a

    total of three students at the Uppsala School of Entrepreneurship, The Establishment of a Small

    Challenger Company in a Segmented High-Technology Life Science Market.

    The review is about immobilized metal ion affinity chromatography (IMAC) and describes this popular

    protein purification technique which has constantly evolved since its first discovery in 1975. It is also

    indeed a technique used by the case company under study in the main report. The mechanism when

    using Histidine-tagged proteins and Nickel-nitrilotriacetate (Ni-NTA) agarose is highlighted.

    The main report aims to identify the challenges and opportunities of a small challenger company in a

    rigid and conservative high technology life science market. Qualitative and quantitative data was

    collected through interviews, an online survey and conjoint analysis which were used as market research

    tools. The data showed that marketing channels should be scientific journals, seminars and conferences

    and that price and quality are important factors for customers in the high-technology life science market.

  • 227.
    Håfström, Therese
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Genome closure and bioinformatic analysis of the parallel sequenced bacterium Brachyspira intermedia PWS/AT2011Självständigt arbete på avancerad nivå (yrkesexamen), 20 poäng / 30 hpStudentuppsats (Examensarbete)
    Abstract [en]

    Brachyspira species are bacteria that colonize the intestines of some mammalian and avian species with different degrees of pathogenicity. Brachyspira intermedia is a mild pig and bird pathogen with an unknown genomic sequence. In this project, we completed the genome of Brachyspira intermedia PWS/AT and did a comparative genomic analysis between B. intermedia PWS/AT and the already completed genomes of B. hyodysenteriae WA1, B. murdochii 56-150T and B. pilosicoli 95/1000. A table containing 15 classes of unique and shared genes was developed and analyzed in order to gain a better understanding of species-specific traits and clues behind the different degree of pathogenicity. Our result shows that genes are overall poorly annotated and further studies are of great importance for understanding different and shared properties. The largest number of unique features was found in B. intermedia and B. murdochii. B. hyodysenteriae and B. pilosicoli has most likely developed independently towards different biological niches and B. pilosicoli has undergone a major reductive evolution. One plasmid and six prophages were found in B. intermedia, where two of the phages appear to be capable of horizontal gene transfer. Further genome sequencing of more strains will probably increase the understanding of species-specific traits even more.

  • 228.
    Ida, Salenby
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Develop an automated staining protocol for ProxHCR2017Självständigt arbete på avancerad nivå (yrkesexamen), 20 poäng / 30 hpStudentuppsats (Examensarbete)
    Abstract [en]

    Proximity hybridization chain reaction (ProxHCR) is a novel in situ hybridization technique capable of detecting protein-protein interactions and post-translational modifications, having the potential to be a diagnostic and prognostic tool in clinical practice. As molecular pathology is becoming an integrated part of clinical evaluations, most staining procedures done today are automated. Compared to other similar methods ProxHCR is suitable for automated staining. The aim of this project was therefore to develop an automated staining protocol for ProxHCR, which could be used in an instrument normally performing immunohistochemistry (IHC). During the developing process, several parameters in the current protocol was tested and adjusted to suit a chosen instrument. The result from this project was an automated ProxHCR protocol which was run in an IHC instrument. A small study was also performed to find suitable biomarkers for ProxHCR, indicating the systems’ capabilities. The conclusion from this project was that ProxHCR can be run on an existing IHC instrument and that the method can be used to study several relevant biomarkers.

  • 229.
    Inda Díaz, Juan Salvador
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Cross Conformal Prediction hyperparameter tuning using Apache Spark2018Självständigt arbete på avancerad nivå (masterexamen), 30 poäng / 45 hpStudentuppsats (Examensarbete)
    Abstract [en]

    Molecular signature fingerprints together with Support Vector Machines and Cross Conformal Prediction were used to train binary classification models for four different unbalanced and highly unbalanced Quantitative High-Throughput Screening. The validity of the predictor models was evaluated using the miscalibration rate, while the efficiency of the predictors was measured with fuzzines, sumP, region size, excess and the proportion of correct singletons predicted. By doing a grid search on the molecular signature height start and height end, the cost parameter in linear Support Vector Machine, and the number of folds in Cross Conformal Prediction, it was confirmed that the combination of height start 0 or 1, with height end 2 or 3 is the most adequate to build the molecular signature fingerprints to be used as input for classification using linear Support Vector Machine. Having fixed the heights to 1 and 3, the cost parameter had little influence on the performance of the predictors but a cost of 1.0 returned better predictors. It was possible to build valid predictors for a single dataset. For the other three datasets the predictors did not result valid for the minority class. It is believed that the validity of the predictors depends on a minimum number of molecules in each fold of the training set in Cross Conformal Prediction. A recommendation of the number of folds is between 20 and 30 provided that each class of molecule is represented by at least 100 observations.

  • 230.
    Inganäs, Hanna
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Identifying exosomal biomarkers to predict cardiac events2011Självständigt arbete på avancerad nivå (masterexamen), 20 poäng / 30 hpStudentuppsats (Examensarbete)
    Abstract [en]

    Every year, millions of people in the world die from cardiovascular diseases. Most of thesevictims show no symptoms of disease for decades as the disease silently progresses, but maysuddenly become afflicted with a myocardial infarction or stroke. At present there is aregrettable lack of important disease markers that could help identify patients at risk withregard to secondary cardiovascular events. Biomarkers for this would of course be extremelyvaluable. If such markers could distinguish between patients with different responses totreatment and overall outcome, that would be of major added value as this potentially couldpave the way for differentiated preventive measures. In this study we show that specificproteins isolated from plasma-derived exosomes are indeed associated with an increased riskfor secondary cardiac events.

  • 231.
    Isabell, Nilsson
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Mitochondrial DNA as a danger-associated molecular pattern in Myalgic encephalitis and endometrial cancer2018Självständigt arbete på avancerad nivå (masterexamen), 30 poäng / 45 hpStudentuppsats (Examensarbete)
    Abstract [en]

    Mitochondria are complex organelles, which are involved in various important metabolic pathways. Due to their proteobacterial evolutionary origin, the mitochondria DNA resemble unmethylated microbial CpG motifs, which possess the ability to interact with pathogen associated DNA sensors, such as TLR9 and activate the NLRP3 inflammasome, inducing pro- inflammatory cytokines. Myalgic encephalitis (ME), also called chronic fatigue syndrome (CFS) is a disease of unknown ethology. A dysfunctional energy production might be a piece of the puzzle, to explain the fatigue. By examine the presence of anti-mitochondrial antibodies (AMA) and anti-cardiolipin antibodies (ACA), as well as evaluating mitochondrial DNA as a danger-associated molecular pattern (DAMP) we aim to provide an important piece of knowledge to further understand the disease. ME patients are at risk of developing B-cell lymphoma. For comparison we have analyzed mtDNA levels in endometrial cancer, which is the most common malignancy of the female genital tract. By measuring both mtDNA and nuclear DNA, our aim was to compare two surgical methods: traditional open abdominal surgery with robot assisted laparoscopic surgery for DAMP-signaling, that is tissue damage and immune activation. We found that neither AMA nor ACA could be detected in ME plasma samples, and the level of circulatory mtDNA did not differ from healthy controls. However, mtDNA levels in cancer patients was significantly increased compared to healthy controls (p<0.0001). No difference in tissue damage and immune activation, as judged from mtDNA and nDNA levels could be identified between the two surgical methods. We conclude that ME patients patient mitochondrial dysfunction cannot be explained by abnormal antibodies or mtDNA. In contrast cancer patients have significantly raised levels of the mtDNA DAMP in circulation.

    Publikationen är tillgänglig i fulltext från 2020-06-01 15:46
  • 232.
    Isak, Sylvin
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Increasing bioinformatics in third world countries: Studies of S.digitata and P.Polymyxa to further bioinformatics in east Africa2016Självständigt arbete på avancerad nivå (masterexamen), 20 poäng / 30 hpStudentuppsats (Examensarbete)
    Abstract [en]

    Despite an increase of biotechnical studies in third world countries, the bioinformatical side is largely lacking. In this paper we attempt to further the bioinformatical capabilities of east Af-rica. The project consisted of two teaching segments for east African doctorates, one as part of an academic workshop at ILRI, Kenya, and one in a small class at SLU, Sweden. The project also included the generation of two simple to use bioinformatical pipelines with the explicit aim to be reused by novice bioinformaticians from the very same region. The viability of the piplines were verified by generating transcriptional expression level differences for Paeni-bacillus polymyxa strain A26 and whole genome annotations for Setaria digitata. Both pipe-lines may have some merit for the collaborative effort between ILRI and SLU to annotate Eleusine coracana, a draught resilient crop, the annotation of which may save lives. The teaching material, source code for the pipelines and overall teaching impression have been included in this paper.

  • 233.
    Isaksson, Mikael
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Occurence of organic micropollutants (OMPs) in Lake Mälaren using zebra mussels (Dreissena polymorpha) and passive water samplers2019Självständigt arbete på avancerad nivå (masterexamen), 20 poäng / 30 hpStudentuppsats (Examensarbete)
    Publikationen är tillgänglig i fulltext från 2020-03-19 11:17
  • 234.
    Isaksson, Simon
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Biogas production at high ammonia levels: The importance of temperature and trace element supplementation on microbial communities2018Självständigt arbete på avancerad nivå (yrkesexamen), 20 poäng / 30 hpStudentuppsats (Examensarbete)
  • 235.
    Ishak, Helena
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Developing a ChIP-seq pipeline that analyzes the human genome and its repetitive sequences2017Självständigt arbete på avancerad nivå (masterexamen), 30 poäng / 45 hpStudentuppsats (Examensarbete)
  • 236.
    Ivermark, Katarina
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Attacking cancer biomarker clusters from all sides: - bispecific, bivalent and polyspecific affinity proteins towards HER family receptors2016Självständigt arbete på avancerad nivå (yrkesexamen), 20 poäng / 30 hpStudentuppsats (Examensarbete)
  • 237.
    Ivermark, Katarina
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Johansson, Caroline
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Karlsson, Caroline
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Lövgren, Jessica
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Yuen, Pikkei
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Ånäs, Sofia
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Optimering av cellodlingsmedia genom kombinering av designade stamlösningar: med experimentell design och multivariat dataanalys2013Självständigt arbete på grundnivå (kandidatexamen), 10 poäng / 15 hpStudentuppsats (Examensarbete)
    Abstract [sv]

    Syftet med projektet är att ta fram en metod för optimering av cellodlingsmedia som kan minska den tid och de resurser som dagens metoder kräver. Fem stamlösningar med adekvata komponenter designas och kombineras med olika flödeshastigheter till ett medium. Kombinationerna testas med experimentell design och analyseras med multivariat dataanalys för att få fram optimerade cellmedia.

    Odlingsmetoden som de fem stamlösningarna anpassas till är fed-batch, ett system där en av lösningarna är en baslösning och de resterande fyra designas till feedlösningar. De senare tillsätts i olika hastigheter till baslösningen anpassat efter cellernas näringsbehov. Strategin som har lagts upp för att designa stamlösningarna bygger på förhållandet mellan komponenternas förbrukningshastighet i de olika tillväxtfaserna. Under odlingen befinner sig cellerna i olika tillväxtfaser, i den exponentiella fasen ökar celldensiteten och i den stationära fasen sker större delen av produktionen av till exempel specifika antikroppar. Komponenterna i baslösningen förbrukas inte, eller i så liten mängd att de inte behöver tillsättas under odlingen, till skillnad från komponenterna i feedlösningarna som behöver tillsättas för att inte utarmas. I den exponentiella celltillväxtfasen, är behovet av de olika feedlösningarna flera gånger större än i den efterföljande stationära fasen. När önskad celldensitet är uppnådd så minskas flödeshastigheten från feedlösningarna och cellerna går in i stationärfas för att ge maximal produktion av önskad produkt.

    Projektet är uppbyggt av fyra delar: En litteraturstudie av nuvarande metoder för mediumutveckling, en beskrivning av framtagna stamlösningar, optimering av flödeshastigheten med experimentell design och multivariat dataanalys samt ett laborativt arbetsflöde av medias tillverkningsprocess.

  • 238.
    Jamal, Sabri
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Stool Detection and Classification in Colorectal Cancer2016Självständigt arbete på avancerad nivå (yrkesexamen), 20 poäng / 30 hpStudentuppsats (Examensarbete)
    Abstract [en]

    This project has been dedicated to the field of medical image analysis concerning the issue of colorectal cancer. Cancers can be evolved in almost any part of the body and is therefore a disease that impacts the whole world. Colorectal cancer is just one of such cancer types and has been coined as one of the more frequent cancer types encountered. Colonoscopy is the accepted screening method for identifying elements known as polyps. Polyps are perceived as swollen tissue found in the colon. Before the search for the polyps begins, an assessment of how clean the bowel is first made to ensure it is safe to identify the above-mentioned elements. This thesis has been focused on detection and classification in order to calculate the percentage of each stool type present in the colon. To address this, k-means clustering was implemented using features such as texture and color to classify the different stool types. Firstly the images were preprocessed, the preprocessing was followed by color segmentation and finally the images were classified. Once the classification of each pixel had been done the classified pixels were assigned a class label. Each label was connected to color and finally a visual representation of the classified image was presented through repainting the entire image. The results show that in a perfect segmentation of the colon the classifier performs well. While in the case of a partial segmentation the frequency of misclassifications increases. 

  • 239.
    Jansson, Linnéa
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Johnson, Gustav
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Wallskog, Amanda
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Svalberg, Linn
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Svärd, Karl
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Engström Kindmark, Hedvig
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Dost, Maryam
    Utvärdering av marknad och analysmetoder för snabbtest av antibiotikaresistens för polymikrobiella blodprover: En studie för utveckling av icke-invasiva optiska metoder och automatisering med maskininlärning2019Självständigt arbete på grundnivå (kandidatexamen), 10 poäng / 15 hpStudentuppsats (Examensarbete)
    Abstract [en]

    Gradientech AB is a company that develops a new ultra-rapid system for antibiotic susceptibility testing and their product will hopefully be used in health care for more efficient diagnosis of sepsis. Today the product has difficulties with the analysis of polymicrobial tests. For our project, the task is therefore to examine the market and the demand for the ability to detect polymicrobial infections. Our project is meant to provide ideas for improvements on their current method for the feasibility to detect several types of bacteria in the same test.

    Through literature studies, we have received an overview of how optical methods using image analysis can work and how they could be implemented in Gradientech's product. Image analysis can make the identification of bacteria possible. Interesting objects in the image can be distinguished from each other with filters that handle, for example, size, shape and light intensity. A potential improvement in the classification of bacteria by optical methods may be to test several different angles and wavelengths. This is to get more training data for machine learning and thus more accurately detect and analyze samples.

    The results from literature studies and interviews with clinicians, a microbiologist, and professor in image analysis have led to a conclusion that techniques that contribute to a decrease of antimicrobial resistance will be crucial for the future. In Sweden, the development of resistant bacteria is pretty low, but in many other parts of the world, there is a different reality. The product’s greatest potential will probably be in countries with a high incidence of resistant bacteria and with educated personnel available to use the product. Ultra-rapid systems for AST can contribute to saving lives by making sure that the right type of antibiotics is given directly. Detection and identification of polymicrobial samples in sepsis are also relevant, but it will not contribute to reduced antibiotic use since the patient's health will always be prioritized as of now. Finally, we reached the conclusion that identification of polymicrobial tests is not a necessary feature for the success of the product. This is above all due to the mass spectrometry method MALDI-TOF, a technique that is already well-established in health care systems. It can quickly and cheaply identify bacteria in clinical samples.

  • 240.
    Janzon, Rebecka
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Undervisning om hållbar utveckling i gymnasieskolan: En studie ur lärarperspektiv2012Självständigt arbete på avancerad nivå (yrkesexamen), 10 poäng / 15 hpStudentuppsats (Examensarbete)
    Abstract [sv]

    De senaste åren har internationella dokument efterfrågat förtydliganden gällande undervisning om hållbar utveckling. Detta är något som svensk regering och Skolverket tagit till sig och i samband med gymnasiereformen 2011 presenterades nya läro- och ämnesplaner med ett tydligare uppdrag gällande undervisning om hållbar utveckling, men bara i vissa ämnen. Däremot preciseras det inte hur och i vilken omfattning undervisningen ska bedrivas vilket medför svårigheter för lärare att veta hur de ska förhålla sig till undervisning om hållbar utveckling. Syftet med föreliggande studie är att belysa några gymnasielärares attityder gällande undervisning om hållbar utveckling, exempelvis vilka lärarkategorier som anser denna undervisning om hållbar utveckling mest relevant samt skildra några lärares önskan av fortbildning inom ämnet. Jag har genomfört en enkätstudie som till viss del ämnar jämföra resultaten med Waxegårds fem år gamla studie, detta för att se hur lärarnas attityder ändrats i frågor gällande undervisning om hållbar utveckling.Min studie visar att 32 % av lärarna aldrig undervisar om hållbar utveckling, jämförande siffra i Waxegårds studie är 37 %, med andra ord har ingen markant ökning av undervisning om hållbar utveckling skett de senaste fem åren. Lärare i samhällsvetenskapliga ämnen är den grupp som både finner det mest relevant och i störst utsträckning undervisar om hållbar utveckling. 62 % av lärarna i min studie upplever att de har tillräckliga kunskaper för att undervisa om hållbar utveckling, jämförande siffra i Waxegårds studie är 37 %. Detta tyder på att kunskapen om undervisning om hållbar utveckling vidgats de senaste fem åren. Min studie visar att lärare önskar fortbildning om hållbar utveckling i samma omfattning som för fem år sedan, samtidigt som andelen lärare som fått fortbildning ökat i omfattning de senaste fem åren, från 25 % till 36 %. Möjlig förklaring kan vara den internationella FN-satsningen om undervisning för hållbar utveckling.

  • 241.
    JIN, TUO
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Dietary effects on late-life mortality rates of male and female Drosophila melanogaster2012Självständigt arbete på avancerad nivå (masterexamen), 30 poäng / 45 hpStudentuppsats (Examensarbete)
  • 242.
    Johansson, Alina
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Molecular mechanisms behind TRIM28expression2015Självständigt arbete på avancerad nivå (masterexamen), 20 poäng / 30 hpStudentuppsats (Examensarbete)
  • 243.
    Johansson, Andreas
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Effects of beaver dams on benthic macroinvertebrates2014Självständigt arbete på avancerad nivå (masterexamen), 30 poäng / 45 hpStudentuppsats (Examensarbete)
    Abstract [en]

    In the 1870's the beaver (Castor fiber), population in Sweden had been exterminated. Thebeaver was reintroduced to Sweden from the Norwegian population between 1922 and 1939.Today the population has recovered and it is estimated that the population of C. fiber in all ofEurope today ranges around 639,000 individuals. The main aim with this study was toinvestigate if there was any difference in species diversity between sites located upstream anddownstream of beaver ponds. I found no significant difference in species diversity betweenthese sites and the geographical location of the streams did not affect the species diversity.This means that in future studies it is possible to consider all streams to be replicates despiteof geographical location. The pond age and size did on the other hand affect the speciesdiversity. Young ponds had a significantly higher diversity compared to medium-aged ponds.Small ponds had a significantly higher diversity compared to medium-sized and large ponds.The upstream and downstream reaches did not differ in terms of CPOM amount but somewater chemistry variables did differ between them. For the functional feeding groups I onlyfound a difference between the sites for predators, which were more abundant downstream ofthe ponds.

  • 244.
    Johansson, Annelie
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Identifying gene regulatory interactions using functional genomics data2014Självständigt arbete på avancerad nivå (yrkesexamen), 20 poäng / 30 hpStudentuppsats (Examensarbete)
    Abstract [en]

    Previously studies used correlation of DNase I hypersensitivity sites sequencing (DNase-seq) experiments to predict interactions between enhancers and its target promoter gene. We investigate the correlation methods Pearson’s correlation and Mutual Information, using DNase-seq data for 100 cell-types in regions on chromosome one. To assess the performances, we compared our results of correlation scores to Hi-C data from Jin et al. 2013. We showed that the performances are low when comparing it to the Hi-C data, and there is a need of improved correlation metrics. We also demonstrate that the use of Hi-C data as a gold standard is limited, because of its low resolution, and we suggest using another gold standard in further studies.

  • 245.
    Johansson, Annelie
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Sundqvist, Henrik
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Hansson, Malin
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Widell, Lars
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Huss, Elisabeth
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Petersson, Rikard
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Nya tillämpningar för utandningstest kopplade till Kibions diagnostikinstrument IRIS ®2012Självständigt arbete på grundnivå (kandidatexamen), 10 poäng / 15 hpStudentuppsats (Examensarbete)
  • 246.
    Johansson, Carolin
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Origin of the Egyptian Domestic Cat2012Självständigt arbete på avancerad nivå (yrkesexamen), 20 poäng / 30 hpStudentuppsats (Examensarbete)
    Abstract [en]

    This study presents mitochondrial genome sequences from 22 Egyptian house cats with the aim of resolving the uncertain origin of the contemporary world-wide population of Domestic cats. Together with data from earlier studies it has been possible to confirm some of the previously suggested haplotype identifications and phylogeny of the Domestic cat lineage. Moreover, by applying a molecular clock, it is proposed that the Domestic cat lineage has experienced several expansions representing domestication and/or breeding in pre-historical and historical times, seemingly in concordance with theories of a domestication origin in the Neolithic Middle East and in Pharaonic Egypt. In addition, the present study also demonstrates the possibility of retrieving long polynucleotide sequences from hair shafts and a time-efficient way to amplify a complete feline mitochondrial genome.

  • 247.
    Johansson, Caroline
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Genome-wide association study of drug-induced angioedema2019Självständigt arbete på avancerad nivå (yrkesexamen), 20 poäng / 30 hpStudentuppsats (Examensarbete)
  • 248.
    Johansson, Fredrik
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Microscale measurement of kinetic binding properties of monoclonal antibodies in solution using Gyrolab2011Självständigt arbete på avancerad nivå (magisterexamen), 20 poäng / 30 hpStudentuppsats (Examensarbete)
    Abstract [en]

    The number of monoclonal antibodies approved for therapeutic use has increased rapidlyover the last decade. As a consequence, precise and robust kinetic characterization techniquesare crucial in order to select the best suitable candidates. A kinetic characterization methodwas developed in Gyrolab with automated sample transfers. The characterization wasperformed in solution in a mixing CD, containing an integrated nanoliter mixing chamberwith affinity binding columns. Association rate constants were determined for four anti-TSHantibodies with values ranging from 3x105 M-1s-1 to 10x105 M-1s-1. The antibodies wereranked according to kass. Reproducibility

  • 249.
    Johansson, Johan
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Optimization of proximity ligationassay based Western blotting2011Självständigt arbete på avancerad nivå (masterexamen), 20 poäng / 30 hpStudentuppsats (Examensarbete)
    Abstract [en]

    Many of today’s methods for the detection of biomolecules suffer from a high limit ofdetection due to poor signal generation upon recognition of target. By applying andoptimizing proximity ligation assay (PLA) in Western blotting (WB), the limit of detectionhas been lowered down to the picomolar range. In this report I have optimized the differentparameters that affect the signal generation and explored possibilities to increase the ease ofuse, by merging protocol steps and performing signal generating reactions at roomtemperature.

  • 250.
    Johansson, Mia
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Individual susceptibility and Acute Exposure Guideline Levels (AEGLs) with focus on asthma2011Självständigt arbete på avancerad nivå (magisterexamen), 20 poäng / 30 hpStudentuppsats (Examensarbete)
2345678 201 - 250 av 558
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