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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.
    Al-Attar, Rima
    University of Skövde, School of Bioscience.
    Characterization of the antimicrobial activity of plantaricin NC8 αß in a viral-bacterial coinfection model2024Independent thesis Basic level (degree of Bachelor), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Viral-bacterial coinfection is a major and life-threatening issue, and it ranks among the primary causes of mortality. Current monotherapies that only target either bacteria or viruses, are deemed insufficient for treating coinfection and may be associated with undesirable consequences. Therefore, the development of novel treatment approaches is necessary, preferably with dual effects against both viruses and bacteria. This study sought to assess the effectiveness of PLNC8 αβ, in specifically targeting both KUNV and S. aureus infection in an in vitro coinfection model using human keratinocyte cells. The LDH cytotoxicity test was performed to evaluate the peptide’s effectiveness in reducing cytotoxicity that is individually caused by S. aureus, KUNV, as well as their coinfection. Additionally, ELISA was utilized to quantify the levels of inflammatory cytokines, namely CXCL8, and IL-6. The results demonstrated that both forms of the PLNC8 αβ effectively decreased the infection-induced cellular cytotoxicity. The D- PLNC8 αβ exhibited superior efficacy compared to the L- PLNC8 αβ, since the latter was more susceptible to enzymatic degradation, resulting in the loss of its functionality. Furthermore, both forms of PLNC8 αβ effectively modulated the levels of inflammatory cytokine and restored cellular viability. In addition, the peptide substantially reduced the number of bacterial colonies in both S. aureus infection and coinfection. Based on these findings D- PLNC8 αβ possesses a dual antimicrobial action and could be further characterized and validated as a promising therapeutic agent against viral-bacterial coinfection.

  • 6.
    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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  • 7.
    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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  • 8.
    Andersson, David
    et al.
    Swedish School of Sport and Health Sciences, GIH, Department of Sport and Health Sciences.
    Boyacioglu, Anders
    Swedish School of Sport and Health Sciences, GIH, Department of Sport and Health Sciences.
    Bilateral deficit vid excentrisk och koncentrisk muskelaktion: En jämförande studie mellan den summerade unilaterala och bilaterala kraftutvecklingen hos roddare visavi sprinters2006Independent thesis Basic level (degree of Bachelor), 10 poäng / 15 hpStudent thesis
    Abstract [en]

    Aim

    The main aim of the study was to investigate the difference in bilateral deficit between rowers and sprinters during maximal eccentric/concentric muscle actions.

    • Are there any significant differences in bilateral deficit between rowers and sprinters?

    • Do the amount of years in practice effect the bilateral deficit?

    Method

    Fourteen male subject participants divided in 2 equal sized groups (7 individuals in each group; rowers and sprinters) performed maximal unilateral/bilateral eccentric and concentric muscle actions in a leg press machine at a velocity of 0.2m/s. The range of motion in the knee joint was 70° – 140°. Dependent t-tests have been performed within each group pre and post test. P was set to 0,05 to prevent type I faults (false positive) a Bonferroni test was made for two comparisons and set to 0,0253.

    Results

    Average bilateral deficit for rowers were: 11% concentric and 33% eccentric. Number of years in practice and bilateral deficit: practiced >8years concentric 7% and eccentric 24%. Practiced <8 years concentric 21% and eccentric 55%.

    Average bilateral deficit for sprinters were: 5% concentric and 24% eccentric. Number of years in practice and bilateral deficit: practiced >8years concentric 4% and eccentric 26%. Practiced <8years concentric 16% and eccentric 11%.

    Conclusions

    The main explanation for the larger differences in bilateral deficit for rowers in eccentric muscle action compared to sprinters may be related for the fact that the rowers have an almost non - eccentric phase during rowing. When comparing the amount of years in practice and bilateral deficit we saw that it decreased with the number of practiced years for booth rowers and sprinters. The reason to this pattern is probably on a neural base.

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  • 9.
    Apró, William
    et al.
    Swedish School of Sport and Health Sciences, GIH, Department of Sport and Health Sciences.
    Tannerstedt, Jörgen
    Swedish School of Sport and Health Sciences, GIH, Department of Sport and Health Sciences.
    Nutrition och muskeluppbyggnad2007Student thesis
    Abstract [sv]

    Senare års studier har gett oss en klarare bild av hur muskeluppbyggnaden stimuleras och regleras av styrketräning och nutrition. Mycket forskning kvarstår dock innan fullständiga rekommendationer kan ges. Vad som dock är klart är att de allmänna rekommendationerna som idag uppgår till 0.8 g protein • kg-1 kroppsvikt • dag-1 i de flesta länder (Lemon, 2000) inte räcker till för fysiskt aktiva individer. Atletens ökade proteinbehov kan dock enkelt tillgodoses via ökat matintag varvid supplementering ur den aspekten inte är nödvändig.

    Vidare vet man att tillgängligheten och tillförseln av aminosyror runt träningen är avgörande för maximal stimulering av proteinsyntesen. Muskeln behöver tillgång till essentiella aminosyror när träningen påbörjas för maximal stimulering av proteinsyntesen. Huruvida aminosyrorna behöver tas i form av en dryck i kosttillskottsform eller kan intas i form av vanlig mat för att tillräckligt fort kunna förse muskeln med EAA är inte utrett.

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  • 10.
    Arama, Charles
    et al.
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute. University of Sciences Techniques and Technologies of Bamako, Mali.
    Troye-Blomberg, Marita
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    The path of malaria vaccine development: challenges and perspectives2014In: Journal of Internal Medicine, ISSN 0954-6820, E-ISSN 1365-2796, Vol. 275, no 5, p. 456-466Article, review/survey (Refereed)
    Abstract [en]

    Malaria is a life-threatening disease caused by parasites of the Plasmodium genus. In many parts of the world, the parasites have developed resistance to a number of antimalarial agents. Key interventions to control malaria include prompt and effective treatment with artemisinin-based combination therapies, use of insecticidal nets by individuals at risk and active research into malaria vaccines. Protection against malaria through vaccination was demonstrated more than 30years ago when individuals were vaccinated via repeated bites by Plasmodium falciparum-infected and irradiated but still metabolically active mosquitoes. However, vaccination with high doses of irradiated sporozoites injected into humans has long been considered impractical. Yet, following recent success using whole-organism vaccines, the approach has received renewed interest; it was recently reported that repeated injections of irradiated sporozoites increased protection in 80 vaccinated individuals. Other approaches include subunit malaria vaccines, such as the current leading candidate RTS,S (consisting of fusion between a portion of the P.falciparum-derived circumsporozoite protein and the hepatitis B surface antigen), which has been demonstrated to induce reasonably good protection. Although results have been encouraging, the level of protection is generally considered to be too low to achieve eradication of malaria. There is great interest in developing new and better formulations and stable delivery systems to improve immunogenicity. In this review, we will discuss recent strategies to develop efficient malaria vaccines.

  • 11.
    Arneson, Sofia
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Att motverka dehydrering hos äldre i teori och praktik2015Independent thesis Basic level (degree of Bachelor), 180 HE creditsStudent thesis
    Abstract [en]

    Objective: To identify similarities and differences in methods and aids used to prevent dehydraton in the elderly as identified from the scientific literature and from interviews with caretakers.

    Method: Literature studies was performed through the University Library search service ”OneSearch” and further from references in key papers. Three interviews were conducted on nursing assistants in two retirement homes and home care services, to offer some insight into the practical activities.

    Results : The following factors were identified as important in both literature and interviews: (1) knowledge of the elderly through documentation, (2) adapted approach when serving drinks after the elderly person's preferences and condition, (3) a homely environment with social interactions, (4) assessments of fluid intake, fluid balance and risk factors through attention, fluid registration and with the help of several other professional groups, and given the history of the elderly, (5) reminders for dementia and a accessibility of large amount of easily absorbed beverages consumed gradually during diarrhea and vomiting, (6) easy-to-use and specially designed drinking aids. For the following factors differences were obeserved between literature survey and interviews: (1) education for caregivers; limited to the investigated sites, (2) technical aids and swallowing therapy (dietary modifications, adapted head positions, swallowing training) in dysphagia; diet modification is used at the investigated sites (3) the importance of cup and jug colours; blue cups used in practice, no support in literature.

    Conclusions: Differences were found in terms of education and the use of swallowing therapy, assistive technology and infusions. Education, more frequent fluid registration and a complete swallowing therapy are improvement opportunites, some of them requires extra resources and/or clear guidelines. Acceptance of technical aids is not self-evident. Investigation of the effect of cup color and design that can encourage the elderly to drink could potentially be a way forward. The results of the interviews are not generalizable because they only aimed to give an insight into the practical activities. Most of the strategies that have been identified are "soft" in nature. It is difficult to get a clear picture of the efficiency of different methods. Methods that have been evaluated with good results in dysphagia and therefore offer potential to improve liquid intake, are swallowing therapy and stimulation of swallowing musculature.

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  • 12.
    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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  • 13.
    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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  • 14.
    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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  • 15.
    Bansal, Ruby
    et al.
    Department of Biology, University of Massachusetts, Amherst, USA.
    Tighe, Daniel
    Department of Biology, University of Massachusetts, Amherst, USA.
    Danai, Amin
    Department of Biology, University of Massachusetts, Amherst, USA.
    Rawn, Dorothea F. K.
    Health Canada, Health Products and Food Branch, Ottawa, Canada.
    Gaertner, Dean W.
    Health Canada, Health Products and Food Branch, Ottawa, Canada.
    Arnold, Doug L.
    Health Canada, Health Products and Food Branch, Ottawa, Canada.
    Gilbert, Mary E.
    Toxicity Assessment Division, US Environmental Protection Agency, USA.
    Zoeller, R. Thomas
    Department of Biology, University of Massachusetts, Amherst, USA; Molecular and Cellular Biology Program, University of Massachusetts, Amherst, USA.
    Polybrominated diphenyl ether (DE-71) interferes with thyroid hormone action independent of effects on circulating levels of thyroid hormone in male rats2014In: Endocrinology, ISSN 0013-7227, E-ISSN 1945-7170, Vol. 155, no 10, p. 4104-4112Article in journal (Refereed)
    Abstract [en]

    Polybrominated diphenyl ethers (PBDEs) are routinely found in human tissues including cord blood and breast milk. PBDEs may interfere with thyroid hormone (TH) during development, which could produce neurobehavioral deficits. An assumption in experimental and epidemiological studies is that PBDE effects on serum TH levels will reflect PBDE effects on TH action in tissues. To test whether this assumption is correct, we performed the following experiments. First, five concentrations of diphenyl ether (0-30 mg/kg) were fed daily to pregnant rats to postnatal day 21. PBDEs were measured in dam liver and heart to estimate internal dose. The results were compared with a separate study in which four concentrations of propylthiouracil (PTU; 0, 1, 2, and 3 ppm) was provided to pregnant rats in drinking water for the same duration as for diphenyl ether. PBDE exposure reduced serum T4 similar in magnitude to PTU, but serum TSH was not elevated by PBDE. PBDE treatment did not affect the expression of TH response genes in the liver or heart as did PTU treatment. PTU treatment reduced T4 in liver and heart, but PBDE treatment reduced T4 only in the heart. Tissue PBDEs were in the micrograms per gram lipid range, only slightly higher than observed in human fetal tissues. Thus, PBDE exposure reduces serum T4 but does not produce effects on tissues typical of low TH produced by PTU, demonstrating that the effects of chemical exposure on serum T4 levels may not always be a faithful proxy measure of chemical effects on the ability of thyroid hormone to regulate development and adult physiology.

  • 16.
    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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  • 17.
    Barranco, Isabel
    et al.
    University of Murcia, Spain.
    Roca, Jordi
    University of Murcia, Spain.
    Tvarijonaviciute, Asta
    University of Murcia, Spain.
    Rubér, Marie
    Linköping University, Department of Clinical and Experimental Medicine, Division of Clinical Sciences. Linköping University, Faculty of Medicine and Health Sciences.
    Vicente Carrillo, Alejandro
    Linköping University, Department of Clinical and Experimental Medicine, Division of Microbiology and Molecular Medicine. Linköping University, Faculty of Health Sciences.
    Atikuzzaman, Mohammad
    Linköping University, Department of Clinical and Experimental Medicine, Division of Clinical Sciences. Linköping University, Faculty of Medicine and Health Sciences.
    Ceron, Jose J.
    University of Murcia, Spain.
    Martinez, Emilio A.
    University of Murcia, Spain.
    Rodriguez-Martinez, Heriberto
    Linköping University, Department of Clinical and Experimental Medicine, Division of Clinical Sciences. Linköping University, Faculty of Medicine and Health Sciences.
    Measurement of Activity and Concentration of Paraoxonase 1 (PON-1) in Seminal Plasma and Identification of PON-2 in the Sperm of Boar Ejaculates2015In: Molecular Reproduction and Development, ISSN 1040-452X, E-ISSN 1098-2795, Vol. 82, no 1, p. 58-65Article in journal (Refereed)
    Abstract [en]

    This study revealed and characterised the presence of the antioxidant enzymes paraoxonase (PON) type 1 (PON-1, extracellular) and type 2 (PON-2, intracellular) in boar semen. To evaluate PON-1, an entire ejaculate from each of ten boars was collected and the seminal plasma was harvested after double centrifugation (1,500g for 10min). Seminal plasma was analysed for concentration as well as enzymatic activity of PON-1 and total cholesterol levels. Seminal-plasma PON-1 concentration ranged from 0.961 to 1.670ng/ml while its enzymatic activity ranged from 0.056 to 0.400 IU/ml, which represent individual variance. Seminal-plasma PON-1 concentration and enzymatic activity were negatively correlated (r=-0.763; Pless than0.01). The activity of seminal-plasma PON-1 negatively correlated with ejaculate volume (r=-0.726, Pless than0.05), but positively correlated with sperm concentration (r=0.654, Pless than0.05). Total seminal-plasma cholesterol concentration positively correlated with PON-1 activity (r=0.773; Pless than0.01), but negatively correlated with PON-1 concentration (r=-0.709; Pless than0.05). The presence of intracellular PON-2 was determined via immunocytochemistry in spermatozoa derived from artificial insemination. PON-2 localised to the post-acrosomal area of the sperm head and principal piece of the tail in membrane-intact spermatozoa. In summary, PON is present in boar semen, with PON-1 at low levels in seminal plasma and PON-2 within the spermatozoa. Further studies are needed to characterise the relationship between antioxidant PONs with sperm and other seminal-plasma parameters. Mol. Reprod. Dev. 82: 58-65, 2015. (c) 2014 Wiley Periodicals, Inc.

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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.
    Berens, Carola
    University of Skövde, School of Bioscience.
    Mutational bypass of aroE auxotrophy in Escherichia coli: Mechanism(s) and strain specificity2024Independent thesis Basic level (degree of Bachelor), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Escherichia coli is an important model organism in scientific research. Different strains can carry different genetic properties, and gene knockouts are used to study effects on phenotype. Deletion of the aroE gene in the MG1655 and ATCC 25922 strains of Escherichia coli, coding for an essential enzyme in the biosynthesis pathway for aromatic amino acids, resulted in auxotrophy. Subsequent selection for prototrophy revealed that the auxotrophic phenotype could be suppressed at a frequency of approximately 10-8 in ATCC 25922 but not in MG1655. The aim of this study was to identify the mutation(s) that suppressed the phenotype of the aroE gene deletion and determine why suppression occurred in ATCC 25922, but not in MG1655. Independently selected mutants were analysed by whole genome sequencing, but no obvious genetic alterations were identified. This prompted an evaluation of the phenotypic stability of the selected mutants. Mutants were growth in rich medium then tested for auxotrophy, which revealed that the mutant phenotype was highly unstable. While the initial research question could not be answered, both the frequency of occurrence and instability of the selected mutant phenotype, are important clues. Genetic instability is associated both with gene duplication, for which no evidence was found in the genome sequence, and epigenetic changes, which are not revealed by standard DNA sequencing. In conclusion, an auxotrophy bypass mechanism has been shown to exist in ATCC 25922 with no obvious genotypic source. Further experimentation, including methylome sequencing, might provide more leads.

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  • 21.
    Berg, Monica
    Karlstad University, Faculty of Arts and Education.
    God hälsa som mål: En textanalys av olika rekommendationer2007Independent thesis Basic level (professional degree), 10 points / 15 hpStudent thesis
    Abstract [sv]

    Syftet med denna uppsats är undersöka om det finns skillnader och likheter i rekommendationer inom tre olika fält där kostsammansättning och fysisk aktivitet behandlas.

    Frågor som besvaras är vilka skillnader och likheter i rekommendationer angående intag av protein, kolhydrater och fett och motion som ges. För att få svar på dessa frågor har en textanalys som baseras på Holliday’s tredimensionella modell för diskursanalys använts. Resultatet visar att de främsta skillnaderna i rekommendationer rör hur man ska fördela det totala energiintaget mellan de energigivande näringsämnena. Likheter som visar sig är att andelen snabba kolhydrater i kosten bör minskas samt att daglig motion påverkar vår hälsa positivt.

  • 22. Berggren, D. Moreno
    et al.
    Folkvaljon, Y.
    Engvall, M.
    Sundberg, J.
    Lehman, S.
    Lambe, M.
    Antunovic, P.
    Garelius, H.
    Hellstrom-Lindberg, E.
    Jadersten, M.
    Lorenz, Fryderyk
    Umeå University, Faculty of Medicine, Department of Medical Biosciences.
    Nilsson, L.
    Ejerblad, E.
    VALIDATION OF PROGNOSTIC SCORING SYSTEMS FOR MYELODYSPLASTIC SYNDROMES IN THE SWEDISH MDS-REGISTER2016In: Haematologica, ISSN 0390-6078, E-ISSN 1592-8721, Vol. 101, p. 243-243Article in journal (Other academic)
  • 23.
    Bergh, Johan
    et al.
    Umeå University, Faculty of Medicine, Department of Medical Biosciences.
    Zetterström, Per
    Umeå University, Faculty of Medicine, Department of Medical Biosciences.
    Andersen, Peter M.
    Umeå University, Faculty of Medicine, Department of Pharmacology and Clinical Neuroscience, Clinical Neuroscience.
    Brännström, Thomas
    Umeå University, Faculty of Medicine, Department of Medical Biosciences.
    Graffmo, Karin Sixtensdotter
    Umeå University, Faculty of Medicine, Department of Medical Biosciences.
    Jonsson, P. Andreas
    Umeå University, Faculty of Medicine, Department of Medical Biosciences.
    Lang, Lisa
    Stockholm, Sweden.
    Danielsson, Jens
    Stockholm, Sweden.
    Oliveberg, Mikael
    Stockholm, Sweden.
    Marklund, Stefan
    Umeå University, Faculty of Medicine, Department of Medical Biosciences.
    Structural and kinetic analysis of protein-aggregate strains in vivo using binary epitope mapping2015In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 112, no 14, p. 4489-4494Article in journal (Refereed)
    Abstract [en]

    Despite considerable progress in uncovering the molecular details of protein aggregation in vitro, the cause and mechanism of protein-aggregation disease remain poorly understood. One reason is that the amount of pathological aggregates in neural tissue is exceedingly low, precluding examination by conventional approaches. We present here a method for determination of the structure and quantity of aggregates in small tissue samples, circumventing the above problem. The method is based on binary epitope mapping using anti-peptide antibodies. We assessed the usefulness and versatility of the method in mice modeling the neurodegenerative disease amyotrophic lateral sclerosis, which accumulate intracellular aggregates of superoxide dismutase-1. Two strains of aggregates were identified with different structural architectures, molecular properties, and growth kinetics. Both were different from superoxide dismutase-1 aggregates generated in vitro under a variety of conditions. The strains, which seem kinetically under fragmentation control, are associated with different disease progressions, complying with and adding detail to the growing evidence that seeding, infectivity, and strain dependence are unifying principles of neurodegenerative disease.

  • 24.
    Bergman, Ingrid-Maria
    et al.
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Edman, Kjell
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Rosengren, K. Johan
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Edfors, Inger
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    European wild boars and domestic pigs display different polymorphic patterns in the Toll-like receptor (TLR)1, TLR2, TLR6, and TLR10 genes.2010In: International Symposium on Animal Genomics for Animal Health Paris, France, 31 May – 2 June 2010: The AGAH 2010 Abstract Book, 2010, p. 35-Conference paper (Other academic)
    Abstract [en]

    The Toll-like receptors (TLR) are vitally important pattern recognition receptors linking innate and adaptive immunity. Several single nucleotide polymorphisms (SNP) in human TLR genes have been associated with disease. There are few studies on associations between polymorphisms in TLR genes and disease in pigs, but the TLR2/TLR6 heterodimer is activated by Mycoplasma hyopneumoniae, and the expression of TLR2, TLR4, and TLR9 is modulated in the presence of different Salmonella serovars. Porcine TLR1, TLR6, and TLR10 are located in a cluster on the p arm of chromosome 8, while TLR2 resides on the q arm. Previously, we identified quantitative trait loci (QTL) for immune-related traits on pig chromosome 8, close to the KIT gene and the microsatellite S0225, respectively. In order to explore polymorphism in some TLR genes in European wild boars and domestic pigs, TLR1, TLR2, and TLR6 were sequenced in 25 wild boars, representing three populations, and in 15 domestic pigs of Hampshire, Landrace, and Large White origin. Similarly, TLR10 was sequenced in 15 wild boars and 15 domestic pigs. In TLR1 and TLR2, more SNP were present in the domestic pigs than in the wild boars. In TLR6, SNP numbers were similar in both animal groups, but the level of heterozygosity was higher in the domestic pigs than in the wild boars. In TLR10, again, more SNP were present in the domestic pigs, and a higher number of nonsynonymous SNP were detected in TLR10 compared to the other genes. This may suggest redundancy for TLR10 in pigs. 

  • 25.
    Betsholtz, Christer
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Cancer and Vascular Biology.
    Keller, Annika
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Cancer and Vascular Biology.
    PDGF, Pericytes and the Pathogenesis of Idiopathic Basal Ganglia Calcification (IBGC)2014In: Brain Pathology, ISSN 1015-6305, E-ISSN 1750-3639, Vol. 24, no 4, p. 387-395Article in journal (Refereed)
    Abstract [en]

    Platelet-derived growth factors (PDGFs) are important mitogens for various types of mesenchymal cells, and as such, they exert critical functions during organogenesis in mammalian embryonic and early postnatal development. Increased or ectopic PDGF activity may also cause or contribute to diseases such as cancer and tissue fibrosis. Until recently, no loss-of-function (LOF) mutations in PDGF or PDGF receptor genes were reported as causally linked to a human disease. This changed in 2013 when reports appeared on presumed LOF mutations in the genes encoding PDGF-B and its receptor PDGF receptor-beta (PDGF-R) in familial idiopathic basal ganglia calcification (IBGC), a brain disease characterized by anatomically localized calcifications in or near the blood microvessels. Here, we review PDGF-B and PDGF-R biology with special reference to their functions in brain-blood vessel development, pericyte recruitment and the regulation of the blood-brain barrier. We also discuss various scenarios for IBGC pathogenesis suggested by observations in patients and genetically engineered animal models of the disease.

  • 26. Bett, B
    et al.
    Kiunga, P
    Gachohi, J
    Sindato, C
    Mbotha, D
    Robinson, T
    Lindahl, J
    Grace, D
    Effects of climate change on the occurrence and distribution of livestock diseases.2017In: Preventive Veterinary Medicine, ISSN 0167-5877, E-ISSN 1873-1716, Vol. 137, no Pt B, p. 119-129, article id S0167-5877(16)30631-6Article in journal (Refereed)
    Abstract [en]

    The planet's mean air and ocean temperatures have been rising over the last century because of increasing greenhouse gas (GHG) emissions. These changes have substantial effects on the epidemiology of infectious diseases. We describe direct and indirect processes linking climate change and infectious diseases in livestock with reference to specific case studies. Some of the studies are used to show a positive association between temperature and expansion of the geographical ranges of arthropod vectors (e.g. Culicoides imicola, which transmits bluetongue virus) while others are used to illustrate an opposite trend (e.g. tsetse flies that transmit a range of trypanosome parasites in sub-Saharan Africa). We further describe a positive association between extreme events: droughts and El Niño/southern oscillation (ENSO) weather patterns and Rift Valley fever outbreaks in East Africa and some adaptation practices used to mitigate the impacts of climate change that may increase risk of exposure to infectious pathogens. We conclude by outlining mitigation and adaptation measures that can be used specifically in the livestock sector to minimize the impacts of climate change-associated livestock diseases.

  • 27.
    Boakai, Wendy
    University of Skövde, School of Bioscience.
    Understanding the role of anaplastic lymphoma kinase in metabolism: Genetic screening of potential molecular players2024Independent thesis Basic level (degree of Bachelor), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Anaplastic lymphoma kinase (Alk) is a receptor tyrosine kinase primarily expressed within the brain, recognized for its pivotal role as an oncogenic driver across various cancers, including neuroblastoma. Recent studies have expanded the current understanding of Alk's function, extending beyond its oncogenic properties to encompass developmental and metabolic functions, suggesting its involvement as a modulator of body weight. Notably, Alk's gain-of-function in Drosophila has been linked to a significant reduction in pupal size. This study aimed to elucidate the signaling pathway between the brain and fat body governed by Alk and identify the molecular players involved using Drosophila as a model organism. Transcriptomic analyses were employed to identify genes upregulated in the fat body under conditions of Alk gain-of-function. Using the Gal4/UAS system, specific genes were manipulated in the fat body based on their upregulation in Alk gain-of-function mutants. Immunofluorescence techniques were utilized to visualize morphological changes in the fat body and the distribution of lipid droplet distribution, which were then quantified and compared to the Alk gain-of-function phenotype. The results demonstrate that Alk gain-of-function mutation disrupts fat body physiology, resulting in an abnormal phenotype. Several genes emerged as potential candidates involved in fat body metabolism, with mthl8 notably upregulated. Targeted expression of mthl8 led to a phenotype like the Alk gain-of-function fat body phenotype, highlighting mthl8 as a potential key player in the Alk-mediated signaling pathway between the brain and fat body. This study provides mechanistic insights into the role of Alk in metabolism.

  • 28.
    Borssén, Magnus
    et al.
    Umeå University, Faculty of Medicine, Department of Medical Biosciences.
    Nordlund, J
    Haider, Z
    Landfors, M
    Larsson, P
    Forestier, E
    Heyman, M
    Hultdin, M
    Lönnerholm, G
    Syvänen, AC
    Degerman, S
    DNA methylation holds prognostic information in relapsed precursor B-cell acute lymphoblastic leukemiaManuscript (preprint) (Other academic)
  • 29.
    Bäcklund Lundahl, Frida
    University of Skövde, School of Bioscience.
    The impact of DNA methylation in forensics criminal investigations: A meta-analysis2024Independent thesis Basic level (degree of Bachelor), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    This study examines the use of DNA methylation as an application in forensic science, namely age estimation and individual identification. DNA methylation is an epigenetic marker that assists forensic analyses by providing information about biological age and tissue types. A meta-analysis methodology that integrated data from 15 research papers was utilized to evaluate the precision and reliability of age predictions based on DNA methylation. The findings indicate that DNA methylation is a valid method for age determination, which is especially useful when traditional forensic methods are insufficient on degraded biological samples. The outcomes suggest a high overall effect, with an effect size (r) of 0.96, and a 95% confidence interval of 0.94 to 0.97. Given the variations in sample sizes and methodologies across the publications, slight differences in the MAD values were expected. Nevertheless, these values remained within a comparable range. The results imply that DNA methylation markers are highly effective for age estimate, particularly in genes KLF14 and ELOVL2 where there is a strong association between CpG sites and age. In conclusion, DNA methylation is a practical and essential technique for establishing age and identifying individuals. The study emphasizes how DNA methylation can improve forensic procedures and age estimation accuracy, potentially aiding in the resolution of criminal cases. 

  • 30.
    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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  • 31.
    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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  • 32.
    Cancar, Anja
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmaceutical Biosciences.
    Serbia’s way to accession with the European Union and the European Medicines Agency: a comparison of regulatory activity in the field of pharmaceuticals in Serbia and Sweden2014Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Introduction:  On 24 January, 2014 Serbia was approved opening negotiations on accession into the European Union (EU). The European Commission is responsible for launching assistance programmes to support preparatory procedures for the candidate countries; one of those programmes is the Instrument for pre-accession Assistance (IPA) programme. The aim of the IPA programme is to build contacts and relationships between the European Medicines Agency (EMA) and Serbia’s Medicines and Medical Devices Agency (ALIMS), for future collaboration in the EMA activities and its relationship with the Member States of EU.

    Aim: The aim is to describe regulatory activities of ALIMS on human medicines, since the country is not yet a Member State of the EU and to put this into relation with Sweden, a Member State of the EU, which may promote new activities to be introduced in ALIMS’s regulatory work.

    Method: This is a descriptive comparative literature report of institutions working with pharmaceutical regulatory activities.

    Findings: The Serbian Law on Medicines and Medical Devices, established in 2010 suggests that the activities of ALIMS are generally in accordance with the EU standards and guidelines. Since Serbia is not yet a member of the EU, the pharmaceutical regulatory system for granting centralized authorization or marketing authorization based on mutual recognition is not yet possible. However, the Law of Medicines and Medical Devices states that exceptions can be made and ALIMS can issue authorization of centrally authorized medicines if it has reasons related to protection of public health.

    Conclusions: ALIMS has a well developed regulatory authority thanks to international collaboration and a desire to become an EU Member State. 

  • 33.
    Cederquist, Kristina
    et al.
    Umeå University, Faculty of Medicine, Department of Medical Biosciences.
    Palmqvist, Richard
    Emanuelsson, Monica
    Golovleva, Irina
    Umeå University, Faculty of Medicine, Department of Medical Biosciences, Medical and Clinical Genetics.
    Grönberg, Henrik
    Retained immunohistochemical staining in a large Swedish HNPCC family with a pathogenic MLH1 missense mutationManuscript (preprint) (Other academic)
  • 34. Cerritelli, Susana M
    et al.
    Iranzo, Jaime
    Sharma, Sushma
    Umeå University, Faculty of Medicine, Department of Medical Biochemistry and Biophysics.
    Chabes, Andrei
    Umeå University, Faculty of Medicine, Department of Medical Biochemistry and Biophysics.
    Crouch, Robert J
    Tollervey, David
    El Hage, Aziz
    High density of unrepaired genomic ribonucleotides leads to Topoisomerase 1-mediated severe growth defects in absence of ribonucleotide reductase2020In: Nucleic Acids Research, ISSN 0305-1048, E-ISSN 1362-4962, Vol. 48, no 8, p. 4274-4297Article in journal (Refereed)
    Abstract [en]

    Cellular levels of ribonucleoside triphosphates (rNTPs) are much higher than those of deoxyribonucleoside triphosphates (dNTPs), thereby influencing the frequency of incorporation of ribonucleoside monophosphates (rNMPs) by DNA polymerases (Pol) into DNA. RNase H2-initiated ribonucleotide excision repair (RER) efficiently removes single rNMPs in genomic DNA. However, processing of rNMPs by Topoisomerase 1 (Top1) in absence of RER induces mutations and genome instability. Here, we greatly increased the abundance of genomic rNMPs in Saccharomyces cerevisiae by depleting Rnr1, the major subunit of ribonucleotide reductase, which converts ribonucleotides to deoxyribonucleotides. We found that in strains that are depleted of Rnr1, RER-deficient, and harbor an rNTP-permissive replicative Pol mutant, excessive accumulation of single genomic rNMPs severely compromised growth, but this was reversed in absence of Top1. Thus, under Rnr1 depletion, limited dNTP pools slow DNA synthesis by replicative Pols and provoke the incorporation of high levels of rNMPs in genomic DNA. If a threshold of single genomic rNMPs is exceeded in absence of RER and presence of limited dNTP pools, Top1-mediated genome instability leads to severe growth defects. Finally, we provide evidence showing that accumulation of RNA/DNA hybrids in absence of RNase H1 and RNase H2 leads to cell lethality under Rnr1 depletion.

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  • 35.
    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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  • 36. Cif, Laura
    et al.
    Hariz, Marwan
    Umeå University, Faculty of Medicine, Department of Pharmacology and Clinical Neuroscience, Clinical Neuroscience. Unit of Functional Neurosurgery, University College London-Institute of Neurology, Queen Square, London, UK.
    Seventy Years of Pallidotomy for Movement Disorders2017In: Movement Disorders, ISSN 0885-3185, E-ISSN 1531-8257, Vol. 32, no 7, p. 972-982Article in journal (Other academic)
    Abstract [en]

    The year 2017 marks the 70th anniversary of the birth of human stereotactic neurosurgery. The first procedure was a pallidotomy for Huntington's disease. However, it was for Parkinson's disease that pallidotomy was soon adopted worldwide. Pallidotomy was abandoned in the late 1950s in favor of thalamotomy because of the latter's more striking effect on tremor. The advent of levodopa put a halt to all surgery for PD. In the mid-1980s, Laitinen reintroduced the posteroventral pallidotomy of Leksell, and this procedure spread worldwide thanks to its efficacy on most parkinsonian symptoms including levodopa-induced dyskinesias and thanks to basic scientific work confirming the role of the globus pallidus internus in the pathophysiology of PD. With the advent of deep brain stimulation of the subthalamic nucleus, pallidotomy was again abandoned, and even DBS of the GPi has been overshadowed by STN DBS. The GPi reemerged in the late 1990s as a major stereotactic target for DBS in dystonia and, recently, in Tourette syndrome. Lately, lesioning of the GPI is being proposed to treat refractory status dystonicus or to treat DBS withdrawal syndrome in PD patients. Hence, the pallidum as a stereotactic target for either lesioning or DBS has been the phoenix of functional stereotactic neurosurgery, constantly abandoned and then rising again from its ashes. This review is a tribute to the pallidum on its 70th anniversary as a surgical target for movement disorders, analyzing its ebbs and flows and highlighting its merits, its versatility, and its resilience.

  • 37.
    Dahlberg, Josef
    et al.
    Swedish Univ Agr Sci, Dept Anim Nutr & Management, Uppsala, Sweden.;Swedish Univ Agr Sci, Dept Clin Sci, Uppsala, Sweden..
    Johnzon, Carl-Fredrik
    Swedish Univ Agr Sci, Dept Anat Physiol & Biochem, Uppsala, Sweden..
    Sun, Li
    Swedish Univ Agr Sci, Dept Mol Sci, Uppsala, Sweden..
    Pejler, Gunnar
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Swedish Univ Agr Sci, Dept Anat Physiol & Biochem, Uppsala, Sweden..
    Östensson, Karin
    Swedish Univ Agr Sci, Dept Clin Sci, Uppsala, Sweden..
    Dicksved, Johan
    Swedish Univ Agr Sci, Dept Anim Nutr & Management, Uppsala, Sweden..
    Absence of changes in the milk microbiota during Escherichia coli endotoxin induced experimental bovine mastitis2023In: Veterinary research (Print), ISSN 0928-4249, E-ISSN 1297-9716, Vol. 54, article id 46Article in journal (Refereed)
    Abstract [en]

    Changes in the milk microbiota during the course of mastitis are due to the nature of a sporadic occurring disease difficult to study. In this study we experimentally induced mastitis by infusion of Escherichia coli endotoxins in one udder quarter each of nine healthy lactating dairy cows and assessed the bacteriological dynamics and the milk microbiota at four time points before and eight time points after infusion. As control, saline was infused in one udder quarter each of additionally nine healthy cows that followed the same sampling protocol. The milk microbiota was assessed by sequencing of the 16 S rRNA gene and a range of positive and negative controls were included for methodological evaluation. Two different data filtration models were used to identify and cure data from contaminating taxa. Endotoxin infused quarters responded with transient clinical signs of inflammation and increased SCC while no response was observed in the control cows. In the milk microbiota data no response to inflammation was identified. The data analysis of the milk microbiota was largely hampered by laboratory and reagent contamination. Application of the filtration models caused a marked reduction in data but did not reveal any associations with the inflammatory reaction. Our results indicate that the microbiota in milk from healthy cows is unaffected by inflammation.

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  • 38. Davies, Brandon S J
    et al.
    Beigneux, Anne P
    Barnes, Richard H
    Tu, Yiping
    Gin, Peter
    Weinstein, Michael M
    Nobumori, Chika
    Nyrén, Rakel
    Umeå University, Faculty of Medicine, Department of Medical Biosciences, Physiological chemistry.
    Goldberg, Ira
    Olivecrona, Gunilla
    Umeå University, Faculty of Medicine, Department of Medical Biosciences, Physiological chemistry.
    Bensadoun, André
    Young, Stephen G
    Fong, Loren G
    GPIHBP1 is responsible for the entry of lipoprotein lipase into capillaries.2010In: Cell metabolism, ISSN 1932-7420, Vol. 12, no 1, p. 42-52Article in journal (Refereed)
    Abstract [en]

    The lipolytic processing of triglyceride-rich lipoproteins by lipoprotein lipase (LPL) is the central event in plasma lipid metabolism, providing lipids for storage in adipose tissue and fuel for vital organs such as the heart. LPL is synthesized and secreted by myocytes and adipocytes, but then finds its way into the lumen of capillaries, where it hydrolyzes lipoprotein triglycerides. The mechanism by which LPL reaches the lumen of capillaries has remained an unresolved problem of plasma lipid metabolism. Here, we show that GPIHBP1 is responsible for the transport of LPL into capillaries. In Gpihbp1-deficient mice, LPL is mislocalized to the interstitial spaces surrounding myocytes and adipocytes. Also, we show that GPIHBP1 is located at the basolateral surface of capillary endothelial cells and actively transports LPL across endothelial cells. Our experiments define the function of GPIHBP1 in triglyceride metabolism and provide a mechanism for the transport of LPL into capillaries.

  • 39.
    Davies, Victoria S.
    et al.
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Lindsund, Erik
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Petrovic, Natasa
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Cannon, Barbara
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Nedergaard, Jan
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Repeated short excursions from thermoneutrality suffice to restructure brown adipose tissue2023In: Biochimie, ISSN 0300-9084, E-ISSN 1638-6183, Vol. 210, p. 40-49Article in journal (Refereed)
    Abstract [en]

    Given the presence of brown adipose tissue in adult humans, an important issue is whether human brown adipose tissue is recruitable. Cold exposure is the canonical recruitment treatment; however, in experimental animals (mice), recruitment of brown adipose tissue is normally induced by placing the mice in constant cold, a procedure not feasible in humans. For possible translational applications, we have therefore investigated whether shorter daily excursions from thermoneutrality would suffice to qualitatively and quantitatively induce recruitment in mice. Mice, housed at thermoneutrality (30 °C) to mimic human conditions, were transferred every day for 4 weeks to cool conditions (18 °C), for 0, 15, 30, 120 and 420 min (or placed constantly in 18 °C). On the examination day, the mice were not exposed to cold. Very short daily exposures (≤30 minutes) were sufficient to induce structural changes in the form of higher protein density in brown adipose tissue, changes that may affect the identification of the tissue in e.g. computer tomography and other scan studies. To estimate thermogenic capacity, UCP1 protein levels were followed. No UCP1 protein was detectable in inguinal white adipose tissue. In the interscapular brown adipose tissue, a remarkable two-phase reaction was seen. Very short daily exposures (≤30 minutes) were sufficient to induce a significant increase in total UCP1 levels. For attainment of full cold acclimation, the mice had, however, to remain exposed to the cold. The studies indicate that marked alterations in brown adipose tissue composition can be induced in mammals through relatively modest stimulation events.

  • 40.
    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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  • 41. de Veer, Simon J.
    et al.
    Swedberg, Joakim E.
    Akcan, Muharrem
    Rosengren, K. Johan
    Brattsand, Maria
    Umeå University, Faculty of Medicine, Department of Medical Biosciences.
    Craik, David J.
    Harris, Jonathan M.
    Engineered protease inhibitors based on sunflower trypsin inhibitor-1 (SFTI-1) provide insights into the role of sequence and conformation in Laskowski mechanism inhibition2015In: Biochemical Journal, ISSN 0264-6021, E-ISSN 1470-8728, Vol. 469, no 2, p. 243-253Article in journal (Refereed)
    Abstract [en]

    Laskowski inhibitors regulate serine proteases by an intriguing mode of action that involves deceiving the protease into synthesizing a peptide bond. Studies exploring naturally occurring Laskowski inhibitors have uncovered several structural features that convey the inhibitor's resistance to hydrolysis and exceptional binding affinity. However, in the context of Laskowski inhibitor engineering, the way that various modifications intended to fine-tune an inhibitor's potency and selectivity impact on its association and dissociation rates remains unclear. This information is important as Laskowski inhibitors are becoming increasingly used as design templates to develop new protease inhibitors for pharmaceutical applications. In this study, we used the cyclic peptide, sunflower trypsin inhibitor-1 (SFTI-1), as a model system to explore how the inhibitor's sequence and structure relate to its binding kinetics and function. Using enzyme assays, MD simulations and NMR spectroscopy to study SFTI variants with diverse sequence and backbone modifications, we show that the geometry of the binding loop mainly influences the inhibitor's potency by modulating the association rate, such that variants lacking a favourable conformation show dramatic losses in activity. Additionally, we show that the inhibitor's sequence (including both the binding loop and its scaffolding) influences its potency and selectivity by modulating both the association and the dissociation rates. These findings provide new insights into protease inhibitor function and design that we apply by engineering novel inhibitors for classical serine proteases, trypsin and chymotrypsin and two kallikrein-related peptidases (KLK5 and KLK14) that are implicated in various cancers and skin diseases.

  • 42.
    Degerman, Sofie
    et al.
    Umeå University, Faculty of Medicine, Department of Medical Biosciences, Pathology.
    Landfors, Mattias
    Umeå University, Faculty of Science and Technology, Department of Mathematics and Mathematical Statistics. Umeå University, Faculty of Medicine, Department of Medical Biosciences, Pathology.
    Siwicki, Jan Konrad
    Revie, John
    Borssen, Magnus
    Umeå University, Faculty of Medicine, Department of Medical Biosciences, Pathology.
    Evelönn, Emma
    Umeå University, Faculty of Medicine, Department of Medical Biosciences, Pathology.
    Forestier, Erik
    Umeå University, Faculty of Medicine, Department of Medical Biosciences, Medical and Clinical Genetics.
    Chrzanowska, Krystyna H.
    Ryden, Patrik
    Umeå University, Faculty of Science and Technology, Department of Mathematics and Mathematical Statistics.
    Keith, W. Nicol
    Roos, Göran
    Umeå University, Faculty of Medicine, Department of Medical Biosciences, Pathology.
    Immortalization of T-Cells Is Accompanied by Gradual Changes in CpG Methylation Resulting in a Profile Resembling a Subset of T-Cell Leukemias2014In: Neoplasia, ISSN 1522-8002, E-ISSN 1476-5586, Vol. 16, no 7, p. 606-615Article in journal (Refereed)
    Abstract [en]

    We have previously described gene expression changes during spontaneous immortalization of T-cells, thereby identifying cellular processes important for cell growth crisis escape and unlimited proliferation. Here, we analyze the same model to investigate the role of genome-wide methylation in the immortalization process at different time points pre-crisis and post-crisis using high-resolution arrays. We show that over time in culture there is an overall accumulation of methylation alterations, with preferential increased methylation close to transcription start sites (TSSs), islands, and shore regions. Methylation and gene expression alterations did not correlate for the majority of genes, but for the fraction that correlated, gain of methylation close to TSS was associated with decreased gene expression. Interestingly, the pattern of CpG site methylation observed in immortal T-cell cultures was similar to clinical T-cell acute lymphoblastic leukemia (T-ALL) samples classified as CpG island methylator phenotype positive. These sites were highly overrepresented by polycomb target genes and involved in developmental, cell adhesion, and cell signaling processes. The presence of non-random methylation events in in vitro immortalized T-cell cultures and diagnostic T-ALL samples indicates altered methylation of CpG sites with a possible role in malignant hematopoiesis.

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  • 43.
    Devad, Martin
    et al.
    Swedish School of Sport and Health Sciences, GIH, Department of Sport and Health Sciences.
    Wallin, Peter
    Swedish School of Sport and Health Sciences, GIH, Department of Sport and Health Sciences.
    Kosttillskott åt folket?!: en kvantitativ studie om användandet av och åsikter om kosttillskott2007Independent thesis Basic level (degree of Bachelor), 10 poäng / 15 hpStudent thesis
    Abstract [sv]

    Syfte & frågeställningar

    Syftet var att undersöka användandet av och uppfattningar om kosttillskott bland människor som tränar på gym. Frågeställningarna löd enligt följande:

    - Vilka kategorier av människor som tränar på gym använder kosttillskott?

    - Skiljer sig åsikterna om kosttillskott beroende på om man använder det eller inte?

    - Har användandet av kosttillskott någon inverkan på attityden till dopning?

    Metod

    Studien baseras på en kvantitativ enkätundersökning vilken utfördes på fyra olika gym inom Storstockholm. Tre utav gymmen representeras av två stora kedjor och det fjärde av ett mindre gym, vilket inte ingick i någon kedja. Gymmen selekterades genom att ta fram de två stora gymkedjornas samtliga anläggningar inom stor Stockholm och sedan numrera dessa varpå lottdragning utfördes. Samma procedur genomfördes gällande det mindre gymmet. Individerna som kom att delta i studien blev 169st varav 105 män och 64 kvinnor. Dessa selekterades genom ett frivilligt urval i samband med att de utvalda gymmen besöktes. Datan analyserades i SPSS där vi använt ett chi-2- samt Man Whitney U- test.

    Resultat

    Resultaten visade att användandet av kosttillskott var störst bland styrketränande män vilkas huvudmål med träningen var att förbättra hälsan samt bygga muskler. Åsikterna om kosttillskott skilde sig åt beroende på om respondenterna använde det eller inte. Detta framkom då de respondenter som nyttjade kosttillskott såg fler fördelar och hade en positivare inställning till användandet. I studien framkom det att majoriteten (85.1 %, n = 168) av respondenterna var emot användandet av dopning. Bland användarna var det 26.7 % (n = 75) som ansåg att det var upp till individen att bestämma om denne ville nyttja dopning.

    Slutsats

    Användandet av kosttillskott var förhållandevis stort då 44,9 % av respondenterna använde det mer eller mindre regelbundet. Majoriteten (59,6 %) av respondenterna uppgav att det var upp till individen att bestämma om denne ville nyttja kosttillskott. Tron på att kosttillskott ger effekt på träningen men att det kan bli skadligt vid överdosering delades också av majoriteten (54,8 %) av respondenterna.

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  • 44.
    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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  • 45. Drager, Luciano F.
    et al.
    Li, Jianguo
    Shin, Mi-Kyung
    Reinke, Christian
    Aggarwal, Neil R.
    Jun, Jonathan C.
    Bevans-Fonti, Shannon
    Sztalryd, Carole
    OByrne, Sheila M.
    Kroupa, Olessia
    Umeå University, Faculty of Medicine, Department of Medical Biosciences, Physiological chemistry.
    Olivecrona, Gunilla
    Umeå University, Faculty of Medicine, Department of Medical Biosciences, Physiological chemistry.
    Blaner, William S.
    Polotsky, Vsevolod Y.
    Intermittent hypoxia inhibits clearance of triglyceride-rich lipoproteins and inactivates adipose lipoprotein lipase in a mouse model of sleep apnoea2012In: European Heart Journal, ISSN 0195-668X, E-ISSN 1522-9645, Vol. 33, no 6, p. 783-U33Article in journal (Refereed)
    Abstract [en]

    Delayed lipoprotein clearance is associated with atherosclerosis. This study examined whether chronic intermittent hypoxia (CIH), a hallmark of obstructive sleep apnoea (OSA), can lead to hyperlipidaemia by inhibiting clearance of triglyceride rich lipoproteins (TRLP). Male C57BL/6J mice on high-cholesterol diet were exposed to 4 weeks of CIH or chronic intermittent air (control). FIO2 was decreased to 6.5 once per minute during the 12 h light phase in the CIH group. After the exposure, we measured fasting lipid profile. TRLP clearance was assessed by oral gavage of retinyl palmitate followed by serum retinyl esters (REs) measurements at 0, 1, 2, 4, 10, and 24 h. Activity of lipoprotein lipase (LpL), a key enzyme of lipoprotein clearance, and levels of angiopoietin-like protein 4 (Angptl4), a potent inhibitor of the LpL activity, were determined in the epididymal fat pads, skeletal muscles, and heart. Chronic intermittent hypoxia induced significant increases in levels of total cholesterol and triglycerides, which occurred in TRLP and LDL fractions (P 0.05 for each comparison). Compared with control mice, animals exposed to CIH showed increases in REs throughout first 10 h after oral gavage of retinyl palmitate (P 0.05), indicating that CIH inhibited TRLP clearance. CIH induced a 5-fold decrease in LpL activity (P 0.01) and an 80 increase in Angptl4 mRNA and protein levels in the epididymal fat, but not in the skeletal muscle or heart. CIH decreases TRLP clearance and inhibits LpL activity in adipose tissue, which may contribute to atherogenesis observed in OSA.

  • 46.
    Edfors, Inger
    et al.
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Torremorrel, M
    Univ Minnesota.
    Escherichia coli and Salmonella in pigs2010In: Breeding for Disease Resistance in Farm Animals / [ed] RFA Axford, S Bishop, F Nicholas, JB Owen, Walllingford, UK: CABI Publishing, 2010, 3rd, p. 232-250Chapter in book (Other academic)
    Abstract [en]

    Diarrhoea due to bacterial infections is a problem mainly in the young growing animal, including the pig. Among the bacteria that cause diarrhoea in pigs are various strains of Escherichia coli and Salmonella. Considerable genetic variation in resistance/susceptibility has been found for both neonatal and post-weaning diarrhoea caused by E. coli carrying F4 fimbriae and post-weaning diarrhoea and oedema disease due to E. coli strains with F18 fimbriae. The loci for the receptors of both types of fimbriae have been mapped: the F4 receptor(s) to chromosome 13 (SSC13) and the F18 receptor to chromosome 6 (SSC6). Several candidate genes have been suggested for the F4 receptor, among them different mucine genes (MUC4, MUC13), and a very close association between a single-nucleotide polymorphism (SNP) in an alpha (1, 2) fucosyltransferase gene (FUT1) and the F18 receptor has been identified.Resistance to Salmonella infections in mice is associated with the antimicrobial activity of macrophages, and some studies have suggested that it is linked with polymorphism in the Nramp1 gene. The gene has been identified in several species including the pig, but data are so far lacking concerning association between polymorphism in the porcine gene and resistance-susceptibility to Salmonella infection. Using transcriptome profiles, several porcine genes that are differentially up or downregulated during Salmonella infection have been identified. Further studies of associations between polymorphisms in these genes and the outcome of Salmonella infection may facilitate the development of tools to identify carrier pigs, and lead towards identification of markers that can be used to select for resistant pigs.Breeding for increased disease resistance can be potentially performed in several ways; excluding susceptible breeding of animals after exposure, marker-assisted selection (MAS) based on closely linked loci or direct selection based on polymorphism in the causative gene. The rapid development in molecular genetics has provided dense genome maps and the tools to identify and study individual genes, both at the deoxyribonuclease acid (DNA) and the expression level. Overall use of genetic markers influencing disease traits is expected to increase significantly in the coming years. This number will grow as large-scale accurate disease phenotypes are collected in pedigreed populations. It is likely that many disease markers will contribute additively to the selection criteria and will be used as part of complex selection indices that will balance other economically significant traits.

  • 47.
    Ekhtiari Bidhendi, Elaheh
    et al.
    Umeå University, Faculty of Medicine, Department of Medical Biosciences.
    Bergh, Johan
    Umeå University, Faculty of Medicine, Department of Medical Biosciences.
    Zetterström, Per
    Umeå University, Faculty of Medicine, Department of Medical Biosciences.
    Andersen, Peter M.
    Umeå University, Faculty of Medicine, Department of Pharmacology and Clinical Neuroscience, Clinical Neuroscience.
    Marklund, Stefan L.
    Umeå University, Faculty of Medicine, Department of Medical Biosciences.
    Brännström, Thomas
    Umeå University, Faculty of Medicine, Department of Medical Biosciences.
    Two superoxide dismutase prion strains transmit amyotrophic lateral sclerosis-like disease2016In: Journal of Clinical Investigation, ISSN 0021-9738, E-ISSN 1558-8238, Vol. 126, no 6, p. 2249-2253Article in journal (Refereed)
    Abstract [en]

    Amyotrophic lateral sclerosis (ALS) is an adult-onset degeneration of motor neurons that is commonly caused by mutations in the gene encoding superoxide dismutase 1 (SOD1). Both patients and Tg mice expressing mutant human SOD1 (hSOD1) develop aggregates of unknown importance. In Tg mice, 2 different strains of hSOD1 aggregates (denoted A and B) can arise; however, the role of these aggregates in disease pathogenesis has not been fully characterized. Here, minute amounts of strain A and B hSOD1 aggregate seeds that were prepared by centrifugation through a density cushion were inoculated into lumbar spinal cords of 100-day-old mice carrying a human SOD1 Tg. Mice seeded with A or B aggregates developed premature signs of ALS and became terminally ill after approximately 100 days, which is 200 days earlier than for mice that had not been inoculated or were given a control preparation. Concomitantly, exponentially growing strain A and B hSOD1 aggregations propagated rostrally throughout the spinal cord and brainstem. The phenotypes provoked by the A and B strains differed regarding progression rates, distribution, end-stage aggregate levels, and histopathology. Together, our data indicate that the aggregate strains are prions that transmit a templated, spreading aggregation of hSOD1, resulting in a fatal ALS-like disease.

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  • 48.
    Ekorn, Bonnie
    et al.
    Swedish School of Sport and Health Sciences, GIH, Department of Sport and Health Sciences.
    Holmgren, Maria
    Swedish School of Sport and Health Sciences, GIH, Department of Sport and Health Sciences.
    Frulle = full rulle?: en kvantitativ studie om frukostens inverkan på elevers fysiska prestation i ämnet idrott och hälsa2007Independent thesis Basic level (degree of Bachelor), 10 poäng / 15 hpStudent thesis
    Abstract [sv]

    Sammanfattning

    Syfte och frågeställningar

    Syftet var att undersöka om frukosten har någon inverkan på den fysiska prestationen i ämnet idrott och hälsa. Frågeställningarna var:

    • Finns det något samband mellan fysisk prestation och frukost hos elever som äter respektive inte äter frukost?

    • Är det någon skillnad i den fysiska prestationen mellan könen, bland de elever som äter respektive inte äter frukost?

    • Finns det något samband mellan fysisk prestation, tidpunkt för frukostintag och idrott och hälsa bland elever som äter respektive inte äter frukost?

    Metod

    Undersökningen är kvantitativ och har genomförts bland 89 elever i skolår 7 och 8. Det externa bortfallet var 28,8 procent. Studien genomfördes i idrott och hälsa där eleverna deltog och sedan svarade på en enkät. I statistikprogrammet SPSS fastställdes resultatet.

    Resultat

    Frukosten har en inverkan på prestationen i form av svett. De elever som äter frukost svettas mer. Det finns ingen skillnad i prestation mellan flickor och pojkar som har ätit respektive inte ätit frukost. Tidpunkten för frukostintaget har en inverkan på prestationen i form av svett. Ju kortare tid mellan frukostintag och aktivitetsutövande, desto mer svettas eleven.

    Slutsats

    Som slutsats kan vi se att frukosten har en inverkan på prestationen i form av svett. De elever som äter frukost svettas mer.

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  • 49.
    Ekstrand, Carl
    et al.
    Swedish Univ Agr Sci, Div Pharmacol & Toxicol, Dept Biomed & Vet Publ Hlth, POB 7028, S-75007 Uppsala, Sweden.
    Ingvast-Larsson, Carina
    Swedish Univ Agr Sci, Div Pharmacol & Toxicol, Dept Biomed & Vet Publ Hlth, POB 7028, S-75007 Uppsala, Sweden.
    Bondesson, Ulf
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Analytical Pharmaceutical Chemistry. Natl Vet Inst, Dept Chem Environm & Feed Hyg, Uppsala, Sweden.
    Hedeland, Mikael
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Analytical Pharmaceutical Chemistry. Natl Vet Inst, Dept Chem Environm & Feed Hyg, Uppsala, Sweden.
    Olsen, Lena
    Swedish Univ Agr Sci, Div Pharmacol & Toxicol, Dept Biomed & Vet Publ Hlth, POB 7028, S-75007 Uppsala, Sweden;Swedish Univ Agr Sci, Div Vet Nursing, Dept Clin Sci, Uppsala, Sweden.
    Cetirizine per os: exposure and antihistamine effect in the dog2018In: Acta Veterinaria Scandinavica, ISSN 0044-605X, E-ISSN 1751-0147, Vol. 60, article id 77Article in journal (Refereed)
    Abstract [en]

    BackgroundCetirizine is an antihistamine used in dogs, but plasma concentrations in relation to effect after oral administration are not well studied. This study investigated cetirizine exposure and the plasma cetirizine concentration-antihistamine response relation in the dog following oral administration of cetirizine.ResultsEight Beagle dogs were included in a cross-over study consisting of two treatments. In treatment one, cetirizine 2-4mg/kg was administered per os once daily for 3days. The other treatment served as a control. Wheal diameter induced by intra-dermal histamine injections served as response-biomarker. Cetirizine plasma concentration was quantified by UHPLC-MS/MS. Median (range) cetirizine plasma terminal half-life was 10h (7.9-16.5). Cetirizine significantly inhibited wheal formation compared with the premedication baseline. Maximum inhibition of wheal formation after treatment with cetirizine per os was 100% compared with premedication wheal diameter. The median (range) IC50-value for reduction in wheal area was 0.33 mu g/mL (0.07-0.45). The median (range) value for the sigmoidicity factor was 1.8 (0.8-3.5). A behavioral study was also conducted and revealed no adverse effects, such as sedation.ConclusionThe results indicate that a once-daily dosing regimen of 2-4mg/kg cetirizine per os clearly provides a sufficient antihistamine effect. Based on this experimental protocol, cetirizine may be an option to treat histamine-mediated inflammation in the dog based on this experimental protocol but additional clinical studies are required.

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  • 50.
    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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