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  • 1.
    Abdullahi, Fardosa
    University of Skövde, School of Bioscience.
    Investigating possible differential expression level of hsa-miR-708-5p in Neuroblastoma2022Independent thesis Basic level (degree of Bachelor), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Neuroblastoma (NB) is one of the most common extracranial cancers found in children under the age of five. The cause of NB is not well understood, about 2% of the cases have been linked to rare germline mutations in the anaplastic lymphoma kinase (ALK) gene. However, NB is thought to be mainly caused by genetic mutation at the early stages of development. Clinically, NB can be grouped into three risk groups: low, intermediate and high-risk disease. The survival rate of patients with high-risk NB is less than 50% of the diagnosed cases. Survival rates emphasizes the necessity for future NB diagnostic therapy. One potential study area is miRNA, studies have demonstrated both prognostic and predictive usefulness to therapies. MiRNA is a single-stranded RNA that is 18-24 nucleotides long. Its function is to regulate numerous cellular activities, and to act as tumor suppressors or oncogenes. Genetic anomalies such as MYCN amplification and 11q deletion cause NB by disrupting the expression patterns of certain miRNAs. In this experiment the miRNA, hsa-miR-708-5p, was examined in three genetically diverse NB cell lines; NB69 without MYCN amplification and 11q deletion, SKNBE with MYCN amplification, and Kelly with a chromosome 11q deletion, the cell lines were used to see if the expression levels of hsa-miR-708-5p differed. The expression level of hsa-miR-708-5p, was assessed using qPCR; variation in gene expression was identified between the cell lines. Therefore, miR-708-5p could be a viable option when looking at gene expression of hsa-miR-708-5p for future diagnostic or prognostic in NB.

  • 2.
    Abela, Sohunda
    University of Skövde, School of Bioscience.
    Molecular detection of Sclerotinia sclerotiorum from petals of oilseed rape by Nanopore sequencing using MinIon2023Independent thesis Advanced level (degree of Master (One Year)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Sclerotinia sclerotiorum is a plant pathogenic fungus that causes Sclerotinia stem rot in oilseed rape. In Sweden, the disease causes severe crop loss that varies by year. Previous studies have shown a relationship between the proportion of infected petals and disease incidence in infected fields in places with high humidity levels before and during flowering. In this study, the aim was to develop a technique to detect S. sclerotiorum and other fungi pathogens in the petals of oilseed rape from naturally infected fields by using nanopore sequencing from Oxford Nanopore Technologies. DNA was extracted from the petals of oilseed rape and subsequently amplified by performing PCR after optimizing the optimal annealing temperature. Using the forward primer ITS1catta and the reverse primer ITS4ngsUni, these primers targeted the ITS region, which is used as a marker for the identification of fungi. The resulting Amplicon concentrations varied. Five amplicon PCR samples were selected for MinION sequencing. These samples were selected since they had the best purity levels. Finally, bioinformatic analysis was done with Kraken2 and the Pavian tool and compared with UNITE databases. The result showed hundreds of thousands of reads were recovered from the Ascomycota and Basidiomycota fungi divisions; S. sclerotiorum was observed in one field sample; other Sclerotiniaceae species like Dumontinia tuberosa, Botrytis cinerea, and Sclerotinia bulborum were detected in two fields; and many other fungal pathogen species affecting rapeseed crops in Sweden were successfully detected. MinION was successful in identifying S. sclerotiorum and other plant pathogens.

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  • 3.
    Adindu Uzowuru, Cosmas
    University of Skövde, School of Bioscience.
    Inflammasome: Investigating the effect of NEK7 in the activation of the NLRP3 Inflammasome2020Independent thesis Basic level (degree of Bachelor), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Inflammation is a biological defence mechanism applied by living organisms against foreign invaders. In the response to DAMPs and PAMPs, organisms use inflammatory multi-protein complexes to fight the attackers. The most studied inflammasome proteins are NLRP3, ASC and Caspase-1. This study is aimed at understanding the role of NEK7 protein in the NLRP3 inflammasome’s activation, using CRISPR/Cas9 system. To determine the effect of CRISPR/Cas9 and transfection, mRNA expression was analyzed. The results obtained suggest that neither the transfection nor the NEK7 protein knockout have sufficiently worked. This study could not experimentally establish that NEK7 triggers NLRP3 inflammasome activation because ELISA was not conducted to verify the levels of cytokines emitted, due to there being no statistical differences between the samples. Above all, the research question in this thesis project was not answered because the instability of the ACTB reference gene negatively influenced the results. However, previous related studies conclude that NEK7 plays a crucial role in the activation of the NLRP3 inflammasome.

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  • 4.
    Ajaj, Asil
    University of Skövde, School of Bioscience.
    The ecotoxicity effect of metronidazole on Raphidocelis subcapitata2022Independent thesis Basic level (degree of Bachelor), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Pseudokirchneriella subcapitata is a sickle-shaped freshwater green microalga that is normally found in unicellular form. It is the best known and most frequently used species of ecotoxicological bioindicator because of its high growth rate and sensitivity to toxicants. Metronidazole (MTZ) is a routinely used nitroimidazole antibiotic that has caused environmental issues owing to incorrect use. A toxicity test was performed in order to understand the relationship between the MTZ concentrations and response at a physiological level. The study found a growth percentage of (0, 4.8571, 4.5714, -15.1429, -37.1429 %) accordingly. The changes on the transcriptomic level were tested by performing a RT-qPCR. Using ∆∆Ct method to compare the treated samples with low and high MTZ concentration against the control sample. The study found that Exposure to MTZ at the low and high concentrations gave rise to 1.45 fold upregulated pcna gene expression that was differentially expressed in control R. subcapitata. The high group of samples in the high group were clearly distinguishable from those in the control and low treatment groups.

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  • 5.
    Alghazali, Raghad
    University of Skövde, School of Bioscience.
    GSK-3 post-transcriptionally regulates TNF-α biosynthesis in THP-1 macrophages2022Independent thesis Basic level (degree of Bachelor), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Few things are more fascinating than finding new interactions between previously unrelated pathways. Glycogen synthase kinase-3 (GSK-3), a ubiquitous kinase initially known for its role in regulating glycogen metabolism, has recently been found to be an indispensable regulator of the TLR4-mediated inflammatory response. GSK-3 inhibition exhibits potent anti-inflammatory effects by acting on both arms of the inflammatory response, reducing the secretion of pro-inflammatory cytokines, and promoting the production of anti-inflammatory cytokines. Tumor Necrosis Factor-α (TNF-α) is among the most important inflammatory cytokines. Aberrant TNF-α expression is associated with various inflammatory conditions, including sepsis and cancer. Thus, understanding the mechanisms regulating TNF-α production could reveal potential therapeutic strategies for TNF-α-associated diseases. Consequently, this study aimed to examine the effect of GSK-3 inhibition on TLR4-induced TNF-a production by THP-1 macrophages. THP-1 macrophages were stimulated with LPS and nigericin in the presence and absence of GSK-3 inhibitor, and TNF-α protein and mRNA levels were evaluated by ELISA and Real-time PCR, respectively. GSK-3 inhibition significantly attenuated TNF-α protein levels in a dose-dependent manner, whereas TNF-α mRNA levels remained unaffected, reflecting a possible post-transcriptional modulation of TNF-α biosynthesis by GSK-3. However, more comprehensive research is needed to elucidate the precise contribution of GSK-3 to TNF-α biosynthesis and to identify novel therapeutic mechanisms to alleviate inflammatory diseases associated with abnormal TNF-α production.

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  • 6.
    Ali, Muhammad
    University of Skövde, School of Life Sciences.
    A COMPARATIVE STUDY OF GENE EXPRESSION NETWORKS USINGBIOLAYOUT, GENENET AND DAVID2012Independent thesis Advanced level (degree of Master (One Year)), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    Deriving clusters of genes by different clustering techniques or finding the statistically significant variations among genes are conventional approaches to study microarray expression data. Nowadays in vitro experiments are being considered to make applications of genetical genomics more widespread in non-model species. Different bioinformatics tools are being used to investigate genetic pathways in the form of correlation based networks. In this study, a comparison was made between in vivo and in vitro gene expression data by using two software: BioLayout and GeneNet. From ten mice, five mice with the wild-type allele and five mice with the gene knock out (KO) for the gene SOCS2, a total of twenty samples were taken: five fresh samples from wildtype mice, five fresh samples from KO mice, five cultured samples from wildtype mice and five cultured samples from KO mice. After obtaining differentially expressed genes from microarray cDNA experiments, network analysis was done using the software BioLayout and GeneNet to make correlation and partial-correlation based networks. The resulting networks, or clusters derived from the networks, were subsequently analyzed for gene set enrichment analysis (GSEA) using the tool DAVID. The results from the GSEA were used to compare all the clusters and networks between the fresh and cultured samples to test for functional overlap. The GSEA results were also used to compare the clusters from BioLayout with the networks from GeneNet to compare overlap between these tools using the same data. When functional enrichment analysis and comparisons were made between the fresh and cultured data set after getting the networks and clusters from BioLayout and GeneNet, only a few functional categories were found in common. This suggested that in vitro samples are unable to give the same biological information as in vivo samples for this particular gene KO. Also the two different network tools showed only limited overlap, suggesting that the correlation based networks from BioLayout show a different type of relationship among the genes than the partial correlations from GeneNet.

    Therefore, the use of different network tools can be recommended to visualize and explore the regulatory pathways among genes.

  • 7.
    Aliakbari, Massume
    et al.
    Department of Crop Production and Plant Breeding, Shiraz University, Shiraz, Iran.
    Cohen, Stephen P.
    Department of Plant Pathology, The Ohio State University, USA.
    Lindlöf, Angelica
    University of Skövde, School of Bioscience. University of Skövde, Systems Biology Research Environment.
    Shamloo-Dashtpagerdi, Roohollah
    Department of Agriculture and Natural Resources, Higher Education Center of Eghlid, Iran.
    Rubisco activase A (RcaA) is a central node in overlapping gene network of drought and salinity in Barley (Hordeum vulgare L.) and may contribute to combined stress tolerance2021In: Plant physiology and biochemistry (Paris), ISSN 0981-9428, E-ISSN 1873-2690, Vol. 161, p. 248-258Article in journal (Refereed)
    Abstract [en]

    Co-occurrence of abiotic stresses, especially drought and salinity, is a natural phenomenon in field conditions and is worse for crop production than any single stress. Nowadays, rigorous methods of meta-analysis and systems biology have made it possible to perform cross-study comparisons of single stress experiments, which can uncover main overlapping mechanisms underlying tolerance to combined stress. In this study, a meta-analysis of RNA-Seq data was conducted to obtain the overlapping gene network of drought and salinity stresses in barley (Hordeum vulgare L.), which identified Rubisco activase A (RcaA) as a hub gene in the dual-stress response. Thereafter, a greenhouse experiment was carried out using two barley genotypes with different abiotic stress tolerance and evaluated several physiochemical properties as well as the expression profile and protein activity of RcaA. Finally, machine learning analysis was applied to uncover relationships among combined stress tolerance and evaluated properties. We identified 441 genes which were differentially expressed under both drought and salinity stress. Results revealed that the photosynthesis pathway and, in particular, the RcaA gene are major components of the dual-stress responsive transcriptome. Comparative physiochemical and molecular evaluations further confirmed that enhanced photosynthesis capability, mainly through regulation of RcaA expression and activity as well as accumulation of proline content, have a significant association with combined drought and salinity stress tolerance in barley. Overall, our results clarify the importance of RcaA in combined stress tolerance and may provide new insights for future investigations. 

  • 8.
    Almqvist, Gustaf
    et al.
    University of Stockholm, Stockholm Sweden.
    Andersen, Michael
    Danish Fishermen’s Association, Fredericia, Denmark.
    Willestofte Berg, Casper
    DTU Aqua – National Institute of Aquatic Resources Section for Fisheries Advice, Charlottenlund, Denmark.
    Broadgate, Wendy
    The Fisheries Secretariat (FISH), Stockholm, Sweden.
    Bryan, Meaghan
    National Oceanic and Atmospheric Administration Southeast Fisheries Science Center, Miami, United States.
    Campana, Steven
    Fisheries and Oceans Canada Bedford Institute of Oceanography, Dartmouth, Canada.
    Cardinale, Max
    Swedish University of Agricultural Sciences Institute of Marine Research, Lysekil, Sweden.
    Casini, Michele
    Swedish University of Agricultural Sciences Institute of Marine Research, Lysekil, Sweden.
    Dierking, Jan
    Leibniz-Institut für Meereswissenschaften, Kiel, Germany.
    von Dorrien, Christian
    Thünen Institute Baltic Sea Fisheries, Rostock, Germany.
    Eero, Margit
    DTU Aqua – National Institute of Aquatic Resources, Charlottenlund, Denmark.
    Efimov, Yuri
    Russian Federal Research Institute of Fisheries & Oceanography (VNIRO), Moscow, Russian Federation.
    Gasyukov, Pavel
    AtlantNIRO, Kaliningrad, Russian Federation.
    Hemmer-Hansen, Jakob
    DTU Aqua – National Institute of Aquatic Resources Department of Inland Fisheries, Silkeborg, Denmark.
    Hjelm, Joakim
    Swedish University of Agricultural Sciences Institute of Marine Research, Lysekil, Sweden.
    Holmgren, Noél
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre.
    Horbowy, Jan
    National Marine Fisheries Research Institute, Gdynia, Poland.
    Hüssy, Karin
    DTU Aqua – National Institute of Aquatic Resources, Charlottenlund, Denmark.
    Johansson, Reine
    Baltic Sea Advisory Council, Dyrön, Sweden.
    Jonusas, Stanislovas
    DGMare, Brussels, Belgium.
    Kornelius, George
    Institute of Food Safety, Animal Health and Environment (BIOR) 8 Daugavgrivas Str. Fish Resources Research Department, Riga, Latvia.
    Köster, Fritz
    DTU Aqua – National Institute of Aquatic Resources Section for Fisheries Advice, Charlottenlund, Denmark.
    Kraak, Sarah
    Thünen Institute, Braunschweig, Germany.
    Krumme, Uwe
    Thünen Institute Baltic Sea Fisheries, Rostock, Germany.
    Large, Scott
    International Council for the Exploration of the Sea, Copenhagen, Denmark.
    Larsson, Staffan
    Swedish Cod Fishermen’s Producer Organisation, Lycke, Sweden.
    Luzenczyk, Anna
    National Marine Fisheries Research Institute, Gdynia, Poland.
    Lövgren, Johan
    Swedish University of Agricultural Sciences Institute of Marine Research, Lysekil, Sweden.
    Maguire, Jean-Jacques
    Godefroy, Quebec, Canada.
    Mosegaard, Henrik
    DTU Aqua – National Institute of Aquatic Resources, Charlottenlund, Denmark.
    Nielsen, Anders
    DTU Aqua – National Institute of Aquatic Resources, Charlottenlund, Denmark.
    Norrström, Niclas
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre.
    Oeberst, Rainer
    Thünen Institute Baltic Sea Fisheries, Rostock, Germany.
    Stepputtis, Daniel
    Thünen Institute Baltic Sea Fisheries, Rostock, Germany.
    Stern, Edward
    The Fisheries Secretariat (FISH), Stockholm, Sweden.
    Storr-Paulsen, Marie
    DTU Aqua – National Institute of Aquatic Resources Section for Fisheries Advice, Charlottenlund, Denmark.
    Strehlow, Harry Vincent
    Thünen Institute Baltic Sea Fisheries, Rostock, Germany.
    Svedäng, Henrik
    Swedish University of Agricultural Sciences Institute of Marine Research, Lysekil, Sweden.
    Trenkel, Verena
    Ifremer Nantes Centre, Nantes, France.
    Wæver Pedersen, Martin
    DTU Aqua – National Institute of Aquatic Resources Section for Fisheries Advice, Charlottenlund, Denmark.
    Zimmermann, Christopher
    Thünen Institute Baltic Sea Fisheries, Rostock, Germany.
    Report of the Benchmark Workshop on Baltic Cod Stocks (WKBALTCOD)2015Report (Other academic)
    Abstract [en]

    The ICES Benchmark Workshop on Baltic Cod Stocks (WKBALTCOD), chaired by External Chair Jean-Jacques Maguire, Canada and ICES Chair Marie Storr-Paulsen, Denmark, and attended by two invited external experts Verena Trenkel, France and Meaghan Bryan, USA met in Rostock, Germany, 2–6 March 2015 with 39 participants and six countries represented. The objective of WKBALTCOD was to evaluate the appropriateness of data and methods to determine stock status and investigate meth-ods appropriate to use in the single-stock assessment for the cod stock in SD 22–24 and cod in SD 25–32 in the Baltic. Participants in the workshop were a large group with diverse backgrounds representing the industry, fisheries, NGOs, managers and scientists.The single-stock analytic assessment of the eastern Baltic stock was not accepted by the assessment working group (WGBFAS) in 2014 due to severe problems with the input data. The advice for the eastern Baltic cod was, therefore, based on the ICES approach for data-limited stocks. As an outcome ICES decided to establish a bench-mark for both cod stocks and to scope an integrated assessment for the Baltic cod stocks. The first meeting (WKSIBCA) was therefore meant to introduce the interces-sional work conducted since the assessment working group in April 2014, and to reach some conclusions on how to proceed both in the short term (Benchmark in March 2015) and longer term (2–3 years) and was seen as a data compilation work-shop, there is produced a separate report from this workshop. The WKBALTCOD was the 2nd meeting in the benchmark process and was intended to come up with a final stock assessment method, stock annex and input data for both stocks. As it was not possible to reach conclusive decision on the final model to be used for the east Baltic cod stock during the benchmark meeting and as more work on the preferable models was needed, it was decided by the ACOM leadership to prolong the bench-mark process until the assessment working group meeting in April 2015. This deci-sion has led to a relatively long process partly mixed with the assessment working group WGBFAS.It became clear during the benchmark process that although large effort has been put into explaining the underlying processes leading to the changes in the Baltic ecosys-tem, there is still some lack of understanding of the present situation in the eastern Baltic cod stock. Therefore, it was not possible to reach firm conclusions on the final model to be used and therefore not possible to set reference points. It was decided to continue to explore the most promising models and to continue to improve the input data until the assessment working group started in April.The main challenges still to be solved for the Eastern Baltic cod stock is the quantifi-cation of increased natural mortality and decrease in growth. Through several presentations during the workshop (both WKSIBCA and WKBALTCOD) it became clear that natural mortality very likely has increased in later years, due to decreased condition and increased parasite infection. A decrease in growth also seems plausible duo to a decrease in condition and/or selectivity-induced mortality of the largest in-dividuals. However, as none of these parameters are easily estimated, especially with the severe ageing problems, different model assumptions made the output very shaky.For the western Baltic cod, stock identification issues were examined in area SD 24, the intermediate area: based on otolith characteristics and genetics. Due to the results showing a large proportion of east cod in this area, it was decided to split the catch2 | ICES WKBALTCOD REPORT 2015and survey from SD 24 into either the western or eastern Baltic cod stock. It was pos-sible to derive proportions of eastern and western cod in SD 24 back to the mid-1990s.For the western Baltic cod stock a modelled survey indices was included in the as-sessment covering the western part of SD 24 and Area 22+23 and based on a smoothed ALK.Both cod stocks have in the past used commercial tuning fleet to have a better cov-ered of older age groups. It was decided to abound this time-series duo quality issues such as a limited coverage and problems with technical creeping.WKBALTCOD was not able to explore and define reference points for the Western Baltic cod stock during the meeting due to time constraints, but these were calculated and decided by correspondence after the meeting. The recent protocols on estimation procedures developed by WKMSYREF3 for stocks with a full analytical assessment and for data-limited stocks served as objective guidelines to obtain reference point estimates.

  • 9.
    Alsayed Ahmad, Alaa
    University of Skövde, School of Bioscience.
    Azithromycin effects on R. subcapitata on molecular levels: Ecotoxicological study on the effects of a pollutant on chlorophyll contents, pcna and cyt P450 genes expression2022Independent thesis Basic level (degree of Bachelor), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Antibiotics are considered a type of antimicrobial that particularly has an impact on bacteria or fungi in humans and animals. The widespread use of common antibiotics, combined with the fact that the majority of active antibiotics and their metabolites are water-soluble, results in persistent pollution in aquatic environments, as well as a potential threat to ecosystems. Moreover, there are inadequate ecotoxicological data on many antibiotics, such as azithromycin, which has been quantified at elevated levels in the aquatic system. Raphidocelis subcapitata is a globally distributed green alga that is commonly used as a model species for evaluating chemical toxicity due to the availability of a sequenced genome and its rapid growth, which allows assessing chemical effects across many generations. the aim of this project is to provide an insight on genotoxicity for R. subcapitata and study the effects of azithromycin antibiotic on algae, on both growth rate and molecular levels by determining gene expression levels, specifically, its effect related to chlorophyll pigments,biosynthesis, and DNA replication levels. In order to do that, toxicity test according to OECD guidelines for 7 days, photosynthetic pigment extraction and qRT-PCR were utilized. In the present study, an EC50 of 24 µg/L was obtained, while low risk in the Swedish water streams was indicated, significant induction in Chlorophyll a and b at high concentrations while no effects on carotenoids were observed, no significant difference in pcna and cyt P450 at LOEC and lower concentrations was obtained. This might suggests testing higher concentrations in upcoming research.

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  • 10.
    Andersen, Michael
    et al.
    Danish Fishermen’s Association Fredericia, Denmark.
    Arula, Timo
    University of Tartu, Estonia.
    Casini, Michele
    Swedish University of Agricultural Sciences, Sweden.
    Clink, Sally
    Baltic Sea Regional Advisory Council, Denmark.
    Collie, Jeremy
    University of Rhode Island, USA.
    Eckeskog, Magnus
    The Fisheries Secretariat (FISH), Sweden.
    Eero, Margit
    DTU Aqua - National Institute of Aquatic Resources, Denmark.
    Eriksson, Pehr E.
    Swedish Fisherman’s Federation Fiskets Hus, Sweden.
    Gasyukov, Pavel
    AtlantNIRO, Russian Federation.
    Gröhsler, Thomas
    Thünen Institute of Baltic Sea Fisheries (TI-OF), Germany.
    Holmgren, Noél
    University of Skövde, School of Life Sciences. University of Skövde, The Systems Biology Research Centre.
    Horbowy, Jan
    National Marine Fisheries Research Institute, Poland.
    Howell, Daniel
    Institute of Marine Research, Norway.
    Jepsena, Ilona
    European Commission, Directorate for Maritime Affairs and Fisheries, Belgium.
    Johansson, Reine J.
    Swedish Fishermen´s Federation, Sweden.
    Janusas, Stanislovas
    European Commission Directorate for Maritime Affairs and Fisheries, Belgium.
    Kaljuste, Olavi
    Swedish University of Agricultural Sciences, Sweden.
    Karpushevskiy, Igor
    AtlantNIRO, Russian Federation.
    Klaas, Kunnar
    Ministry of the Environment of Estonia, Estonia.
    Kornilovs, Georgs
    Institute of Food Safety, Animal Health and Environment (BIOR), Latvia.
    Krumme, Uwe
    Thûnen Institute of Baltic Sea Fisheries (TI-OF), Germany.
    Linke, Sebastian
    University of Gothenburg, Sweden.
    Lövgren, Johan
    Swedish Unniversity of Agricultural Sciences, Sweden.
    Luzenczyk, Anna
    National Marine Fisheries Research Institute, Poland.
    Maguire, Jean-Jacques
    International Council for the Exploration of the Sea, Canada.
    Neuenfeldt, Stefan
    DTU Aqua - National Institute of Aquatic Resources, Denmark.
    Norrström, Niclas
    University of Skövde, School of Life Sciences. University of Skövde, The Systems Biology Research Centre.
    Oeberst, Rainer
    Thünen Institute of Baltic Sea Fisheries (TI-OF), Germany.
    Plaganyi, Eva
    CSIRO Marine and Atmospheric Research (CMAR), Australia.
    Plikshs, Maris
    Institute of Food Safety, Animal Health and Environment (BIOR), Latvia.
    Raid, Tiit
    Estonian Marine Institute, University of Tartu, Estonia.
    Reeves, Stuart
    European Commission Directorate for Maritime Affairs and Fisheries , Belgium.
    Rindorf, Anna
    DTU Aqua - National Institute of Aquatic Resources, Denmark.
    Storr- Paulsen, Marie
    DTU Aqua - National Institute of Aquatic Resources, Denmark.
    Strehlow, Harry V.
    Thünen Institute of Baltic Sea Fisheries (TI-OF), Germany.
    Vinther, Morten
    DTU Aqua - National Institute of Aquatic Resources, Denmark.
    Walther, Yvonne
    Swedish University of Agricultural Sciences, Sweden.
    Report of the Benchmark Workshop on Baltic Multispecies Assessments (WKBALT): 4–8 February 2013, Copenhagen, Denmark2013Report (Refereed)
  • 11.
    Aps, R.
    et al.
    University of Tartu.
    Fetissov, M.
    University of Tartu.
    Holmgren, Noel
    University of Skövde, School of Life Sciences. University of Skövde, The Systems Biology Research Centre.
    Norrström, Niclas
    University of Skövde, School of Life Sciences. University of Skövde, The Systems Biology Research Centre.
    Kuikka, S.
    University of Helsinki.
    Central Baltic Sea herring: effect of environmental trends and fishery management2011In: Ecosystems and Sustainable Development VIII / [ed] Y. Villacampa & C. A. Brebbia, Southampton: BioMed Central Ltd. , 2011, p. 69-80Conference paper (Refereed)
    Abstract [en]

    Uncertainty is an endemic condition of the Baltic Sea herring (Clupea harengus membras, L) fishery management. It is a condition exacerbated by the fishing fleet overcapacity and consequent exploitation of the herring stock at a level believed to be unsustainable. Some sources of uncertainty are mainly related to biology and fishing technique: the unsolved problem of herring assessment and management units, the recruitment–environment relationship and the reduction in mean weights-at-age, uncertain ageing of fish, the problem of unaccounted fishing mortality caused by the fish selection through the trawl net. Fishing fleet overcapacity is believed to be behind of the regulatory overfishing when setting the Total Allowable Catches (TACs) higher than the scientific advice (decision overfishing) and tolerating the extensive underreporting of catches (implementation overfishing). Two scenarios for the Central Baltic Sea herring fishery management options are constructed and the Bayesian networks are used to represent and update uncertainties encountered in the process of the management related situation assessment. First scenario represents the current status of the fishery management resulting in fishing mortality (F) higher than FMSY – the fishing mortality that corresponds to the Maximum Sustainable Yield (MSY). The second scenario demonstrates the assumed potential impact of economic incentives (e.g.zoning, individual transferable quotas (ITQs), territorial use rights etc.) on the reduction of excessive fishing capacity and bringing actual fishing mortality closer to FMSY.

  • 12.
    Arvidsson, D.
    et al.
    Univ Gothenburg, Sahlgrenska Acad, Dept Clin Nutr, SE-40530 Gothenburg, Sweden.
    Slinde, Frode
    University of Skövde, School of Life Sciences.
    Larsson, S.
    Univ Gothenburg, Sahlgrenska Acad, Dept Internal Med Respirat Med & Allergology, Gothenburg, Sweden.
    Hulthén, L.
    Univ Gothenburg, Sahlgrenska Acad, Dept Clin Nutr, SE-40530 Gothenburg, Sweden.
    Energy cost of physical activities in children: Validation of SenseWear Armband2007In: Medicine & Science in Sports & Exercise, ISSN 0195-9131, E-ISSN 1530-0315, Vol. 39, no 11, p. 2076-2084Article in journal (Refereed)
    Abstract [en]

    PURPOSE: To examine the validity of SenseWear Pro2 Armband in assessing energy cost of physical activities in children, and to contribute with values of energy costs in an overview of physical activities in children. METHODS: Energy cost was assessed by SenseWear Pro2 Armband in 20 healthy children, 11-13 yr, while lying down resting, sitting playing games on mobile phone, stepping up and down on a step board, bicycling on a stationary bike, jumping on a trampoline, playing basketball, and walking/running on a treadmill at the speeds 2, 3, 4, 5, 6, 7, 8, and 10 km x h(-1). During these activities, energy cost was also assessed from VO2 and VCO2 measured by Oxycon Mobile portable metabolic system, which was used as criterion method. RESULTS: The difference in energy cost between SenseWear Pro2 Armband and Oxycon Mobile was -0.7 (0.5) (P < 0.001) for resting, -2.0 (0.9) (P < 0.001) for playing games on mobile phone, -6.6 (2.3) (P < 0.001) for stepping on the step board, -12.0 (3.7) (P < 0.001) for bicycling, -2.7 (11.9) (P = 0.34) for jumping on the trampoline, and -14.8 (6.4) kJ x min(-1) (P < 0.001) for playing basketball. The difference in energy cost between SenseWear Pro2 Armband and Oxycon Mobile for increasing treadmill speed was 1.3 (3.1) (P = 0.048), 0.1 (2.9) (P = 0.82), -1.2 (2.6) (P = 0.049), -1.6 (3.2) (P = 0.044), -3.1 (3.7) (P = 0.0013), -4.9 (3.7) (P < 0.001), -5.3 (3.7) (P < 0.001), and -11.1 (3.5) kJ x min(-1) (P < 0.001). CONCLUSIONS: SenseWear Pro2 Armband underestimated energy cost of most activities in this study, an underestimation that increased with increased physical activity intensity. A table of energy costs (MET values) of physical activities in children measured by indirect calorimetry is presented as an initiation of the creation of a compendium of physical activities in children

  • 13.
    Babena, Omar
    University of Skövde, School of Bioscience.
    Expression of the chloride channel CLCC1 is downregulated after 24 hours in LPS-primed THP-1 monocyte-like cell line2021Independent thesis Basic level (degree of Bachelor), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Inflammation is the body's response to infection or injury and is mediated by the innate immune system. The NLRP3 inflammasome is a multi-protein complex that is a major contributor to many inflammatory disorders. Emerging evidence suggests the involvement of the Endoplasmic reticulum stress with the NLRP3 inflammasome. The endoplasmic reticulum stress is a series of stress signals that can activate the unfolded protein response and usually accompanies inflammation and eventually causes cell death. Recently, a localized endoplasmic reticulum micro-protein called the chloride clic like-1 channel was found to be involved in the endoplasmic reticulum homeostasis. Recent evidence suggests the involvement of endoplasmic reticulum stress in the inflammation pathways of the NLRP3 inflammasome. The relationship between the ER and the NLRP3 inflammasome has not been clearly described. This study aimed at investigating the expression levels of the microprotein CLCC1 to shed a light on the relationship between the endoplasmic reticulum stress and the NLRP3 inflammasome. The expression levels of CLCC1 were analyzed by qPCR in cultured monocytes under different time points of Lipopolysachaaride immuno-stimulation. The stability of expression in candidate reference genes was investigated for normalization purposes. This study reported the regulation of CLCC1 as a novel finding under prolonged LPS exposure of monocytes and stable reference genes such as GUSB and ACTB were identified. The relationship between CLCC1 and NLRP3 inflammasome priming by LPS indicated that CLCC1 is regulated and may be involved in the inflammatory mechanisms of endoplasmic reticulum stress and NLRP3 inflammasome inflammatory diseases, contributing to a potential therapeutic target in the endoplasmic reticulum and inflammasome related diseases.

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  • 14.
    Backlund, Kristina
    University of Skövde, School of Bioscience.
    microRNA-200 Family Expression Level Changes in Stimulated THP-1 Cells Following NLRP3 Inflammasome Activation2020Independent thesis Basic level (degree of Bachelor), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Innate immunity is the immune systems rapid responses to infection after being attacked by a pathogen. Inflammatory responses are activated by the detection of pathogen-associated molecular patterns and danger-associated molecular patterns through pattern recognition receptors on inflammatory cells. NLRs are activated by intracellular PAMPs which warn cells of damage and have a major role in initiating the innate inflammatory responses as well as the development of infectious and inflammatory diseases. NLRP3 is a very large multiprotein complex and is the most studied inflammasome. The NLRP3 Inflammasome follows a two-signal model for activation, signal one forms the NLRP3 complex and signal two activates the inflammasome. NLRP3 initiates an inflammatory form of cell death called pyroptosis and triggers the release of pro-inflammatory cytokines IL-1β and IL-18. The miR-200 family has five members, miR-200a, miR-200b and miR-429 located on chromosome 1 and miR-200c and miR-141 located on chromosome 12. In this study, THP-1 cells were differentiated with PMA then stimulated with LPS and ATP. Various time samples were collected and isolated to obtain miRNA. Two-step RT-qPCR was then performed to quantitively monitor the changes in miRNA-200 family expression levels. The purpose of this study was to observe how miRNA-200 family expression levels change in stimulated THP-1 cells as the NLRP3 inflammasome is activated. This became a pilot study as all biological replicates could not be analyzed, miR-200 family is showing a potential response to the activation of the NLRP3 inflammasome and they should be investigated further.

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  • 15.
    Badekar, Karishma
    University of Skövde, School of Bioscience.
    Cloning of two arsenic reponsive arsB and arsC genes from Lysinibacillus sphaericus and construction of binary vectors for T-DNA mediated transformation of tobacco plants.2017Independent thesis Advanced level (degree of Master (One Year)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Arsenic is classified to be a heavy metal that severely contaminates human foods, drinking water and the environment in many regions of the world. Long term exposure to arsenic can create chronic poisoning of human health leading to many life threatening and lethal diseases such as cancer, keratosis, gangrene, damage of lung, kidney and liver and also many other neuro vascular disorders.

    To cope with this problem, the researchers of the Biotechnology Research group at the University of Skövde has previously identified and isolated a bacterial strain Lysinibacillus sphaericus sp. B1-CDA from arsenic contaminated soil. These strains are resistant to arsenic, can uptake arsenic from the contaminated source and store it inside the cells thus reducing the arsenic content in the contaminated source. Genome sequencing of this strain revealed that the bacterium harbors several arsenic responsive genes. The research group has also performed several in silico studies on these genes to determine their molecular functions. Two of these genes arsB and arsC were predicted to be involved in uptake and storage of arsenics inside the cells. In this thesis work the arsB and arsC genes were cloned from the genomic DNA of bacterium by PCR using database sequences as primers. These genes were then transferred into two cloning vectors pMAN1080 and pMAN0385, respectively. The pCAMBIA1301 vector was utilized to construct the binary vectors for transferring these genes to tobacco plants by using Agrobacterium tumefaciens T-DNA mediated gene transfer. Two binary vectors each harboring the respective arsenic responsive genes arsB and arsC were successfully constructed. Transgenic calli derived from leaf disk transformation were successfully selected. Transgenic shoots were generated but with a very low transformation frequency (<6%).

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  • 16.
    Bansal, Divya
    University of Skövde, School of Bioscience.
    Adipocytes from SERCA2 knockout mice exhibit a dysregulation in the secretion of adiponectin and resistin2020Independent thesis Advanced level (degree of Master (One Year)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Obesity leading to Type-2-diabetes is a major health issue all over the world. Obesity characterized by expansion of adipose tissue, in particular white adipose tissue (WAT) which controls the metabolic physiology in the body by secreting proteins like adiponectin and resistin. Adiponectin has a protective role against diabetes development whereas resistin causes insulin resistance. Protein folding, maturation and translocation is performed by the Endoplasmic reticulum using calcium ions. The calcium homeostasis is maintained by calcium pumps and channels, chief of this is sarco-/endoplasmic reticulum (SR/ER) Ca2+ ATPase pump (SERCA) which restores calcium back to the ER. To study the effect of SERCA2 on adiponectin and resistin secretion in different adipose tissue depots using an adipocyte specific tamoxifen-inducible SERCA2 Knock-out mice, short term secretion experiments were performed. Chemical inhibition of SERCA2 and ER stress was performed in in-vitro experiments using adipocyte like 3T3-L1 cell line. The experiments revealed that SERCA2 dysfunction led to decrease in adiponectin and resistin secretion in normal and stimulant conditions in both male and female mice. In-vitro experiments revealed that ER stress led to misfolded protein accumulation affecting exocytotic events of adiponectin containing vesicles. Therapeutic agents can be formulated to tackle the SERCA2 dysfunction and to maintain calcium homeostasis by identifying these key mechanisms for diabetes and related metabolic disorders.

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  • 17.
    Bansal, Vanisha
    University of Skövde, School of Bioscience.
    Blood interactions with bioactive peptidefunctionalized nanocellulose: An evaluation of the activation of the coagulation and complement system2022Independent thesis Advanced level (degree of Master (One Year)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    A current trend utilizing the biomedical approach in the field of wound care is focused on the increased potential to develop wound healing materials designed to address specific types of wounds or underlying pathologies to achieve improved healing. The work presented in this thesis evaluates the blood response to wood-derived nanocellulose functionalized with a peptide, with the ultimate aim of characterizing the material as a potential wound dressing for chronic wound care. The material was evaluated based on the response toward the innate immune system. These interactions between the material and blood were studied using an in vitro whole blood loop model, and then, the coagulation and complement system activation markers were quantified using enzyme-linked immunosorbent assays. The platelet count and the levels of the thrombin-antithrombin complex reported for the material showed no activation of the coagulation cascade whereas there was an activation caused in the complement system showing higher levels of C3a and s-C5b9 components as compared to the controls. The observations obtained from this interdisciplinary project can be considered as a stepping stone toward the need for further analysis of the material in advanced wound care applications. This can be achieved by targeting the specific phases of the wound healing process in order to promote effective wound management. 

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  • 18.
    Belekar, Prajakta Ashok
    University of Skövde, School of Bioscience.
    Quantifying extracellular vesicle secretion from single neuro-endocrine cells to understand how they affect hormonal secretion2020Independent thesis Advanced level (degree of Master (One Year)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Extracellular vesicles (EV’s) are small lipid bilayer vesicles that are generated by almost all kind of cells in a body. EV’s are considered as one of the key intercellular messengers regulating cell signalling mechanisms. Earlier studies have shown that, in metabolic diseases like diabetes and obesity, as well as during hypertension and neurodegenerative disease there is increased production and secretion of EV’s. Secretion mechanism of EV’s is yet unknown. The aim of this study was to investigate the EV production and secretion mechanism in type-2-diabetes and in parallel to EV studies, measurement of SST secretion, to elucidate how it is influenced by EV’s. Tetraspanin was used to label EV’s and the efficiency was evaluated by using TIRFM and considering how many exosomes they label per cell and how well they express. Further, the EV marker were exploited in studying trafficking events of EV’s at the plasma membrane. This included EV approach to PM through docking/visiting, and EV loss from PM through undocking. EV labelling showed that CD63 and CD151 were two efficient markers for live-cell imaging by TIRF microscopy (TIRFM). Trafficking analysis of EV’s showed that number of visiting events were significantly higher compared to docking and undocking events. To know how many of total EV’s in a cell are ready to fuse with plasma membrane, rate of displacement of EV’s was monitored. This showed, small fraction of EV’s were slow-moving, probably docked at the PM while rest EV’s were fast-moving, either visiting or undocking EV’s. Docked EV’s fuse with plasma membrane. SST secretion from δ-cells was studied using pancreatic islets. There are no currently reliable means to measure δ-cells SST secretion. Commercially available antibodies against SST were evaluated compared to antibodies developed in the lab. Efficiency of the antibodies was studied by analyzing number of δ-cells and their distribution in an islet. The results showed that the antibodies against SST that were developed in the lab have a higher efficiency compared to the commercially available antibodies in δ-cells in an islets and tissue. These antibodies were used for staining δ-cells in type-2 diabetic vs healthy islets. Decrease in number of δ-cells in diabetic islets was observed. Therefore, these developed antibodies can be used for future hormone secretion studies.

  • 19.
    Beniamin, Armanos
    University of Skövde, School of Life Sciences.
    Establishment of an Expression and Purification System for Plasmodium falciparum Multi Drug Resistance (pfmdr) Transporter2007Independent thesis Advanced level (degree of Master (One Year)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Malaria is a life threatening parasite disease caused and transmitted by infected female anopheles mosquito. However, the parasite, Plasmodium falciparum, has become resistant to most anti malarial drugs, such as chloroquine, which contributes to fever and anaemia because of its ability to digest the haemoglobin in the red blood cells. The aims of this project were to establish whether “Bac to Bac” Baculoviral Expression System is suitable for expression of pfmdr 1 gene and for purification of the pgh 1 protein. The pfmdr 1 gene encodes an ABC transporter protein, pgh 1, fixed in the cell membrane of the Plasmodium falciparuum gut, which assist in elimination of drug compounds. Furthermore, “Bac to Bac” Baculoviral Expression System uses vectors with histidine tags to clone the pfmdr 1 gene and subsequently transform these into DH10Bac cells to produce the recombinant bacmid DNA. Since pfmdr 1 gene is an AT-rich sequence, PCR was optimized, by lowering the annealing and extension temperature to 47Co and 66Co respectively. The results show that “Bac to Bac” Baculoviral Expression System can be used to express the pfmdr 1 gene, though further experiments has to be performed.

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  • 20.
    Bergenius, Mikaela
    et al.
    Swedish University of Agricultural Sciences, Department of Aquatic Resources, Institute of Marine Research, Lysekil, Sweden.
    Boje, Jesper
    The National Institute of Aquatic Resources Section for Fisheries Advice, Charlottenlund, Denmark.
    Casini, Michele
    Swedish University of Agricultural Sciences, Department of Aquatic Resources, Institute of Marine Research, Lysekil, Sweden.
    Degel, Henrik
    The National Institute of Aquatic Resources Section for Fisheries Advice, Charlottenlund, Denmark.
    Eero, Margit
    The National Institute of Aquatic Resources Section for Management Systems, Charlottenlund, Denmark.
    Florin, Ann-Britt
    Swedish University of Agricultural Sciences, Department of Aquatic Resources, Institute of Coastal Research, Öregrund, Sweden.
    Gasyukov, Pavel
    AtlantNIRO, Kaliningrad, Russian Federation.
    Grygiel, Wlodzimierz
    Sea Fisheries Institute, Gdynia, Poland.
    Gröhsler, Tomas
    Thünen Institute of Baltic Sea Fisheries (TI-OF), Rostock, Germany.
    Hjelm, Joakim
    Swedish University of Agricultural Sciences, Institute of Marine Research, Sweden.
    Horbowy, Jan
    Sea Fisheries Institute, Gdynia, Poland.
    Holmgren, Noél
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre.
    Norrström, Niclas
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre.
    Kaljuste, Olavi
    Swedish University of Agricultural Sciences, Department of Aquatic Resources, Institute of Coastal Research, Öregrund, Sweden.
    Karpushevskiy, Igor
    AtlantNIRO, Kaliningrad, Russian Federation.
    Karpushevskaia, Anastasiia
    AtlantNIRO, Kaliningrad, Russian Federation.
    Kornilovs, Georgs
    Latvian Fish Resources Agency, Riga, Latvia.
    Krumme, Uwe
    Thünen Institute of Baltic Sea Fisheries (TI-OF), Rostock, Germany.
    Luzenczyk, Anna
    National Marine Fisheries Research Institute, Gdynia, Poland.
    Lövgren, Johan
    Swedish University of Agricultural Sciences, Department of Aquatic Resources, Institute of Marine Research, Lysekil, Sweden.
    Pönni, Jukka
    Finnish Game and Fisheries Research, Institute Kotka Unit, Kotka, Finland.
    Oeberst, Rainer
    Thünen Institute of Baltic Sea Fisheries (TI-OF), Rostock, Germany.
    Raid, Tiit
    Estonian Marine Institute, University of Tartu, Tallinn, Estonia.
    Raitaniemi, Jari
    Finnish Game and Fisheries Research Institute Turku Game and Fisheries Research, Turku, Finland.
    Statkus, Romas
    Division of fishery research and science, Fishery service under Ministry of Agriculture, Klaipeda, Lithuania.
    Stoetera, Sven
    Thünen Institute of Baltic Sea Fisheries (TI-OF), Rostock, Germany.
    Storr-Paulsen, Marie
    DTU Aqua - National Institute of Aquatic Resources Section for Fisheries Advice, Charlottenlund, Denmark.
    Ustups, Didzis
    Institute of Food Safety, Animal Health and Environment (BIOR), Fish Resources Research Department, Riga, Latvia.
    Walther, Yvonne
    Swedish University of Agricultural Sciences, Institute of Marine Research, Karlskrona, Sweden.
    Report of the Baltic Fisheries Assessment Working Group (WGBFAS): 14-21 April 2015, ICES HQ, Copenhagen, Denmark2015Report (Other academic)
    Abstract [en]

    The ICES Baltic Fisheries Assessment Working Group (WGBFAS) met 14-21 April 2015 (Chair: Mare Storr-Paulsen, Denmark), with 28 participants and 9 countries represented. The objective of WGBFAS was to assess the status of the following stocks:

    1 ) Sole in Division IIIa, SDs 20-22

    2 ) Cod in Kattegat, Cod in SD 22-24, Cod in SD 25-32

    3 ) Herring in SD 25-27, 28.2, 29 and 32, Herring in SD 28.1 (Gulf of Riga), Herring in SD 30, Herring SD 31.

    4 ) Sprat in SD 22-32

    5 ) Plaice 21-23, Plaice 2425

    6 ) Flounder 22-23; 24-25; 26+28 and 27+29-32, Brill 2232, Dab 2232, and Turbot 2232 (survey trends)

    WGBFAS also identified the data needed, for next year’s data call with some suggestions for improvements in the data call as well as in InterCatch. The report contains an introduction with the summary of other WGs relevant for the WGBFAS, country specific fishery description, the methods used, and ecosystem considerations. The results of the analytical stock assessment or survey trends for the species listed above are then presented with all the stocks with the same species in the same sections. The report ends with references, list of Working Documents, recommendations and Stock Annexes. In first quarter 2015 the Baltic cod stocks and the plaice stocks were benchmarked. As a result the Baltic cod stocks now have to apply a splitting key in SD 24 were both stocks are present. This has changed the assessment from being an area based assessment to now being a stock based assessments and has implications for the advice. The principle analytical models used for the stock assessments were XSA and SAM. For most flatfishes, CPUE trends from bottom trawl surveys were presented (except plaice 2425 and her31 using relative SSB from SAM and XSA, respectively). Ecosystem changes have been analytically considered in the following stock assessments: Herring in SD 25-27, 28.2, 29 and 32, and Sprat in SD 22-32, in form of cod predation mortality. Last year a very large retrospective pattern in the Eastern Baltic cod stock caused that the WG rejected the analytic assessment. Several uncertainties in the data lead to this conclusion i.a age reading problems with large inconsistency between and within nations as well as a change in growth and natural mortality. However, even though a data compilation workshop and a benchmark have been conducted in the intermediate time it was not possible to solve the main issue on growth. The lack of knowledge on growth caused to that even the length based data required in the data call was very uncertain for the models and in the end the WG was not able to produce a better model than was presented last year which is based on survey trends. The Her-30 (Herring in the Botnian Sea) was by the working group down scaled from a category 1 stock to a category 3 stock due to the commercial tuning fleet used in the assessment having very uncertain estimates in the last couples of years. However, during the Baltic ADG an alternative assessment was suggested were the stock is still considered a category 1 stock but the last 8 years of the commercial tuning fleet was terminated. This assessment was conducted after the working group but has been included in the report.

  • 21.
    Bergenius, Mikaela
    et al.
    Swedish University of Agricultural Sciences.
    Cadigan, Noel
    Memorial University of Newfoundland, Canada.
    Gröhsler, Tomas
    Johann-Heinrich von Thünen-Institute, Germany .
    Holmgren, Noél
    University of Skövde, School of Life Sciences. University of Skövde, The Systems Biology Research Centre.
    Morgado, Cristina
    International Council for the Exploration of the Sea, Denmark.
    Pönni, Jukka
    Finnish Game and Fisheries Research Institute, Finland.
    Raitaniemi, Jari
    Finnish Game and Fisheries Research Institute, Finland.
    Storr-Paulsen, Marie
    DTU Aqua - National Institute of Aquatic Resources, Denmark.
    Trenkel, Verena
    Ifremer Nantes Centre, France.
    Report of the Inter-Benchmark Protocol for Herring in Subdivision 30 (IBP Her30): 11–15 March 2013, By correspondence2013Report (Refereed)
    Abstract [en]

    The Inter-Benchmark Protocol for Herring in Subdivision 30 (IBP-Her30) worked by correspondence  between  February  28  and  March  28  2013. Verena Trenkel  (France) served as Chair with invited expert Noel Cadigan (Canada). There were six participants. The objectives of the groups were to review the work carried out in response to the benchmark working group WKPELA in 2012.

  • 22.
    Bergström, Lena
    et al.
    Swedish Univeristy of Agricultural Sciences, Department of Aquatic Resources, Öregrund, Sweden.
    Blenckner, Thorsten
    Stockholm Resilience Centre, Stockholm University, Stockholm, Sweden.
    Grimvall, Anders
    Swedish Institute for the Marine Environment, Gothenburg, Sweden.
    Gårdmark, Anna
    Swedish Univeristy of Agricultural Sciences, Department of Aquatic Resources, Öregrund, Sweden.
    Hamrén, Henrik
    Baltic Sea Centre, Stockholm University, Stockholm, Sweden.
    Holmgren, Noél
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre.
    Jacob, Ute
    University of Hamburg, Institute of Hydrobiology and Fishery Science, Hamburg, Germany.
    Kininmonth, Stuart
    Stockholm Resilience Centre, Stockholm University, Stockholm, Sweden.
    Large, Scott
    ICES, Copenhagen, Denmark.
    Levin, Phil
    Northwest Fisheries Science Center, Seattle, USA.
    Lehikoinen, Annukka
    Helsinki University, Kotka Maritime Research Centre, Kotka, Finland.
    Llope, Marcos
    Instituto Español de Oceanografía, Centro Oceanográfico de Cádiz, Spain.
    Luzenczyk, Anna
    National Marine Fisheries Research Institute, Gdynia, Poland.
    Müller-Karulis, Bärbel
    Baltic Sea Centre, Stockholm university, Stockholm, Sweden.
    Möllmann, Christian
    University of Hamburg, Institute of Hydrobiology and Fishery Science, Hamburg, Germany.
    Neuenfeldt, Stefan
    DTU Aqua, Charlottenlund, Denmark.
    Norrström, Niclas
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre.
    Olsson, Jens
    Swedish Univeristy of Agricultural Sciences, Department of Aquatic Resources, Öregrund, Sweden.
    Otto, Saskia
    University of Hamburg, Institute of Hydrobiology and Fishery Science, Hamburg, Germany.
    Pekcan-Hekim, Zeynep
    Swedish Univeristy of Agricultural Sciences, Department of Aquatic Resources, Öregrund, Sweden.
    Rau, Andrea
    Thuenen-Institute of Baltic Sea Fisheries, Rostock, Germany.
    Reid, David
    Marine Institute, Rinville, Galway, Ireland.
    Tomczak, Maciej, T.
    Baltic Sea Centre, Stockholm university, Stockholm, Sweden.
    Torres, Marian
    Swedish Univeristy of Agricultural Sciences, Department of Aquatic Resources, Öregrund, Sweden.
    Ustups, Didzis
    Institute of Food safety, Animal Health and Environment, Riga, Latvia.
    Uusitalo, Laura
    Finnish Environment Institute, Marine Research Centre, Helsinki, Finland.
    Wesslander, Karin
    Swedish Meteorological and Hydrological Institute, Marine Environment, Västra Frölunda, Sweden.
    Report of the ICES/HELCOM Working Group on Integrated Assessments of the Baltic Sea (WGIAB)2015Report (Other academic)
    Abstract [en]

    The ICES/HELCOM Working Group on Integrated Assessments of the Baltic Sea(WGIAB) was established in 2007 as a forum for developing and combining ecosystembasedmanagement efforts for the Baltic Sea. The group intends to serve as a scientificcounterpart and support for the ICES Baltic Fisheries Assessment Working Group(WGBFAS) as well as for efforts and projects related to Integrated Ecosystem Assessments(IEA) within ICES and HELCOM. The group works in cooperation with similargroups within the ACOM/SCICOM Steering Group on Integrated Ecosystem Assessments(SSGIEA).The 2015 WGIAB meeting was held in Cádiz, Spain, from 9–13 March, back-to-backwith the meeting of its counterpart in the Working Group on Ecosystem Assessmentof Western European Shelf Seas (WGEAWESS). The meetings had joint sessions as wellas WG specific work, and some participants effectively participated in both meetings.The WGIAB meeting was attended by 27 participants from nine countries. The meetingwas chaired by Christian Möllmann, Germany, Laura Uusitalo, Finland and Lena Bergström,Sweden.This was the last year of the ongoing three-year Terms of Reference (ToR) for WGIAB.The main working activities in 2015 were to i) conduct studies on Baltic Sea ecosystemfunctioning with the goal to publish case studies from different parts of the Baltic Seain peer-reviewed journals, ii) work on the demonstration exercise to develop ecosystem-based assessment and advice for Baltic fish stocks focusing on cod (DEMO) withmultiple approaches, iii) plan further how to integrate the social and economic aspectsmore tightly in the WGIAB work, and iv) discuss the future focus and format of theWGIAB work.The Baltic ecosystem functioning activity focused on identifying and exploring keytrends and linkages in the Baltic Sea foodweb. This was pursued by presentation andfurther discussion of ongoing intersessional work on foodweb modelling and integratedanalyses, and by exercises to develop conceptual models Baltic Sea foodwebsand the links to ecosystem function. Long-term monitoring datasets on the abiotic andbiotic parts of the Baltic Sea Proper ecosystem were updated for use in the continuedwork to develop environmental indicators for fisheries and marine management.The focus of the DEMO 3 (DEMOnstration exercise for Integrated Ecosystem Assessmentand Advice of Baltic Sea cod) was on finding a way to use the results from theDEMO1 and DEMO2 workshops in short and midterm projections/scenarios of Balticcod dynamics based on different types of modelling, as well as designing methodologyand modelling data for practical implementation of Integrated Advice for Baltic cod.The WGIAB was positively inclined towards including social and economic aspectsinto the integrated assessment. Openings to this path were provided by presentationon ongoing project work, and discussing their linkages to ecological aspects. It wasseen as crucial that experts on social and economic analysis should be included andtake an active part in the future work of the group.The group concluded that its upcoming work should focus more closely on functionaldiversity, which was identified as a recurring issue in the Baltic Sea. This approach wasalso identified as a useful connection point between scientific and management aspectsin order for the group to continue serving as a forum for developing ecosystem-basedmanagement efforts in the Baltic Sea. A focus on functional diversity was also seen as2 | ICES WGIAB REPORT 2015a potentially feasible way of bringing together management aspects for different sectors,by linking to ecosystem services concepts.The group proposed Saskia Otto, Germany and Martin Lindegren, Denmark as newincoming Chairs, together with Lena Bergström, Sweden and Laura Uusitalo, Finland.Having four Chairs is justified due to the wide scope of the group's work, as well asthe increased work load due to the planned new foci.

  • 23.
    Biswas, M. K.
    et al.
    Huazhong Agricultural University, China.
    Ahmed, M. B.
    University of Skövde, School of Life Sciences. University of Skövde, The Systems Biology Research Centre.
    Mondal, M. A. A.
    University of Rajshahi, Bangladesh.
    Razvy, M. A.
    Huazhong Agricultural University, China.
    Hoque, A.
    University of Rajshahi, Bangladesh.
    Islam, R.
    University of Rajshahi, Bangladesh.
    Hossaina, M.
    University of Rajshahi, Bangladesh.
    Mandal, Abul
    University of Skövde, School of Life Sciences. University of Skövde, The Systems Biology Research Centre.
    In exploitation of genetic diversity in potato breeding2010In: Agronomski Glasnik (Agronomy Journal), ISSN 1848-8900, Vol. 72, no 4-5, p. 261-276Article in journal (Refereed)
    Abstract [en]

    With a view to select divergent parents genetic diversity was estimated among twenty genotypes. Thirty F1 progenies developed by line-tester mating were studied from seedling generation to first clonal generation for five important agronomic traits. Cluster analysis reveals that the parents could be grouped into seven different clusters. Cluster means showed wide range of variation for several traits among singles as well as multi genotypic clusters. Considering diversity pattern, parents should select from cluster I, III, IV, and V for the improvement of potato. Analysis of variance revealed that all most all the sources of variation were highly significant for all the studied traits in both generations. Parents Challisha, Lalpakri, Patnai, Chamak, Sadagoti, TPS-67 and TPS-364 were found to be good general combiners for tuber yield and yield contribution traits due to their gca effects. The sca effects showed that out of 30 hybrids 12 were found to have specific combining ability for tuber yield and those hybrids also exhibited considerable heterosis for tuber yield and yield contributing traits.

  • 24.
    Callado Prat, Elia
    University of Skövde, School of Bioscience.
    Comparison of manual and semi-automatic RNA extraction methods using two-tailed RT-qPCR for absolute quantification as part of the sepsis diagnosis research2023Independent thesis Basic level (degree of Bachelor), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Nowadays, sepsis has become a major healthcare problem. Its variance of symptoms and the lack of time to act makes it greatly difficult to treat. An early diagnosis using biomarkers, particularly miRNA, could potentially increase the patient’s prognosis as well as reduce the use of antibiotics for the treatment. The lack of method optimization for miRNA extraction and quantification calls for investigation prior to the construction of a multi-biomarker panel for sepsis diagnosis. The aim of this project was to examine and compare manual and semi-automatic extraction methodologies through the small RNA quantity and RNA quality, as well as test the detection and quantification abilities of the novel technique, two-tailed RT-qPCR. 30 extractions have been performed, their extracted elutions have been subjected to quality and quantity control and detection and absolute quantification through the two-tailed RT-qPCR. The results show no significant differences between the quantity and quality of the RNA extracted using both methods. Time management, on the contrary, reported significant differences between the two methods. On the other hand, the two-tailed RT-qPCR successfully amplified the miRNA candidate from as little as 100 µL of healthy plasma. The absolute quantification showed the miRNA candidate’s low concentration in plasma. Moreover, the qPCR efficiency was irregular during the project which may alert of contamination or unspecific primers. However, the melt curve showed a single amplicon which suggests great specificity. The detection and quantification of the miRNA candidate have been successful, though further investigation is recommended.

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  • 25.
    Camargo Romera, Paula
    University of Skövde, School of Bioscience.
    Isoform 2 of DLG2 gene as a possible candidate tumour suppressor of neuroblastoma2021Independent thesis Basic level (degree of Bachelor), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Neuroblastoma (NB) is the most frequent extracranial solid tumour in childhood. The clinical diagnosis of NB is difficult due to the age of the patient and the vague appearance of the symptoms. Moreover, there are two groups of aggressive NBs, one with MYCN amplification and the other with an 11q deletion. Some genes could be a candidate suppressor for NB, e.g., the DLG2 gene that resides within the 11q-deleted region. The DLG2 gene has a large number of exons and multiple isoforms depending on the alternative splicing process. Moreover, these isoforms can include the L27 domain or not. This study aimed to analyse, by applying bioinformatic tools, if isoform 2, which does not have L27 domain, could be a candidate suppressor for this disease. RNA-seq samples from different human cell lines were collected from NCBI and a quality analysis was performed. The filtered samples were run in R and Python programs to do a visualization of the exon expression level and the prediction of Rsubread for exon-exon junctions. The results showed that isoform 2 of DLG2 gene was not expressed in the samples of NB, which is a promising result for being a candidate suppressor of NB. Furthermore, the prediction of exon-exon junctions by Rsubread was confirmed to be very accurate. In conclusion, this study shows that isoform 2 of DLG2 gene could be a candidate tumour suppressor in NB that could, in the future, be used as a target to help to detect earlier the presence of NB and increase the life expectancy of children who suffer from this disease.

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  • 26.
    Chawade, Aakash
    et al.
    CropTailor AB, Lund, Sweden.
    Lindlöf, Angelica
    University of Skövde, School of Life Sciences. University of Skövde, The Systems Biology Research Centre. CropTailor AB, Lund, Sweden.
    Olsson, Björn
    University of Skövde, School of Life Sciences. University of Skövde, The Systems Biology Research Centre.
    Olsson, Olof
    CropTailor AB, Lund, Sweden ; Department of Pure and Applied Biochemistry, Lund University, Sweden.
    Global expression profiling of low temperature induced genes in the chilling tolerant japonica rice jumli marshi2013In: PLOS ONE, E-ISSN 1932-6203, Vol. 8, no 12, p. e81729-, article id e81729Article in journal (Refereed)
    Abstract [en]

    Low temperature is a key factor that limits growth and productivity of many important agronomical crops worldwide. Rice (Oryza sativa L.) is negatively affected already at temperatures below +10°C and is therefore denoted as chilling sensitive. However, chilling tolerant rice cultivars exist and can be commercially cultivated at altitudes up to 3,050 meters with temperatures reaching as low as +4°C. In this work, the global transcriptional response to cold stress (+4°C) was studied in the Nepalese highland variety Jumli Marshi (spp. japonica) and 4,636 genes were identified as significantly differentially expressed within 24 hours of cold stress. Comparison with previously published microarray data from one chilling tolerant and two sensitive rice cultivars identified 182 genes differentially expressed (DE) upon cold stress in all four rice cultivars and 511 genes DE only in the chilling tolerant rice. Promoter analysis of the 182 genes suggests a complex cross-talk between ABRE and CBF regulons. Promoter analysis of the 511 genes identified over-represented ABRE motifs but not DRE motifs, suggesting a role for ABA signaling in cold tolerance. Moreover, 2,101 genes were DE in Jumli Marshi alone. By chromosomal localization analysis, 473 of these cold responsive genes were located within 13 different QTLs previously identified as cold associated.

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  • 27.
    Chrifi, Wail
    University of Skövde, School of Bioscience.
    The effect of temperature on the innate immune response in the lungs against RSV2020Independent thesis Basic level (degree of Bachelor), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    A constant flow of various pathogens enters the respiratory system on daily basis through the involuntary mechanism of breathing. Respiratory viral infections are common yet can be fatal in vulnerable populations. Respiratory syncytial virus (RSV) is one of the first and most common viruses that the human population acquire in the first two years of life. Despite the ability of most infants to recover from a RSV infection, many require hospitalization and, in few cases, die from such an infection. The pattern of seasonality of respiratory viruses also applies to RSV. In this work the temperature dependence of infectivity was studied in Hep-2 cells infected with RSV that had been incubated with bronchoalveolar lavage (BAL) fluid. The results indicate a temperature dependence of infectivity. Inhibition of the viral infectivity was observed at three different temperatures 37 ̊C, 40 ̊C and 42 ̊C. The inhibition appears to be linked to the appearance of large agglutinates that appear to reduce the infectivity of RSV. Such a study found that viral neutralization is dependent on a temperature-dependent agglutination reaction. The causality of agglutination formation requires further investigation in order to conclusively confirm the immunological component(s) of this reaction, and how temperature is contributing to this reaction.

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  • 28.
    de Jong, Anton
    University of Skövde, School of Bioscience.
    Drosophila Melanogaster as a model for studies on fertility associated biomarkers2015Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    Many of the processes that regulate male fertility are intricate and subfertility strikes hard against both couples trying to concieve and cattle farmers where the fertility of males used for artificial insemination is the single most important factor viewed in relative economic terms. A recently published study by Fagerlind and collegues showed that seven microRNA sequences differed significantly in expression between bulls with moderate and high fertility.

    In order to study the effect these might have on fertility, a model organism is needed. The present study aim to assess if the fruit fly Drosophila Melanogaster could be used as such. It have served science for over a century, is cheap to grow and has a short generation time. A secondary objective of the present study was to elucidate if any of the observed microRNAs was expressed at a higher concentration at a specific life stage of the fly. Samples from eggs, the three larval stages and adult males and females were collected. Subsequently, after conversion into cDNA with primers for miR-34, miR-1249, miR-148b and miR-15b, the microRNA concentrations were evaluated  with Quantitative Real-Time PCR. Three out of four microRNA sequenses showed expression in the fly and for one of them, miR-34, a marked difference in expression between the developmental stages could be observed, but not confirmed statistically due to the low number of samples. This result enables further studies on these sequences and their role in male fertility.

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  • 29.
    Dello Russo, Marika
    et al.
    Institute of Food Sciences, National Research Council, Avellino, Italy.
    Formisano, Annarita
    Institute of Food Sciences, National Research Council, Avellino, Italy.
    Lauria, Fabio
    Institute of Food Sciences, National Research Council, Avellino, Italy.
    Ahrens, Wolfgang
    Leibniz Institute for Prevention Research and Epidemiology—BIPS, Bremen, Germany ; Institute of Statistics, Faculty of Mathematics and Computer Science, Bremen University, Germany.
    Bogl, Leonie H.
    School of Health Professions, Bern University of Applied Sciences, Switzerland ; Finnish Institute of Molecular Medicine, University of Helsinki, Finland.
    Eiben, Gabriele
    University of Skövde, School of Health Sciences. University of Skövde, Digital Health Research (DHEAR). Department of Public Health and Community Medicine, University of Gothenburg, Sweden.
    De Henauw, Stefaan
    Department of Public Health and Primary Care, Ghent University, Belgium.
    Hebestreit, Antje
    Leibniz Institute for Prevention Research and Epidemiology—BIPS, Bremen, Germany.
    Intemann, Timm
    Leibniz Institute for Prevention Research and Epidemiology—BIPS, Bremen, Germany.
    Hunsberger, Monica
    Department of Public Health and Community Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Sweden.
    Lissner, Lauren
    Department of Public Health and Community Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Sweden.
    Molnar, Denes
    Department of Pediatrics, Medical School, University of Pécs, Hungary.
    Pala, Valeria
    Department of Preventive and Predictive Medicine, Fondazione IRCCS, Istituto Nazionale dei Tumori, Milan, Italy.
    Papoutsou, Stalo
    Research and Education Institute of Child Health, Strovolos, Cyprus.
    Santaliestra-Pasias, Alba M.
    NUTRI-GENUD (Growth, Exercise, Nutrition and Development) Research Group, Faculty of Health Sciences and Sports, Instituto Agroalimentario de Aragón (IA2), Instituto de Investigación Sanitaria Aragón (IIS Aragón), Universidad de Zaragoza, Spain ; CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Instituto de Salud Carlos III, Madrid, Spain.
    Veidebaum, Toomas
    National Institute for Health Development, Center of Health and Behavioral Science, Tallinn, Estonia.
    Wolters, Maike
    Leibniz Institute for Prevention Research and Epidemiology—BIPS, Bremen, Germany.
    Siani, Alfonso
    Institute of Food Sciences, National Research Council, Avellino, Italy.
    Russo, Paola
    Institute of Food Sciences, National Research Council, Avellino, Italy.
    I.Family Consortium,
    Dietary Diversity and Its Association with Diet Quality and Health Status of European Children, Adolescents, and Adults: Results from the I.Family Study2023In: Foods, E-ISSN 2304-8158, Vol. 12, no 24, article id 4458Article in journal (Refereed)
    Abstract [en]

    Dietary diversity (DD) plays a crucial role in fostering high-quality diets, but its association with health outcomes, particularly body adiposity and non-communicable diseases (NCDs), is inconsistent. This may be due to a lack of a standardized method for estimating DD. Our study investigates the association between two DD indices, namely the dietary diversity score (DDS) and food variety score (FVS), and anthropometric measures, biochemical parameters, and diet quality in a large population sample from the I.Family study across research centers in eight European countries. In our cross-sectional analysis of 3035 participants, DDSs varied among countries, with a higher prevalence in the third DDS tertile among those with higher education. DDS showed a positive association with diet quality across all age groups. Higher DDS tertile individuals showed increased fiber, fruit, and vegetable intake, greater meal frequency, and lower ultra-processed food consumption. No relevant biochemical differences were observed across DDS tertiles, and a higher DDS was associated with lower overweight/obesity prevalence only in adults. No significant associations were found with FVS. Our findings emphasize the need to consider food groups for a more accurate estimation of diet quality. This aligns with studies suggesting DDS alone is not an independent risk factor for obesity in children and adolescents. Public health programs should prioritize food diversity to promote improved nutrition and overall well-being in communities. 

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  • 30.
    Diaz Rivera, Alicia
    University of Skövde, School of Bioscience.
    Future diagnosis of sepsis: Evaluating the mNGS approach by using the MinION device2022Independent thesis Basic level (degree of Bachelor), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Sepsis is an irregular systemic response to an infection, in which a pathogen or some of its component(s)reaches the bloodstream of the host or sterile tissue, triggering a disproportionate immune reaction. The first three hours are critical in the diagnosis of sepsis, in order to ensure an effective treatment with less impact on the patient. Culture-dependent diagnosis is the present standard procedure which can take up to several days. Metagenomics Next Generation Sequencing (mNGS) is a culture independent diagnostics method which could be used to identify the presence of pathogens from DNA extracted from human whole blood enabling a more effective treatment procedure of infected patients. The aim of this research was to utilize the sequencing data obtained with the MinION Nanopore sequencing device, in order to systematize its use as a tool for the early detection of sepsis; furthermore, determine if this technology is effective to use on DNA extracted from whole blood. The main research question of this thesis focused on whether the MinION Nanopore sequencing is a reliable tool for the early detection of sepsis. Whole blood samples from healthy donors was spiked with bacteria and DNA was extracted and sequenced with MinION device. The sequencing results were interpreted with the MinKNOW v2.0 software, through the application What’s In My Pot (WIMP). Also, the web tool PATRIC 3.6.12. and KRAKEN2 algorithm. The reads from the taxonomic family where the bacteria belong to was analyzed, presuming the bacterial DNA was present in the DNA extracted but the genus was not detected. According to the KRAKEN2 and WIMP analysis, the bacteria used to spike the whole blood samples was detected up to the taxonomic family level. Thus, confirming the presence of the spiked bacteria in the purified DNA samples.

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  • 31.
    Eero, Margit
    et al.
    National Institute of Aquatic Resources, Technical University of Denmark, Charlottenlund, Denmark.
    Hjelm, Joakim
    Department of Aquatic Resources, Institute of Marine Research, Swedish University of Agricultural Sciences, Lysekil, Sweden.
    Behrens, Jane
    National Institute of Aquatic Resources, Technical University of Denmark, Charlottenlund, Denmark.
    Buchmann, Kurt
    Department of Veterinary Disease Biology, University of Copenhagen, Copenhagen, Denmark.
    Cardinale, Massimiliano
    Department of Aquatic Resources, Institute of Marine Research, Swedish University of Agricultural Sciences, Lysekil, Sweden.
    Casini, Michele
    Department of Aquatic Resources, Institute of Marine Research, Swedish University of Agricultural Sciences, Lysekil, Sweden.
    Gasyukov, Pavel
    AtlantNIRO, Kaliningrad, Russian Federation.
    Holmgren, Noél
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre.
    Horbowy, Jan
    National Marine Fisheries Research Institute, Gdynia, Poland.
    Hüssy, Karin
    National Institute of Aquatic Resources, Technical University of Denmark, Charlottenlund, Denmark.
    Kirkegaard, Eskil
    International Council for the Exploration of the Sea (ICES), Copenhagen, Denmark.
    Kornilovs, Georgs
    Institute of Food Safety, Animal Health and Environment “BIOR”, Riga, Latvia.
    Krumme, Uwe
    Thünen Institute of Baltic Sea Fisheries, Rostock, Germany.
    Köster, Friedrich W.
    National Institute of Aquatic Resources, Technical University of Denmark, Charlottenlund, Denmark.
    Oeberst, Rainer
    Thünen Institute of Baltic Sea Fisheries, Rostock, Germany.
    Plikshs, Maris
    Institute of Food Safety, Animal Health and Environment “BIOR”, Riga, Latvia.
    Radtke, Krzysztof
    National Marine Fisheries Research Institute, Gdynia, Poland.
    Raid, Tiit
    Estonian Marine Institute, University of Tartu, Tallinn, Estonia.
    Schmidt, Jörn
    Department of Economics, Christian-Albrechts University of Kiel, Kiel, Germany.
    Tomczak, Maciej T.
    Stockholm University, Baltic Sea Centre, Stockholm, Sweden.
    Vinther, Morten
    National Institute of Aquatic Resources, Technical University of Denmark, Charlottenlund, Denmark.
    Zimmermann, Christopher
    Thünen Institute of Baltic Sea Fisheries, Rostock, Germany.
    Storr-Paulsen, Marie
    National Institute of Aquatic Resources, Technical University of Denmark, Charlottenlund, Denmark.
    Eastern Baltic cod in distress: biological changes and challenges for stock assessment2015In: ICES Journal of Marine Science, ISSN 1054-3139, E-ISSN 1095-9289, Vol. 72, no 8, p. 2180-2186Article in journal (Refereed)
    Abstract [en]

    The eastern Baltic (EB) cod (Gadus morhua) stock was depleted and overexploited for decades until the mid-2000s, when fishing mortality rapidlydeclined and biomass started to increase, as shown by stock assessments. These positive developments were partly assigned to effective managementmeasures, and the EB cod was considered one of the most successful stock recoveries in recent times. In contrast to this optimistic view, theanalytical stock assessment failed in 2014, leaving the present stock status unclear. Deteriorated quality of some basic input data for stock assessmentin combination with changes in environmental and ecological conditions has led to an unusual situation for cod in the Baltic Sea, which posesnew challenges for stock assessment and management advice.Anumber of adverse developments such as low nutritional condition and disappearanceof larger individuals indicate that the stock is in distress. In this study, we (i) summarize the knowledge of recent changes in cod biology andecosystem conditions, (ii) describe the subsequent challenges for stock assessment, and (iii) highlight the key questions where answers are urgentlyneeded to understand the present stock status and provide scientifically solid support for cod management in the Baltic Sea.

  • 32.
    Ekström, Anette
    et al.
    University of Skövde, School of Life Sciences.
    Nissen, Eva
    University of Skövde, School of Life Sciences.
    Process-oriented training in breastfeeding attitudes and continuity of care improve mothers perception of support2007In: Health Education Research Trends / [ed] Peter R. Hong, Nova Science Publishers, Inc., 2007, p. 211-225Chapter in book (Refereed)
  • 33.
    Elawad, Hazzim
    University of Skövde, School of Bioscience.
    Sepsis and circulating miRNA: The road towards absolute quantification of unknown miRNA levels in plasma utilizing two-tailed RT-qPCR, while testing two extraction methods, striving to create multi-marker panel for sepsis diagnosis2021Independent thesis Advanced level (degree of Master (One Year)), 20 credits / 30 HE creditsStudent thesis
    Abstract [sv]

    Sepsis is a preventable yet life threatening condition, resulting from body response to infection. Time is crucial in sepsis diagnosis since deterioration in patients’ health can occur rapidly. Blood culturing is the gold standard for diagnosis, along with clinical assessment. The discovery of miRNA in biofluids as a biomarker, founded the way for extensive research on its capabilities. MiRNA showed promises in diagnosing, assessing outcome and reporting sepsis progression. Since being delicate to handle while present in biofluid, the need was uttermost to find an effective way for miRNA isolation and detection, to facilitate developing multi-marker panel that help diagnosing sepsis, more efficiently than blood culturing. The current study aimed at using manual and robotic (QIAcube) methods, with MiRNeasy Serum/Plasma Advanced (Qiagen) as kit and protocol, to extract miRNA from human plasma samples. Plasma was either spiked with synthetic miR-223 to act as a positive control, or non-spiked. Once extraction was done, quality-quantity assessment was conducted using Qubit and Nanodrop. Two-tailed RT-qPCR (TATAA Biocenter) was used for miRNA quantification. QIAcube showed better results in quantity, hands-on and turn-around time compared to manual extraction, while better purity was scored for the manual method. While amplification appeared in all spiked samples, absolute quantification detected miRNA in some of the non-spiked samples. The study verified using the extraction kit with 100 μl of plasma is effective for miRNA extraction. Although faced with difficulties, absolute quantification using two-tailed RT-qPCR demonstrates its success in detecting lowly expressed miRNA. Future studies are needed for more optimized verification.

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  • 34.
    Erixon, Rebecka
    University of Skövde, School of Bioscience.
    Cytochrome P450 expression and growth inhibition in R. subcapitata in response to pharmaceutical cocktail exposure: An ecotoxicological study of metoprolol, omeprazole, paracetamol and diclofenac2022Independent thesis Basic level (degree of Bachelor), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Pharmaceuticals and their metabolites are present in the environment, with levels expected to rise in the future. The effects on off-target organisms are still mostly unknown and of increasing concern, as are combination cocktail effects. Microalgae are of importance to ecosystems due to being primary producers and responsible for approximately half the global photosynthetic activity. Additionally, in some algal species a detoxification ability has been uncovered, linked to the enzymatic metabolism of cytochrome P450. However, the molecular mechanisms involved in the xenobiotic metabolism of algae are poorly studied, especially regarding cocktail effects. The aim of this study was to investigate the cocktail effect on growth inhibition and gene expression in Raphidocelis subcapitata, from environmentally relevant levels of pharmaceuticals. This was achieved by performing a growth inhibition test, according to the OECD 201 guidelines. Four of the most prescribed pharmaceuticals in Sweden, paracetamol, metoprolol, omeprazole and diclofenac were tested as a cocktail and compared to metoprolol exposure. Test concentrations ranged from naturally occurring levels up to that of a tenfold. In addition to optimization of RNA extraction, a transcriptomic analysis was performed on cocktail treated groups to evaluate expression of cytochrome P450. For all concentrations, metoprolol exposure resulted in algal growth inhibition, while cocktail exposure surprisingly promoted growth. Here the lowest and medium concentrations tested yielded a downregulation of the gene, while the highest concentration elicited an upregulation. The prospect of predicting cocktail toxicity is discussed, likewise the possibility of drug-drug interactions in microalgae due to cocktail exposure. 

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  • 35.
    Fagerlind, Magnus
    et al.
    University of Skövde, The Systems Biology Research Centre. University of Skövde, School of Bioscience.
    Stålhammar, Hans
    VikingGenetics, Skara.
    Olsson, Björn
    University of Skövde, The Systems Biology Research Centre. University of Skövde, School of Bioscience.
    Klinga-Levan, Karin
    University of Skövde, The Systems Biology Research Centre. University of Skövde, School of Bioscience.
    Expression of miRNAs in Bull Spermatozoa Correlates with Fertility Rates2015In: Reproduction in domestic animals, ISSN 0936-6768, E-ISSN 1439-0531, Vol. 50, no 4, p. 587-594Article in journal (Refereed)
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  • 36.
    Farrokgi, Moloud
    University of Skövde, School of Bioscience.
    Association of RABL6 withAP3 in trafficking membrane2022Independent thesis Advanced level (degree of Master (One Year)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Via the membrane trafficking system, proteins and macromolecules dispense in different pathways into cells. Moreover, it transports proteins inside and outside of cells. AP3 and LAMP1 are crucial in the biogenesis of lysosomes and sorting the cargo proteins in the trafficking membrane. The result of immunoprecipitation and mass spectrometry proteomics that Paul Manna carried out showed that the RABL6 protein has a relation to AP3. RABL6 has been known as a proto-oncogene previously, and this is the first time that RABL6 may have a function in trafficking membrane. This study aimed to find the association of RABL6 with AP3 and the function of RABL6 via the distribution of LAMP1. HeLa cell line was transfected by a plasmid containing RABL6/GFP. The cells transfected by RABL6/GFP plasmids and wild-type cells were fixed and prepared for immunostaining. After immunostaining, confocal microscopy was used to show the interaction of AP3 and RABL6 and the distribution of LAMP1. In addition, HeLa cells were knockout for RABL6 to show the function of AP3 in RABL6 knockout cells. Optimizing immunostaining, the ratio of 1:100 for RABL6 antibody with PFA fixing shows the best result. The colocalization of RABL6 and AP3 was calculated in cells transfected by RABL6/GFP plasmid and wild-type cells and interpreted the association to each other. The knockout RABL6 cells were unsuccessful, although some differences were observed in the size of the cells. The distribution of LAMP1 in wild-type cells and RABL6 cells transfected by RABL6/GFP plasmid displayed statistical differences. In overexpressed cells, LAMP1 showed more intensity. In conclusion, the RABL6 is involved in trafficking membrane with AP3 and LAMP1.

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  • 37.
    Flos Berga, Mario
    University of Skövde, School of Bioscience.
    Effect of Ibuprofen on the growth of Pseudokirchneriella subcapitata2022Independent thesis Basic level (degree of Bachelor), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Pharmaceuticals are an important class of pollutants in aquatic ecosystems. Detected concentration are typically in the range 1 ng/L – 1 μg/L. Traditional wastewater treatment does not provide a complete removal of these contaminants; hence, they may have a negative impact on the environment. In addition, microalgae are an ecologically-meaningful target group of species for bioindication purposes as well as primary production and oxygen supply. The present work aimed to investigate the effect of Ibuprofen on the green alga Pseudokirchneriella subcapitata. Algal cultures were exposed to five different concentrations of the drug (5, 15, 45, 135, 405 mg/L) for four days. Absorbance measured at 680 nm was determined every day and obtained data were transformed into cell concentration (cells/mL) by a previously prepared calibration curve. Specific growth rate, generation time, percent inhibition and effective concentration were calculated. Moreover, one way ANOVA with Tukey’s test were applied to observe differences between groups and time periods. Based on this study, all the cultures treated with Ibuprofen had a growth inhibition as well as presenting a lag phase. Increasing the Non-Steroidal Anti-Inflammatory drug (NSAID) concentration reduced the growth rate and consequently, increased the percent inhibition in a concentration-dependent manner. According to this report, new research should be focused on the development of hybrid systems for degradation and removal of pharmaceuticals. NSAID pollution may lead to a reduction in the diversity and number of functional groups of eukaryotic algae. Finally, more research should be devoted to the toxicity of drugs in a variety of test organisms and development of reliable methods for toxicity test at low and chronic exposures to achieve more realistic conclusions.

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  • 38.
    Fransson, Cristian
    University of Skövde, School of Bioscience.
    The initial steps in the pursuit to diagnose trimethylaminuria with liquid chromatography-tandem mass spectrometry and UniSpray ionization at CMMS2022Independent thesis Basic level (degree of Bachelor), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Trimethylaminuria is an autosomal recessive disorder characterized by a decreased oxidation capacity of trimethylamine to trimethylamine-N-oxide in the liver. The condition is diagnosed by estimating concentrations of trimethylamine and trimethylamine-N-oxide in human urine and then evaluating their respective creatinine ratios and the oxidation efficiency percentage. Values previously retrieved with liquid chromatography-tandem mass spectrometry with electrospray ionization but not the novel ionization interface UniSpray. Thus, this project aims to initiate the development of a liquid chromatography-tandem mass spectrometry diagnostic method for trimethylaminuria with UniSpray ionization. The analytes were extracted from urine with a liquid-liquid extraction method and separated with hydrophilic interaction liquid chromatography using an isocratic profile with 5 mM of ammonium formate in water and methanol and multiple reaction monitoring. Overall, the mean coefficient of variation and recovery percentage from trimethylamine spiked urine samples were lower than expected, whereas the intra-precision for trimethylamine-N-oxide was acceptable. Three urine samples had estimated oxidation percentages, but only one had derived comparable creatinine ratios to an external laboratory. Due to the inadequacy of comparative data and the precision and recovery percentage deviations, the results presented in this report need cautious interpretation. Future development of the method could include manual tuning, reconsidering the calibration curve and reference values, and comparisons to the extraction method. Although there are apparent discrepancies in the precision and reliability of the derived trimethylamine and trimethylamineN-oxide concentrations, the initial steps in the pursuit of a liquid chromatography-tandem mass spectrometry diagnostic method for trimethylaminuria provide a practical foundation to continue the development.

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  • 39.
    Frisk, Mikael
    et al.
    Department of Physics, Chemistry and Biology (IFM), Linköping University, Linköping, Sweden.
    Jonsson, Annie
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre.
    Sellman, Stefan
    Department of Physics, Chemistry and Biology (IFM), Linköping University, Linköping, Sweden.
    Flisberg, Patrik
    The Forestry Research Institute of Sweden, Uppsala, Sweden.
    Rönnqvist, Mikael
    Département de génie mécanique, Université Laval, Québec, Canada.
    Wennergren, Uno
    Department of Physics, Chemistry and Biology (IFM), Linköping University, Linköping, Sweden.
    Route optimization as an instrument to improve animal welfare and economics in pre-slaughter logistics2018In: PLOS ONE, E-ISSN 1932-6203, Vol. 13, no 3, article id e0193223Article in journal (Refereed)
    Abstract [en]

    Each year, more than three million animals are transported from farms to abattoirs in Sweden. Animal transport is related to economic and environmental costs and a negative impact on animal welfare. Time and the number of pick-up stops between farms and abattoirs are two key parameters for animal welfare. Both are highly dependent on efficient and qualitative transportation planning, which may be difficult if done manually. We have examined the benefits of using route optimization in cattle transportation planning. To simulate the effects of various planning time windows and transportation time regulations and number of pick-up stops along each route, we have used data that represent one year of cattle transport. Our optimization model is a development of a model used in forestry transport that solves a general pick-up and delivery vehicle routing problem. The objective is to minimize transportation costs. We have shown that the length of the planning time window has a significant impact on the animal transport time, the total driving time and the total distance driven; these parameters that will not only affect animal welfare but also affect the economy and environment in the pre-slaughter logistic chain. In addition, we have shown that changes in animal transportation regulations, such as minimizing the number of allowed pick-up stops on each route or minimizing animal transportation time, will have positive effects on animal welfare measured in transportation hours and number of pick-up stops. However, this leads to an increase in working time and driven distances, leading to higher transportation costs for the transport and negative environmental impact.

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  • 40.
    Frössling, Jenny
    et al.
    Department of Disease Control and Epidemiology, National Veterinary Institute, Uppsala, Sweden / Department of Animal Environment and Health, Swedish University of Agricultural Sciences, Skara, Sweden.
    Ohlson, Anna
    Department of Disease Control and Epidemiology, National Veterinary Institute, Uppsala, Sweden / Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Björkman, Camilla
    Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Håkansson, Nina
    University of Skövde, School of Life Sciences. University of Skövde, The Systems Biology Research Centre. Division of Theoretical Biology, IFM Theory and Modelling, Linköping University, Linköping, Sweden.
    Nöremark, Maria
    Department of Disease Control and Epidemiology, National Veterinary Institute, Uppsala, Sweden.
    Application of network analysis parameters in risk-based surveillance - Examples based on cattle trade data and bovine infections in Sweden2012In: Preventive Veterinary Medicine, ISSN 0167-5877, E-ISSN 1873-1716, Vol. 105, no 3, p. 202-208Article in journal (Refereed)
    Abstract [en]

    Financial resources may limit the number of samples that can be collected and analysed in disease surveillance programmes. When the aim of surveillance is disease detection and identification of case herds, a risk-based approach can increase the sensitivity of the surveillance system. In this paper, the association between two network analysis measures, i.e. ‘in-degree’ and ‘ingoing infection chain’, and signs of infection is investigated. It is shown that based on regression analysis of combined data from a recent cross-sectional study for endemic viral infections and network analysis of animal movements, a positive serological result for bovine coronavirus (BCV) and bovine respiratory syncytial virus (BRSV) is significantly associated with the purchase of animals. For BCV, this association was significant also when accounting for herd size and regional cattle density, but not for BRSV. Examples are given for different approaches to include cattle movement data in risk-based surveillance by selecting herds based on network analysis measures. Results show that compared to completely random sampling these approaches increase the number of detected positives, both for BCV and BRSV in our study population. It is concluded that network measures for the relevant time period based on updated databases of animal movements can provide a simple and straight forward tool for risk-based sampling.

  • 41.
    Geetha, Bandhumithra
    University of Skövde, School of Bioscience.
    The severity of human papillomavirus- 16/18 infection and its prevention to cervical cancer: A systematic review and meta-analysis2022Independent thesis Advanced level (degree of Master (One Year)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Infectious diseases caused by human papillomavirus (HPV) are among the most common sexually transmitted diseases in the world. Currently, all countries of the WHO Eastern Mediterranean Region (EMRO) except the United Arab Emirates and Libya do not have a national vaccination program including the HPV vaccine. Cervical cancer risk can be reduced through the use of prophylactic HPV vaccines. Hence, the aim of this study was to examine the severity of HPV-16/18 infection in cervical cancer through a systematic review and to evaluate the effectiveness of vaccines against HPV-16/18 variants to prevent cervical cancer via a meta-analysis. Both the systematic review and meta-analysis contain nine relevant studies with 66154 and 78308 cervical cancer participants respectively. Statistical analyses were performed using pooled odds ratios (OR) with 95% confidence intervals (95% CI). Publication bias was examined using the funnel plot graph. The findings stated that overall 70% of cervical cancer was attributed to either HPV 16 or HPV 18. Heterogeneity for this meta-analysis was found to be I2= 80% with a p-value<0.01 and overall OR (odds ratio) was 0.09 (95% CI= 0.04-0.20) for the random effect model. The lower odds ratio (less than 1) indicated fewer occurrences of cervical cancer in the HPV 16/18 vaccinated group than in the unvaccinated individuals. The overall vaccination efficiency was found to be 91% from the odds ratio ((1-0.09)x100=91). Thus, the present findings support that a prophylactic vaccine against HPV16/18 prevents the severity of HPV-associated cervical cancer.

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  • 42.
    Ghiasvand, Mohammad
    University of Skövde, School of Bioscience.
    Bacterial cell detection limits using Oxford Nanopore’s MinION2022Independent thesis Basic level (degree of Bachelor), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Sepsis is a potentially fatal emergency medical condition that reflects the presence of the body’s systematic inflammation. Around 260 biomarkers have been determined to sepsis. The gold standard of blood culturing has remained the best technique for finding sepsis etiology up to this data. However, some vital drawbacks, such as laboriousness, have encouraged a global attempt to find new techniques. This study aimed to optimize a method from which earlier sepsis diagnosis compared to the gold standard could be resulted. DNA was extracted from both spiked and non-spiked whole blood samples. After quality control of the DNA elutions, library preparation and nanopore sequencing using the MinION device were carried out. Basecalling and demultiplexing were done using Guppy GPU and barcoded FASTQ-files were analyzed using What’s-In-My-Pot and Kraken2 taxonomy classification programs. Three different DNA extraction methods were compared from which the second and third methods opted as the optimized methods. Although spiked species were not found in the used taxonomy classification databases, their respective families were spotted. Kraken2 program indicated a relationship between the read percentage of the families and the spiking level of initial blood samples. On the other hand, What’s-In-My-Pot did not show such a trend and only the highest spiking concentration had indicated the families within the reads. A possible justification for not finding the species within the reads is the patchiness of the two databases. Despite the failure in determining the species within FASTQ-files, the whole experiment has gathered valuable experiences for future studies.

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  • 43.
    Ghobadi, Bita
    University of Skövde, School of Bioscience.
    Suggestions for optimal biomarker miRNA extraction from plasma of sepsis patients2020Independent thesis Basic level (degree of Bachelor), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Sepsis is a life-threatening organ disfunction, which is caused by a dysfunctional immuneresponse and develops when an infection overwhelms the body’s defense mechanism and causesand uncontrolled inflammatory response. Biomarkers have a great impact on helping diagnosisand treatments of sepsis. The biomarkers, like miRNA, are needed for both more accurate andquicker diagnosis of sepsis in patients. The future diagnostics are looking at other types ofbiomarkers, e.g. miRNA, but low amounts of miRNA are present in biofluids and make itchallenging to quantify. A new methodology is needed which is both accurate and does notrequire a lot of fluid. The aim of this project was to identify which kit of two kits and which oftwo volumes of plasma would lead to the highest concentration of miRNA and highest quality ofmiRNA extracted. This was quantified by using two different volumes, 100 μl and 200 μl, andextracting the two volumes with both exoRNeasy Serum/Plasma midi kit (Qiagen) and TotalRNA Purification kit (Norgen). There was no statistical difference between median miRNAconcentrations between the two volumes within the Qiagen kit. However, the mean miRNAconcentration (0.833 ng/μl) obtained from the Norgen kit (100 μl plasma starting volume) wasstatistically higher than the mean miRNA concentration (0.570 ng/μl) obtained from the samekit with 200 μl, p = 0.033. The optimal kit and volume of this study is the Norgen kit with 100 μl.Further studies are needed to verify these results.

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  • 44.
    Gordobil, Oihana
    et al.
    University of the Basque Country, Donostia-San Sebastián, Spain.
    Moriana, Rosana
    KTH Royal Institute of technology.
    Zhang, Liming
    KTH Royal Institute of technology.
    Labidi, Jalel
    University of the Basque Country, Donostia-San Sebastián, Spain.
    Sevastyanova, Olena
    KTH Royal Institute of technology.
    Assesment of technical lignins for uses in biofuels and biomaterials: Structure-related properties, proximate analysis and chemical modification2016In: Industrial crops and products (Print), ISSN 0926-6690, E-ISSN 1872-633X, Vol. 83, p. 155-165Article in journal (Refereed)
    Abstract [en]

    The potential of organosolv and kraft eucalyptus and spruce lignin as feedstock for polymeric materials and biofuel applications was assessed. Proximate analysis was used to predict the heating values and char formation. Chemical modification, based on the esterification reaction with methacryloyl chloride, was applied to introduce vinyl groups into the lignin macromolecules for enhanced reactivity. Kraft eucalyptus and spruce lignins had a more condensed structure than organosolv lignins, which resulted in greater thermal stability for these lignins. For different species within the same process, the thermal parameters showed a correlation with certain structural and compositional parameters (ash and sugars content, molecular weight and degree of condensation). Organosolv spruce lignin produced the highest heating value of 24. MJ/Kg, which is suitable for biofuel applications. The content of phenolic OH groups was higher for kraft lignins and especially higher for softwood lignins, both organosolv and kraft. The degree of methacrylation, estimated from the content of vinyl groups per C9 lignin unit, was significantly greater for organosolv lignins than for kraft lignins despite the higher OH-groups content in the latter.

  • 45.
    Groenewald, Lourens
    University of Skövde, School of Bioscience.
    Manual and robotic RNA extraction from human plasma with absolute quantification of miRNA through two-tailed RT-qPCR as part of research into early diagnosis of sepsis2022Independent thesis Basic level (degree of Bachelor), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Each hour´s delay in administering antibiotics has been shown to result in a 9% increase in the odds of mortality in sepsis cases. It is thus evident that the development of a diagnostic method that ensures an early time to diagnosis of sepsis is essential. MiRNAs have shown promise with regards to diagnostic capabilities concerning sepsis, with differential expression of circulatory miRNAs seen during various diseased states. MiRNA can be quantified directly from a blood plasma sample, greatly decreasing the time to diagnosis, as the requirement for culturing is eliminated. Quantification of miRNA by means of qPCR has proven rather challenging, due to their short length. A solution might be two-tailed RT-qPCR, a method which utilizes a two-tailed RT primer. The aim of the project was to optimize the extraction and quantification of miRNAs from minimal amounts of human blood plasma samples, as to create a standardized and reproduceable method for measuring biomarker miRNAs within human blood plasma. In this study, a significant difference between manual and semi-automated extraction of miRNA from plasma with regards to A260/A280 ratios (p = 0.00) was observed. It was also found that a correlation exists between A260/A280 ratios and miR-seps6 quantified, using the two-tailed RT-qPCR method. This method has shown to be effective at amplifying circulating miR-seps6 arising from 100 µL of human blood plasma. A linear standard curve, constructed from synthetic miR-seps 6 produced optimal amplification efficiencies, and the melt curve indicated a single product, which correlates with good specificity. As successful detection and amplification of miR-seps 6 had been achieved during this study, the next phase of the project can be initiated, where it will be attempted to detect miR-seps 6 from plasma stored in a human biological material bank (biobank). 

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  • 46.
    Halan Söderberg, Jessica
    University of Skövde, School of Bioscience.
    The GSK-3 inhibitor has no effect on production of IL-1β in LPS- and Nigericin-stimulated THP-1 macrophages2022Independent thesis Basic level (degree of Bachelor), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Inflammation is the body's natural defense reaction and is known since ancient times. The inflammation is divided into two main phases, acute and chronic inflammation dependent on the process and cellular mechanisms of the inflammation. Inflammation has become to be an important field in research by biomedical research where it is included in many cellular processes thus being phagocytosis, chemotaxis, mitosis, and cell differentiation. Inflammasomes are pro-inflammatory intracellular multimeric protein complexes that introduce the activation of pro-inflammatory cytokines, such as interleukin-1β and interleukin-18, upon trigger by PAMPs and DAMPs signals. The most studied inflammasome is the NLRP3 inflammasome that is activated by various trigger signals, like DAMPs, ATP, uric acid crystals and amyloid-β fibrils. GSK-3β is a kinase that controls various cellular processes, such as inflammation by regulating the activity of abundant transcription factors that are valuable for cytokine production. The aim of this thesis project was to investigate if GSK-3 Inhibitor IV, SB-216763, in a concentration-dependent manner had an effect on production of IL-1β in LPS- and Nigericin-stimulated THP-1 ASC-GFP-macrophages. In addition to the gene expression analysis of IL-1β, the amount of secreted IL-1β, and the possible correlation between treated THP-1 cells with and without GSK-3 inhibitor evaluated. The gene expression analysis was performed by using qPCR and the amount of secreted IL-1β was done using sandwich enzyme-linked immunosorbent assay. The results from this study showed no significant difference in gene expression and amount secreted of IL-1β in THP-1 cells when treated with the GSK-3 Inhibitor IV, SB-216763. 

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  • 47.
    Handlin, Linda
    University of Skövde, School of Life Sciences. University of Skövde, The Systems Biology Research Centre. Swedish University of Agricultural Sciences, Department of Animal Environment and Health, Skara, Sweden.
    Human-Human and Human-Animal Interaction: Some Common Physiological and Psychological Effects2010Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The aim of the present thesis was to investigate hormonal and physiological effects in mothers during a breastfeeding session and in dogs and their owners in response to short-term interaction. In study one, sixty-six mothers receiving either exogenous oxytocin infusion and/or epidural analgesia (EDA) during labor or intramuscular oxytocin injection post partum were studied. Oxytocin, prolactin, adrenocorticotrophic hormone (ACTH) and cortisol levels, as well as blood pressure were measured during a breastfeeding session two days after birth. In response to breastfeeding two days after birth, the mothers displayed a pulsatile release of oxytocin and increasing prolactin levels. In addition, the activity in the HPA-axis was reduced and maternal blood pressure decreased. The results also show that EDA administration in combination with oxytocin during labor resulted insignificantly lower oxytocin levels and higher cortisol levels, as well as higher bloodpressure in response to breastfeeding two days after birth, compared to EDA administration alone. In addition, oxytocin infusions dose-dependently lowered the mothers’ endogenous oxytocin levels two days after birth. In study two, ten female dog owners and their male Labrador dogs participated, together with ten controls. Their levels of oxytocin, cortisol and insulin, as well as their heart rate, were measured. The connection between the quality of the dogowner relationship and hormone levels was also explored. Short-term interaction between dogs and their owners resulted in oxytocin release in both species and their cortisol levels and heart rate were also affected. Oxytocin levels and positive attitudes regarding the dog-owner relationship were positively correlated. In conclusion, both human-human and human-animal interactions induce oxytocin release and promote oxytocin mediated effects, such as decreasing cortisol levels and blood pressure. In addition, social interaction and oxytocin levels arepositively related.

  • 48.
    Handlin, Linda
    et al.
    University of Skövde, School of Life Sciences. University of Skövde, The Systems Biology Research Centre. Department of Animal Environment and Health, Swedish University of Agricultural Sciences, Skara, Sweden.
    Hydbring-Sandberg, Eva
    Department of Anatomy, Physiology, and Biochemistry, Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Nilsson, Anne
    Department of Animal Environment and Health, Swedish University of Agricultural Sciences, Skara, Sweden.
    Ejdebäck, Mikael
    University of Skövde, School of Life Sciences. University of Skövde, The Systems Biology Research Centre.
    Jansson, Anna
    Department of Animal Nutrition and Management, Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Uvnäs-Moberg, Kerstin
    University of Skövde, School of Life Sciences. University of Skövde, The Systems Biology Research Centre. Department of Animal Environment and Health, Swedish University of Agricultural Sciences, Skara, Sweden.
    Short-Term Interaction between Dogs and Their Owners: Effects on Oxytocin, Cortisol, Insulin and Heart Rate-An Exploratory Study2011In: Anthrozoos, ISSN 0892-7936, E-ISSN 1753-0377, Vol. 24, no 3, p. 301-315Article in journal (Refereed)
    Abstract [en]

    The aim of this exploratory study was to determine heart rate and the levels of oxytocin, cortisol, and insulin in dogs and their owners in response to a short-term interaction. In addition, the dogs' behavior was studied. The owners' responses were compared with those obtained from a control group. Ten female volunteers and their own male Labrador dogs participated in an experiment during which the owner stroked, petted, and talked with her dog during the first 3 minutes. Blood samples were collected from both dog and owner before (0) and at 1, 3, 5, 15, 30, and 60 minutes after the start of the interaction. Blood samples were analyzed by EIA. Heart rate was monitored telemetrically. The data were analyzed using linear mixed models and paired t-tests. The dogs' oxytocin levels were significantly increased 3 minutes after the start of the interaction (p = 0.027). Cortisol levels were significantly increased after 15 and 30 minutes (p = 0.004 and p = 0.022, respectively), and heart rate was significantly decreased after 55 minutes (p = 0.008). The dogs displayed normal behaviors during the experiment. The owners' oxylocin levels peaked between 1 and 5 minutes after interaction (p = 0.026). No such effect was seen in the controls. Cortisol levels displayed a significant decrease at 15 or 30 minutes in both owners and controls, and insulin levels did so at 60 minutes (p = 0.030, p = 0.002 and p = 0.002, p < 0.0001, respectively). Heart rate decreased significantly in the owners at 55 and 60 minutes (p = 0.0008) but not in the controls. In conclusion, short-term sensory interaction between dogs and their owners influences hormonal levels and heart rate. However, further studies need to be performed in order to better understand the effects of interaction between dogs and their owners.

  • 49.
    Handlin, Linda
    et al.
    University of Skövde, School of Life Sciences. University of Skövde, The Systems Biology Research Centre. Department of Animal Environment and Health, Swedish University of Agricultural Sciences, Skara, Sweden.
    Nilsson, Anne
    University of Skövde, School of Life Sciences. University of Skövde, The Systems Biology Research Centre. Department of Animal Environment and Health, Swedish University of Agricultural Sciences, Skara, Sweden.
    Ejdebäck, Mikael
    University of Skövde, School of Life Sciences. University of Skövde, The Systems Biology Research Centre.
    Hydbring-Sandberg, Eva
    Department of Anatomy, Physiology, and Biochemistry, Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Uvnäs-Moberg, Kerstin
    University of Skövde, School of Life Sciences. University of Skövde, The Systems Biology Research Centre. Department of Animal Environment and Health, Swedish University of Agricultural Sciences, Skara, Sweden.
    Associations between the Psychological Characteristics of the Human-Dog Relationship and Oxytocin and Cortisol Levels2012In: Anthrozoos, ISSN 0892-7936, E-ISSN 1753-0377, Vol. 25, no 2, p. 215-228Article in journal (Refereed)
    Abstract [en]

    The aim of the present study was to explore possible correlations between dog owners' relationships with their dogs, as measured with the Monash Dog Owner Relationship Scale (MDORS), and oxytocin and cortisol levels in both the owners and their dogs. Ten female owners of male Labrador Retrievers completed the MDORS. The scores obtained from the single items, subscales, and total score of the MDORS were calculated. Ten blood samples were collected from each dog owner and her dog during a 60-minute interaction. Blood samples were analyzed for oxytocin and cortisol by Enzyme Immuno Assay (EIA) and mean values of oxytocin and cortisol were calculated in both owners and dogs. The MDORS scores obtained were correlated with basal and mean oxytocin and cortisol levels. The correlation analysis revealed some relationships between the scores of items in the MDORS that reflect the character of the dog-owner-relationship and the owners' hormone levels. For example, higher oxytocin levels in the owners were associated with greater frequency in kissing their dogs (rs = 0.864, p = 0.001). Lower cortisol levels in the owners were associated with their perception that it will be more traumatic when their dog dies (rs = -0.730, p = 0.025). The correlation analysis also revealed some relationships between the scores of items in the MDORS and the dogs' hormone levels. For example, greater frequency in owners kissing their dogs was associated with higher oxytocin levels in the dogs (rs = 0.753, p = 0.029). Six items in the subscale Perceived Costs, as well as the subscale itself, correlated significantly with the dogs' oxytocin levels (rs = 0.820, p = 0.007), that is, the lower the perceived cost, the higher the dogs' oxytocin levels. In addition, significant correlations between the oxytocin levels of the owners and the dogs were demonstrated. Possible mechanisms behind these correlations are discussed. In conclusion, the scores of some items and the subscales of the MDORS correlated with oxytocin, and to a lesser extent cortisol, levels in both the owners and dogs.

  • 50.
    Hassano, Ragad
    University of Skövde, School of Bioscience.
    GSK-3 and ROS (reactive oxygen species) inhibition modulate Vimentin expression2022Independent thesis Basic level (degree of Bachelor), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    When exposed to pathogenic stress, cellular processes and survival are dependent on cytoskeletal proteins for structure and organisation of the cell to adapt and maintain homeostasis during inflammation. Vimentin is type III cytoskeletal protein, with an extensive cytoplasmic meshwork, across the cell and regulate the cell structure and cellular space and expressed strongly under tumorigenic events. GSK-3, a regulatory component of inflammation expressed in abundance of cell together with reactive oxygen species (ROS), a group of key complex signalling molecules that are oxygen metabolites which are partially reduced, with robust oxidising abilities, are believed to influence inflammasome formation and specifically vimentin expression upon inflammation. This project investigated the potential modulation vimentin mRNA expression utilising the two signal NLRP3 inflammasome activation theory, by inhibiting GSK-3 and ROS in signal I and or signal II in LPS and nigericin stimulated THP-1 cells, compared to non-inhibited LPS and nigericin THP-1 cells. Inhibition of GSK-3 in signal II downregulated vimentin expression, reflecting repressed phosphorylation of GSK-3 hence also the components required for vimentin; whilst upregulation of vimentin in signal I, reflects possible alternative pathways phosphorylating vimentin components. Overall upregulation of vimentin upon inhibiting ROS in both signal I and II, further proved that inflammasome activation is independent of ROS in the priming step. More research is required integrating vimentin activity and either GSK-3 or ROS, as the potential of these prominent inflammatory markers and their major regulatory presence across an abundance of cell may contribute to the future of drug development for inflammatory diseases.  

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