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  • 301.
    Larsson, Erika
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Endocrine disruption of the fungicide propiconazole in the frog Xenopus tropicalis: Effects on the aromatase activity and egg development2015Independent thesis Advanced level (degree of Master (One Year)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Amphibian populations around the world are decreasing, and endocrine disrupting chemicals have been suggested as a part of the problem. The fungicide propiconazole is used in agriculture in many countries. It works as a fungicide by inhibiting CYP51, affecting the fungi cell membrane, but it has also been proven to inhibit aromatase, CYP19. Aromatase converts androgens to estrogen and is important for sexual differentiation in the early development and in reproduction in vertebrates. The aim of this study was to investigate the effect of propiconazole on the aromatase activity in brains from the West African clawed frog (Xenopus tropicalis), after larval and adult exposure and on aromatase activity in ovaries after adult exposure. Furthermore, effects on egg development was determined after adult exposure.

    Tadpoles were exposed to propiconazole (0, 25, and 250 µg/L) from three days after hatching until metamorphosis. In a former study, female adult X. tropicalis were exposed to 0 and 250 µg/L propiconazole during 4 weeks. The result of the aromatase activity measurements showed that 250 µg/L propiconazole increased brain aromatase activity after larval exposure. Brain and ovarian aromatase activity was also increased compared to the controls after adult exposure to 250µg/L propiconazole. The increased aromatase activity could reflect a compensatory response to decreased estrogen levels. Propiconazole had a significant impact on egg development, with an increased proportion of atretic oocytes and a decreased proportion of vitellogenic oocytes compared to the controls. The effect on egg development seems to be the result of a low estrogen level. The results suggest that exposure to propiconazole 250 µg/L could have a negative impact on X. tropicalis fertility.  Further studies to determine impacts of environmental exposure concentrations are needed to evaluate the risk of azoles to amphibian reproduction.

  • 302.
    Larsson, Hanna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Den smältande polarisens effekt på de endemiska valarna i Arktis2014Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [sv]

    Klimatförändringarna har en stor påverkan på de arktiska valarna grönlandsval (Balaena mysticetus), vitval (Delphinapterus leucas) och narval (Monodon monoceros), mer än vad som tros vid en första tanke. I dagsläget får dessa valar utstå stora utmaningar som troligenkan komma att förvärras i framtiden om inte isens smältande kan bromsas. En del av utmaningarna innebär att valarna måste genomgå stora förändringar för att överleva, vilket innebär att deras förmåga att anpassa sig spelar en stor roll. Människans jakt på valen har alltid varit ett stort problem för de arktiska valarna, tack vare restriktioner om fångstkvoter och vem som får jaga val ser framtiden ljusare ut i alla fall för grönlandsvalen och vitvalen. För narvalen ser det dock inte lika ljust ut eftersom det är en art som är känsligare än många andra arktiska arter för effekterna som den globala uppvärmningen har på den arktiska miljön.

    I dagsläget har en del effekter på valarna blivit synliga såsom ändrade migrationsvanor och ökad predation. På grund av bristande data från perioden innan klimatförändringarna är detsvårt att dra konkreta slutsatser, därför fokuserar mycket forskning på att förutse vad som kommer att ske i framtiden. Fokus på framtiden är viktigt eftersom det som sker idag redan är försent att göra någonting åt, det vi kan göra är att se till att det inte blir ännu värre.

    Den smältande isens effekter är svåra att skilja på då de överlappar en del, till exempel leder tillgången på föda till förändringar i habitat. Man har i dagsläget sett små skillnader i tillgång på föda, beståndet av istorsken har minskat, eftersom det är en viktig föda för de arktiska valarna kan det ha en effekt. En minskning av en viss typ av plankton har också observerats och eftersom ingen ersättande art har setts kommer detta få effekter på näringsväven i de arktiska haven och därmed alla arter som lever där inklusive de arktiska valarna. I framtiden tror man att primärproduktionen kommer att öka på grund av den höjda vattentemperaturen och den ökande ytan med öppet vatten, detta kommer eventuellt ha en positiv effekt på de arktiska valarna.

  • 303.
    Leal, Luis
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Before speciation: adaptive evolution of diapause regulation in common wood-white butterflies (Leptidea sinapis)2017Independent thesis Advanced level (degree of Master (Two Years)), 30 credits / 45 HE creditsStudent thesis
  • 304.
    Lee, Hyeun-Ji
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Compensatory growth: the relationship between body size and mass at emergence and subsequent mass gain in the emerald damselfly, Lestes sponsa2014Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
  • 305.
    Lee, Iwa
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Environmental Toxicology. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Quantification of p53-expressing cells and neurodegenerative cells in neonatal mouse brain after exposure to PBDE 99, TBBPA or ketamine2011Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
  • 306.
    Leggatt, Rosalind A.
    et al.
    Fisheries & Oceans Canada, Ctr Aquaculture & Environm Res, 4160 Marine Dr, W Vancouver, BC V7V 1N6, Canada..
    Sundström, L. Fredrik
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre. Fisheries & Oceans Canada, Ctr Aquaculture & Environm Res, 4160 Marine Dr, W Vancouver, BC V7V 1N6, Canada..
    Vandersteen, Wendy E.
    Fisheries & Oceans Canada, Ctr Aquaculture & Environm Res, 4160 Marine Dr, W Vancouver, BC V7V 1N6, Canada.;Miracle Springs Inc, 12443 Stave Lake Rd, Mission, BC V2V 0A6, Canada..
    Devlin, Robert H.
    Fisheries & Oceans Canada, Ctr Aquaculture & Environm Res, 4160 Marine Dr, W Vancouver, BC V7V 1N6, Canada..
    Alternate Directed Anthropogenic Shifts in Genotype Result in Different Ecological Outcomes in Coho Salmon Oncorhynchus kisutch Fry2016In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 11, no 2, article id e0148687Article in journal (Refereed)
    Abstract [en]

    Domesticated and growth hormone (GH) transgenic salmon provide an interesting model to compare effects of selected versus engineered phenotypic change on relative fitness in an ecological context. Phenotype in domestication is altered via polygenic selection of traits over multiple generations, whereas in transgenesis is altered by a single locus in one generation. These established and emerging technologies both result in elevated growth rates in culture, and are associated with similar secondary effects such as increased foraging, decreased predator avoidance, and similar endocrine and gene expression profiles. As such, there is concern regarding ecological consequences should fish that have been genetically altered escape to natural ecosystems. To determine if the type of genetic change influences fitness components associated with ecological success outside of the culture environments they were produced for, we examined growth and survival of domesticated, transgenic, and wild-type coho salmon fry under different environmental conditions. In simple conditions (i. e. culture) with unlimited food, transgenic fish had the greatest growth, while in naturalized stream tanks (limited natural food, with or without predators) domesticated fish had greatest growth and survival of the three fish groups. As such, the largest growth in culture conditions may not translate to the greatest ecological effects in natural conditions, and shifts in phenotype over multiple rather than one loci may result in greater success in a wider range of conditions. These differences may arise from very different historical opportunities of transgenic and domesticated strains to select for multiple growth pathways or counter-select against negative secondary changes arising from elevated capacity for growth, with domesticated fish potentially obtaining or retaining adaptive responses to multiple environmental conditions not yet acquired in recently generated transgenic strains.

  • 307.
    Leggatt, Rosalind A.
    et al.
    Fisheries & Oceans Canada, Ctr Aquaculture & Environm Res, Ctr Aquat Biotechnol Regulatory Res, W Vancouver, BC, Canada..
    Sundström, L. Fredrik
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre. Fisheries & Oceans Canada, Ctr Aquaculture & Environm Res, Ctr Aquat Biotechnol Regulatory Res, W Vancouver, BC, Canada..
    Woodward, Krista
    Fisheries & Oceans Canada, Ctr Aquaculture & Environm Res, Ctr Aquat Biotechnol Regulatory Res, W Vancouver, BC, Canada..
    Devlin, Robert H.
    Fisheries & Oceans Canada, Ctr Aquaculture & Environm Res, Ctr Aquat Biotechnol Regulatory Res, W Vancouver, BC, Canada..
    Growth-Enhanced Transgenic Coho Salmon (Oncorhynchus kisutch) Strains Have Varied Success in Simulated Streams: Implications for Risk Assessment2017In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 12, no 1, article id e0169991Article in journal (Refereed)
    Abstract [en]

    Growth hormone (GH) transgenic fish have accelerated growth and could improve production efficiency in aquaculture. However, concern exists regarding potential environmental risks of GH transgenic fish should they escape rearing facilities. While environmental effects have been examined in some GH transgenic models, there is a lack of information on whether effects differ among different constructs or strains of transgenic fish. We compared growth and survival of wild-type coho salmon (Oncorhynchus kisutch) fry, a fast-growing GH transgenic strain containing a metallothionein promoter (T-MT), and three lines/strains containing a reportedly weaker histone-3 promoter (T-H3) in hatchery conditions and semi-natural stream tanks with varying levels of natural food and predators. Rank order of genotype size and survival differed with varying environmental conditions, both within and among experiments. Despite accelerated growth in hatchery conditions, T-MT fry gained little or no growth enhancement in stream conditions, had enhanced survival when food was limiting, and inconsistent survival under other conditions. Rank growth was inconsistent in T-H3 strains, with one strain having highest, and two strains having the lowest growth in stream conditions, although all T-H3 strains had consistently poor survival. These studies demonstrate the importance of determining risk estimates for each unique transgenic model independent of other models.

  • 308.
    Lehtonen, Emily
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Breeding Site Selection and Breeding Success in Red-throated Divers (Gavia stellata): Implications for Wind Power Development2016Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Our alarming rate of resource exploitation and its consequences on the environment is fuelling an increase in sustainable energy production around the world. Wind power appears to be a particularly promising energy source relative to its environmental footprint, with the exception of potential negative effects of wind power on birds. Varying results from impact assessments around the world indicate that knowledge of both abiotic and biotic factors, as well as bird behavior and ecology, is required to assess the cumulative impact of any given wind farm on local bird communities. This study aims to assess the cumulative impact of a proposed wind farm on a threatened seabird, the red-throated diver (Gavia stellata), at one of its breeding "hotspots" in Sweden: the Holmöarna islands. Measurements of environmental variables in lakes on Holmöarna are combined with breeding surveys from 2012 to 2015 to assess which environmental variables may be associated with lakes that red-throated divers do or do not breed in, and which variables are correlated with breeding success. These results are combined with a literature review to assess the potential negative effects of the proposed wind farm on the breeding population on Holmöarna. The results show that average breeding success over the survey period was 0.35 fledged young per pair per year. No difference was found in environmental variables between lakes that divers had or had not bred in. Lake area/perimeter ratio and distance to the sea were significantly negatively correlated with breeding success, although distance to the sea was only significant for lakes with at least one successful breeding attempt during the survey period. Based on these correlations, 33 of a total 40 breeding lakes are shown to have relatively high area/perimeter ratios and long distances to the sea, which may pre-dispose divers breeding within them to low breeding success. These lakes are, therefore, identified as being at high-to-moderate risk of increased breeding failure if breeding success is further reduced as a result of external factors, including that of any negative impacts of the proposed wind farm. 31 of the 40 breeding lakes are also within 1 km of the proposed wind turbine sites, which may render red-throated divers breeding within them vulnerable to displacement as a result of wind farm-related disturbance. The literature review highlights the mechanisms that may determine the cumulative impact of the wind farm on red-throated divers in terms of collision mortality, habitat displacement, and barriers to movement. The strong sensitivity of red-throated divers to disturbance is considered to be the most likely driver of any negative effects of the wind farm. In this context, I thus argue the need for a precautionary approach to planning wind power developments in the vicinity of breeding red-throated diver populations.

  • 309.
    Lehtonen, Emily
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    The Behavioural Ecology of a Potentially Undescribed Morph of Saki Monkey (genus Pithecia) in a Highly Diverse Primate Community2017Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    The importance of tropical forests for global diversity and ecosystem function is well established in scientific literature, but is undermined by gaps in our knowledge of tropical ecosystems and species. Primates play important functional roles in these ecosystems, and despite constituting one of the most well-recognised taxa in the world, many species remain poorly studied. The Area de Conservación Regional Communal Tamshiyacu-Tahuayo (ACRCTT), located in the northeastern Peruvian Amazon, harbours one of the most diverse primate assemblages in the world and presents an ideal opportunity for the study of primate communities and mechanisms of their coexistence. Previous research has recorded the presence of an atypically coloured morph of monk saki monkeys (Pithecia monachus, sensu Marsh 2014) living in sympatry with a population of burnished sakis (Pithecia inusta, sensu Marsh 2014) in the reserve. In this study, the behavioural ecology of this potentially undescribed morph of saki monkey is described, using continuous focal data collected during the early wet season in the ACRCTT. The sakis were most often encountered in multi-adult groups and in the upper forest strata. The observed feeding strategies suggest that fruits and/or seeds constitute the sakis' primary food source in the wet season, although arthropods were also ingested during a large proportion of feeding records. Sex differences in behavioural patterns provide support for a difference in male and female investment in group defence. As only the monk saki morph was encountered during the study, the potential for seasonal habitat differentiation between the saki populations at the ACRCTT is discussed. A survey of primates in flooded and non-flooded forest areas at the ACRCTT was also conducted, in which nine of the 14 primate species recorded at the ACRCTT were encountered. Significant differences in the vertical distribution of primate groups provide evidence for vertical stratification in the ACRCTT primate community. This study contributes to previous research on the poorly-studied Pithecia genus, and provides insights into the mechanisms of niche differentiation between Pithecia and other primates.

  • 310.
    Leijon, Fredrik
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Active machine learning for quantitative kinetic analyses of ligand cell-surface interactions.2017Independent thesis Advanced level (professional degree), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    In the analysis of a ligand-target interaction the kinetic constants are of high interest. Making a good estimation on the kinetic constants is governed by using the best model that describes the data the best. It also of great importance to choose experiments such that certainty on the kinetic constants increases to the highest degree possible. This project is part of a collaboration between UU (Cancer Pharmacology and Computational Medicine, Dept Medical Sciences) and Ridgeview Instruments AB in Uppsala with the aim to implement model selection procedure followed by a plotting of probability density maps, this is referred to as probability distribution of unknown kinetic interaction constants (PDUKC). The project also aims to implement an active learning algorithm to propose optimal experiments so that the parameter certainty increases. It is all implemented in the framework of Bayesian statistics. The implemented active learning algorithm shows promising results in terms of precision evaluation, but does not show any improved accuracy compared to random experimental sampling. The model selection in PDUKC performs well in low noise examples but struggles when noise is increased. It shows PDUKC got some promising potential in good visualization of the unknown kinetic constants.

  • 311.
    Leijon, Fredrik
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Varela, Inés
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Annala, Katja
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Braesch-Andersen, Ken
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Nilsson, Martina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Dahlman, Michelle
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Hållbart expressionssystem för rekombinanta proteiner i Escherichia coli 2015Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
  • 312.
    Leoo, Hampus
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Suppressing fabulous mutants: A search for vascular regulators in Arabidopsis2019Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
  • 313.
    Lewin, Marcus
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Taxonomic revision of the genus Chamaecrista (Fabaceae) in Ecuador2015Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    A revision of the genus Chamaecrista (Leguminosae) in Ecuador is presented. The work is based on morphometric studies of herbarium material and information from the literature and the Internet. The purpose of the study was to get a better knowledge of the distribution, taxonomic status and conservation of Chamaecrista in Ecuador. The study recognizes in all six species and several varieties, viz. Ch. nictitans with var. jaliscensis, var. disandea, var. pilosa, var. paraguariensis and var. glabrata, Ch. glandulosa with var. flavicoma and var. andicola, Ch. absus and Ch. rotundifolia.

    Keys, descriptions and illustrations are provided for all taxa.

  • 314.
    Leyhr, Jake
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Characterisation of Transcription Factor Regulation During the Development of Zebrafish Craniofacial Structures2018Independent thesis Advanced level (degree of Master (Two Years)), 30 credits / 45 HE creditsStudent thesis
    Abstract [en]

    The appearance of jaws approximately 420 million years ago was a major event in vertebrate evolution. This new structure allowed gnathostomes to take on roles as active predators and increase their energy intake, facilitating their success as a group. Craniofacial musculoskeletal structures evolved in concert with the jaw to support its function, including the connective tissues that connect muscles and bones. Understanding the development of these tendons and ligaments in extant gnathostomes will shed light on how they originated and diversified. The expression patterns of Scleraxis and Mohawk, two transcription factors known to be embryonic markers of tendon and ligament tissues, were determined in the early stages of zebrafish development using whole mount in situ hybridization and mapped to specific connective elements. In order to progress our understanding of the regulation of Mohawk expression, a bioinformatic pipeline involving searches for evolutionarily conserved elements with relevant transcription factor binding motifs was undertaken. This led to the identification of CNS.8 as a promising enhancer candidate. Orthologous sequences of CNS.8 from eight different vertebrate species were isolated and cloned into plasmids containing a fluorescent reporter gene for functional validation using transgenesis in the future. The regenerative abilities of the jaw joint between Meckel’s cartilage and the palatoquadrate are another intriguing unknown, so an expression clone containing a Nitroreductase-based chemical ablation system was constructed under the control of a previously-identified conserved enhancer of the nkx3.2 transcription factor gene that marks the joint interzone tissue. A stable transgenic zebrafish line was generated containing this construct and preliminary experiments indicate the promise of this system for specifically ablating the jaw joint interzone tissue to study its regeneration. Together, these results extend our knowledge of the regulation and expression of transcription factors in developing craniofacial connective tissues, and provide a potentially powerful zebrafish model for joint regeneration.

    The full text will be freely available from 2020-09-30 12:25
  • 315.
    LH, Srilakshmy
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Sequence and expression evolution of duplicated genes in Salix2015Independent thesis Advanced level (degree of Master (Two Years)), 30 credits / 45 HE creditsStudent thesis
  • 316.
    Li, Daoyi
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Effect of 6OHDA-induced dopaminergic neuron loss on level of astakine 1 cytokine in crayfish brain and blood cells2017Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    Prokineticin 2 has been recently discovered to be up regulated in the mice having the Parkinson's disease. The homologue protein of prokineticin 2 in the crayfish, named astatine 1, has been reported to be highly expressed in crayfish blood cells and have very similar functions with the prokineticin 2. However, the role of astakine 1 in the Parkinson's disease has never been researched. Therefore, in this study 6OHDA which is a compound widely used to induce Parkinson’s disease model organisms such as mice and rats was injected into crayfish. After injection, levels of astakine 1 in crayfish brain and blood cells were examined by the western blot. In addition, the number of blood cells was determined and movement of crayfish was observed.

  • 317.
    Li, Xiaofei
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology.
    The IL-33/ST2 pathway in CNS: Traumatic brain injury and brain tumour2012Independent thesis Advanced level (degree of Master (Two Years)), 30 credits / 45 HE creditsStudent thesis
    Abstract [en]

    Interleukin 33 (IL-33) is a dual function cytokine. It is a member of the IL-1 family and it acts as a pro-inflammatory factor (18 kilo Dalton, 18 kD) like other cytokines in IL-1 family. IL-33 is also a transcription factor (32 kD - form) which can suppress or activate gene transcription in diverse cases. A variety of cell types and tissues in the central nervous system (CNS) can release IL-33 after injury. The 18 kD IL-33 binds to the membrane receptor protein ST2 ligand, then regulates downstream gene expression, triggers cytokine synthesis, and modulates the immune system response. After traumatic brain injury (TBI) in the CNS, glial cells become key players in the nervous tissue response. Astrocytes undergo activation, proliferation, release pro-inflammatory factors and, as a consequence, a glial scar barrier around the injury is formed. Simultaneously, resting microglia are activated and able to remove debris. Lastly, oligodendrocytes together with microglia and astrocytes are activated and communicate with the immune system. In addition, as a severe kind of injury to the CNS, brain tumours share some similar characteristics of brain injury, such as hypoxia and inflammation. Therefore, IL-33 may play a role in neuroinflammation and also in brain tumours. In this project, our aim was to investigate the role of IL-33 and the IL-33/ST2 pathway in traumatic brain injury and brain tumours (e.g glioma). We found that IL-33 can influence the CNS immune resonse, and may be important in CNS pathology. 

  • 318.
    Li, Zhiwei
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology.
    Characterising copy number polymorphisms using next generation sequencing data2019Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    We developed a pipeline to identify the copy number polymorphisms (CNPs) in the Northern Swedish population using whole genome sequencing (WGS) data. Two different methodologies were applied to discover CNPs in more than 1,000 individuals. We also studied the association between the identified CNPs with the expression level of 438 plasma proteins collected in the same population.

    The identified CNPs were summarized and filtered as a population copy number matrix for 1,021 individuals in 243,987 non-overlapping CNP loci. For the 872 individuals with both WGS and plasma protein biomarkers data, we conducted linear regression analyses with age and sex as covariance. From the analyses, we detected 382 CNP loci, clustered in 30 collapsed copy number variable regions (CNVRs) that were significantly associated with the levels of 17 plasma protein biomarkers (p < 4.68×10-10).

  • 319.
    Lichancova, Hana
    et al.
    Comenius Univ, Fac Nat Sci, Dept Biochem, Bratislava, Slovakia.
    Hodorova, Viktoria
    Comenius Univ, Fac Nat Sci, Dept Biochem, Bratislava, Slovakia.
    Sienkiewicz, Karolina
    Univ Warsaw, Fac Math Informat & Mech, Warsaw, Poland.
    Penir, Sarah Mae U.
    Univ Philippines Diliman, Philippine Genome Ctr, Natl Sci Complex, Quezon City, Philippines.
    Afanasyev, Philipp
    Vavilov Inst Gen Genet, Lab Evolutionary Genom, Moscow, Russia.
    Boceck, Dominic
    Univ Tubingen, ZBIT Ctr Bioinformat, Algorithms Bioinformat, Tubingen, Germany.
    Bonnin, Sarah
    Barcelona Inst Sci & Technol, Ctr Genom Regulat CRG, Barcelona, Spain.
    Hakobyan, Siras
    Inst Mol Biol NAS RA, Yerevan, Armenia.
    Krawczyk, Pawel S.
    Polish Acad Sci, Inst Biochem & Biophys, Lab RNA Biol & Funct Genom, Warsaw, Poland.
    Smyczynska, Urszula
    Med Univ Lodz, Dept Biostat & Translat Med, Lodz, Poland.
    Zhivkoplias, Erik
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Zlatohurska, Maryna
    Natl Acad Sci Ukraine, Inst Microbiol & Virolo, Kiev, Ukraine.
    Odrzywolski, Adrian
    Med Univ Lublin, Lublin, Poland.
    Tralle, Eugeniusz
    Int Inst Mol & Cell Biol Warsaw, Warsaw, Poland.
    Frolova, Alina
    Natl Acad Sci Ukraine, Inst Mol Biol & Genet, Kiev, Ukraine.
    Pryszcz, Leszek P.
    Int Inst Mol & Cell Biol Warsaw, Warsaw, Poland.
    Brejova, Brona
    Comenius Univ, Fac Math Phys & Informat, Dept Comp Sci, Bratislava, Slovakia.
    Vinar, Tomas
    Comenius Univ, Fac Math Phys & Informat, Dept Appl Informat, Bratislava, Slovakia.
    Nosek, Jozef
    Comenius Univ, Fac Nat Sci, Dept Biochem, Bratislava, Slovakia.
    Genome Sequence of Flavor-Producing Yeast Saprochaete suaveolens NRRL Y-175712019In: MICROBIOLOGY RESOURCE ANNOUNCEMENTS, ISSN 2576-098X, Vol. 8, no 9, article id e00094-19Article in journal (Refereed)
    Abstract [en]

    Saprochaete suaveolens is an ascomycetous yeast that produces a range of fruity flavors and fragrances. Here, we report the high-contiguity genome sequence of the ex-holotype strain, NRRL Y-17571 (CBS 152.25). The nuclear genome sequence contains 24.4 Mbp and codes for 8,119 predicted proteins.

  • 320.
    Liljeruhm, Josefine
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Biology.
    Funk, Saskia K.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Tietscher, Sandra
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Edlund, Anders D.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology. Uppsala Univ, iGEM Uppsala, Uppsala, Sweden.
    Jamal, Sabri
    Uppsala Univ, iGEM Uppsala, Uppsala, Sweden.
    Yuen, Pikkei
    Uppsala Univ, iGEM Uppsala, Uppsala, Sweden.
    Dyrhage, Karl
    Uppsala Univ, iGEM Uppsala, Uppsala, Sweden.
    Gynnå, Arvid H.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Systems Biology. Uppsala Univ, iGEM Uppsala, Uppsala, Sweden.
    Ivermark, Katarina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Lövgren, Jessica
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Törnblom, Viktor
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Virtanen, Anders
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Microbiology.
    Lundin, Erik
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala Univ, iGEM Uppsala, Uppsala, Sweden.
    Wistand-Yuen, Erik
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Forster, Anthony C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Engineering a palette of eukaryotic chromoproteins for bacterial synthetic biology2018In: Journal of Biological Engineering, ISSN 1754-1611, E-ISSN 1754-1611, Vol. 12, article id 8Article in journal (Refereed)
    Abstract [en]

    Background: Coral reefs are colored by eukaryotic chromoproteins (CPs) that are homologous to green fluorescent protein. CPs differ from fluorescent proteins (FPs) by intensely absorbing visible light to give strong colors in ambient light. This endows CPs with certain advantages over FPs, such as instrument-free detection uncomplicated by ultra-violet light damage or background fluorescence, efficient Forster resonance energy transfer (FRET) quenching, and photoacoustic imaging. Thus, CPs have found utility as genetic markers and in teaching, and are attractive for potential cell biosensor applications in the field. Most near-term applications of CPs require expression in a different domain of life: bacteria. However, it is unclear which of the eukaryotic CP genes might be suitable and how best to assay them.

    Results: Here, taking advantage of codon optimization programs in 12 cases, we engineered 14 CP sequences (meffRed, eforRed, asPink, spisPink, scOrange, fwYellow, amilGFP, amajLime, cjBlue, mefiBlue, aeBlue, amilCP, tsPurple and gfasPurple) into a palette of Escherichia coil BioBrick plasmids. BioBricks comply with synthetic biology's most widely used, simplified, cloning standard. Differences in color intensities, maturation times and fitness costs of expression were compared under the same conditions, and visible readout of gene expression was quantitated. A surprisingly large variation in cellular fitness costs was found, resulting in loss of color in some overnight liquid cultures of certain high-copy-plasmid-borne CPs, and cautioning the use of multiple CPs as markers in competition assays. We solved these two problems by integrating pairs of these genes into the chromosome and by engineering versions of the same CP with very different colors.

    Conclusion: Availability of 14 engineered CP genes compared in E coil, together with chromosomal mutants suitable for competition assays, should simplify and expand CP study and applications. There was no single plasmid-borne CP that combined all of the most desirable features of intense color, fast maturation and low fitness cost, so this study should help direct future engineering efforts.

  • 321.
    Lind, Simon
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Distributed Ensemble Learning With Apache Spark2016Independent thesis Advanced level (professional degree), 20 credits / 30 HE creditsStudent thesis
  • 322.
    Lindborg, Marcus
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organism Biology, Systematic Biology. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    GC-MS analysis for Polyaromatic Hydrocarbons (PAH) in Moroccan medicinal tars: An ethnobotanical study and chemical investigation of the use and safety of medicinal tars in Marrakesh and the High Atlas Mountains, Morocco2008Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
  • 323.
    Linde, Anton
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Site directed mutagenesis on a recombinant lectin domain with the aim for increased solubility2013Independent thesis Advanced level (professional degree), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    A series of mutations were performed on a recombinant fucose binding lectin domain from the fungi Aleuria aurantia in order to break oligomer formation. The mutated variants showed lowered solubility than wild type, indicating that the oligomer formation was inhibited and is important to solubilize the protein

  • 324.
    Lindh, Hanna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Mothers, Markets and Medicine: The role of traditional herbal medicine in primary women and child health care in the Dar es Salaam region, Tanzania.2015Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    Traditional medicine is still the most common primary healthcare used in Tanzania, especially among women. The ethnobotanical studies performed in Tanzania have not explored women’s traditional medicine, with the result that we do not know that much about it, including if women’s usage of medicinal plants create a threat against the medicinal flora’s biodiversity or not. Field studies consisting of interviews and collections of medicinal plants were carried out in the Dar es Salaam region in Tanzania before identifying the collected specimens by DNA barcoding, literature and morphology in Uppsala, Sweden. The 33 informants belonged to 15 different ethnic groups and 79% of them had migrated to Dar es Salaam. A total of 249 plant species were mentioned for women’s healthcare and 140 for children’s healthcare. The medicinal plants frequently reported as used for women’s health and childcare during structured interviews and free-listing exercises were Senna occidentalis/ Cassia abbreviata, Zanthoxylum sp., Clausena anisata, Acalypha ornata and Ximenia sp. The most salient uses of medicinal plants by women were during pregnancy, childbirth, menstruation, to induce abortion, and for cleansing infants and treating convulsions in children. Most of the fresh specimens were collected from disturbance vegetation. The informants having most interview answers in common were the market vendors, healers and herbalists and they were the only informants that mentioned species listed as vulnerable on the IUCN Red List of Threatened Species. These results were similar to the outcomes from studies of women’s traditional health care in West Africa. Out of 343 collected specimens, 19% were identified by DNA barcoding and 33% by literature sources. Out of 98 voucher samples, 61% were identified by comparisons of morphology, results from DNA analysis and literature. DNA barcoding was necessary to use as method since most medicines were sold in powdered shape. With more time and experience it should be possible to chart the majority of the medicinal plants up to species level. A difference between medicinal plant harvest for domestic and commercial use was observed where the commercial harvesting meant a greater threat to the Tanzanian medicinal plant biodiversity due to unsustainable harvesting methods. Previous studies have shown that an increased commercial harvesting and trade of plants often result in a decreased biodiversity. High population growth and quick urbanization mean that domestic harvesting of women’s medicinal plants will not be able to continue as previously and women in Tanzania will be more dependent on commercial trade for their traditional medicine.

  • 325.
    Lindvall, Jenny
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Green and red fluorescent protein tagging of endogenous proteins in glioblastoma using the CRISPR (clustered regularly interspaced short palindromic repeats)-Cas9 system2016Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Glioblastoma multiforme is the most malignant primary brain tumor that affects adults, recognized by the World Health Organization as an aggressive grade IV astrocytoma. Patients diagnosed with this type of tumor are left with a poor prognosis even with the most advanced treatment available. The cancer is quite heterogeneous and is typically categorized into four different subtypes depending on genetic aberrations and patient characteristics. Furthermore, researchers have discovered a subpopulation of glioblastoma cells, known as cancer stem cells, which are thought to be resistant to current therapies and responsible for tumor reoccurrence and relapse. Previous studies, in addition to this one, have found that the differentiation of glioblastoma cells downregulate nestin protein expression, the selected stem cell marker, and upregulate glial fibrillary acid protein expression, the selected differentiation marker, using immunofluorescence. Thus, one alternative treatment option is to understand the mechanism underlying the differentiation of cancer stem cells. Four cell cultures representative of each glioblastoma subtype will be endogenously tagged using the genome editing system, Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR/Cas9). The representative stem cell marker, nestin, will be tagged with a green fluorescent protein, while the chosen differentiation marker, glial fibrillary acid protein, will be tagged with a red fluorescent protein. Several drugs were screened to analyze whether the drugs had a differentiation effect on the glioblastoma cells. As a result, strong evidence indicated that bone morphogenetic protein four upregulated glial fibrillary acid protein expression levels to the same extent as the differentiation control media using 5% fetal bovine serum. The goal of this study is to establish a method to directly monitor the differentiation process of glioblastoma cells as a novel molecular screening method. In this case, all glioblastoma cells, even the ones resistant to treatment, can be eliminated through an initial “pre-treatment” by forcing differentiation of cancer stem cells, making the cells more susceptible to the chemotherapy drugs. In the long run, glioblastoma patients would have a chance at a more positive prognosis; a longer life that is free of glioblastoma.

  • 326.
    Ling, Shen
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Effects of in utero and lactational exposure to bisphenol A on bone tissue in rats2013Independent thesis Advanced level (degree of Master (Two Years)), 80 credits / 120 HE creditsStudent thesis
    Abstract [en]

    Bisphenol A (BPA) is an industrial chemical that is used in the production of polycarbonate plastics and epoxy resins. The applications result in consumer exposure to BPA via the diet.The toxicity and hormonal activity of BPA in laboratory animals have been studied and hormone related cancers and metabolic disorders have been observed in rodents. The objective of this project was to study effects on bone tissues of rats exposed to low doses of BPA in utero and during lactation. 110 pregnant Wistar rats were randomly distributed into five groups and gavaged with (0, 0.025, 0.25, 5 or 50 mg BPA/kg body weight (b.w.)/day) from gestation day 7 until weaning at pup day 22, offspring were exposed in utero and during lactation. Body weights of the offspring were recorded and right femurs were collected for geometry and densitometry measurements using peripheral quantitative computed tomography and also for analysis of biomechanical properties via three-point bending. The major findings of the study: Increased femur length in female offspring of dams exposed to 0.025 mg BPA/kg b.w./day or 5 mg BPA/kg b.w./day; Increased cortical thickness of male offspring of dams exposed to 0.025 mg BPA/kg b.w./day. No effects of biomechanical properties were seen on the bones of either sex offspring.

    In conclusion, this study demonstrates that in utero and lactational exposure to BPA at levels relevant to current human exposure alters femoral geometry in rat offspring. BPA showed endocrine disruptive effects on both female and male offspring bone tissue. The mechanisms behind these differences are unknown.

  • 327.
    Little, Chelsea
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Community, Functional Group, and Species Responses to Decades of Experimental Warming in the High and Low Arctic2014Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    While manipulative warming experiments have detected significant changes to alpine and arctic ecosystems, the nature of these changes appear to vary significantly in space (i.e., regionally and at the neighborhood level) and time (i.e., short- versus long-term effects). To further understand the variation in climate change effects on high-latitude vegetation communities, I measured the responses of a high Arctic meadow community in Adventdalen, Svalbard, to 11 years of open-top chamber (OTC) warming, and three low Arctic plant communities in Latnjajaure, Sweden, to 21 years of warming. In the low Arctic sites the abundance of living material was significantly higher in OTC’s than control plots, but this pattern did not hold in the high Arctic. In all sites, however, there was a significant, sometimes threefold increase in dead plant material in warmed plots. There were also shifts in the functional group composition of communities in the OTC plots at all the sites, but the nature of these shifts differed by community. After 21 years of warming in the low Arctic there was a significant decrease in lichen and moss cover, and different vascular plant functional groups expanded depending on community type. In the high Arctic, forbs and rushes expanded in cover at the expense of the dominant shrub, Salix polaris. Surprisingly, there were few effects of warming on community diversity or evenness at any site. Individual species at sites showed various responses to warming, from positive to negative effects on both abundance, growth, and reproduction. For instance, S. polaris flowering increased in OTC’s in the high Arctic, but S. herbacea flowering decreased in OTC’s in the low Arctic. My results show that the abundance of living and dead biomass will be strongly affected by long-term warming. This is particularly important given the strong linkages between community productivity, litter accumulation and decomposition, and nutrient and carbon cycling. Changes to community composition and effects on individual populations, however, must be assessed at a local scale in order to draw reliable conclusions about the future trajectories of these communities. Responses to warming from the species to the community level have important implications for ecosystem functioning. 

  • 328.
    Liu, Xiaodong
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Prediction of drug class and adverse sideeffects based on induced gene expressionprofiles - a feasability study2013Independent thesis Advanced level (degree of Master (Two Years)), 30 credits / 45 HE creditsStudent thesis
    Abstract [en]

    One of the core businesses of biomedical study is to establish diseases/genes/drugs connections, which still remains as a fundamental challenge in today’s pharmacological and medical research due to the limited numbers of effective tools. Gene-expression profiling has historically served as a valuable resource for elucidating the mechanisms underlying biological pathways, for instance, the molecular pathological mechanism of certain diseases in biomedicine. However, few efforts have been put into exploring deeper knowledge of medication by means of gene expression profiling. The aim of the project reported here was to establish a systematic approach to the discovery of functional connections among gene expression, drug classification and drug action using statistical (machine) learning techniques available and refined in R and in RapidMiner. Based on the data derived from “Connectivity Map”resource (a large collection of 22000-dimensional gene-expression profiles induced in cultured human cells when treated with 1309 different drug molecules) the feasibility to establish a well performing classifier which can predict drug groups according to the Anatomical Therapeutic Chemical (ATC) system was explored. The same kind of classification approach was also applied to predict adverse side effects of drugs, available in the SIDER online database, using the same “Connectivity Map” gene expression data. In order to avoid information leaks between the classifier design and the subsequent test on new examples, which could future lead to over-optimistic conclusions, all feasibility studies were performed using carefully designed cross validation procedures. Although we succeeded in building a well performing classifier for one certain ATC group on the second level, the overall performance of classifiers when evaluated properly (no information leaks) was less promising than expected, for both ATC and side effect prediction. Therefore the main conclusion is that the “Connectivity Map” resource seems to contain surprisingly limited information with respect to these two prediction tasks.

  • 329.
    Liu, Yuchen
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Invasion of Babesia microti in Northeastern USA2012Independent thesis Advanced level (degree of Master (Two Years)), 30 credits / 45 HE creditsStudent thesis
  • 330.
    Ljungberg, Jennie
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Consequences of stagnant algal mats for the benthic fauna on shallow soft bottoms at northern Gotland, Baltic Sea2015Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Earlier studies have shown that dense drifting algal mats influence the marine benthic fauna negatively. The purpose of this study was to evaluate the effects of drifting filamentous algae on the benthic fauna on soft bottom shallow bays. Sampling of the benthic fauna in areas with drifting algal mats and areas with bare sand was conducted in two shallow bays of northern Gotland, Baltic Sea. An additional experiment was carried out in situ including cages with and without algae, respectively. The opportunity to investigate a drifting algal mat from the start to the final stage of decomposition occurred. The abundance of the benthic fauna increased significantly more in cages without algae compared to the initial data and cages with algae. The number of taxa was also higher in cages without algae when compared to the initial data, cages with algae and under the algal mat. Oxygen levels declined in cages with algae and under the algal mat, but this was most pronounced under the algal mat. Under the drifting algal mat, only species with higher tolerance to reduced oxygen levels were recorded. This study shows that dense algal mats that become stagnant for a longer period of time influence the benthic fauna negatively because of reduced oxygen levels.

  • 331.
    Ljungberg, Jennie
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Food choice of different size classes of flounder (Platichthys flesus) in the Baltic Sea2015Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Flounder, Platichthys flesus, is considered to be an important predator on blue mussels, Mytilus edulis, in the Baltic Sea. The purpose of this study was to investigate if flounder diet, i.e. blue mussels, could have an impact on the relationship between weight and length of flounders, i.e. their condition. Flounders and blue mussels were captured in August 2013 outside Herrvik, on eastern Gotland. Experiments on feeding preference and weight changes of flounders feeding on either small or larger mussels took place at Ar Research Station, Uppsala University. Blue mussels were kept in aquaria. The fish were kept in basins (2 × 2 m), with sea water (about 19°C and 6.3 ‰). The fish were divided into different size classes and some of them tagged individually. Analyses of substance in flounder stomachs as well as calculations of mussel weight/length relation were accomplished with data from 2012. Results from the experiments showed that all flounders, independent of size, preferred small mussels before larger ones. They all lost weight during the experiments. The weight/length ratio (shellfree dry weight/shell length) of blue mussels was proved to be positively correlated with shell length. Because of this it was concluded that the size of ingested blue mussels does not have any impact on the differences in condition between larger and smaller flounders.

  • 332.
    Ljunggren, Elin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre. Department of Aquatic Resources, Swedish University of Agricultural Sciences.
    Prey choice of great cormorants (Phalacrocorax carbo) in a marine protected area: potential impact on collapsed fish stocks and implications for future monitoring2017Independent thesis Advanced level (degree of Master (Two Years)), 30 credits / 45 HE creditsStudent thesis
    Abstract [en]

    Great cormorant (Phalacrocorax carbo) populations have experienced a rapid growth in Europe since the 1980s, resulting in conflicts with fisheries over local fish resources. The 8-fjords area is a marine protected area on the Swedish west coast, where long term overfishing has led to a collapse of several local demersal fish stocks. Subsequently, fishing regulations have been implemented to protect and re-establish the stocks of cod- and flatfish species, at the same time as cormorants have increased largely in numbers. The increased predation pressure has raised concerns about the recovery of local fish stocks, although knowledge about cormorant feeding habits are lacking. Here, cormorant prey choice in two subareas of the 8-fjords area is investigated, using morphological identification of prey remains in regurgitated pellets. An estimated 15 077 fishes were identified from a total of 480 pellets. The most important prey families based on relative abundance were flatfish (Pleuronectidae 48%), gobies (Gobiidae 21%) and codfish (Gadidae 13%). Pairwise ANOSIM analyses showed extremely small differences in diet composition between sites (p≤0.003, R<0.08). In comparison to available monitoring fishery data, the diet did not correspond to prey abundance. Estimated fish sizes of a subsample of flat- and codfish showed that juveniles seemed to be preferred. Pellet analysis provided limited information about consumed species and should be combined with other methods for more detailed assessments of cormorant prey choice in the 8-fjords area.

  • 333.
    Llavero Pasquina, Marcel
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Photochemistry and Molecular Science, Microbial Chemistry. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Engineered light controlled cell development for enhanced hydrogen production in Nostoc punctiforme ATCC 291332016Independent thesis Advanced level (degree of Master (Two Years)), 30 credits / 45 HE creditsStudent thesis
    Abstract [en]

    The aim of this thesis is to enhance heterocyst-based hydrogen production inNostoc punctiforme ATCC 29133. We envision to do so by finely regulatingthe ratio of heterocyst in order to optimize the filament energy balance. Wehereby report the development of an optogenetic synthetic switch basedon the native PcpeC promoter. The optogenetic switch featured a 24-folddynamic range when measuring reporter sfGFP fluorescence. Such a geneticgate was conceived to artificially drive the expression of hetR, the masterregulator of heterocyst development. We achieved to induce enhancedheterocyst differentiation in the presence of ammonia only by changing thechromatic properties of the light source. Thus, the natural cell developmentregulation was substituted by effectively introducing a full person-drivencontrol over the process.

  • 334.
    Lu, Jiaqi
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    The effect of sexual selection and mating on personality traits and behavior consistency of Callosobruchus maculatus2019Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    Animals’ personality traits are defined as consistent behavior tendencies and the function of them in life-history strategy and reproductive success has been given a lot of explanations in a large amount of research. However, the behavior consistency of individuals in different sexes, mating status and selection regimes is rarely mentioned. In this research, we were interested in personality traits and their consistency in inter-individuals and intra-individuals, and proposed that with the removal of fecundity selection males would evolve to be more female-like and decrease their locomotor activity, and copulation would change the physiological status of females and thus alter their levels of activity.

     

    In the experiment, seed beetles (Callosobruchus maculatus) that were artificially selected in monogamy, polygamy and male-limited selection regimes were weighed, dropped in a designed arena and their behaviors were recorded with a camera for four minutes in the first day when they were newborn and virgin. In the next day, the virgin beetles were randomly paired to mate, weighed afterwards, and dropped in the arena again for videoing the same setting as yesterday. In data collection step, with these videos four behaviors types including walking, entering squares, time spent on roof and entering a new area were observed, scored and noted down. To process the data, we made correlation analysis and it was found that walking, entering square and a new area were positively correlated. After building the linear mixed effect models we found that sex together with mating significantly act in modifying beetles’ behaviors, males were more active than females but the difference was narrowed after mating, and copulation caused a significant increase in the level of locomotor activity in females. To our disappointment, selection regimes did not have any significant impact on locomotor activity. Our work gave an insight that copulation changed individuals’ behaviors more in females than in males and dimorphic expression of sex-biased genes differed due to mating effect.

     

  • 335.
    Lundberg, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Optimization of the multiplexed Proximity Ligation Assay for detection of blood-based biomarkers2014Independent thesis Advanced level (professional degree), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    The Proximity Ligation Assay (PLA) is a relatively new method which utilizes the strength of both immunoassays and DNA detection. PLA has the capacity of high multiplexing due to the high specificity achieved with both dual protein-binding and dual primer binding during detection with Real-Time PCR. We developed a multiplexed PLA protocol that can measure 28 biomarkers in human EDTA plasma. The method was tested on 46 individuals diagnosed with colorectal cancer and 48 age matched healthy controls. The results are very promising as we re-discover the most well-known biomarkers for colorectal cancer and also find some potential new markers (significance tested with students T-test with p<0.05). Further improvements of the protocol are needed to decrease the variation.

  • 336.
    Lundberg, Sofia
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Populationsutveckling hos indikatorarten flodpärlmussla (Margaritifera margaritifera) i Värmland2016Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
  • 337.
    Lundgren, Christian
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Immune responses in urogenital cancer2015Independent thesis Advanced level (professional degree), 20 credits / 30 HE creditsStudent thesis
  • 338.
    Lundh, Emma
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organism Biology, Systematic Biology. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Plant Use in Ante- and Postpartum Health Care in Lao PDR2007Independent thesis Advanced level (degree of Master (One Year)), 20 credits / 30 HE creditsStudent thesis
  • 339.
    Lundin, Erik
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    AutoPhylo, a bioinformatic tool for identifying and retrieving sequences2010Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    The task of constructing a molecular phylogenetic tree consists of finding homologous sequences, making a multiple sequence alignment, perhaps removing gaps and ambiguous positions in the alignment and finally phylogenetically inferring the tree with various evolutionary models. Often there is a need to refine the tree by removing inappropriate sequences. For each step of this process there is a tool to accomplish the task. Starting with a sequence of interest BLAST (Basic Local Alignment Search Tool) is used to find homologous sequences from various databases. Then multiple sequence alignment programs such as MUSCLE or CLUSTAL can be used to align the sequences. In the alignment there are often regions of gaps and ambiguous positions that can be identified and removed with programs such as GBlocks. Finally, using the alignment a phylogenetic tree can be reconstructed using selected methods and models. Depending on the scientific goals and data, this process generally needs to be repeated several times in order to “refine” the tree. To construct a tree of correct phylogeny “true” homologous positions in an alignment must beused. In addition, if the tree is to reconstruct the correct relationship among species (rather than just the genes), then it is also necessary to use orthologous sequences, rather than sequences that have undergone duplications (paralogs). To further complicate tree reconstruction there are technical problems such as long branch attraction (where fast evolving sequences cluster together even if they are unrelated) and horizontal gene transfer (where cells that can be unrelated exchange genes) that could mislead the phylogeny. At present there is no effective program that is sophisticated enough to correct these kinds of problems without careful manual examination. However, many of these steps are simple and repetitive. It is the goal of bioinformatics to automate as many of these simple tedious steps as possible, in order to allow large amounts of data to be processed quickly and accurately. In this paper a tool that streamlines the phylogenetic tree reconstruction process is presented. The tool, named AutoPhylo, identifies and retrieves sequences from NCBI (database collection) or a user-defined local database via BLAST searches. These sequences are then used to construct a tree that can be examined with a graphical user interface (GUI). The GUI allows the user to identify and remove unwanted sequences in order to refine the tree. The sequences are retrieved in groups that have one or more queries that limits the selection to specific species, genes or others valid NCBI queries. Some tests are applied to show that the program is useful and is able to accelerate subroutines of the process.

  • 340.
    Lundin, Sigrid
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Schedin, Johan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Olsson, Robin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Sundh, Andrea
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Wegelius, Adam
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Smarta val av metall‐kelatorkomplex optimerar proteinrening med IMAC2012Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [sv]

    På beställning av GE Healthcare AB har en sammanställning gjorts över interaktionen mellan metalljoner och kelatorer samt metalljoner och proteiner vid immobiliserad metalljonsaffinitetskromatografi (IMAC). Kelatorer är kemiska föreningar som kan användas för att binda metalljoner. Denna sammanställning kan användas som en vägledning för optimering av IMAC.

    Det är ett vedertaget faktum att bindningsstyrkan mellan metalljoner och proteiner, bland annat, beror på hur många bindningsställen på metalljonen som finns kvar för proteiner att binda till. Desto fler bindningsställen kelatorn upptar på metalljonen, desto svagare blir interaktionen med proteinet. Denna sammanställning är begränsad till ett antal metalljoner, som till exempel Cu2+, Ni2+, Co2+, Zn2+ och Fe3+, och kelatorerna ”Iminodiacetic acid” (IDA), ”tris(2-aminoethyl)amine” (TREN), ”1,4,7-triazacyclononane” (tacn), ”tris(carboxymethyl)ethylenediamine” (TED) och ”nitrilotriacetic acid” (NTA).

    Några intressanta skillnader i bindningsstyrkan mellan ett antal intermediära metalljoner, kopplade till en kelator, och proteiner har framkommit i denna studie. Dessa relationer, för kelatorerna IDA, TREN och tacn, finns redovisade nedan (starkast bindningsaffinitet längst till vänster).

    IDA: Cu2+ > Ni2+>Zn2+>Co2+

    TREN: Cu2+ > Ni2+

    Tacn: Cu2+ > Ni2+ > Zn2+ > Co2+ > Cr2+ ≈ Mn2+

  • 341.
    Lundström, Alexander
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Sarkisjan, Arusjak
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Isgård, Caroline
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Brorsson, Gustaf
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Rashyna, Marina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Jillefors Olsson, Sofia
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Att sälja fluorescerande dextraner - var, hur och varför?2015Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [sv]

    Syftet med detta projekt var att ge företaget TdB Consultancy AB en djupare förståelse för hur och inom vilka forskningsområden fluorescerande dextraner används och även ge dem information som hjälper dem marknadsföra sig och sina produkter.

    För detta gjordes en litteraturundersökning där 87 artiklar lästes om fluorescerande dextraner och deras biotekniska applikationer. Fortsättningsvis gjordes en marknadsföringsstudie och en enkätstudie. Enkäter skickades ut till 160 av TdB Consultancy AB’s kunder och 17 av deras konkurrenter. De personer som svarade på enkäterna var spridda över hela världen och arbetade inom olika områden. Under marknadsföringsstudien gjordes en undersökning av intressanta konferenser för TdB Consultancy AB, där de skulle kunna ställa ut sina produkter. Vi tittade även på konkurrenternas prissättning av sina produkter och deras hemsidor.

    Litteraturundersökningen visade att de två mest dominerande biotekniska områdena där fluorescerande dextraner används är vid studier av permeabilitet hos olika vävnader i kroppen, främst inom blod-hjärn-barriären och membranstudier. Marknadsföringsstudien och enkätstudien visade att god kundkontakt och tillgänglighet på internet är de främsta sätten att nå kunder för TdB Consultancy AB.

    Av samtliga studier har det kommit fram att:

    • de största biotekniska användningsområdena för fluorescerande dextraner är studier på blod-hjärn-barriären och membranstudier
    • god kundkontakt och tillgänglighet på internet är de viktigaste marknadsföringsstrategierna för TdB Consultancy AB
    • ingen av TdB Consultancy AB’s kunder som vi kommit i kontakt med har fått kännedom om företaget via de bekostade marknadsföringskanaler TdB Consultancy AB använt sig av
    • priset på TdB Consultancy AB’s fluorescerande dextraner står sig bra mot de konkurrenters produkter vi analyserat
    • de fyra konferenserna Neuroscience 2015, Pharmapack, AAPS National Biotechnology Conference och WPC: Blood-Brain Barrier, är relevanta för TdB Consultancy AB med avseende på användningsområdena, priset och geografisk placering
  • 342.
    Lundén, Mattias
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Mathematical modeling of insulin response in encapsulated islets of Langerhans2014Independent thesis Advanced level (professional degree), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Transplantation of the islets of Langerhans is a promising technique for restoring the impairedinsulin production in brittle type 1 diabetics. The downside is that the patient will have to takeimmunosuppressant drugs in order to protect the islet cells from the immune system. Donorsare also sparse, making the quest of finding sufficient amounts of islets for transplantationhard. Encapsulation of the islets of Langerhans has been proposed as a means of protectingthe cells from the immune system taking away the need for immunosuppresives. The mostcommon encapsulation technique is extravascular capsules, which are categorized into micro-and macrocapsules. The microcapsules hold only one or a small set of islet whereas themacrocapsules hold a large quantity of islets.This thesis investigates the encapsulation impact on the beta-cells rapid insulin response torising plasma glucose levels. This was done by simulating the glucose-insulin system inMATLAB with included encapsulation of the islets. Two current macro-encapsulation set upswere used in the model, Beta-Air and ViaCyte devices, and they were compared against anormal case. The results showed that the Beta-Air device would not be able to restorenormoglycemia in a T1DM patient but rather showed a delay in insulin response, while theViaCyte device could mimic the normal case well.

  • 343.
    Lustenhouwer, Monique
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Population and Conservation Biology.
    Local adaptation of larval life history in the moor frog Rana arvalis across a landscape mosaic2012Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Growth rate is an important life history trait, which impacts fitness indirectly through its effect on the age and size at maturity, as well as directly through costs associated with accelerated growth such as increased predation risk. Genetic variation and plasticity in growth are widespread in nature, and local adaptation of growth rate may evolve due to divergent selection in different environments, for example related to predation risk, temperature or time constraints. I studied local adaptation of larval life history in the moor frog Rana arvalis, in a local network of ponds close to Uppsala. Local adaptation of growth rate and survival was studied in a reciprocal transplant experiment between ponds with different habitat characteristics. Meanwhile, differences among the populations in intrinsic growth, activity and response to predation were studied in a common garden experiment in the laboratory, where tadpoles were raised in the presence or absence of a predator and tested in direct predation trials. In the field, differences in growth among populations were found, independent of which pond the tadpoles were raised in, indicating that the ponds were similar growth environments. Survival differences among the populations depended on the pond, but local populations did not do better than foreign ones. In the laboratory, similar patterns in growth rate were found. All populations were highly plastic in their response to predation, having lower growth and activity in the predator-induced treatment and decreased mortality in the predation trials. Tadpole size was an important factor in escaping predation. One population clearly grew faster than the others in the field and in the lab, which could be explained in terms of its habitat of origin but was most likely related to the relatively late hatching of this population. Future studies are necessary concerning the possible costs of this accelerated growth and the importance of breeding phenology. Apart from the one differential population, I did not find evidence of local adaptation in the field or in the laboratory. The influence of habitat characteristics on tadpole life history was difficult to study, due to the limited number of ponds and many environmental differences among them. However, this thesis was a valuable pilot study concerning the design of experiments to study factors promoting and constraining local adaptation in landscape mosaics. An understanding of local adaptation at the scale at which gene flow occurs is important for the conservation of populations in fragmented landscapes as well as for the study of ecological speciation.

  • 344.
    Långström, Elisabeth
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Genetiska studier av spädlosta på Tjörn (Bromus pseudosecalinus)2008Report (Other academic)
  • 345.
    Långström, Elisabeth
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Åtgärdsprogramför sötgräs 2009–2013 (Cinna latifolia)2009Report (Other academic)
  • 346.
    López Olvera, Enrique Argenis
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre. Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC.
    Kinetic studies of carrier conjugated protease inhibitors2019Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Conjugates of soybean trypsin inhibitor (SBTI) and potato serine protease inhibitor (PSPI) immobilized on metal oxide particles of ~100nm diameter were prepared. Inhibition of trypsin hydrolysis of BAPA by these conjugates was measured and enzyme kinetics constants kcat, KM, kcat/KM and ki were determined. Metal oxide particles presented an inhibitory effect similar to that of a competitive inhibitor, noticed through the increase value of the K M constant. Furthermore, PSPI conjugates had the highest inhibition of trypsin, illustrated by the significantly higher value of KM relative to the value for particles only.

  • 347. Lönn, Mikael
    et al.
    Alexandersson, Ronny
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Gustafsson, Susanne
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Functional Genomics.
    Hybrids and fruit set in a mixed flowering-time population of Gymnadenia conopsea (Orchidaceae)2006In: Hereditas, ISSN 0018-0661, E-ISSN 1601-5223, Vol. 143, no 1, p. 222-228Article in journal (Refereed)
    Abstract [en]

    We have recently found that the morphologically determined subspecies Gymnadenia conopsea ssp conopsea in Sweden includes early and late flowering individuals. We were interested in the interactions between the flowering time groups; if there were gene flow between them and if so this was detrimental or advantageous. A spatially mixed population of early and late flowering individuals was studied using three microsatellite loci. We measured patterns in genetic differentiation and inferred occurrence of hybridisation and introgression. Variation in flowering time, fertility and relative and absolute fruit set was measured. The pattern of introgression between flowering-time groups differed between loci. In two of the three investigated loci, allele separation was distinct between early and late flowering plants and one genetically obvious hybrid was infertile. In the third locus, several alleles were shared between the two flowering time variants. The degree of introgression was associated to fruit set failure, which was higher in the late flowering plants and lower in early flowering plants. A small group of early flowering individuals with somewhat delayed flowering compared to the main group was genetically distinct and had lower relative and absolute fruit set. This group was not genetically intermediate, but rather constituting an independent group, with lower fruit set possibly caused by absence of pollinators. There seem to be a strong barrier against introgression into the late flowering group which is kept genetically distinct and less diverse. The early flowering group is diverse, includes two subgroups and seems to benefit from gene flow.

  • 348.
    Lövgren, Jessica
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Site-specific labelling of anti-HER2 ADAPT proteins for molecular imaging applications2016Independent thesis Advanced level (professional degree), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Cancer is one of the leading causes of death worldwide. It is of great importance to use reliable diagnostic methods before determining treatment methods. Molecular imaging is a non-invasive approach of visualising tumours in vivo. This method requires imaging agents that are detectable and binds specifically to the tumour. The aim of this degree project was to produce and characterise a protein-based imaging agent, called ADAPT, that has been engineered to bind the breast cancer associated receptor HER2. This protein has previously been labelled with radionuclides in the N-terminal and tested in vivo with promising results. However, due to the fact that the position of the radiolabel can affect the biodistribution of the imaging agent, a comparison to C-terminal radiolabelled variants is of high interest. Radiolabelling can be performed by first attaching a chelator to the protein and later bind the radionuclide through the chelator. The chelator used in this project binds to a thiol group and therefore a unique cysteine was added to the C-termini. The N-termini were altered to both generate variants with and without purification tag. Proteins with altered N-termini and C-termini were produced and later characterised by circular dichroism and surface plasmon resonance. None of the non-tagged variants could be produced to a sufficient amount and was discarded for further studies. However, all variants with a purification tag could be produced and the shortest variant was chosen to be tested in vivo.

  • 349.
    Marklund, Emil
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Bayesian inference in aggregated hidden Markov models2015Independent thesis Advanced level (professional degree), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Single molecule experiments study the kinetics of molecular biological systems. Many such studies generate data that can be described by aggregated hidden Markov models, whereby there is a need of doing inference on such data and models. In this study, model selection in aggregated Hidden Markov models was performed with a criterion of maximum Bayesian evidence. Variational Bayes inference was seen to underestimate the evidence for aggregated model fits. Estimation of the evidence integral by brute force Monte Carlo integration theoretically always converges to the correct value, but it converges in far from tractable time. Nested sampling is a promising method for solving this problem by doing faster Monte Carlo integration, but it was here seen to have difficulties generating uncorrelated samples.

  • 350.
    Markstedt, Olof
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Kubernetes as an approach for solving bioinformatic problems.2017Independent thesis Advanced level (professional degree), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    The cluster orchestration tool Kubernetes enables easy deployment and

    reproducibility of life science research by utilizing the advantages

    of the container technology. The container technology allows for easy

    tool creation, sharing and runs on any Linux system once it has been

    built. The applicability of Kubernetes as an approach to run

    bioinformatic workflows was evaluated and resulted in some examples

    of how Kubernetes and containers could be used within the field of

    life science and how they should not be used. The resulting examples

    serves as proof of concepts and the general idea of how

    implementation is done. Kubernetes allows for easy resource

    management and includes automatic scheduling of workloads. It scales

    rapidly and has some interesting components that are beneficial when

    conducting life science research.