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  • 1.
    Abbey-Lee, Robin N.
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Kreshchenko, Anastasia
    Mechanical and Aeronautical Engineering Division L5, Department of Mechanical, Aerospace & Civil Engineering, Dalton Nuclear Institute, FSE Research Institutes,The University of Manchester, UK.
    Fernandez Sala, Xavier
    Linköping University, Faculty of Science & Engineering. Linköping University, Department of Physics, Chemistry and Biology, Biology.
    Petkova, Irina
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering. School of Biological Sciences, Centre for Ecology,Evolution and Behaviour, Royal Holloway University of London, Egham UK.
    Løvlie, Hanne
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Effects of monoamine manipulations on the personality and gene expression of three-spined sticklebacks2019In: Journal of Experimental Biology, ISSN 0022-0949, E-ISSN 1477-9145, Vol. 222, no 20, article id jeb211888Article in journal (Refereed)
    Abstract [en]

    Among-individual behavioral differences (i.e. animal personality) are commonly observed across taxa, although the underlying, causal mechanisms of such differences are poorly understood. Animal personality has been correlated with physiological functions as well as fitness-related traits. Variation in many aspects of monoamine systems, such as metabolite levels and gene polymorphisms, has been linked to behavioral variation. Therefore, here we experimentally investigated the potential role of monoamines in explaining individual variation in personality, using two common pharmaceuticals that respectively alter the levels of serotonin and dopamine in the brain: fluoxetine and ropinirole. We exposed three-spined sticklebacks, a species that shows animal personality, to either chemical alone or to a combination of the two chemicals, for 18 days. During the experiment, fish were assayed at four time points for the following personality traits: exploration, boldness, aggression and sociability. To quantify brain gene expression on short- and longer-term scales, fish were sampled at two time points. Our results show that monoamine manipulations influence fish behavior. Specifically, fish exposed to either fluoxetine or ropinirole were significantly bolder, and fish exposed to the two chemicals together tended to be bolder than control fish. Our monoamine manipulations did not alter the gene expression of monoamine or stress-associated neurotransmitter genes, but control, untreated fish showed covariation between gene expression and behavior. Specifically, exploration and boldness were predicted by genes in the dopaminergic, serotonergic and stress pathways, and sociability was predicted by genes in the dopaminergic and stress pathways. These results add further support to the links between monoaminergic systems and personality, and show that exposure to monoamines can causally alter animal personality.

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  • 2.
    Abrouk, Michael
    et al.
    Institute of Experimental Botany, Centre of the Region Hana for Biotechnological and Agricultural Research, Olomouc, Czech Republic.
    Balcarkova, Barbora
    Institute of Experimental Botany, Centre of the Region Hana for Biotechnological and Agricultural Research, Olomouc, Czech Republic.
    Simkova, Hana
    Institute of Experimental Botany, Centre of the Region Hana for Biotechnological and Agricultural Research, Olomouc, Czech Republic.
    Kominkova, Eva
    Institute of Experimental Botany, Centre of the Region Hana for Biotechnological and Agricultural Research, Olomouc, Czech Republic.
    Martis, Mihaela-Maria
    Linköping University, Department of Clinical and Experimental Medicine, Division of Cell Biology. Linköping University, Faculty of Medicine and Health Sciences. Institute for Bioinformatics and Systems Biology, Helmholtz Center Munich, Neuherberg, Germany.
    Jakobson, Irena
    Department of Gene Technology, Tallinn University of Technology, Akadeemia tee 15, Tallinn 19086, Estonia.
    Timofejeva, Ljudmilla
    Department of Gene Technology, Tallinn University of Technology, Akadeemia tee 15, Tallinn 19086, Estonia.
    Rey, Elodie
    Institute of Experimental Botany, Centre of the Region Hana for Biotechnological and Agricultural Research, Olomouc, Czech Republic.
    Vrana, Jan
    Institute of Experimental Botany, Centre of the Region Hana for Biotechnological and Agricultural Research, Olomouc, Czech Republic.
    Kilian, Andrzej
    Diversity Arrays Technology Pty Ltd, Yarralumla, ACT2600, Australia.
    Järve, Kadri
    Department of Gene Technology, Tallinn University of Technology, Akadeemia tee 15, Tallinn 19086, Estonia.
    Dolezel, Jaroslav
    Institute of Experimental Botany, Centre of the Region Hana for Biotechnological and Agricultural Research, Olomouc, Czech Republic.
    Valarik, Miroslav
    Institute of Experimental Botany, Centre of the Region Hana for Biotechnological and Agricultural Research, Olomouc, Czech Republic.
    The in silico identification and characterization of a bread wheat/Triticum militinae introgression line: Characterization of alien introgression in wheat2017In: Plant Biotechnology Journal, ISSN 1467-7644, E-ISSN 1467-7652, Vol. 15, no 2, p. 249-256Article in journal (Refereed)
    Abstract [en]

    The capacity of the bread wheat (Triticum aestivum) genome to tolerate introgression from related genomes can be exploited for wheat improvement. A resistance to powdery mildew expressed by a derivative of the cross bread wheat cv. Tähti ⨯ T. militinae (Tm) is known to be due to the incorporation of a Tm segment into the long arm of chromosome 4A. Here, a newly developed in silico method termed RICh (rearrangement identification and characterization) has been applied to characterize the introgression. A virtual gene order, assembled using the GenomeZipper approach, was obtained for the native copy of chromosome 4A; it incorporated 570 4A DArTseq markers to produce a zipper comprising 2,132 loci. A comparison between the native and introgressed forms of the 4AL chromosome arm showed that the introgressed region is located at the distal part of the arm. The Tm segment, derived from chromosome 7G, harbors 131 homoeologs out of the 357 genes present on the corresponding region of Chinese Spring 4AL. The estimated number of Tm genes transferred along with the disease resistance gene was 169. Characterizing the introgression's position, gene content and internal gene order should facilitate not only gene isolation, but may also be informative with respect to chromatin structure and behavior studies.

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

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

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

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  • 4.
    Ahrné, Karin
    et al.
    SLU.
    Bengtsson, Bengt Åke
    Björklund, Jan-Olof
    Cederberg, Björn
    Eliasson, Claes
    Hydén, Nils
    Jonasson, Jan
    Lindeborg, Mats
    Lst Kalmar Län.
    Ohlsson, Anders
    Palmqvist, Göran
    Ryrholm, Nils
    University of Gävle, Faculty of Health and Occupational Studies, Department of Occupational and Public Health Sciences, Biology.
    Rödlista över fjärilar Lepidoptera2015In: Rödlistade arter i Sverige 2015 / [ed] Westling, Anna, Uppsala: ArtDatabanken SLU , 2015, p. 98-112Chapter in book (Other academic)
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  • 5.
    Ajawatanawong, Pravech
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Baldauf, Sandra
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    An automatable method for high throughput analysis of evolutionary patterns in slightly complex indels and its application to the deep phylogeny of Metazoa2014Manuscript (preprint) (Other academic)
    Abstract [en]

    Insertions/deletions (indels) in protein sequences are potential powerful evolutionary markers. However, these characters have rarely been explored systematically at deep phylogenetic levels. Previous analyses of simple (2-state) clade defining indels (CDIs) in universal eukaryotic proteins found none to support any major animal clade. We hypothesized that CDIs might still be found in the remaining population of indels, which we term complex indels. Here, we propose a method for analyzing the simplest class of complex indels the “slightly complex indels”, and use these to investigate deep branches in animal phylogeny. Complex indels with two states, called bi-state indels, show similar evolutionary patterns to singleton simple indels and confirms that insertion mutations are more common than deletions. Exploration of CDIs in 2- to 9-state complex indels shows strong support for all examined branches of fungi and Archaeplastida. Surprisingly, we also found CDIs supporting major branches in animals, particular in vertebrates. We then expanded the search to non-bilaterial animals (Porifera, Cnidaria and Ctenophora). The phylogenetic tree reconstructed by CDIs places the Ctenophore Mnemiopsis leidyi as the deepest branch of animals with 6 CDIs support. Trichoplax adhaerens is closely related to the Bilateria. Moreover, the indel phylogeny shows Nematostella vectensis and Hydra magnipapillata are paraphyletic group and position of Cnidarian branches seems to be problematic in the indel phylogeny because of homoplasy. This might be solved if we discover CDIs from animal specific proteins, which emerged after the universal orthologous proteins.Evolutionary Patterns in Slightly Complex Protein Insertions/Deletions (Indels) and Their Application to the Study of Deep Phylogeny in Metazoa

  • 6.
    Aktar, Farjana
    Stockholm University, Faculty of Science, Stockholm Resilience Centre.
    ‘Hazaribagh’- development trajectory or trap? – A case study of a leather processing unit in Bangladesh2017Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    The extensive alteration of global ecosystems, especially the changes caused by globalized and industrialized economic development activities over the last fifty years, have urged for a better understanding of the human-in-nature management system. Bangladesh, a densely populated developing country, is witnessing rapid environmental degradation while passing through different phases of industrial growth. Leather, one of the oldest industries in this country, provides a very positive picture in the country’s national economy and at the same time produces severe ecological and social crisis in a mutually reinforcing way. At first sight, it seems to fit the SES concept of social ecological trap. The previous scientific studies on ‘Hazaribagh’ leather processing unit in Bangladesh have investigated social, economic, ecological and stakeholder’s perspectives but did not address the pathway that has shaped the present situation. The objective of this case study was therefore to explore the reasons why change of this ‘Hazaribagh system’ has been impeded for so long and if the social-ecological trap concept could help to clarify the reasons for the chronic delay of the relocation of ‘Hazaribagh’ leather processing unit. This study has observed, through a historical investigation that a path dependent social ecological trap situation is persisting in the ‘Hazaribagh system’ where the economic opportunity is playing the role as a juncture between the phases of the process; and power mechanism and the disconnected SES has influenced and strengthened the claim. This study has also addressed some other underlying substantial social issues, which are influencing the process and might contribute to outline further research, and consequently provide insight to escape from the trap situation.

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  • 7.
    Al Saleem, Evan
    KTH, School of Biotechnology (BIO).
    Improving unnatural amino acid mutagensis efficiency and selectivity in mammalian cell2016Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Genetically encoded, site-specific incorporation of unnatural amino acids (UAA)into proteins through selective recoding of an amber stop codon provides apowerful route for expressing synthetic proteins in living cells. Recoding of theamber stop codon is achieved by introducing an amber suppressortRNA/synthetase pair orthogonal to the endogenous tRNA complement intocells. Methanosarcina is a methane producing archaea with the unusualcapability of suppressing the stop codon (specifically the amber codon). Bysuppressing the amber codon Methanosarcina facilitate the incorporation of thenon-canonical amino acid pyrrolysine (pyl). The suppressing mechanismoriginates from a evolutionary unique Pyrrolysyl-tRNA synthetase (PylRS) and itsmatching tRNApyl. The PylRS has been further evolved and modified to allowincorporation of a wide range of UAAs. Amber suppression is today used tocontrol and study protein function in living cells. By making a series of wellcontrolledexperiments with HEK293T cells we aimed to develop this techniqueinto a robust and general tool for mammalian cell biology. Specifically we weretesting the incorporation of the unnatural amino acid bicyclononyne (BCN) by aset of known PylRS mutants. Our results suggest the mutant aaRS PylRS “AF” isthe most robust and efficient synthetase for BCN. We have improved ambersuppression by determining which factors leads to a more efficient method andsimultaneously decreasing the cost of the method.

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  • 8. Alava, Mikko
    et al.
    Ardelius, John
    KTH, School of Computer Science and Communication (CSC), Computational Biology, CB.
    Aurell, Erik
    KTH, School of Computer Science and Communication (CSC), Computational Biology, CB.
    Kaski, P.
    Krishnamurthy, S.
    Orponen, P.
    Seitz, S
    Circumspect descent prevails in solving random constraint satisfaction problems2008In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 105, no 40, p. 15253-15257Article in journal (Refereed)
    Abstract [en]

    We study the performance of stochastic local search algorithms for random instances of the K-satisfiability (K-SAT) problem. We present a stochastic local search algorithm, ChainSAT, which moves in the energy landscape of a problem instance by never going upwards in energy. ChainSAT is a focused algorithm in the sense that it focuses on variables occurring in unsatisfied clauses. We show by extensive numerical investigations that ChainSAT and other focused algorithms solve large K-SAT instances almost surely in linear time, up to high clause-to-variable ratios a; for example, for K = 4 we observe linear-time performance well beyond the recently postulated clustering and condensation transitions in the solution space. The performance of ChainSAT is a surprise given that by design the algorithm gets trapped into the first local energy minimum it encounters, yet no such minima are encountered. We also study the geometry of the solution space as accessed by stochastic local search algorithms.

  • 9.
    Albers, Eva
    et al.
    Chalmers Univ Technol, Dept Biol & Biol Engn, Div Ind Biotechnol, SE-41296 Gothenburg, Sweden..
    Malmhall-Bah, Eric
    Chalmers Univ Technol, Dept Biol & Biol Engn, Div Ind Biotechnol, SE-41296 Gothenburg, Sweden..
    Olsson, Joakim
    Chalmers Univ Technol, Dept Biol & Biol Engn, Div Ind Biotechnol, SE-41296 Gothenburg, Sweden..
    Sterner, Martin
    KTH, School of Architecture and the Built Environment (ABE), Sustainable development, Environmental science and Engineering, Water and Environmental Engineering.
    Mayers, Joshua J.
    Chalmers Univ Technol, Dept Biol & Biol Engn, Div Ind Biotechnol, SE-41296 Gothenburg, Sweden..
    Nylund, Goran M.
    Univ Gothenburg, Dept Marine Sci Tjarno, SE-45296 Stromstad, Sweden..
    Rupar-Gadd, Katarina
    Linnaeus Univ, Dept Built Environm & Energy Technol, Luckligs Plats 3, SE-35195 Växjö, Sweden..
    Abdollahi, Mehdi
    Chalmers Univ Technol, Dept Biol & Biol Engn, Div Food & Nutr Sci, SE-41296 Gothenburg, Sweden..
    Cvijetinovic, Suzana
    Chalmers Univ Technol, Dept Biol & Biol Engn, Div Ind Biotechnol, SE-41296 Gothenburg, Sweden..
    Welander, Ulrika
    Linnaeus Univ, Dept Built Environm & Energy Technol, Luckligs Plats 3, SE-35195 Växjö, Sweden..
    Edlund, Ulrica
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Fibre- and Polymer Technology.
    Pavia, Henrik
    Univ Gothenburg, Dept Marine Sci Tjarno, SE-45296 Stromstad, Sweden..
    Undeland, Ingrid
    Chalmers Univ Technol, Dept Biol & Biol Engn, Div Food & Nutr Sci, SE-41296 Gothenburg, Sweden..
    Influence of preservation methods on biochemical composition and downstream processing of cultivated Saccharina latissima biomass2021In: Algal Research, ISSN 2211-9264, Vol. 55, article id 102261Article in journal (Refereed)
    Abstract [en]

    Saccharina latissima biomass cultivated along the Swedish west coast was subjected to four different scalable preservation methods after harvest; freezing, sun-drying, oven-drying and ensiling. Freeze-drying and freezing at -80 ?C were also included to provide dry and wet references. The effects of the different preservation methods on the composition of Saccharina biomass (on dry weight, DW, basis), and the recovery as well as properties of high-quality protein, alginate and biogas were evaluated. Sun-drying significantly reduced protein, alginate and fatty acid content of the seaweeds and thereby concentrated ash in the biomass compared to the other methods. Protein/amino acids and fatty acids were significantly concentrated in ensiled biomass, while mannitol and laminarin were reduced compared to the other biomasses. Oven-drying and -20 ?C freezing affected the composition the least, with lower ash content and alterations in some specific amino and fatty acids. Sun-drying and ensiling resulted in significantly lower protein solubility at high pH compared to the other biomasses which translated into the lowest total seaweed protein recovery using the pH-shift process. Highest protein yield was obtained with the freeze-dried reference. Ensiling lead to a significant decrease in the molecular weight of alginate, while sun-drying caused a negative effect on alginate by inducing a shift in the guluronic and mannuronic acids composition of alginate. Sun-drying gave the lowest methane yield in the anaerobic digestion experiments while freezing at -80 ?C gave the highest yield, closely followed by freezing at -20 ?C and ensiling. To conclude, preservation methods must be carefully chosen to protect the valuable component in Saccharina latissima, and to achieve an efficient downstream processing ultimately yielding high quality products as part of a seaweed biorefinery.

  • 10.
    Alfjorden, Anders
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Experimental Spironucleus infections in Atlantic salmon (Salmo salar): Hidden secrets of the life cycle of Spironucleus salmonicida revealed2018Independent thesis Advanced level (degree of Master (One Year)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

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

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  • 11.
    Alhamar, Sarah
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science.
    Extraction of the Coagulant Protein from Oil Waste2022Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Human health relies on clean water, and yet many developing countries have areas of poor water quality. This is either due to a lack of infrastructure and poor sanitation, or financial restrictions. One of the first steps of water treatment involves a process called flocculation. 

    Currently, aluminum sulfate (alum) is the most popular flocculation agent, but it has significant health implications. In contrast, the Moringa oleifera seed is a nonchemical additive which has historically been used in water treatment as a flocculation agent in addition to other applications in the cosmetic and food industries. 

    While Moringa oleifera seeds are one of the original plants used in water treatment, many others also show potential. The waste product from cold press oil industries was analyzed to test its viability as an alternative flocculation agent and to avoid competition with human consumption and industrial processes. Different oil wastes were screened to find a suitable coagulation agent. 

    Ion exchange chromatography and antimicrobial tests were conducted using simple assays. The screening was focused on the protein concentration and the coagulation activity of the oil cake presses. Moringa oleifera, rapeseed, linseed, peanut, and sesame seed oil press cakes were tested, of which two showed promising results and potential for use in water treatment. 

    The oil cake presses of Moringa seed and rapeseed showed the presence of coagulant proteins which are comparable to the seed extracts. The coagulant protein from the oil cake press has a similar molecular mass to that of seed extracts. The purified proteins displayed antibacterial properties, and their nutrient outputs were minimal. 

  • 12. Ali, Imran
    et al.
    Penttinen-Damdimopoulou, Pauliina E
    Mäkelä, Sari I
    Berglund, Marika
    Stenius, Ulla
    Akesson, Agneta
    Håkansson, Helen
    Halldin, Krister
    Institutet för miljömedicin, Karolinska Institutet.
    Estrogen-like effects of cadmium in vivo do not appear to be mediated via the classical estrogen receptor transcriptional pathway.2010In: Journal of Environmental Health Perspectives, ISSN 0091-6765, E-ISSN 1552-9924, Vol. 118, no 10, p. 1389-94Article in journal (Refereed)
    Abstract [en]

    BACKGROUND: Cadmium (Cd), a ubiquitous food contaminant, has been proposed to be an endocrine disruptor by inducing estrogenic responses in vivo. Several in vitro studies suggested that these effects are mediated via estrogen receptors (ERs).

    OBJECTIVE: We performed this study to clarify whether Cd-induced effects in vivo are mediated via classical ER signaling through estrogen responsive element (ERE)-regulated genes or if other signaling pathways are involved.

    METHODS: We investigated the estrogenic effects of cadmium chloride (CdCl2) exposure in vivo by applying the Organisation for Economic Co-operation and Development (OECD) rodent uterotrophic bioassay to transgenic ERE-luciferase reporter mice. Immature female mice were injected subcutaneously with CdCl2 (5, 50, or 500 µg/kg body weight) or with 17α-ethinylestradiol (EE2) on 3 consecutive days. We examined uterine weight and histology, vaginal opening, body and organ weights, Cd tissue retention, activation of mitogen-activated protein kinase (MAPK) pathways, and ERE-dependent luciferase expression.

    RESULTS: CdCl2 increased the height of the uterine luminal epithelium in a dose-dependent manner without increasing the uterine wet weight, altering the timing of vaginal opening, or affecting the luciferase activity in reproductive or nonreproductive organs. However, we observed changes in the phosphorylation of mouse double minute 2 oncoprotein (Mdm2) and extracellular signal-regulated kinase (Erk1/2) in the liver after CdCl2 exposure. As we expected, EE2 advanced vaginal opening and increased uterine epithelial height, uterine wet weight, and luciferase activity in various tissues.

    CONCLUSION: Our data suggest that Cd exposure induces a limited spectrum of estrogenic responses in vivo and that, in certain targets, effects of Cd might not be mediated via classical ER signaling through ERE-regulated genes.

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

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

  • 14.
    Alkaissi, Hammoudi
    et al.
    Linköping University, Department of Clinical and Experimental Medicine, Division of Neuro and Inflammation Science. Linköping University, Faculty of Medicine and Health Sciences. Region Östergötland, Center for Diagnostics, Department of Clinical Pathology and Clinical Genetics.
    Ekstrand, Jimmy
    Linköping University, Department of Clinical and Experimental Medicine. Linköping University, Faculty of Medicine and Health Sciences. Region Östergötland, Center for Diagnostics, Department of Clinical Pathology and Clinical Genetics.
    Jawad, Aksa
    Linköping University, Department of Clinical and Experimental Medicine, Division of Cell Biology. Linköping University, Faculty of Medicine and Health Sciences. Region Östergötland, Center for Diagnostics, Department of Clinical Pathology and Clinical Genetics.
    Nielsen, Jesper Bo
    University of Southern Denmark, Denmark.
    Havarinasab, Said
    Linköping University, Department of Clinical and Experimental Medicine, Division of Neuro and Inflammation Science. Linköping University, Faculty of Medicine and Health Sciences. Region Östergötland, Center for Diagnostics, Department of Clinical Pathology and Clinical Genetics.
    Söderkvist, Peter
    Linköping University, Department of Clinical and Experimental Medicine, Division of Cell Biology. Linköping University, Faculty of Medicine and Health Sciences. Region Östergötland, Center for Diagnostics, Department of Clinical Pathology and Clinical Genetics.
    Hultman, Per
    Linköping University, Department of Clinical and Experimental Medicine, Division of Neuro and Inflammation Science. Linköping University, Faculty of Medicine and Health Sciences. Region Östergötland, Center for Diagnostics, Department of Clinical Pathology and Clinical Genetics.
    Genome-Wide Association Study to Identify Genes Related to Renal Mercury Concentrations in Mice2016In: Journal of Environmental Health Perspectives, ISSN 0091-6765, E-ISSN 1552-9924, Vol. 124, no 7, p. 920-926Article in journal (Refereed)
    Abstract [en]

    BACKGROUND: Following human mercury (Hg) exposure, the metal accumulates in considerable concentrations in kidney, liver, and brain. Although the toxicokinetics of Hg have been studied extensively, factors responsible for interindividual variation in humans are largely unknown. Differences in accumulation of renal Hg between inbred mouse strains suggest a genetic interstrain variation regulating retention or/and excretion of Hg. A. SW, DBA/2 and BALB/C mouse strains accumulate higher amounts of Hg than B10.S.

    OBJECTIVES: We aimed to find candidate genes associated with regulation of renal Hg concentrations.

    METHODS: A. SW, B10.S and their F1 and F2 offspring were exposed for 6 weeks to 2.0 mg Hg/L drinking water. Genotyping with microsatellites was conducted on 84 F2 mice for genome-wide scanning with ion pair reverse-phase high-performance liquid chromatography (IP RP HPLC). Quantitative trait loci (QTL) were established. Denaturing HPLC was used to detect single nucleotide polymorphisms for haplotyping and fine mapping in 184 and 32 F2 mice, respectively. Candidate genes (Pprc1, Btrc and Nfkb2) verified by fine mapping and QTL were further investigated by real-time polymerase chain reaction. Genes enhanced by Pprc1 (Nrf1 and Nrf2) were included for gene expression analysis.

    RESULTS: Renal Hg concentrations differed significantly between A. SW and B10. S mice and between males and females within each strain. QTL analysis showed a peak logarithm of odds ratio score 5.78 on chromosome 19 (p = 0.002). Haplotype and fine mapping associated the Hg accumulation with Pprc1, which encodes PGC-1-related coactivator (PRC), a coactivator for proteins involved in detoxification. Pprc1 and two genes coactivated by Pprc1 (Nrf1 and Nrf2) had significantly lower gene expression in the A. SW strain than in the B10. S strain.

    CONCLUSIONS: This study supports Pprc1 as a key regulator for renal Hg excretion.

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  • 15.
    Alkufai, Meysah
    Kristianstad University, Faculty of Natural Sciences.
    Fungerar AHA-metoden för epifytiska lavar och mossor?: En studie av naturvärdesindikatorer hos träd i park- och kyrkliga kulturmiljöer2021Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    Old trees in cultural environments are receiving increasing attention in nature conservation due to their high conservation values and provide important habitat for endangered plant and animal species. The purposes of the study were to investigate whether Sörensson's AHA-method is applicable also to mosses and lichens, as well as to compare two environments with old trees. 443 trees were inventoried in Kristianstad, of which 230 in Tivoliparken and 213 in Östra begravningsplatsen. The trees were assessed based on the occurrence of: cavities, barkless areas, and so on. These findings were used to assign each tree to the five AHA classes of varying conservation value. Trees were also searched for predetermined lichens and mosses signalling high conservation value, and a simple count was made of the total number of trivial cryptogam species on each tree. Tivoliparken had a wider scatter of trees among the AHA classes; 56 in the highest value classes (class I and II), 114 in class III, and 60 as resource trees. At Östra begravningsplatsen, half of the oldest trees were in the two highest value classes and 93 in class III. The remaining trees ended up as resource trees. In total, 89 records of 6 signal species were made, and one wood fungus. There was a significant association between AHA class and richness of trivial species when trees of all species were pooled, but no association when beech and linden were assessed separately. These results suggest that the AHA method does not work on cryptogams.

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  • 16.
    Alriksson, Claes-Göran
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Texturvariationer i skogsmark - effekter på tillväxt och gödslingsrespons?: Studie i ett försök med behovsanpassad gödsling i Ebbegärde2019Independent thesis Advanced level (degree of Master (One Year)), 20 credits / 30 HE creditsStudent thesis
    Abstract [sv]

    En mängd olika ståndortsfaktorer påverkar trädens tillväxt. Några av dessa kan påverkas genom olika skogsskötselmetoder, t ex näringstillförsel. I ett flertal försök de senaste decennierna har skogsgödsling visat sig kunna öka tillväxten markant. Faktorer som inte är påverkbara, som t ex markens textur och markens jorddjup kan då bli begränsande för tillväxten eftersom en finkornig textur oftast är gynnsam ur tillväxtsynpunkt. Föreliggande undersökning syftar till att se om det finns en texturvariation inom en begränsad yta och dess effekter på tillväxten. Texturen undersöktes genom torrsiktning. Resultaten visar att det förelåg en stor variation av texturen på beståndsnivå och att det kan påverka tillväxten i kombination med andra begränsande faktorer såsom vattentillgång.

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  • 17.
    Amalia, Clausson
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Hormonet leptin och dess funktioner2014Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
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  • 18.
    Amnebrink, Dennis
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Transcriptomic profiling of marine bacteria between development and senescence phases of a phytoplankton bloom2018Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Bacterioplankton provide important ecosystem functions by carrying out biogeochemical cycling of organic matter. Playing an important role in the microbial loop they help remineralize carbon and nutrients. Bacteria also interact with phytoplankton during phytoplankton blooms. However, fundamental understanding on the underlying molecular mechanisms involved in the degradation of phytoplankton-derived organic matter is still in its infancy. Therefore, we analysed data from a mesocosm experiment following a natural phytoplankton-bloom from an upwelling system in the North- East Atlantic Ocean. The purpose was to contribute a mechanistic understanding based on functional gene expression analysis of natural microbial assemblages. Our results show the difference in functional gene expression within a bacterial metacommunity and how this functional response drastically switches between bloom build up and senescence. Transcripts showed a broad change in gene expression involving major SEED categories, with the bloom senescence phase exhibiting a higher relative abundance in major categories such as Carbohydrates, Protein Metabolism and Amino Acids and Derivatives. Within these categories genes connected to carbon utilization and transport systems (Ton and Tol) as well as chemotaxis showed a higher abundance during bloom senescence. The change in functionality based on transcripts showed a different bacterial community composition appearing over a very short time. We thus conclude that the bacterial functional gene expression response between build-up and degradation bloom phases is remarkably different and associated with a change in the identity of bacteria with active expression. Our findings highlight the importance of bacterial substrate specialists with different functional roles during different time points of phytoplankton blooms.

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  • 19.
    Anderson, Jennifer L
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Nieuwenhuis, Bart P. S.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Division of Evolutionary Biology, Faculty of Biology, Ludwig- Maximilians-Universität München.
    Johannesson, Hanna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Asexual reproduction and growth rate: independent and plastic lifehistory traits in Neurospora crassa2019In: The ISME Journal, ISSN 1751-7362, E-ISSN 1751-7370, Vol. 13, no 3, p. 780-788Article in journal (Refereed)
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  • 20.
    Andersson, Emelie
    et al.
    Halmstad University, School of Business, Innovation and Sustainability.
    Trulsson, Alexander
    Halmstad University, School of Business, Innovation and Sustainability.
    Vilka invasiva främmande växter utgör ett hot mot ekskogar i Västra Götalands län?2022Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    Invasive alien species pose one of the greatest threats against biodiversity, in Sweden and globally. The northern location of Sweden has limited the distribution of invasive alien species, however, issues concerning invasives are predicted to increase with future climate change. The Swedish University of Agricultural Sciences has compiled a report containing a list of more than 1000 invasive alien species which have been classified based on their ecological effect and invasion potential. The report will be the basis of the future national list of legislated species.

    In our report, we examine which invasive alien land-based plant species pose the greatest threats against oak tree forests in the county of Västra Götaland. Our results can be used to prioritize which invasive alien plant species the County Administrative Board, in an early stage, could direct measures against to protect oak tree forests in conservation management. The protection of oak is crucial since it is one of the most important genera in Europe, both economically and ecologically, entailing a national responsibility. Shading and competition are major threats, affecting oak trees negatively and prohibiting rejuvenation.  

    The species selected for analysis in our report was based on the list of invasive alien species compiled by the Swedish University of Agricultural Sciences in combination with the EU’s list of species of union concern. This report contains a GIS analysis and a field study. The GIS analysis was based on observational data in SLU Artportalen and in the field study, 4 protected oak tree forests were surveyed. The difference in results may indicate inadequate data in SLU Artportalen. Our GIS analysis showed that Japanese knotweed (Reynoutria japonica) posed the largest present and future threat against analyzed oak tree forests, while red-berried elder (Sambucus racemosa) posed the largest present threat against examined oak tree forest according to the survey in our field study. The number of observations of selected invasive alien plant species in oak tree forests, with associated surrounding buffer zones of 2 km, close to urban areas was higher than in oak tree forest, with associated buffer zones, not close to urban areas. The difference in number of observations was significant. Our result can confirm that invasive alien plant species are more numerous in urban areas than in non-urban areas, meaning the threat against oak tree forest close to urban areas may be greater. This corresponds with previous research showing that the dispersal of invasive alien plant species is promoted by human activities, such as gardening and the disposal and transportation of waste from excavations. 

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  • 21.
    Andersson, Fredrika
    Karlstad University, Faculty of Social and Life Sciences.
    Barns tankar om den egna kroppen!: Vad vet fyraåringar och sexåringar om sin kropp!2009Independent thesis Basic level (professional degree), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    The aim of this research was to investigate the concepts among five and six year old children regarding the human body. Six children were interviewed by means of qualitative interviews. The children's concept regarding the human body differed depending on their age. The six year old children knew more about the body than the four year old children. Spontaneously the children knew we had heart, brain, blood, brain cells, muscles and skeleton

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  • 22.
    Andersson, Helene
    et al.
    KTH, School of Electrical Engineering (EES), Signal Processing. University of Twente, Netherlands .
    Van Den Berg, A.
    From LOC to LIC: Using individual cells as experimentation platforms2005In: Nanobiotechnology, ISSN 1551-1286, Vol. 1, no 3, p. 319-321Article in journal (Refereed)
    Abstract [en]

    There are many efforts today trying to mimic the properties of single cells in order to design chips that are as efficient as cells. However, cells are nature's nanotechnology engineering at the scale of atoms and molecules. Therefore, it might be better to vision a microchip that utilizes a single cell as experimentation platform. A novel, so-called Lab-in-a-Cell (LIC) concept is described, where advantage is taken of micro/nanotechnological tools to enable precise control of the biochemical cellular environment and possibility to analyze the composition of single cells.

  • 23.
    Andersson, Johanna
    Kristianstad University, Faculty of Natural Science.
    Heteronormativa blommor och könsrollsbundna bin, är naturen verkligen så normativ?: en analys av hur läroböcker i biologi och naturkunskap rekonstruerar normer om kön och sexualitet vid beskriviningar av djurs beteende2020Independent thesis Advanced level (professional degree), 10 credits / 15 HE creditsStudent thesis
    Abstract [sv]

    Detta arbete handlar om hur normer om kön och sexualitet (re)konstrueras i biologiundervisningen, och fokuserar på innehåll om hur djurs beteende beskrivs. Tidigare forskning pekar på att undervisningen och läroböcker inom biologi och naturkunskap är mycket heteronormativ och förklarar kvinnor och män i dikotomiska termer. En del av forskningsrapporterna uppmärksammade också att det finns en svårighet att sammanföra det biologiska innehållet och innehåll som behandlar sexualitet, genus och relationer i undervisningen. Endast två studier är gjorda på hur normer om kön och sexualitet konstrueras då djurs beteende beskrivs. Då forskning visar att biologin och dess förklaringar på djurs beteende har betydelse för vad vi människor ser som naturliga beteenden för oss, kan innehåll om djurs beteende i undervisnngen ge normativa föreställningar om kön och sexualitet. Undersökningen gjordes utifrån frågeställningarna: 

    Vilka förklaringar om djurs beteende utifrån kön och sexuella strategier framställs i läroböcker för kurserna biologi 1 och naturkunskap 2 för gymnasieskolan?

    Vilka följemeningar om kön och sexualitet kan dessa beskrivningar ge elever? 

    Tre läroböcker i biologi och tre läroböcker i naturkunskap analyserades med diskursanalys som analysmetod. Resultatet visade bland annat att det fanns betydligt mer innehåll i biologiböckerna än naturkunskapsböckerna, att antalet normativa beskrivnngar skiljde sig mycket åt mellan böckerna, och att en del böcker riskerar att ge eleverna normativa föreställningar om kön och sexualitet. Följemeningar som identifierades för några av böckerna var bland annat att beteendemässiga könsskillnader är biologiskt bestämt och att heterosexualiteten är naturlig. Perspektiv som är viktiga för arbetet och som är utgångspunkter är teorin om diskurser, normer, queerteori, samt queer- och genusperspektiv på biologi.

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  • 24.
    Andersson, Johanna
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Hornen och djurskyddet: Bedömning av inväxta horn hos nöt och får i svenska domstolar2022Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    Ingrown horns are something that occurs on both cattle and sheep, throughout Sweden. This can be due to many different reasons; for example a dehorning gone wrong, a trauma or a horn growing in the wrong direction. If a horn starts to penetrate the tissue it will cause the affected animal pain and suffering, which will affect the welfare in a negative way. The owner will have plenty of time to cut of the tip of the horn before it penetrates any tissue, since horns grow slowly. Despite this, ingrown horns are detected at both slaughterhouses and in the inspections of the länsstyrelse. To investigate how common it is to report ingrown horns in Sweden and to find out how the Swedish courts views the problem, a total of 42 Swedish verdicts were studied. This study includes 33 verdicts of which 9 were appealed to a higher court. The severity of the cases varied, the skin of the animal was penetrated in 72 % of them. 81 % of the cases refered to cattle and 19 % of the cases refered to sheep. It occured throughout Sweden, from Ystad in the south to Östersund in the north, 91 % of the accused were men and 6 % were women. In 3 % the accused were both a man and a woman. In Sweden 10 % of the farming companies with cattle and 31 % of the farming companies with sheep and goats are run by women. The largest part of the cases (63 %) were discovered by länsstyrelsen during an inspection and 34 % of the cases were discovered at the slaughterhouse. The remaining 3 % were discovered by an employee looking after the animals. Among the reasons as to why the accused failed to act before the horn became ingrown, the most common was difficulty to supervise the animals or that the accused completely denies that the horn was grown in. The results of the study suggests that the animal welfare regulations need to include the horns and their supervision. The Swedish courts need to become further aware of how serious and long a suffering with an ingrown horn can be.

  • 25.
    Andersson, Johanna
    et al.
    Linköping University, Department of Social and Welfare Studies, Learning, Aesthetics, Natural science. Linköping University, Faculty of Educational Sciences.
    Tibell, Lena
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Educational Sciences.
    Exploring childrens' views of what's inside the body2012Conference paper (Refereed)
    Abstract [en]

    The importance of living a healthy life in an everyday context is promoted in schools and preschools. The discussion often focuses on what food is healthy, and that one should eat enough but not too much. The connection between food and beverages and their role in the body is seldom discussed. Students’ ideas about how the human body functions have been investigated in several studies but few have focused on young children. In this study, we investigate young children’s conceptions related to this topic and how their ideas develop. Seventy-nine pre- and primary school children, aged 4-11, participated in individual focus interviews wherein the children were asked to draw and explain their understanding. Our results confirm several findings observed by other workers. However, in contrast with earlier studies, 10 of seventeen 4-5 year-old children indicated the stomach, and more than half of those children described how food can be utilized in the body to extract energy. Furthermore, the brain was among the most commonly mentioned organs cross all age groups. Interestingly, the level of expertise varied and did not covariate with age. For example, five of eight of the 4 year-old children draw 5-8 organs, while a single 10 year-old child could only mention three. Similarly, two of thirteen 7-year old children provided an almost completely correct description of the digestive tract and its function, while most of the older children expressed a much less developed understanding. The results reflect the wide range of different conceptual ideas that teachers confront in a day-to-day classroom context.

  • 26.
    Andersson, Johanna
    et al.
    Linköping University, Department of Social and Welfare Studies, Learning, Aesthetics, Natural science. Linköping University, Faculty of Educational Sciences.
    Tibell, Lena A.E.
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Educational Sciences.
    Children's reasoning and representations about living and non-living things2013Conference paper (Refereed)
    Abstract [en]

    Understanding of the concept ‘life’ and what characterise ‘living things’ is important as a foundation for learning in biology. In a more general view, this understanding can make children develop awareness, respect and responsibility for life as members of a society and in decision making for sustainable development. The present pilot study aim to investigate 5-6 year old pre-school children’s reasoning and representations about living and nonliving things. In cognitive developmental research, the concept of life is well investigated but, questions still remain regarding how children reason around and represent these concepts. Previous research has found that children have difficulties in including plants as living things. Moreover, it is found that young children include e.g. the sun, clouds and rocks as living things. The methods that have been used are often quantitative and use picture-cards with different objects for the children to categorize. In the present pilot study a modified methodology was applied. Children’s drawings of what they consider as living and non-living were collected and picture-cards were used as point of departure for reasoning. In interviews the children were encouraged to explain and express their ideas. The drawings and the cards mainly worked as a meaning making tool for the children. Results from the study will be presented and discussed. 

  • 27.
    Andersson, Jonathan
    et al.
    Linköping University, Department of Mathematics, Mathematics and Applied Mathematics. Linköping University, Faculty of Science & Engineering.
    Kozlov, Vladimir
    Linköping University, Department of Mathematics, Mathematics and Applied Mathematics. Linköping University, Faculty of Science & Engineering.
    Radosavljevic, Sonja
    Stockholm Resilience Centre, Stockholm University, Stockholm, Sweden.
    Tkachev, Vladimir
    Linköping University, Department of Mathematics, Mathematics and Applied Mathematics. Linköping University, Faculty of Science & Engineering.
    Wennergren, Uno
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology. Linköping University, Faculty of Science & Engineering.
    Density-Dependent Feedback in Age-Structured Populations2019In: Journal of Mathematical Sciences, ISSN 1072-3374, E-ISSN 1573-8795, Vol. 242, no 1, p. 2-24Article in journal (Refereed)
    Abstract [en]

    The population size has far-reaching effects on the fitness of the population, that, in its turn influences the population extinction or persistence. Understanding the density- and age-dependent factors will facilitate more accurate predictions about the population dynamics and its asymptotic behaviour. In this paper, we develop a rigourous mathematical analysis to study positive and negative effects of increased population density in the classical nonlinear age-structured population model introduced by Gurtin \& MacCamy in the late 1970s. One of our main results expresses the global stability of the system in terms of the newborn function only. We also derive the existence of a threshold population size implying the population extinction, which is well-known in population dynamics as an Allee effect.

  • 28.
    Andersson, Magnus
    University of Gävle, Faculty of Engineering and Sustainable Development, Department of Electronics, Mathematics and Natural Sciences.
    Bergviksäpplet och dess fruktsättning2014Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    Trees of Bergvik apple (Bergviksäpple) planted between 2001 and 2007 have shown varying harvest. This study investigates why some trees gets low or no harvest while others get significantly higher harvest. The aim is to identify some reasons why fruiting differs between the trees and if possible suggest and/or enlighten the tree owners what can be done to improve fruiting. The study includes 25 trees, mostly located in Hälsingland, Sweden. The tree owners have answered two questionnaires, first in the spring with questions regarding flowering and the second in the autumn, regarding harvest. The answers to these questionnaires form the foundation for this work.

    The result of the study reveals differences in harvest. Older trees and/or trees with good vegetative growth have larger harvest while trees with poor growth in some cases didn’t even get flowers. Younger trees with good growth gave good harvest. This concludes that the single most important factor to get good harvest is good vegetative growth.

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  • 29.
    Andersson, Nelly
    et al.
    Halmstad University, School of Business, Innovation and Sustainability.
    Lindeberg, Richard
    Halmstad University, School of Business, Innovation and Sustainability.
    Nattbelysningens påverkan på förekomsten av nattfjärilar i Halmstads urbana grönområden.2023Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    Abstract

    Moths are a vulnerable group when exposed to night lighting, it affects their basic drives such as foraging and reproduction and increases their mortality through stress and increased risk of predation. Dark and illuminated localities in Halmstads’ urban green areas were inventoried to study the impact of night illumination on the number of individuals and species diversity of moths. In the study, significant differences were found in the individual number of moths and species diversity between the dark and illuminated localities, which could not be significantly correlated to illuminance present in the localities. However, there were indications that illuminance may still have negatively affected the number of individuals and species diversity of moths in this study. There was one illuminated locality that stood out from the rest where species diversity was the third highest measurement from the entire study, which can possibly be attributed to the presence of flowering shrubs. Therefore we suggest that flowering shrubbery can be implemented as a measure to prevent the impact of night illumination on moth populations and becomes the basis for supplementary and follow-up studies of the subject.

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  • 30.
    Andersson, Niki
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Biology and biodiversity of tardigrades in the world and in Sweden: Current status and future visions2017Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Tardigrades are small water-dwelling invertebrates that can live almost anywhere in the world. Even though they are well-known our knowledge about them is still scarce. The aim of this study was therefore to explore our current knowledge about tardigrades by: (1) explore their global phylogeny and biogeography based on bioinformatics (2) screen for tardigrades in select locations of northern Sweden and compare with other Swedish locations, and (3) identify at least one tardigrade from northern Sweden and explore the published biomarkers for further identification. The bulk of this thesis was based on evaluation of the Silva database for analyzing SSU (small subunit) and LSU (large subunit) tardigrade sequences and create phylogenetic trees. Some initial lab work was performed using samples of moss and lichen from Piteå, Vindeln and Öland. Results show that only few countries have been explored with regard to tardigrades, and in Sweden more research have been performed in the south compared to the north. The phylogenetic trees give a rough overview of tardigrade relatedness but many of the sequences need to be improved and more sequence work from additional environments is needed. In the lab tardigrades were only found from the Piteå samples, and one of those was identified as Macrobiotus hufelandi, for which a new biomarker was created. Overall, tardigrade research need to continue and expand to other regions in order to understand how these organisms differ between different environments, and more work is needed to ensure higher quality of sequences added to databases.

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  • 31.
    Andersson, Rebecca
    Linköping University, Department of Physics, Chemistry and Biology, Biology.
    An Evaluation of Two Presumptive Blood Tests and Three Methods to Visualise Blood2017Independent thesis Basic level (degree of Bachelor), 10,5 credits / 16 HE creditsStudent thesis
    Abstract [en]

    The aim of this study was to validate the two presumptive blood tests LMG, LCV and the three visualising blood methods Bluestar Forensics, Lumiscene and the Ruhoff method. The methods’ sensitivity, durability, matrices effects, false positive results and the methods effect on subsequent DNA analysis were studied. DNA analyses were also performed to assess the detection limit of the forensic DNA analysis. Drops of diluted blood were applied on different absorptive matrices and the sensitivity was investigated. The solutions were also placed under different conditions to investigate the durability of the solutions. The solutions were applied upon panels using different chemicals and materials and the false positive results were studied. The DNA analyses were performed by diluting the blood with Bluestar Forensics, the hydrogen peroxide method, the Ruhoff method and deionised water. The study showed that the LMG with a 3 % H2O2 concentration performs the best and it is suited for practical casework. The positive results of LMG was easier to interpret than those of LCV, this is probably due to the fixative agent of the used LCV solution. Bluestar Forensics and Lumiscene did perform similar on the different matrices tested, but the Lumiscene solution had a slightly higher durability. The results strongly indicate that the Ruhoff method can be used without luminol, hence only as a hydrogen peroxide solution (the hydrogen peroxide method). All three visualising blood methods decreases chances of retrieving a positive DNA profile, however the visualising blood methods could be used if the blood cannot be found in any other way. A DNA profile was obtained from the one blood sample analysed at dilution of 1:256 in deionized water.

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  • 32.
    Andin, Josefine
    Linköping University, Department of Behavioural Sciences and Learning, Disability Research. Linköping University, Faculty of Arts and Sciences. Linköping University, The Swedish Institute for Disability Research.
    Biologisk nivå2021In: Att leva som andra: biopsykosociala perspektiv på funktionsnedsättning och funktionshinder / [ed] Lisa Kilman, Josefine Andin, Håkan Hua, Jerker Rönnberg, Lund: Studentlitteratur AB, 2021, p. 39-66Chapter in book (Other academic)
  • 33.
    Ansmark, Julia
    Karlstad University, Faculty of Health, Science and Technology (starting 2013).
    Utomhusundervisning och elevers relation till naturen: En intervjustudie med lärare kring deras utomhusundervisning2020Independent thesis Advanced level (professional degree), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    In today’s digitalised society we spend a lot of time indoors, kids included, and not as much time outdoors in nature. Thoughts that might appear because of this include what children’s relation to nature looks like and what we as teachers can do to improve this relation. The purpose of this study is therefore to contribute with knowledge about teachers’ thoughts and use of outdoor education, and how they view pupils’ relation to nature based on their outdoor education.

    The method used in this study was to conduct interviews with five different teachers about their work with outdoor education, along with their thoughts and views on it. A thematic analysis was used to extract different themes from the teachers’ interview answers. This analysis resulted in six different themes covering teachers’ thoughts and outdoor education. The results show that outdoor education often consists of group-based activities with a focus on practical work where many senses are activated and stimulated. According to the teachers, the way that they work with outdoor education also contributes to a more positive relation between pupils and nature, by improving their interest, but also by giving a better understanding of the interaction between humans, animals and plants, as well as our connection to them. Based on these findings, it is important that teachers try to use more of this kind of outdoor education to help develop and improve the pupils’ relation to nature, while ensuring a productive and healthy environment.

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  • 34.
    Anstrén, Ludwig
    Halmstad University, School of Business, Engineering and Science.
    The Reliability of Cooper ́s Test in Subjects Between 28-60 Years of Age2015Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    Background: Maximal oxygen uptake (VO2max) is a determinant of an individual’s ability to handle oxygen during maximal exercise. To measure VO2max expensive equipment and expertise personnel are required. To make the process of measuring VO2max easier, several submaximal and maximal tests have been created in which an estimation of VO2max could be made. Cooper’s 12-minute run (12MR) was created in 1968 and was tested on 115 military men with a mean age of 22 years. Since then the 12MR test has been re- tested and validated towards maximal treadmill tests on several occasions. When an age of 30 years is reached, VO2max starts to decline with 9-10 percent per decade but can be halted by different forms of exercise. With exercise of moderate to high intensity the decline can be halted by almost 50 percent. Objective: To investigate the reliability of estimated VO2max in a test retest scenario of Cooper ́s 12MR on a mixed healthy population between the ages of 28-60. Method: Nine women and five men, healthy subjects with a mean age of 43 ± 8 participated in the present study. A test retest of Cooper ́s 12MR took place with a minimum of seven days between tests. The subjects had to run as many laps as possible on the track during a 12-minute period. Finished laps were then counted and the fraction of the last lap was measured with a measuring wheel and then added to the total distance. To estimate the subjects’ VO2max Cooper ́s table was used. Results: The single measure Intraclass correlation (ICC) that was found, between the estimated VO2max made from the initial test to the retest on Cooper ́s 12MR, was 0.979. ICC showed a small error variance correlation between the tests and was close to the optimal correlation of 1.0. Conclusion: A standardized protocol for performing Cooper ́s 12MR showed good repeatability for estimating VO2max in two separate tests for a mixed population between 28 to 60 years of age. 

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  • 35.
    Antman Molin, Helena
    et al.
    Linköping University, Department of Physics, Chemistry and Biology.
    Sjöstrand, Mikael
    Linköping University, Department of Physics, Chemistry and Biology.
    Sojans roll i världen: En studie i sojans användning, ekosystemtjänstavtryck och framtida användning: ett underlag för undervisning mot en hållbar utveckling2019Independent thesis Basic level (professional degree), 10 credits / 15 HE creditsStudent thesis
    Abstract [sv]

    Syftet med denna litteraturstudie var att undersöka världens konsumtion och produktion av soja samt den påverkan sojaodlingarna har på ekosystem och ekosystemtjänster. Sojan är rik på protein vilket har gjort den till en viktig gröda för människan, framförallt för vår utfodring av djur. Men den används också i framställningen av biobränsle. Konsumtionen av sojabönorna är störst i Kina men mycket av sojan stannar också kvar i produktionsländerna. Vi har identifierat USA och Brasilien som nutidens största producenter och har fördjupat oss i deras sojaproduktion. I USA påverkar produktionen främst inlandsvåtmarker, gräsmarker och lövskog. Ekosystemtjänster som vattenreglering, kolinlagring och uppväxtmiljöer går förlorade. I Brasilien odlas soja i Amazonas där tropisk regnskog är det ursprungliga ekosystemet, och på Cerradon, vilket är ett tropiskt gräs- och skogslandskap. De främsta förlusterna av ekosystemtjänster är den biologiska mångfalden och flödet av vatten. En för kraftig avskogning av regnskogen har potential till att orsaka en kollaps av ekosystemet som då ersätts av savann. Utöver detta finns en tvåvägsinteraktion i flödet av vatten mellan Cerradon och Amazonas, där båda ekosystemen stöttar varandra. Sojaodlingarna bidrar med ekosystemtjänster i form av mat och råmaterial och har potential till att kompensera en del av sitt ekosystemtjänstavtryck via vattenfiltrering, pollinering och skadedjursbekämpning. Vår slutsats är att sojan även i framtiden kommer vara en viktig gröda på grund av sitt proteininnehåll. Dock behövs en förändring i hur den används då direkt konsumtion av växtprotein är mer effektivt än protein från animaliska källor i en värld där resurserna blir alltmer knappa. 

    Syftet var även att skapa ett didaktiskt arbetsområde grundat i kunskapen om sojan och dess roll i världen vilken tagits fram i litteraturstudien. Arbetsområdet hittas under rubrik 10. ”Pedagogisk planering”.

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  • 36.
    Antonsson, Rebecka
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Behavioral effects of deep brain stimulation in the subthalamic nucleus in obsessive compulsive disorder2021Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    Obsessive compulsive disorder (OCD) is one of the most disabling psychiatric disorder. About 10% of patients with OCD do not respond to pharmacological treatment. However, deep brain stimulation (DBS) has advanced as an alternative treatment. In 2002, two patients who suffered from co-morbidity of Parkinson’s disease (PD) and OCD were treated with DBS for their PD, with DBS-electrodes placed in the subthalamic nucleus (STN). Surprisingly, not only PD symptoms but also OCD symptoms were improved. This was the first time that patients with OCD were treated with DBS in STN and it was found to markedly improve their symptoms. When performing DBS in patients with OCD, as well as for treating PD, several side-effectshave been observed. The side-effects can be both physical and psychological. In this project,the aim is to investigate the efficiency and side-effects of DBS in OCD, correlated with the position of the electrode in, or near, the STN. To address the aim, 10 published reports were analysed. It was found that all electrode positions reported resulted in great improvement of OCD symptoms. In fact, 88% of patients had significant improvement. There was no clear correlation between position of the electrode and number or type of side-effect. However, there was a trend that patients with the electrode placed in associative/limbic STN suffered from more side-effects. In conclusion, this project demonstrates that there might be a correlation between target for electrode stimulation and side-effects. It would be interesting analyse this closer, including additional electrode target areas, but also consider other possible explanations for the variety of side-effects caused by DBS for OCD. 

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  • 37.
    Appel, Madeleine
    University of Gävle, Faculty of Engineering and Sustainable Development, Department of Electronics, Mathematics and Natural Sciences.
    Kulturarvets mosaiklandskap i ny tappning för trädgårdar och balkonger: En litteraturstudie med designförslag som bidrag för bevarandet av mångfalden för solitära bins överlevnad2015Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    Abstract. The purpose of this study is to find out what can be done in gardens and balconies for solitary bees survival, species have already been lost or are red-listed because of poor conditions in terms of habitat. What can design-proposals look like for gardens and balconies? What do suitable habitats contain and what do threats look like for solitary bees?The goal with this literature study was to find answers to my questions. Based on facts that emerged from the results, design proposals have been made for gardens and balconies. Increased biotope-surface from ancient times mosaic-landscape can in modern environments like gardens and balconies be designed as non-toxic and flower-rich meadows, flowering border zones, ditches and flower beds, potted plants, flowering trees and shrubs. Solitary bees need shelter, water to drink and food to eat as in nectar and pollen-rich plants. They need flowering plants from early spring to late autumn to survive. It´s important to spread knowledge and understanding how solitary bees live their lives, that people can cooperate to achieve long-term sustainable habitat solutions. Solitary bees need many flowering plant-surfaces that can act as dispersal corridors in to urban environments, where every single square meter flowering-surface is of importance. Solitary bees increase in number with increasing biotope-surfaces which are facts that design proposals are based on. Devastating threats for solitary bees are floral shortage in urban areas, spraying with various poisons, domestic bees spreading diseases, human fear of small insects and altered habitats.

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  • 38.
    Ardabili, Sahar
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology.
    Microfluidic bases sample preparation for blood stream infections2014Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Microfluidics promises to re-shape the current health-care system by transferring diagnostic tools from central laboratories to close vicinity of the patient (point-of-care). One of the most important operational steps in any diagnostic platform is sample preparation, which is the main subject in this thesis. The goal of sample preparation is to isolate targets of interest from their surroundings. The work in this thesis is based on three ways to isolate bacteria:  immune-based isolation, selective cell lysis, size-based separation.

    The first sample-preparation approach uses antibodies against lipopolysaccharides (LPS), which are surface molecules found on all gram-negative bacteria. There are two characteristics that make this surface molecule interesting. First, it is highly abundant: one bacterium has approximately a million LPS molecules on its cell-wall. Second, the molecule has a conserved region within all gram-negative bacteria, so using one affinity molecule to isolate disease-causing gram-negative bacteria is an attractive option, particularly from the point of view of sample preparation. The main challenge, however, is antigen accessibility. To address this, we have developed a treatment protocol that improves the capturing efficiency.

    The strategy behind selective cell lysis takes advantage of the differences between the blood-cell membrane and the bacterial cell-wall. These fundamental differences make it possible to lyse (destroy) blood-cells selectively while keeping the target of interest, here the bacteria, intact and, what is more important alive. Viability plays an important role in determining antibiotic susceptibility.

    Difference in size is another well-used characteristic for sample- separation. Inertial microfluidics can focus size-dependent particle at high flow-rates. Thus, particles of 10 µm diameter were positioned in precise streamlines within a curved channel.  The focused particles can then be collected at defined outlets.  This approach was then used to isolate white blood cells, which account for approximately 1% of the whole blood.  In such a device particles of 2µm diameter (size of bacteria) would not be focused and thereby present at every outlet. To separate bacteria from blood elasto-inertial microfluidics was used. Here, e blood components are diverted to center of the channels while smaller bacteria remain in the side streams and can subsequently be separated.

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  • 39.
    Ardenstedt, Jonathan
    et al.
    Halmstad University, School of Business, Innovation and Sustainability.
    Fridefors, Patricia
    Halmstad University, School of Business, Innovation and Sustainability.
    Effekter av en toxisk cocktail av Roundup och livsmedelsklassad polypropylenplast på vattenloppan Daphnia Magna2023Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    Toxins and pollutants rarely come alone and studies about various toxic substances are often performed with only one substance at a time. There are studies that have examined different cocktails of substances, but sometimes it can be difficult to identify all sources that affect an organism. We have investigated how a combination of the herbicide Roundup and Food Safe polypropylene plastic affect the freshwater crustacean Daphnia magna. We found that Roundup causes 100% mortality before reaching fertility in higher doses, but that in small doses does not result in lower fitness compared to the control group, but even increases the initial survival rate when Roundup is added to plastic jars. A cocktail of Roundup and plastic resulted in a doubled development time for the eggs. Eggs from individuals in plastic jars also had a longer development time but there was also a much higher number of eggs from these individuals. Futiure studies ought to investigate the fitness of the offspring. Early in the study we discovered that there was most likely a third factor influencing the daphnia negatively, that could not be explained by plastic jars or Roundup, but one that we could not identify. Therefore, we also wish to urge that experiments can easily be influenced by unknown factors.   

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  • 40.
    Arinell, Karin
    et al.
    Örebro University, School of Health Sciences. Department of Cardiology, Örebro University Hospital, Örebro, Sweden.
    Sahdo, Berolla
    Department of Clinical Medicine, Örebro University, Örebro, Sweden.
    Evans, Alina L.
    Faculty of Forestry and Wildlife Management, Hedmark University College, Evenstad, Norway; Section of Arctic Veterinary Medicine, Norwegian School of Veterinary Science, Tromsø, Norway.
    Arnemo, Jon M.
    Faculty of Forestry and Wildlife Management, Hedmark University College, Evenstad, Norway; Department of Wildlife Fish and Environmental Studies, Faculty of Forest Sciences, Swedish University of Agricultural Sciences, Umeå, Sweden.
    Baandrup, Ulrik
    Department of Pathology, Vendsyssel Hospital, Hjørring, Denmark; Faculty of Medical Sciences, Aalborg, Denmark.
    Fröbert, Ole
    Örebro University Hospital. Örebro University, School of Medical Sciences. Department of Cardiology, Örebro University Hospital, Örebro, Sweden.
    Brown Bears (Ursus arctos) Seem Resistant to Atherosclerosis Despite Highly Elevated Plasma Lipids during Hibernation and Active State2012In: Clinical and Translational Science, ISSN 1752-8054, E-ISSN 1752-8062, Vol. 5, no 3, p. 269-272Article in journal (Refereed)
    Abstract [en]

    Hibernation is an extreme physiological challenge for the brown bear (Ursus arctos) in which metabolism is based mainly on lipids. The study objective was to compare plasma lipids in hibernating and active free-ranging brown bears and relate them to arterial histopathology. Blood was drawn from seven immobilized free-ranging brown bears (three females, 23 years old) during hibernation in February and from the same bears while active in June and analyzed by enzymatic and automated hematology methods within 48 hours of sampling. Left anterior descending coronary arteries and aortic arches from 12 bears (six females, 1.512 years old) killed in hunting were examined by histopathology. Total plasma cholesterol decreased from hibernation to the active period (11.08 +/- 1.04 mmol/L vs. 7.89 +/- 1.96 mmol/L, P= 0.0028) as did triglyceride (3.16 +/- 0.62 mmol/L vs. 1.44 +/- 0.27 mmol/L, P= 0.00012) and LDL cholesterol (4.30 +/- 0.71 mmol/L vs. 2.02 +/- 1.03 mmol/L, P= 0.0075), whereas HDL cholesterol was unchanged. No atherosclerosis, fatty streaks, foam cell infiltration, or inflammation were seen in any arterial samples. Brown bears tolerate elevated cholesterol levels, obesity, physical inactivity, and circulatory slow flow during hibernation without signs of -atherosclerosis. This species might serve as a reverse translational model for atherosclerosis resistance.

  • 41.
    Arnroth, Cornelia
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    A study of protein aggregation processes using Dynamic Light Scattering: Validation of the technique and experimental trial with an active pharmaceutical ingredient2020Independent thesis Advanced level (professional degree), 300 HE creditsStudent thesis
    Abstract [en]

    Protein pharmaceuticals is one of the fastest growing class of therapeutics today. However, they pose a lot of challenges in production lines due to their poor stability. Protein aggregation is one of the most common results of protein instability and is a risk factor regarding the quality of therapeutics.

    This master thesis at RISE focused on validating the techniques Dynamic Light Scattering (DLS) and multi angle DLS (MADLS) with respect to detection of aggregation. The model protein B-lactoglobulin was used to assess the robustness and accuracy of DLS. A comparison between two instruments from Malvern, Zetasizer Nano (2006) and Zetasizer Ultra (2018) was done with respect to DLS. It was determined that they were in many ways equivalent, but the newer model Ultra was favourable due to reduced noise and its ability to detect a lower concentration of aggregates. MADLS produced more precise results which is reflected in narrower distributions and has a higher sensitivity than DLS with regards to separating particles near in size. Both techniques proved sensitive enough to differentiate between aggregates and native protein.

    Experimental trials were performed with an active pharmaceutical ingredient, API. The experimental trials with the API aimed to investigate what conditions and surface-interfaces that might pose a risk for aggregation. Despite efforts put in creating an environment where aggregation could be monitored, aggregation could not be established. Measurements with the API generated less reliable results due to noisy data and a lack of reproducibility between individual measurements.

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  • 42.
    Askvärn, Elisabeth
    University of Gävle, Faculty of Engineering and Sustainable Development, Department of Electronics, Mathematics and Natural Sciences.
    Kan växter lindra klimakteriebesvär?: Behandling av vasomotoriska symptom med hjälp av örtmedicin2016Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    The aim of this study was to investigate the use of herbal medicine for vasomotor symptoms during menopause. The questions posed were which herbs that were used, what parts of the herbs that were used, and how the plant parts were prepared and utilized. The last question covered how much the plants alleviated the vasomotor symptoms.

    A review of the scientific literature was carried out. In the articles, 20 herbs and plants were used, but only five of them were said to relieve the vasomotor symptoms. The five plants were Actaea racemosa, Angelica sinensis, Ginkgo biloba, Glycine sp. and Pimpinella anisum.  The most commonly used parts of the herbs were the roots, often through extracts that were processed in order to increase the concentration and to transform the plant parts into powder. The powder was then for the most part transformed to tablets and capsules. Sometimes, information was missing, such as the scientific names of the plants, what parts of the plants that were used and how the herbs were prepared and utilized.

    On average, the herbs alleviated the vasomotor symptoms by 60 %. Most of the herbs appeared to relieve mild symptoms more than they alleviated strong symptoms. An exception was P. anisum, which decreased both the amount of and the strength of the flushes by 74 %.

    This literature study shows that there are plants that influence the vasomotor symptoms in a positive direction. At the same time, it shows that the information in the articles is sometimes incomplete and that the scientists do not always study if the herbs can give side effects.

    Herbal medicine could be an alternative for women who, for different reasons, cannot or do not want to take synthetic hormones or other pharmacological medicines. However, in order to make herbal medicine part of the treatment offered by public health care, longitudinal studies that also investigate possible side effects or risks are needed for securing the effect of the herbs on the human body.

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  • 43.
    Attorps, Iiris
    et al.
    University of Gävle, Faculty of Engineering and Sustainable Development, Department of Electrical Engineering, Mathematics and Science, Mathematics.
    Kellner, Eva
    University of Gävle, Faculty of Engineering and Sustainable Development, Department of Electrical Engineering, Mathematics and Science, Biology.
    Ett helhetsgrepp för likvärdig skola2021In: Nämnaren : tidskrift för matematikundervisning, ISSN 0348-2723, no 3, p. 35-39Article in journal (Other (popular science, discussion, etc.))
  • 44.
    Awoga, Roseline Ayowumi
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Environmental toxicology. Biology Education Centre (IBG).
    Optimization of an In-Vitro System for Testing Developmental Neurotoxicity Induced by Oestrogen, Androgen and Thyroid Disruption2021Independent thesis Advanced level (degree of Master (Two Years)), 40 credits / 60 HE creditsStudent thesis
    Abstract [en]

    In recent times, endocrine disrupting chemicals (EDCs) have been associated with the rise in neurodevelopmental disorders such as autism, attention deficit hyperactivity disorder (ADHD) and decreased intelligence quotient (IQ) in children. This effect is suspected to be induced at pre-/peri-natal development, via an alteration in hormonal signaling, thus interfering with neuronal differentiation, with subsequent effect on normal brain development and function in exposed children. This issue increases the need for chemical screening for potential developmental neurotoxicity (DNT) effect. The current available EDC induced DNT test guideline is based on in-vivo testing that requires animal use. Here, a multipotent neural progenitor cell line, the C17.2 cell-line, generated from neural stem cells of the external germinal layer of mouse cerebellum, with potential to differentiate to neurons or astrocytes, is introduced for in-vitro EDC induced DNT testing. This project focused on optimizing the C17.2 cell-line for the detection of EDC-induced DNT with emphasis on the disruption of the oestrogen, androgen, and thyroid hormone systems. It aimed at validating the involvement of oestrogen, androgen, and thyroid hormone on molecular and cellular endpoints relevant for the differentiation of the C17.2 cells.  Herein, the cells were exposed to the hormonal agonist and antagonist at a range of concentrations for a 10-day differentiation period. After exposure, LDH, viability assay and morphological changes (percentage of neurons in culture and neurite outgrowth) were evaluated. The results showed no morphological changes induced by androgen receptor (AR) agonist/antagonist at relevant physiological concentrations. The thyroid receptor (TR) agonist and antagonist on the other hand showed a response in the form of increased neurite outgrowth in relation to the negative control at a concentration range of 40-200 nM and 40 nM respectively. The oestrogen receptor (ER) antagonist at 100 nM also increased percentage neuron in culture. Additionally, in-silico analysis of microarray and RNA sequencing data were used to map out target genes regulated by ER, AR and TR and involved in neurodevelopment. With this approach, 29 marker genes were identified. Validation of the marker genes by means of gene expression (qPCR) was carried out, ER and TR agonist/antagonist were observed to modulate the expression of examined genes. In summary, the model could not be established for detecting EDC induced DNT via androgenic and oestrogenic pathway, while it is a promising model for identifying DNT induced by thyroid hormone signalling disruption.

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  • 45.
    Axelsson, Amanda
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Åtgärder för att minska humushalten i en dricksvattentäkt2019Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [sv]

    Vedborme träsk är en utdikad sjö på norra Öland som utreds för restaurering till en funktionell våtmark. Åtgäderna syftar till förbättrad vattenkvalitet och biologisk mångfald. Hornsjöns ytvattentäkt som ligger nedströms avrinningsområdet behöver skyddas genom att minska belastningen av humusämnen. Humusämnen leder till brunifiering, en process som färgar vatten brunt. Höga halter kan ge negativa effekter på både vattenrening och ekosystemet. idag är Vedborme träsk torrlagt större delen av året. Jordmånen består av torv i olika nedbrytninsstadier. Tidigare utredning tyder på att våtmarken både läcker och faastlägger humus. Även andra torvmarker i området tros bidra till uppmätta höga halter av humusämnen. Åtgärder för ökad uppehållstid på vattnet och minskning av torv i träsket förelås. Detta examensarbete syftar till att undersöka de föreslagna åtärderna från tidigare utredning och få bättre kunskap om våtmarkens effekter på humusretentionen. För att svara på frågan har ett laboratorieexperiment utförts. Ett mesokosomexperiment utfördes i ett konstantrum med tre olika substrat av torv, gyttja och vatten från Vedborme träsk. Varje substrat hade 10 replikat varav hälften av replikaten blev behandlade med ljus och andra hälften utan ljus. Resultaten visar att underliggande gyttjor har en bättre renande effekt på humus jämfört med torv i testerna. Gruppen men torv skiljde sig från övriga grupper i färgtal när de hade exponerats för ljus (Medianvärden: Torv=125, Gyttja=85, Vatten=125 mg/l Pt). Samma skillnad kunde visas i testet med TOC som responsvariabel. Ljusexponering indikerade en renande effekt på substratet vatten och skulle kunna utredas vidare genom fler analyser av insamlad data från detta experiment. 

    Slutsatserna av detta experiment är följande:

    -Experimenten visar att substatet gyttja från träsket har en bättre renande effekt i ljus och mörker jämfört med torv. Vilket motiverar en bortforsling av torv för att öka reningen i våtmarken. 

    -Torv hade högst TOC och färgtal i experimenten jämfört med andra grupper.

    -Ljuset verkar ha ahft en renande effekt på vattnets halt av humus.

    -Resultaten var förväntade baserat på tidigare forskning.  

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  • 46.
    Ayranci, Diyar
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Design, expression and purification of virus-like particles derived from metagenomic studies: Virus-like Particles (VLP) of novel Partitiviridae species, Hubei.PLV 11, and novel Soutern pygmy squid flavilike virus were designed, expressed using the bac-to-bac expression system and then pruified using various methods2021Independent thesis Advanced level (degree of Master (Two Years)), 30 credits / 45 HE creditsStudent thesis
    Abstract [en]

    Viruses are entities which are made of a few genes and are reliant on obligate parasitism to propagate. Due to the obligate connection to their hosts, virus evolution is constrained to the type of host. Viruses however do transmit to evolutionary distinct hosts; in these cases, the phylogenetic relationship of the hosts usually are close. In some instances, RNA-viruses have made host jumps between evolutionary distant hosts, such as the host jump from invertebrates to vertebrates, and fungi to arthropod. Partitiviruses are double stranded RNA viruses which mainly infect fungi and plants. The defining characteristic of these double stranded RNA viruses are the double layered capsids which are formed by a single open reading frame (ORF). The capsid proteins form icosahedral virus particles which are in the magnitude of 30-40 nm. Metagenomic studies have discovered partitiviruses originating from an insect in the Odanata family, a finding which contradicts the fungal host specificity of partitiviruses. The finding of the Hubei.PLV 11 thus implies the existence of a partitiviruses containing structural elements in their capsids which could be involved in the infection of arthropods. Thus, this virus could be used as a model for a structural comparison with its fungi infecting relatives with hopes to identify common viral structural factors necessary for the infection of arthropods. For this purpose, the Hubei.PLV ORF was cloned and then transfected into insect Spodoptera frugiperda (Sf-9) cells using a baculovirus expression system, “bac-to-bac” expression system. The FLAG-tagged capsid proteins were expressed by the Sf-9 cells to be approximately 60 kDa. After ultra-centrifugation in a sucrose gradient, some spontaneous assembly into the expected ~40 nm icosahedral virus-like particles were observed using low resolution scanning electron microscopy. The observed particles were also confirmed by a dynamic light scattering experiment (DLS) and a higher resolution cryo-EM microscope. Thus, the bac-to-bac expression system can be used to produce VLPs from this genus of viruses, and this metagenomically derived virus genome. However, for future success in defining a high-resolution model of this virus, it is recommended that the Sf-9 culture volume is sufficiently high for enough particle production which is necessary for a high-resolution map. The other virus, the Southern pygmy squid Flavilike virus (SpSFV) has been suggested to be the oldest relative of the land based flaviviruses. The SpSFV was found to be the most divergent of the flaviviruses, and to infect invertebrates. Solving for the structure of the SpSFV and comparing it to vertebrate infecting flaviviruses could therefore lead to the identification of factors necessary for the adaptation to vertebrates and thus the humoral immunity by flaviviruses. The soluble E-protein was expressed using the bac-to-bac expression system. The protein was indicated to be multiglycosylated and approximately 50 kDa which is in line with other strains in the genus. Affinity chromatography did not elute this protein, likely due to the His-tag not being spatially available. Cation exchange could elute some protein, but not much from the small ~30 mL culture. To conclude, VLP assembly was confirmed by the Hubei.PLV, thus, solving for the structure is a distinct possibility when a larger Sf-9 culture is used to produce the VLPs. For the SpSFV soluble E-protein, the protein is secreted into the supernatant of the Sf-9 cultures, making purification a possibility. For this, a large Sf-9 culture can be used to produce this protein and then purify it with a cat-ion exchange chromatography.

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  • 47.
    Azinas, Stavros
    et al.
    Stockholm University, Science for Life Laboratory (SciLifeLab). Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Carroni, Marta
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).
    Cryo-EM uniqueness in structure determination of macromolecular complexes: A selected structural anthology2023In: Current opinion in structural biology, ISSN 0959-440X, E-ISSN 1879-033X, Vol. 81, article id 102621Article in journal (Refereed)
    Abstract [en]

    Cryogenic electron microscopy (cryo-EM) has become in the past 10 years one of the major tools for the structure determination of proteins. Nowadays, the structure prediction field is experiencing the same revolution and, using AlphaFold2, it is possible to have high-confidence atomic models for virtually any polypeptide chain, smaller than 4000 amino acids, in a simple click. Even in a scenario where all polypeptide chain folding were to be known, cryo-EM retains specific characteristics that make it a unique tool for the structure determination of macromolecular complexes. Using cryo-EM, it is possible to obtain near-atomic structures of large and flexible megacomplexes, describe conformational panoramas, and potentially develop a structural proteomic approach from fully ex vivo specimens.

  • 48.
    Baas, Pauline
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    van der Valk, Tom
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Vigilant, Linda
    Ngobobo, Urbain
    Binyinyi, Escobar
    Nishuli, Radar
    Caillaud, Damien
    Guschanski, Katerina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Population-level assessment of genetic diversity and habitat fragmentation in critically endangered Grauer's gorillas2018In: American Journal of Physical Anthropology, ISSN 0002-9483, E-ISSN 1096-8644, Vol. 165, no 3, p. 565-575Article in journal (Refereed)
    Abstract [en]

    Objectives: The critically endangered Grauer's gorilla (Gorilla beringei graueri) has experienced an estimated 77% population decline within a single generation. Although crucial for informed conservation decisions, there is no clear understanding about population structure and distribution of genetic diversity across the species' highly fragmented range. We fill this gap by studying several core and peripheral Grauer's gorilla populations throughout their distribution range.

    Materials and Methods: We generated genetic profiles for a sampling of an unstudied population of Grauer's gorillas from within the species' core range at 13 autosomal microsatellite loci and combined them with previously published and newly generated data from four other Grauer's gorilla populations, two mountain gorilla populations, and one western lowland gorilla population.

    Results: In agreement with previous studies, the genetic diversity of Grauer's gorillas is intermediate, falling between western lowland and mountain gorillas. Among Grauer's gorilla populations, we observe lower genetic diversity and high differentiation in peripheral compared with central populations, indicating a strong effect of genetic drift and limited gene flow among small, isolated forest fragments.

    Discussion: Although genetically less diverse, peripheral populations are frequently essential for the long-term persistence of a species and migration between peripheral and core populations may significantly enrich the overall species genetic diversity. Thus, in addition to central Grauer's gorilla populations from the core of the distribution range that clearly deserve conservation attention, we argue that conservation strategies aiming to ensure long-term species viability should include preserving peripheral populations and enhancing habitat connectivity.

  • 49.
    Babateen, Omar
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience, Physiology.
    Korol, Sergiy V.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience, Physiology.
    Jin, Zhe
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience, Physiology.
    Bhandage, Amol K.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience, Physiology.
    Ahemaiti, Aikeremu
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience, Developmental Genetics.
    Birnir, Bryndis
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience, Physiology.
    Liraglutide modulates GABAergic signaling in rat hippocampal CA3 pyramidal neurons predominantly by presynaptic mechanism2017In: BMC Pharmacology & Toxicology, E-ISSN 2050-6511, Vol. 18, article id 83Article in journal (Refereed)
    Abstract [en]

    Background

    γ-Aminobutyric acid (GABA) is the main inhibitory neurotransmitter in the brain where it regulates activity of neuronal networks. The receptor for glucagon-like peptide-1 (GLP-1) is expressed in the hippocampus, which is the center for memory and learning. In this study we examined effects of liraglutide, a GLP-1 analog, on GABA signaling in CA3 hippocampal pyramidal neurons.

    Methods

    We used patch-clamp electrophysiology to record synaptic and tonic GABA-activated currents in CA3 pyramidal neurons in rat hippocampal brain slices.

    Results

    We examined the effects of liraglutide on the neurons at concentrations ranging from one nM to one μM. Significant changes of the spontaneous inhibitory postsynaptic currents (sIPSCs) were only recorded with 100 nM liraglutide and then in just ≈50% of the neurons tested at this concentration. In neurons affected by liraglutide both the sIPSC frequency and the most probable amplitudes increased. When the action potential firing was inhibited by tetrodotoxin (TTX) the frequency and amplitude of IPSCs in TTX and in TTX plus 100 nM liraglutide were similar.

    Conclusions

    The results demonstrate that liraglutide regulation of GABA signaling of CA3 pyramidal neurons is predominantly presynaptic and more limited than has been observed for GLP-1 and exendin-4 in hippocampal neurons.

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  • 50.
    Backius, Helena
    Karlstad University, Faculty of Social and Life Sciences, Department of Biology.
    Förändring av kärlväxters artsammansättning vid återupptagen hävd i skogligt avgränsade ängs- och hagmarker2011Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    Old agricultural landscapes house a great biodiversity. To conserve this diversity the European Union award financial support in the form of environmental grants to encourage farmers to maintain pastures and hay meadows using old-fashioned methods. But are the measures effective and do they meet their purpose? The purpose of this study was to re-inventory ten sample plots from 2002 on the farm Brofallet to see how species composition of vascular plants had been affected by the nine seasons of using these old-fashioned methods management. The farm is completely surrounded by forest, isolated from other agricultural land. No significant overall change was observed concerning the composition of vascular plant species favored by traditional management. Qualitative observations, however, showed an increase in some species favored by traditional management. The conclusion is that the five-year commitment that farmers make to receive the environmental grants is not adequate enough to be able to detect changes in total diversity of vascular plants on a farm such as Brofallet, but that changes may occur faster at other levels in the ecosystem. Moreover, a ramification of this study is the idea that even environmental measures and documentation should be characterized by diversity. In summary, small-scale extensive farming may prove to be important in the overall quest for a sustainable society, both to exploit land for food production using extensive farming, and to maintain biodiversity at the landscape level.

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