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  • 101.
    Bajalan, Amanj
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Improved methods for virus detection and discovery in metagenomic sequence data2020Independent thesis Advanced level (degree of Master (Two Years)), 30 credits / 45 HE creditsStudent thesis
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  • 102.
    Balakrishna Kaje, Divya
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre. KTH Royal Institute of Technology.
    Characterization of a carbohydrate- active enzyme from the fish pathogen Saprolegnia parasitica2022Independent thesis Advanced level (degree of Master (Two Years)), 30 credits / 45 HE creditsStudent thesis
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  • 103.
    Balck, Marianne
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Phthalates in preschool dust: the relation between phthalates and parameters in the preschool environment2015Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

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

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

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

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

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    thesis
  • 104.
    Balck, Marianne
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Utgör användning av p-piller ett hot mot livskraftiga grodpopulationer?: Etinylöstradiols och levonorgestrels effekter hos arterna Xenopus leavis, Xenopus tropicalis och Rana temporaria2013Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [sv]

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

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  • 105.
    Balk, Pauline
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Removal of organic matter by NaOCl: An improved method to characterize organic microbial food sources2024Independent thesis Advanced level (degree of Master (Two Years)), 30 credits / 45 HE creditsStudent thesis
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  • 106.
    Ballhaus, Florentine
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Investigating plant autophagy with new chemical modulators2020Independent thesis Advanced level (degree of Master (Two Years)), 30 credits / 45 HE creditsStudent thesis
    Abstract [en]

    Autophagy is a major catabolic pathway in which cell components get sequestered in a double membrane vesicle, transported to the vacuole, degraded by vacuolar hydrolases and recycled.  Through this process, cells ensure cell homeostasis and remobilise nutrients. The autophagic flux can be enhanced as an adaptive stress response, improving plants resistance against stress, reducing aging and ultimately increasing yield. However, autophagy regulation in plants remains poorly understood. 

    Novel plant-specific modulators can be used in a chemical genetic approach for identification of proteins involved in the autophagy pathway. Furthermore, autophagy enhancers can find their application in agriculture for improved plant fitness. Known autophagy modulators have severe off-target effects, affecting plant growth and development. A recent screening identified two potential autophagy modulators. We developed a novel method for photoaffinity labelling and pulldown assay in Arabidopsis thaliana to identify potential interactors of the modulators. The identification of autophagy-related proteins will help to further elucidate the autophagic pathway in plants.

    The effect of the new autophagy enhancers on plant growth and development was analysed by automated growth assays. In comparison with a currently available autophagy enhancer, treated plants showed higher viability, indicating possible further applications for the new autophagy modulators in planta.

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  • 107.
    BALTEKIN, ÖZDEN
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Experimental Evolution of Persister Fractions in Escherichia coli2014Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
  • 108.
    Bampalikis, Dimitrios
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Recognizing biological and technical differences in scRNAseq: A comparison of two protocols2018Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Recent advances in sequencing technology have given access to information extracted on a single cell level. Single cell RNA sequencing enables for transcriptomes to be sequenced, allowing for studies within and between cell types. A recently developed protocol, based on Smart-seq2, and the Proximity ligation essay, allows for the detection of protein data from single cells, in parallel with RNA. The combination of the transcriptomic and proteomic data will enhance researchers’ ability to explore cell states. In this study, we are comparing a new pulldown protocol with the widely-used Smart-seq2, as well as against FACS sorted cells. Our results show differences in the RNA sequenced between the two protocols, as well the prediction of cell cycle state based on their data. Using RNA extracted from the pulldown protocol in different time points, we also calculate the direction of development for the cells. We expect that the incorporation of proteomic data will shed light to relevant biological questions related to the cell function.

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  • 109.
    Bantounas, Alexandros
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Host plant selection in closely related butterfly species due to reproductive interference: Modelling a tritrophic system2021Independent thesis Advanced level (degree of Master (Two Years)), 30 credits / 45 HE creditsStudent thesis
    Abstract [en]

    Host plant selection is an important process during the life cycle of lepidopterans, providing ovipositing sites for adults and food resources for the larvae. The processes behind host plant selection have been extensively studied, especially in closely related species in the context of niche separation. Empirical and theoretical studies have shown that multiple processes, such as resource competition, parasitoid avoidance and reproductive interference between interspecific individuals can affect host plant selection, often leading to niche separation. The aim of this study was to create and analyze a mathematical model using the adaptive dynamics techniques, in order to study the evolution of habitat selection. Our model incorporated three processes: Resource competition in the form of density dependent growth, parasitoid attacks and repro- ductive interference in a two species-two habitat system. It was hypothesized that the presence of parasitoids would promote co-existence through top-down control, while reproductive inter- ference would promote niche separation. The results confirmed both hypotheses. The analysis incorporating only the effect of parasitism showed the evolution of habitat separation when parasitoids attacked randomly and the evolution of co-existence in both habitats in the case of switching parasitoids. On the other hand, incorporating reproductive interference promoted the evolution of partial or complete niche separation. The extent of this process was shown to depend on the strength of reproductive interference and the initial habitat choice of the two species. Stronger reproductive interference increased the size of the set of initial conditions leading to the evolution of complete niche separation. The analysis conducted in this study demonstrated the opposing effects of parasitism and reproductive interference on the evolution of habitat selection, promoting co-existence and separation respectively.

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  • 110.
    Barkenäs, Emelie
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Automation of a solid-phase proximity ligation assay for biodefense applications2013Independent thesis Advanced level (professional degree), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

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

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  • 111.
    Barros, Carolina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre. IMBIM.
    Causality in Coexpression2020Independent thesis Advanced level (degree of Master (Two Years)), 30 credits / 45 HE creditsStudent thesis
    Abstract [en]

    One of the main goals of genetics has been to understand the link between genotype and phenotype. Using yeast (Saccharomyces cerevisiae) as our model organism, we take a closer look at the connection between genetic variation and gene expression to learn more about the mechanisms of gene regulation.

    We propose an algorithm based on ANOVA to detect causal relationships between coexpressed genes. We first identify expression quantitative trait loci (eQTLs) with strong effects on gene expression. The algorithm then uses these eQTLs with strong effects and the expression of all genes to identify how genes are affecting each other. This is done by analysing coexpressed gene pairs where both genes have an eQTL and finding if the eQTL of one gene affects the expression of the other. Genes that were found to affect the expression of other genes were named “causal genes”. We evaluate our method by comparing its results with known causal genes and conclude that it is a good predictor of known interactions.

    Using this algorithm, we found 741 genes having causal effects on gene expression, many of which affected the gene expression of many other genes across the genome (2278 total affected genes). Some of the causal genes clustered at six hotspot regions in the genome. Genes in hotspot regions were found to have lower heritability than genes outside these regions. We hypothesize that hotspot regions may be enriched for essential and/or fitness related genes.

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  • 112.
    Barrow, Rasmus Robert
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Single Cell RNA Detection using SuperRCA with Flow Cytometry Readout2024Independent thesis Advanced level (degree of Master (Two Years)), 80 credits / 120 HE creditsStudent thesis
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  • 113.
    Bartish, Margarita
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Establishing iPSCs as a method to model neurodevelopment in Down’s syndrome2012Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    The derivation of pluripotent stem cells (now termed induced pluripotent stem cells, iPSC) from mature somatic cells was a finding of seminal importance to fundamental cell biology. Thus established iPSC technology has been predicted to advance fields that previously relied on the ethically disputed use of embryonic stem cells. Being pluripotent (able to differentiate into every cell type present in the human body) and sharing most other characteristics with embryonic stem cells, but being much readier obtainable and their derivation free from ethical restraints, human induced pluripotent stem cells (hiPSC) provide access to cell types and insights into cell processes previously unattainable to researches. For this thesis, a hiPSC line was established from a skin biopsy donated by a Down’s syndrome patient. Most of what is known today about the molecular neurobiology behind this disease has been gathered from mice models or human post mortem studies, but this has a limited extrapolation potential to early human brain development in DS patients, as Down’s syndrome is an inherently human disease whose defining phenotype is established early during embryonic development. Having access to human pluripotent cells able to recapitulate the events of early neurogenesis is thus invaluable to the understanding of the mechanisms of this disorder. In parallel, work has been performed on optimizing iPSC reprogramming protocol. By exchanging one of the transcription factors used for reprogramming with a reporter gene, genomic integration of reprogramming factors has become possible to be traced visually, enabling more efficient selection of reprogrammed iPSC colonies.  

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  • 114.
    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. 

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  • 115.
    Basu, Alex
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Hedén Gynnå, Arvid
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Nordin, Jessika
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Reivant Munters, Arielle
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Åslin, Matilda
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Framtidens bioinformatikstöd för forskargrupper: En studie av SciLifeLabs användarstöd2012Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [sv]

    Science for Life Laboratory:s (SciLifeLabs) användarstöd inom bioinformatik brister inom en del områden som användarutbildning, organisation och kommunikation. För att kunna tillgodose den snabba utvecklingen av biotekniken (till exempel nästa generations sekvensering) och inte minst SciLifeLab är det viktigt att dessa brister åtgärdas. 

    Efter att ha utfört en serie intervjuer med användare och leverantörer av SciLifeLabs sekvenseringstjänster har vi kommit fram till sex förslag för att täcka problemen inom de olika områdena. Förslagen sträcker sig från att vara enkla till mer omfattande att implementera. 

    Resultaten är riktade mot SciLifeLabs sekvenseringsplattform och är utformade för att kunna implementeras i dagsläget samt anpassas till framtida utvecklingar. Vi tror också att förslagen kan, med enkla modifieringar, användas av andra plattformar hos SciLifeLab.

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  • 116.
    Bate Holmberg, Kristina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    En skogsträdgårds näringspotential2018Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [sv]

    I agroforestry brukas marken genom att kombinera vedartade växter, perenner och annueller.Skogsträdgårdar, som är en typ av agroforestry, vilka besitter flera olika nyttoegenskaper som tillexempel bevarandet av biologiska mångfalden, är en markanvändning av delvis eller endast perennaväxter, som ibland kompletteras av annueller. Några av skogsträdgårdars positiva egenskaper är attväxterna gynnar varandra och producerar/bidrar med livsmedelsproduktion, kolbindning ochkvävefixering. Intressant är att ta reda på huruvida livsmedlen som en skogsträdgård i Sverige kanbidra med kan täcka en människas dagliga näringsintag och även hur växternas kulinariskaegenskaper fungerar. Genom att besöka och samla in växter från två av tretton skogsträdgårdar, medgemensam odlingsdesign, som deltagit i forskningsprojektet Hållbar livsmedelsproduktion – attodla och äta från perenna system har näringsvärdena med avseende på kolhydrater, proteiner ochfett undersökts. Med hjälp av optimeringsmodellen dietproblemet visade det sig att gårdarna kantäcka en vuxen människas dagliga intag med avseende på energi, fett, kolhydrater och protein sålänge växterna ger tillräckligt, minst 600 gram skörd per dygn. Hasselnöt (Corylus avellana),bärhäggmispel (Amelanchier alnifolia), frön från sibirisk ärtbuske (Caragana arborescens) och frönfrån lungrot (Chenopodium bonushenricus) är de mest energitäta och därmed nyckelarterna. Detfinns stort behov av att utveckla beståndet av skogsodlingar för att se ytterligare se potentialen hosperenna växter i Sverige som livsmedelskälla.

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  • 117.
    Baudin, Sammi
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Fjellström, Hillevi
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Kraft, Aron
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Lamberg, Erica
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Rosenbaum, Måns
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Sjöstrand, Hanna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Detection and quantification of post-translational modifications in non-invasive samples: Phosphoproteins as biomarkers and a market analysis of protein quantification technologies2023Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    Post-translational modifications (PTMs) of proteins can be a sign and/or cause of disease. These modified proteins have the potential to be used as biomarkers for diagnostic purposes. However, research in the field is limited. The challenge of having an accessible way of diagnosing patients in time and at a low cost is crucial to improve public health. Blood samples or other non-invasive methods to detect diseases such as Alzheimer’s disease, Parkinson’s disease, Amyotrophic lateral sclerosis and cancers are of urgent need. This report investigates PTMs as possible biomarkers measurable in biofluids, such as blood, for diagnosis and prognosis. Biomarkers like phospho-tau and amyloid-beta are examined in the context of neurodegenerative diseases, as well as phosphorylations on neurofilaments, TAR DNA-binding protein 43 and α-synuclein. All of these are detectable in blood. Several PTMs with connection to different types of cancers are also investigated, such as F3-phosphopeptide and AFP-L3. It was found that many biomarkers for the detection of cancers can potentially be found in extracellular vesicles in blood. Methods such as ELISA, PEA, SomaScan, xMAP, SIMOA and mass spectrometry (MS) are all now available on the market to quantify these PTMs. MS has revolutionized the fields of protein detection in the past and has further evolved to being capable of protein quantification. ELISA has been prevalent for decades and laid the groundwork for improved methods such as xMAP and SIMOA that are easy to use and provide adequate sensitivity. SomaScan and PEA lead the way in dynamic range and multiplexing capacity with around 7000 and 3000 protein assays. The soon-to-be-released technology NULISA, with promising values in sensitivity and dynamic range, is also investigated here. Additionally, a written ethical analysis regarding the process and consequences of biomarker quantification through these technologies was performed. Although the investigated biomarkers are detectable in biofluids, using them as clinical diagnostic markers still poses a challenge, which is why further research in the field is needed. Through an increased knowledge of PTMs of proteins and the right use of platforms, clinical diagnostics and population screenings can be done more efficiently improving public health around the world.

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    Slutrapport23X1
  • 118.
    Bauer, Sofia
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre. Koch Institute for Integrative Cancer Research, M.I.T..
    The in vivo role of Cpt1a and whether a HFD renders ISCs, progenitors or established tumors metabolically reliant on fatty acid oxidation for their maintenance2019Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    The mammalian intestine is made of the small intestine and the colon. The small intestine is arranged into two fundamental structures called villi and crypts. Lgr5+ cells represent the intestinal stem cells (ISCs) and are identified by marker gene Lgr5, which is expressed at the bottom of mouse crypts, i.e. mucosal glands found in the intestinal epithelium. The mammalian intestine is said to respond to signals from the diet. Increased ISC numbers and progenitor proliferation have been associated with the effects of a high-fat diet (HFD) and these cells can, under HFD conditions initiate organoids i.e. small intestine-like structures cultured in vitro. In relation to cancer it has been shown that a HFD acts through the nuclear receptor PPAR-δ in ISCs and progenitors, and that PPAR-δ is also involved in fatty acid oxidation (FAO) as a master transcriptional regulator of the key FAO gene Cpt1a. The aim of this Master’s thesis seeks to assess whether a HFD renders ISCs, progenitors or established tumors metabolically reliant on FAO for their maintenance. Lineage tracing analysis in vivo with the computer software Aperio ImageScope, after βgalactosidase staining experiments contributed to confirm the reduced effects of a HFD in ISCs and progenitors as consequence of Cpt1a loss. The inhibition of FAO through in vitro and in vivo organoid experiments with genotypes APCΔ; P53Δ; Rosa-LSL-ZsGreen; Vil-CreER (APZV) and APCΔ; P53Δ; Cpt1afl/fl; Rosa-LSL-tdTomato; Vil-CreER (APCTV) also showed adverse effects on tumor maintenance. This from the clonogenicity assay after cell/organoid count analysis with the computer software ImageJ. In conclusion from the results obtained, which confirmed the hypothesis in the aims to a large extent Cpt1a could serve as a potential future therapeutic target. However, more experimental trials are needed to ascertain whether Cpt1a is the main contributor to mediate the HFD phenotype, but it is a promising start in the right direction. Increased knowledge of the impacts of diet in health and disease pursues to assist both in the prevention, as well as in the cure of established diseases in patients such as cancer. In the future, it would also be of interest to focus on and confirm whether the effects of the diet on various pathologies is reversible.

  • 119.
    Bazi, Hadi
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre. Karolinska Institute.
    Investigating The Nuclear Translocation of Mitochondrial Factor (MF) Upon Low Insulin/IGF Signaling In C. elegans2023Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    The full text will be freely available from 2033-08-14 00:28
  • 120.
    Bazyan, Saloume
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Sexual selection and extinction in deer2013Independent thesis Advanced level (degree of Master (Two Years)), 80 credits / 120 HE creditsStudent thesis
    Abstract [en]

    By performing a comparative analysis and using phylogenetic relationships of the Cervidaefamily this study aimed to address whether or not sexual selection may play a role in the extinctionof species by making species more vulnerable to extinction. The role of sexual selection in makingspecies more vulnerable to extinction is largely unexplored, and several factors such as ecologicaland life history traits may increase the risk of extinction.In all species of the family Cervidae (Gilbert et al. 2006, Geist 1998,Groves and Grubb2011,Meijaardand Groves2004,Price et al. 2005, Goss 1983) sexually selected characters plays amain role in determining species status and thus potentially their probability of extinction. In thisstudy the intensity of sexual selection (measured as sexual size dimorphism, antler size and matingsystem) and the rate of extinction (IUCN classification and anthropogenic effect) were counted asfactors to determine the role of sexual selection intensity in both species-rich and species-poorclades.By using the programme MESQUITE and phylogenetic trees, the results show an associationbetween species with larger body size and dimorphism, living in open habitats and having largerantler size expanded to more than three tines; such species are mostly non-territorial and formharems during the rutting season. The small species are territorial, live in closed habitats, aremonomorphic and have small antler size limited to two tines or less. Moreover species that aremore subjected to habitat degradation and anthropogenic effects tend to become smaller in size.Extinction risk for the species-rich clades with small sized, territorial and small antler sizedspecies is lower than for those consisting of species with larger antler size, larger body size, livingin open habitats and using harems as mating system.To sum up, the intensity of sexual selection in larger species in deer family put them in risk ofextinction; but on the other site, small species are more adapted to the environment by choosingdifferent strategy in mating system, and reducing antler and body size thus diminishing theextinction risk.

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  • 121.
    Bebris, Kristaps
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Local adaptation of Grauer's gorilla gut microbiome2017Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    The availability of high-throughput sequencing technologies has enabled metagenomicinvestigations into complex bacterial communities with unprecedented resolution andthroughput. The production of dedicated data sets for metagenomic analyses is, however, acostly process and, frequently, the first research questions focus on the study species itself. Ifthe source material is represented by fecal samples, target capture of host-specific sequencesis applied to enrich the complex DNA mixtures contained within a typical fecal DNA extract.Yet, even after this enrichment, the samples still contain a large amount of environmentalDNA that is usually left unanalysed. In my study I investigate the possibility of using shotgunsequencing data that has been subjected to target enrichment for mtDNA from the hostspecies, Grauer’s gorilla (Gorilla beringei graueri), for further analysis of the microbialcommunity present in these samples. The purpose of these analyses is to study the differencesin the bacterial communities present within a high-altitude Grauer’s gorilla, low-altitudeGrauer’s gorilla, and a sympatric chimpanzee population. Additionally, I explore the adaptivepotential of the gut microbiota within these great ape populations.I evaluated the impact that the enrichment process had on the microbial community by usingpre- and post-capture museum preserved samples. In addition to this, I also analysed the effectof two different extraction methods on the bacterial communities.My results show that the relative abundances of the bacterial taxa remain relatively unaffectedby the enrichment process and the extraction methods. The overall number of taxa is,however, reduced by each additional capture round and is not consistent between theextraction methods. This means that both the enrichment and extraction processes introducebiases that require the usage of abundance-based distance measures for biological inferences.Additionally, even if the data cannot be used to study the bacterial communities in anunbiased manner, it provides useful comparative insights for samples that were treated in thesame fashion.With this background, I used museum and fecal samples to perform cluster analysis to explorethe relationships between the gut microbiota of the three great ape populations. I found thatpopulations cluster by species first, and only then group according to habitat. I further foundthat a bacterial taxon that degrades plant matter is enriched in the gut microbiota of all threegreat ape species, where it could help with the digestion of vegetative foods. Another bacterialtaxon that consumes glucose is enriched in the gut microbiota of the low-altitude gorilla andchimpanzee populations, where it could help with the modulation of the host’s mucosalimmune system, and could point to the availability of fruit in the animals diet. In addition, Ifound a bacterial taxon that is linked with diarrhea in humans to be part of the gut microbiotaof the habituated high-altitude gorilla population, which could indicate that this pathogen hasbeen transmitted to the gorillas from their interaction with humans, or it could be indicative ofthe presence of a contaminated water source.

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  • 122.
    Beckman, S
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Giertz, Tobias
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Högqvist Bandefur, Hampus
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Levin, Mattias
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Ridderström, Linnéa
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Rosenblad, Elsa
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Single-cell proteomics in blood samples2024Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    Single-cell proteomics is a useful tool for measuring differences in cell populations for clinical trials. In this report we have conducted a literary review where we looked at 23 different single-cell proteomics methods and their advantages and disadvantages. We have looked at both mass spectrometry-based and affinity-based methods to find upcoming methods in the field of single-cell proteomics. Our findings show that there are multiple promising techniques that can be applied in different contexts. Moreover, we recommended combining different protocols, for instance Capillary zone electrophoresis (CZE) with a microfluidic platform or Optidrop with one of the barcoding methods for better results. When conducting this review it became clear that most methods could be improved by implementing software programs such as PEPerMINT and Infinity flow. Therefore, we encourage that such data acquisition and analysis methods are implemented to yield more accurate characterization and quantification of the single-cell proteome.

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    Rapport
  • 123.
    Belin, Stella
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Transparent Machine Learning for Multi-Omics Analysis of Mental Disorders2020Independent thesis Advanced level (professional degree), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Schizophrenia and bipolar disorder are two severe mental disorders that affect more than 65 million individuals worldwide. The aim of thisproject was to find co-prediction mechanisms for genes associated with schizophrenia and bipolar disorder using a multi-omics data set and a transparent machine learning approach. The overall purpose of theproject was to further understand the biological mechanisms of these complex disorders. In this work, publicly available multi-omics data collected from post-mortem brain tissue were used. The omics types included were gene expression, DNA methylation, and SNP array data. The data consisted of samples from individuals with schizophrenia, bipolar disorder, and healthy controls. Individuals with schizophrenia or bipolar disorder were considered as a combined CASE class.

    Using machine learning techniques, a multi-omics pipeline was developedto integrate these data in a manner such that all types were adequately represented. A feature selection was performed on methylation and SNP data, where the most important sites were estimated and mapped to their corresponding genes. Next, those genes were intersected with the gene expression data, and another feature selection was performed on the gene expression data. The most important genes were used to develop an interpretable rule-based model with an accuracy of 88%. The model wasthen visualized as a network. The graph highlighted genes that may be of biological importance, including CACNG8, RTN4, TERT, OSBPL8, and ANTXR1. Moreover, strong co-predictions were found, most notable between CNKSR4 and KDM4C in CASE samples. However, further investigations would need to be performed in order to prove that these are real biological interactions.

    Through the methods developed and the results found in this project, we hope to shed new light towards analyzing multi-omics data as well as to reveal more about the underlying mechanisms of psychiatric disorders.

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  • 124.
    Bella, Sinclair
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Felicia, Wallnäs
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Stella, Belin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Erik, Olby
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Hampus, Söderberg
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    A Prediction of Antibiotic Resistance with Regard to Urinary and Respiratory Tract Infections2018Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    In this project we set out to find when the resistance level against first line antibiotics would reach 20%. This was executed by first defining relevant bacteria and antibiotics for urinary and respiratory tract infections (UTI's, RTI's). The data was collected from the European Center for Disease Control (ECDC) and the Center for Disease Dynamics, Economics & Policy (CDDEP). The data included the level of resistance for specific years for countries in Europe, as well as for the USA. A prediction model was made using the programming language R. A linear model was used to make a five and ten year prediction. The accuracy was tested. The results were then visualized using R and MATLAB.

    The results show a big variation between different bacteria and antibiotic combinations. For the two E. coli combinations the resistance is already near 20% for many countries and the resistance is increasing. For the three K. pneumoniae combinations the resistance is high in Southern Europe, meaning many countries have reached or are near 20%. For the two P. aeruginosa combinations there is also a higher resistance in Southern Europe but the resistance is decreasing in most countries. The resistance for E. faecalis is also decreasing and is generally very low in all of Europe. For the only RTI relevant combination, S. pneumoniae and penicillins, the resistance is low and many countries except for Sweden show a decrease in resistance.

    The USA did not have data for the same time span as Europe and was therefore analyzed separately. For many combinations the USA are near the 20% limit. Only for two combinations the USA showed a decrease in resistance level, and for one of those combinations the prediction is too uncertain to make any assumptions about. For the USA there were two more combinations for RTI than for Europe. For the S. pneumoniae and penicillins combination they have, just as most of Europe, a decreasing resistance. The two combinations with Acinetobacter spp. have a high resistance that is increasing.

    The main challenge during this project was finding relevant data with a long timespan and with high certainty. The data found is based on invasive isolates which means that the disease which the samples are taken from is not known. The timespan and the certainty of the data affected the accuracy of the prediction model and how long period that could be predicted. The prediction model generated 202 predictions that were visualized.

    An ethical analysis was made concerning both research ethics and general ethics on the topic of antibiotic resistance. This analysis is meant to acknowledge these questions since we believe they are important when discussing antibiotic resistance.

    The objective of this project turned out to be more difficult to attain than first believed. This was because of the lack of quality data. Even though we cannot give a clear answer when each country will reach a resistance of 20% this report gives a good understanding of how the situation looks for UTI and RTI relevant bacteria.

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  • 125.
    Bendz, Kajsa
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Nikkanen, Leo
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Lundström, Ines
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Andersson, Malin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Idofsson, Annie
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Purification of exosomes - a comparison of methods and market analysis2024Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
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  • 126.
    Benevides, Kristina
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Broström, Oscar
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Elison Kalman, Grim
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Swenson, Hugo
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Vlassov, Andrei
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Ågren, Josefin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Stabil och antibiotikafri läkemedelsproduktion i rekombinant Escherichia coli2017Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [sv]

    Den här rapporten presenterar ett antibiotikafritt, stabilt och kromosombaserat expressionssystem för läkemedelsproduktion i Escherichia coli på beställning av företaget Affibody AB. E. coli-stammen BL21(DE3) valdes som värdorganism för expressionssystemet. Systemet består av en genkassett som innehåller en T7-promotor, en 5′-UTR från genen ompA och en terminatorsekvens från RNA-operonet rrnB. Fyra kopior av genkassetten ska integreras i pseudogenerna caiB, yjjM, hsdS och yjiV. En datormodell som modellerar det egentliga kopietalet i cellerna har skapats i mjukvaran MATLAB, vilket visar att det uppskattas vara maximalt 32 kopior av genkassetten per cell på grund av replikation av kromosomen. Ett högt pH i fermentorn; att använda fed-batch och blandade kolhydratkällor; och att använda stammen BL21(DE3) minskar acetatproduktionen i cellen. En lägre acetatproduktion kan leda till en högre produkthalt. En proteinutbytesmodell för mjukvaran MATLAB har konstruerats för att uppskatta koncentrationen av Affibody®-molekylen i en E. coli cell.

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  • 127.
    Beretta-Piccoli, Jonas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    The floating menace: Evaluation of methods to eradicate Nymphoides peltata in Lake Mälaren2020Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Invasive alien species are the second biggest threat to global biodiversity. Biodiversity loss results in loss of ecosystem functions and resilience. Freshwater ecosystems are more sensitive to invasions; therefore, their biodiversity is decreasing at a much faster rate in comparison to terrestrial ones. This thesis focuses on one of three invasive alien aquatic plants present in Sweden: Nymphoides peltata, a sediment-rooted, floating-leaved plant originating from middle Europe and Asia. Since the early 1980’s N. peltata has been present in Lake Galten, the most western part of Mälaren. The current eradication work is carried out by light depletion through floating frames that shade the N. peltata colony. The aim of this work was to evaluate the efficiency of this method by assessing eventual recolonization of N. peltata in eradicated sites and suggesting possible improvements. Information and data were collected by reviewing existing literature on invasive species eradication as well as conducting interviews with experts followed by field observations in Munkhammar bay of Lake Galten. The choice of floating frames as the main eradication method has been proven valid since it counters N. peltata clonal growth and fragmentation capacity. Despite a reduction by 1.7% of total N. peltata coverage from 2019 to 2020, correlated with the increase in frame coverage, field observations showed that recolonization is happening. Suggested improvements are the use of frames as spreading barrier, to reduce clonal growth and fragmentation of large colonies, together with introducing a free-floating fiber sheet to properly seal the gap between shoreline and frames. A proactive covering of vulnerable shores with fiber sheet is also recommended. However, the lack of a coordinated national action plan and laws’ inadequacy weakens the possibility of a successful eradication. Tempestive adjustments of current legislations are needed since climate change will allow N. peltata to spread further north and produce viable seeds.

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  • 128.
    Berg, Josefine
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    In situ detection of genomic DNA regions by padlock probes and rolling circle amplification for quick diagnosis2023Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    The full text will be freely available from 2033-06-13 09:10
  • 129.
    Berg Jöesaar, Märta
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Taxonomy of the Lesser Whitethroat Curruca curruca evaluated by song2022Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
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  • 130.
    Berg, Maria
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Floral scent in relation to flower morphology and mating system - a comparaitive analysis of Brassicaceae species pairs.2017Independent thesis Advanced level (degree of Master (Two Years)), 30 credits / 45 HE creditsStudent thesis
  • 131.
    Bergman, Ebba
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Blomkvist, Viktor
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Erkers, Julia
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Handin, Niklas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Hellner, Joakim
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Nettelblad, Jessica
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Mot en effektiv data- och informationshantering på SiCell2013Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [sv]

    Denna projektrapport är avsedd att vara ett hjälpmedel för SiCell, en del av SciLifeLab Uppsala som ska bli Europas första plattform för enkelcellgenomik till hösten 2013. SiCell har bett projektgruppen om undersökningar gällande ett Laboratory Information Management System, LIMS. På svenska ett datahanteringsystem för laboratorier. Ett sådant system skulle kunna effektivisera SiCells verksamhet. Undersökningarna har resulterat i en kravspecifikation som ett LIMS för SiCell ska uppfylla och en sammanställning av tillgängliga mjukvaror som bäst uppfyller dessa krav. Screensaver, MISO och Gnomex är de tre gratisprogram med öppen källkod som hamnade högst upp i listan. Inget av dem uppfyller alla krav men med modifieringar av programmerare tros detta vara möjligt.

    SiCell bad också om lägre prioriterade undersökningar av några av de metoder som används inom plattformen. Cellysering, Alternativa amplifieringsmetoder och transkriptomik har undersökts av projektgruppen. Detta resulterade i en sammanställning av vilka alternativ som finns och vad som är under utveckling inom respektive område.

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  • 132.
    Bergman, Ingrid
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Top - down control: parasitism and predation on Gonyostomum semen in Swedish brown water lakes2022Independent thesis Advanced level (degree of Master (Two Years)), 30 credits / 45 HE creditsStudent thesis
    Abstract [en]

    Gonyostomum semen is a raphidophyte microalgae that can be found in brown water lakes all over Sweden. The species forms substantial summer blooms that can completely dominate the phytoplankton community, largely due to its limited grazing pressure. To test whether parasites control the abundance of G. semen, as well as to study a newly discovered predator – prey interaction, three experiments were set up. The first experiment aimed to look at potential parasite interactions by screening for infections in natural environments, but none could be found. The second experiment built on the first by testing if the lack of parasites was due to physiological characteristics of G. semen, by exposing the species to diatom parasites and observing the cell’s response. The third experiment investigated the impact of a predatory ciliate on G. semen cell abundance. This predator – prey interaction was first observed in fresh lake water samples and had so far not been described in the literature. First, G. semen alone was exposed to the ciliate, and later the prey preference of the ciliate was examined by offering it four different potential prey species. The results from the first and second experiment suggested that G. semen does not have any parasites, potentially due to lack of a supportive cell wall. When interacting with parasite zoospores, the G. semen cells burst open, meaning that a successful infection would not be possible. The third experiment showed that the ciliate does feed on G. semen, and that it likely prefers G. semen over other types of prey. The limited top – down control on G. semen gives the species an ecological advantage and is seemingly one of the main reasons for G. semen’s success in spreading to new habitats. 

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  • 133.
    Bergquist, Johan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Improved resolution for antibiotic susceptibility in QuickMIC®2022Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    Background: The crisis of antibiotics resistance demand faster, more accurate diagnostics tools for antibiotic susceptibility testing (AST). I studied the effect of an alternative analysis chamber construction in a novel rapid AST system named QuickMIC®, to improve the detection resolution and range. The test chamber is localized in a part of the test cassette called the “slider” and is the part where the test for minimum inhibition concentration (MIC) is located. The test resolution is dependent on optical quality, and with the current production method there are horizontally stretched bacterial colonies in some of the regions. The goal of this project was to see if it was possible to decrease the frequency of these optically bad regions by improving the slider production method.                   Method: An improved production method was examined, using post-laser polishing to finalize slider dimensions. The alternative slider was cut from thicker material compared to the current slider and had the sides polished to reduce the diameter, to avoid the formation of a cylindrical lens shaped inlet and outlet of the microfluidics chamber. The performance of the sliders was compared by looking at the frequency of horizontally stretched colonies. Results: The bacterial colonies of regions near the inlets, outlets and the middle of the test chamber were studied in both the current- and alternatives slider. The result show that colonies in the middle were highly similar in both sliders, showing a large variety in stretch direction and low accuracy. Similar results could be observed in the edge-located colonies of the alternative slider. The edge-located colonies of the current slider are the only one observed to greatly differ from the rest, showing horizontal stretch colonies and high accuracy.                                                                                                     Conclusion: The conclusion from this is that the colonies at the edges of the alternative slider is more like the middle colonies then the edge colonies in the current slider. This shows that the frequency of horizontally stretched colonies decrease in the alternative slider.

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    populärvetenskaplig sammanfattning
    The full text will be freely available from 2025-01-19 08:28
  • 134.
    Bergqwist, Katarina
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Onsbring, Henning
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Vu, Emy
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Wahlin, Malin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Zarelius, Peter
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Åhlin, Mikaela
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Nya sensorsystem för kombinationseffekter av antibiotika2013Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [sv]

    Idag är antibiotikaresistens ett allvarligt problem. En tillfällig lösning på problemet är att utnyttja synergieffekter som kan uppstå mellan olika typer av antibiotika. Det innebär att antibiotika skulle kunna ha effekt mot bakterier som har utvecklat resistens.

    I denna rapport har flera olika metoder, för att mäta bakterietillväxt, utvärderats. Dessa metoder indikerar om antibiotikakombinationerna har en effekt. Däribland har både kommersiella och nyligen publicerade metoder undersökts. De kommersiella metoderna granskades genom en marknadsanalys. De krav som har satts på systemet är att det ska gå att köra flera prov samtidigt, analysen ska kunna utföras på kort tid, metoden ska inte vara destruktiv mot bakterierna samt att datan bör vara på formen av cellkoncentration levande celler.

    Bland de kommersiella mätmetoderna valdes tre metoder ut som verkade vara bland de bästa utifrån kraven. Dessa var ATP-analys, LIVE/DEAD® BacLight™ samt SYBR Green I. Från artiklar hittades fyra nyligen publicerade system som var av intresse utifrån kraven. Dessa var BioMEMS (eng. Biomedical Micro-Electro-Mechanical Sensor), odling i slutna mikrokanaler, SMR (sluten mikrokanalresonator) samt mikroflödessystem med pH-sensor.

    Utifrån vad som finns på marknaden idag och de nyligen publicerade systemen som har undersökts ansåg gruppen att BioMEMS och användande av mikrokanaler är de två bäst lämpade metoderna för ändamålet.

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  • 135.
    Bergström, Linnéa
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Modifications of Escherichia coli 23S rRNA: Do they even matter?2024Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    Modifications of the ribosomal RNAs are seen in all domains of life and are often clustered in regions of functional importance. This suggests that modifications are important, but their specific functions still remain unclear. In this study, a total of 28 single, double, and triple gene deletions of the enzymes that modify the 23S rRNA in E. coli were constructed and analysed for their effects on growth fitness and susceptibility to antibiotics. Growth assays in 20 °C revealed reduced fitness for mutans lacking the modifying enzymes encoded by the genes rluB and rluD, indicating that their modifications are needed for optimal growth atlower temperatures. The deletion of rluD also led to increases sensitivity towards 4/5 tested ribosome-targeting antibiotics which might be due to the loss of the modifications, or a consequence of the growth defect this deletion leads to in the K-12 strain of E. coli used in this study. Significant change in susceptibility to antibiotics were also observed for ΔrluBC which leads to increased sensitivity to chloramphenicol and for ΔrluC which leads to loss of resistance towards clindamycin.

    The full text will be freely available from 2025-06-08 18:13
  • 136.
    Berkelind, Ellinor
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    In vitro bioassays for toxicity testing of wastewater - an evaulation of different sample treatment techniques2020Independent thesis Advanced level (degree of Master (Two Years)), 30 credits / 45 HE creditsStudent thesis
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  • 137.
    Bernedal Nordström, Clara
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Bürger, Erik
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Engberg, Jonas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Jansson, Ylva
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Thorell, Hannes
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Vaivade, Aina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Sluta gnata, hantera din data - Ta fram en kravspecifikation för ett LIMS2019Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    Excel is a great tool, however it has its flaws. Files quickly become slow as they increase in size, and Excel has no built-in feature to easily search through several documents for a specific word, phrase or value. This can be resolved through a LIMS, a Laboratory Information Management System, which is a database solution that can be used to store and trace laboratory data and information. Our task was to evaluate what system requirements the company Olink Proteomics AB has for a LIMS. By interviewing several departments at Olink, we gained information about what each group wanted from such a system and condensed it into a needs assessment. The interviews showed that traceability was needed for every single department, as well as having easy features for adding data into the system. We were also tasked by Olink to research which Swedish laws apply to old patient data, as the company wants to reuse the data for R&D. Our conclusions are that if data is made fully anonymous, there are no issues in using it for R&D. However, this can be difficult as many criteria have to be fulfilled in order for the data to become fully anonymous.

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  • 138.
    Berntsson, Elina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    The effect of Edaravone on Amyloid beta aggregation2019Independent thesis Advanced level (degree of Master (Two Years)), 30 credits / 45 HE creditsStudent thesis
    Abstract [en]

    Alzheimer’s disease (AD) is a devastating neurodegenerative disease that affect millions of people worldwide. Aggregation of Amyloid-β (Aβ) monomers create toxic oligomers that can interact with cellular membranes and disturb cellular functions, resulting in cell death and neurological dysfunction. Increased levels of oxidative stress have been shown in the brains of AD patients, something that besides the obvious cell and tissue toxicity, also favors the amyloidogenic pathway and generates more Aβ monomers. Here we show that Edaravone, a free radical scavenger can affect the aggregation rate of different lengths of Aβ. We show that Aβ-40 that is more commonly found in vivo aggregates faster with addition of Edaravone, while Aβ-42 aggregates slower or not at all. These findings add up to previous findings where free radical scavengers and antioxidants such as Edaravone have been suggested as a potential treatment in Alzheimer’s disease.

  • 139.
    Bertilsson, Filippa
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Spatial mapping of motile cilia proteins in respiratory and female reproductive tissues2024Independent thesis Advanced level (degree of Master (Two Years)), 40 credits / 60 HE creditsStudent thesis
    Abstract [en]

    Motile cilia play critical roles in the human body, including expelling mucus from the lungs and facilitating the transport of oocytes and sperm through the fallopian tubes. Understanding the complex structure and motility of cilia, as well as the diseases associated with them, is of big importance. This study investigates the proteins expressed in ciliated cells from both respiratory and reproductive tissues using multiplex immunofluorescence. We determined the subcellular localization of 134 proteins in the fallopian tube, endometrium, cervix, nasopharynx, and bronchus, focusing on five subcellular regions: the cilia tip, transition zone, basal body, cytoplasm, and nucleus. This analysis was conducted using an automated image analysis method developed specifically for this project. Our findings revealed a high correlation in protein expression across all tissues, although several proteins exhibited distinct expression patterns between different tissues. Notably, the fallopian tube showed a higher correlation with the nasopharynx and bronchus than with the endometrium and cervix. Within these proteins, six gene clusters were identified, with the two largest clusters being strongly associated with ciliary structure. This study enhances our understanding of motile ciliary structures and ciliated cells, identifying key proteins for further research into cilia motion, function, and related diseases.

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  • 140.
    Bertilsson, Filippa
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre. Statens Veterinärmedicinska anstalt.
    Using the eminent toolkit of Wolbachia to study Culex pipiens populations and their relations in Europe2022Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    Culex pipiens, in the family Culicidae, has emerged as one of the biggest vectors for West Nile virus. It has two bioforms, pipiens and molestus, which differ from each other regarding habitat, diapause, and prey. Pipiens prefers to bite birds, and molestus prefers to bite humans. There is to some extent hybridization between the two, which creates a bridge-vector between birds and humans. One way to study the relationships and spreading of the mosquitos is using the intracellular bacteria Wolbachia pipientis which is present in at least 99% of al Culex mosquitoes. The bacteria have two fast evolving genes, pk1 and ank2 which are suitable for this. Not only are the bacteria suitable for genetics, but it is also manipulating the reproductive system of the mosquitoes through Cytoplasmic Incompatibility, which changes structures of populations and allows for the bacteria to spread fast and efficient. We wanted to investigate levels of Wolbachia in different populations, as well as if the two bioforms prefer a prey, together with mapping the relationships between populations using the two genes. We found that Wolbachia was present in all tested mosquitoes, with higher levels of it in the abdomen than in the thorax. We also found that the theory of a preferred prey was false within the tested populations, since both bioforms preferred birds. Lastly, we could identify five different strains of Wolbachia pipientis concentrated to different locations. This study has shown that Wolbachia is present in all tested mosquitoes and is a useful tool to determine relationships within and between populations. This is important to be able to gain understanding of the spread of West Nile virus and other vector borne diseases spread by Culex pipiens mosquitoes. 

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  • 141.
    Betnér, Ellinor
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    The midbrain dopaminergic system - development and heterogeneity in animal models of Parkinson's disease2019Independent thesis Advanced level (degree of Master (Two Years)), 30 credits / 45 HE creditsStudent thesis
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    Examensarbete
  • 142.
    Beyer, Alexander
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Development of Therapeutic Vaccines against IL-18 and Thymic Stromal Lymphopoietin (TSLP)2010Independent thesis Advanced level (degree of Master (Two Years)), 30 credits / 45 HE creditsStudent thesis
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    FULLTEXT01
  • 143.
    Bhawe, Harshal Kunal
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Phylogenomics of Ascetosporea2022Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Ascetosporea is a class of poorly studied unicellular eukaryotes that function as parasites of marine invertebrates. These parasites cause mass mortality events in aquaculture species such as oysters and mussels. The economic importance of these aquaculture species should lead to more attention on the genomics of Ascetosporea and their place on the evolutionary tree of life. With the onset of global warming and rising sea levels and temperatures, many emerging pathogens have been seen and until these are sequenced and analysed, it is difficult to make any conclusions about their relationships and evolution. As there aren’t many genomes and transcriptomes available for Ascetosporea, their position in the larger eukaryotic tree of life remains hypothetical. To attempt to remedy this lack of information, the Burki lab has recently generated sequencing data through sample collection and sequencing for these organisms (genomes and transcriptomes).

    A curated dataset of the various eukaryotic species was previously created and newly sampled and sequenced Ascetosporean genomes of Paramarteilia sp., Marteilia pararefringens, Paramikrocytos canceri, etc. from multiple sampling locations like Ireland, Norway, Sweden, and the UK were included. These could increase the genomic and transcriptomic data available for Ascetosporea and help to resolve the relationships within Ascetosporea. A few reasons why this group has not yet been placed on the tree of life are that the samples are from host tissue, which makes it difficult to sequence these parasites. These Ascetosporeans have also been seen to be very fast-evolving.

    After building phylogenetic relationships with single gene trees to allow for the identification of possible contaminants and paralogs, it was seen that there was a lot of contamination in Ascetosporea, due to the sampling being from host tissue material (hosts are open to the environment). After cleaning and filtering the possible contaminated genes, the trees were remade and a possible link between a fungal group called Microsporidia and Ascetosporea was observed in a few genes. This was hypothesized to be lateral gene transfer between the two groups resulting from their similar lifestyles and infection of invertebrates.

    There were complications like contamination and short blast hits that arose during analysis, and these could be caused by problems by fragmentation in the genome. This fragmentation could have negative effects on genome annotation predictions and consequently phylogenetic and phylogenomic analysis. Due to this and the challenging nature of collecting samples, the read coverage for the genomes is low but it can be used to perform phylogenetic and phylogenomic studies using currently available data and methods. Another expected result was that the sequenced data had contaminants, and a thorough and comprehensive search would have to be conducted on a dataset-wide level to remove any contaminants.

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  • 144.
    Bhutia, Pema choden
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Accuracy of TransferRNA Selection in Protein synthesis2011Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    ACCURACY OF TRANSFER RNA SELECTION IN PROTEIN SY

    The ribosome is a rapid magnificent molecular machine that plays an important role in proteinsynthesis and it consists of RNA and protein. The 70S bacterial ribosome comprises twosubunits, 30S and 50S. The 30S small subunit of the bacterial ribosome contains a protein calledS12, encoded by the rpsL gene. The function of this S12 protein is to help arrange the mRNAcorrectly to the ribosome and to interact with transfer RNA (tRNA) to initiate translation.Mutations in the rpsL gene generate phenotypes like resistance, dependence or pseudodependenceto the antibiotic streptomycin in bacteria. It is believed that mutations in the rpsLgene can increase the accuracy of tRNA selection in protein synthesis.The ribosome conducts the selection of tRNA in two steps: the initial selection and theproofreading step. During these multiple steps, the ribosome chooses the cognate aminoacyltRNAsin a ternary complex with EF-Tu and GTP and accommodates in the A site of ribosome.Therefore, the accuracy of the ribosome in selection of cognate aminoacyl-tRNA is crucial for the production of functional polypeptide sequences. Here, three different Escherichia coli strains; wild type MG1655, streptomycin restrictive (SmR) strain res222, and a streptomycin pseudo-dependent (SmP) strain w3110 are used, for studying the accuracy of tRNA selection inprotein synthesis. The mutant SmR shows hyper-accurate phenotype, which means, it has lowerpeptide bond formation efficiency and higher accuracy than the wild type. SmP shows pseudodependentto streptomycin phenotype which means it has higher peptide bond formation efficiency in the presence of antibiotic streptomycin. I have estimated the accuracy of tRNA selection in protein synthesis with enzyme kinetics. The kinetics data of these experiments display that mutant streptomycin restrictive is hyper-accurate and lower peptide bond formation efficiency than the wild type. SmP for the near cognate reaction in presence of antibiotic streptomycin has higher peptide bond formation efficiency than the SmP in absence of antibiotic streptomycin. SmP in presence antibiotic streptomycin has lower accuracy than the SmP in absence of antibiotic streptomycin.

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  • 145.
    Biradar, Megha
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Improvement of RCA initiation on genomic DNA2015Independent thesis Advanced level (degree of Master (Two Years)), 30 credits / 45 HE creditsStudent thesis
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  • 146.
    Bjorklund, Geir
    et al.
    Council Nutr & Environm Med CONEM, Toften 24, N-8610 Mo I Rana, Norway.
    Chirumbolo, Salvatore
    Univ Verona, Dept Neurosci Biomed & Movement Sci, Verona, Italy;CONEM Sci Secretary, Verona, Italy.
    Dadar, Maryam
    AREEO, Razi Vaccine & Serum Res Inst, Karaj, Iran.
    Pivina, Lyudmila
    Semey Med Univ, Semey, Kazakhstan;Semey Med Univ, CONEM Kazakhstan Environm Hlth & Safety Res Grp, Semey, Kazakhstan.
    Lindh, Ulf
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Butnariu, Monica
    Banats Univ Agr Sci & Vet Med King Michael I Roma, Timisoara, Romania;Banats Univ Agr Sci & Vet Med King Michael I Roma, CONEM Romania Biotechnol & Environm Sci Grp, Timisoara, Romania.
    Aaseth, Jan
    Innlandet Hosp Trust, Res Dept, Brumunddal, Norway;Inland Norway Univ Appl Sci, Elverum, Norway.
    Mercury exposure and its effects on fertility and pregnancy outcome2019In: Basic & Clinical Pharmacology & Toxicology, ISSN 1742-7835, E-ISSN 1742-7843, Vol. 125, no 4, p. 317-327Article, review/survey (Refereed)
    Abstract [en]

    Mercury (Hg), a highly toxic environmental pollutant, shows harmfulness which still represents a big concern for human health, including hazards to fertility and pregnancy outcome. Research has shown that Hg could induce impairments in the reproductive function, cellular deformation of the Leydig cells and the seminiferous tubules, and testicular degeneration as well as abnormal menstrual cycles. Some studies investigated spontaneous abortion and complicated fertility outcome due to occupational Hg exposure. Moreover, there is a relation between inhaled Hg vapour and reproductive outcome. This MiniReview evaluates the hypothesis that exposure to Hg may increase the risk of reduced fertility, spontaneous abortion and congenital deficits or abnormalities.

  • 147.
    Björkenstig, Caroline
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    ANALYSRESULTAT FRÅN ENSKILDA BRUNNAR PÅ GOTLAND: TILLGÄNGLIGGÖRANDE OCH ANVÄNDNINGSOMRÅDEN2019Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    The water supply on Gotland mainly consists of withdrawal from groundwater wells both for public and private use. The groundwater on Gotland is especially vulnerable for contamination and effects of climate change because of the geology and thin soil layer. The data collection regarding the quality of the groundwater is limited today and it is desirable that information and knowledge about the groundwater improves. Primarily, this concerns Gotland’s 14000 private wells where analysis results are not available for authorities to use, for example, for work with environmental goals and water management. Therefore, this work aims to produce a proposition on how to make analysis results available and which use and applications they can have, and hopefully this can be a starting point for a practical implementation on Gotland. The Water laboratory on Gotland, SGU (Geological Survey of Sweden) and the County Administrative Board answered a questionnaire about their area of work and involvement in this. The answers provided a basis for this work, resulting in two suggestions on how to make the analysis results available and in a consent form. In summary, it is possible to start to collect data on analysis results, which can be of importance and use in the water management on Gotland. This will be more easily implemented and easier when the Water laboratory get their new computer system.

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  • 148.
    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.

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    UPTEC X 14 001 Johan Björkesten
  • 149.
    Björklund, Gabriella
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Hur den urbana miljön driver evolutionen hos vilda djur och växter2022Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [sv]

    Det är väl känt att urbaniseringen av våra landskap har minskat den biologiska mångfalden och bidragit till utrotningen av flertalet arter som inte kunnat anpassa sig till den nya miljön. För de arter som lyckats överleva i staden så finns det forskning som talar för att urbaniseringen nu driver deras evolution inom loppet av några få generationer. I den här uppsatsen undersöker jag tre aspekter av stadsmiljön som driver evolutionen hos vilda djur och växter: (1) habitatfragmenteringen, (2) den urbana värmeön och (3) föroreningar. Mitt syfte är att belysa detta fenomen, visa vidden av det, samt åskådliggöra hur urban evolution kan påvisas experimentellt genom att fördjupa mig i ett antal studier.

     

    Forskningen visar att den urbana miljön påverkar evolutionen av en mångfald av arter från samtliga trofiska nivåer, både i form av anpassningar och genom stokastiska händelser. En studie visar hur stadens habitatfragmentering leder till minskad genetisk variation hos urbana populationer och hur genetisk drift tillsammans med minskat genflöde resulterar i genetiskt skilda urban och lantliga populationer. Andra studier påvisar anpassningar till stadens föroreningar och lokala klimat, vilket leder till genetisk divergens mellan urbana och lantliga populationer. En annan studie visar hur mutationer som induceras genom föroreningar resulterar i en ökad mutationshastighet hos populationer nära industrier. Utifrån de undersökta studierna så diskuteras hur de genetiska förändringarna orsakade av stadsmiljön får populationsdynamiska konsekvenser. Ett flertal arter har lyckats anpassa sig till den extrema urbana miljön och en diskussion förs om huruvida det kan införliva hopp om evolutionär räddning från de massutrotningar vi ser idag som följd av de mänskliga miljöförändringarna. Till sist utreds om och hur kunskapen om urban evolution kan användas för att utforma städer med grön infrastruktur som gynnar den biologiska mångfalden. 

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  • 150.
    Björklund, Geir
    et al.
    Council Nutr & Environm Med, Toften 24, N-8610 Mo I Rana, Norway.
    Hilt, Björn
    St Olavs Univ Hosp, Dept Occupat Med, Trondheim, Norway;Norwegian Univ Sci & Technol, Dept Publ Hlth & Nursing, Trondheim, Norway.
    Dadar, Maryam
    AREEO, Razi Vaccine & Serum Res Inst, Karaj, Iran.
    Lindh, Ulf
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Aaseth, Jan
    Innlandet Hosp Trust, Res Dept, Brumunddal, Norway;Inland Norway Univ Appl Sci, Fac Hlth & Social Sci, Elverum, Norway.
    Neurotoxic effects of mercury exposure in dental personnel2019In: Basic & Clinical Pharmacology & Toxicology, ISSN 1742-7835, E-ISSN 1742-7843, Vol. 124, no 5, p. 568-574Article, review/survey (Refereed)
    Abstract [en]

    Numerous studies have reported neurobehavioural effects in dental personnel occupationally exposed to chronic low levels of mercury (Hg). Hg exposure from dental work may also induce various chronic conditions such as elevation of amyloid protein expression, deterioration of microtubules and increase or inhibition of transmitter release at motor nerve terminal endings. Therefore, clinical studies of Hg toxicity in dentistry may provide new knowledge about disturbed metal homeostasis in neurodegenerative diseases such as Alzheimer's disease, multiple sclerosis and mood disorders. The purpose of this MiniReview is to evaluate the evidence of possible relevance between Hg exposure in dentistry and idiopathic disturbances in motor functions, cognitive skills and affective reactions, as well as dose-response relationships.

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