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  • 1.
    Al Shobky, Mohamed
    University of Skövde, School of Bioscience.
    Utilization of cancer-specific genome-scale metabolic models in pancreatic ductal adenocarcinomas for biomarkers discovery and patient stratification2019Independent thesis Advanced level (degree of Master (Two Years)), 40 credits / 60 HE creditsStudent thesis
    Abstract [en]

    Pancreatic Ductal Adenocarcinomas initiates in the exocrine part of the pancreatic tissue and represents over 90% of all the pancreatic cancers. Pancreatic Ductal Adenocarcinomas are extremely aggressive and are one of the most lethal malignant neoplasms. The five-year relative survival is currently less than 8% of the patients. The main reason behind such a low survival rate is that most of the cases are diagnosed at a very late stage. Although substantial advancement in pancreatic cancer research has been done, there has not been any remarkable significance in the mortality to incidence ratio. This is mainly a result of the scarce of early diagnostic characteristic symptoms and reliable biomarkers besides the unresponsiveness to the treatments. In this study, transcriptomics and proteomics data were used for the construction of a genome-scale metabolic model that was used in the detection of altered metabolic pathways, genes and metabolites using gene set analysis and reporter metabolites analysis. As a result, altered metabolic pathways in PDAC tumours were detected, including the lipid metabolism-related pathways as well as carbohydrate metabolism, in addition to nucleotide metabolism, which are considered as potential candidates for diagnostic biomarkers. Moreover, classification of the filtered DIRAC tightly regulated network genes, based on their prognostic values from the pathology atlas, detected two groups of PDAC patients that have significantly different survival outcome. The differential expression analysis of the two groups showed that six of the eight genes used in clustering were showing significantly altered expression, which suggests their importance in PDAC patient stratification. As a conclusion, this study shows the valuable outcome of the GEM reconstructions and other systems-level analyses for elucidating the underlying altered metabolic mechanisms of PDAC. Such analyses results should provide more insights into the biomarker discovery and developing of potential treatments.

    The full text will be freely available from 2020-08-01 19:28
  • 2.
    Alade, Larry
    et al.
    University of Massachusetts.
    Barbosa, Alexandra
    ANICP.
    Bartolino, Valerio
    Swedish University of Agricultural Sciences.
    Beggs, Steven
    Agri-food and Biosciences Institute.
    Bergenius, Mikaela
    Swedish University of Agricultural Sciences.
    Casini, Michele
    Swedish University of Agricultural Sciences.
    Clarke, Maurice
    Marine Institute Rinville.
    Coers, Aukje
    Pelagic RAC Secretariat.
    Deroba, Jonathan
    Woods Hole Oceanographic Institution.
    Dickey-Collas, Mark
    Wageningen IMARES.
    Enberg, Katja
    Institute of Marine Research.
    Gårdmark, Anna
    Swedish University of Agricultural Sciences.
    Gudmundsdóttir, Asta
    Marine Research Institute.
    Hansson, Sture
    University of Stockholm.
    Hatfield, Emma
    Marine Scotland Science Marine Laboratory.
    Hintzen, Niels
    Wageningen IMARES.
    Holmgren, Noél
    University of Skövde, The Systems Biology Research Centre. University of Skövde, School of Life Sciences.
    Hoines, Åge
    Institute of Marine Research.
    Arge Jacobsen, Jan
    Faroe Marine Research Institute.
    Keating, James
    Galway-Mayo Institute of Technology.
    Krysov, Alexander
    Knipovich Polar Research Institute of Marine Fisheries and Oceanography (PINRO).
    Maersk Lusseau, Susan
    Marine Scotland Science Marine Laboratory.
    Mäntyniemi, Samu
    University of Helsinki.
    McCulla, Alan
    Anglo North Irish Fish Producers' Organization.
    Miller, David
    Wageningen IMARES.
    Mosegård, Henrik
    DTU Aqua - National Institute of Aquatic Resources.
    O'Donoghue, Sean
    Killybegs Fishermen's Organization Ltd..
    Olesen, Christian
    Danish Pelagic Producers' Organization.
    Payne, Mark
    DTU Aqua - National Institute of Aquatic Resources Section for Fisheries Advice.
    Pönni, Jukka
    Finnish Game and Fisheries Research Institute.
    Power, Michael
    St Andrew's Biological Station.
    Raitaniemi, Jari
    Finnish Game and Fisheries Research Institute.
    Riveiro, Isabel
    Instituto Español de Oceanografia Centro .
    Roel, Beatriz
    Centre for Environment, Fisheries and Aquaculture Science.
    Rohlf, Norbert
    Johann Heinrich von Thünen-Institute Federal Research Institute for Rural Areas, Forestry and Fisheries Institute for Sea Fisheries.
    Schoute, Barbara
    International Council for the Exploration of the Sea.
    Schön, Pieter-Jan
    Agri-food and Biosciences Institute.
    Silva, Alexandra
    INRB-IPIMAR.
    Timoshenko, Nikolay
    AtlantNIRO.
    Trenkel, Verena
    Ifremer Nantes Centre.
    Report of the Benchmark Workshop on Pelagic Stocks (WKPELA 2012), 13–17 February 2012 Copenhagen, Denmark2012Report (Refereed)
  • 3.
    Al-Bayati, Omar
    University of Skövde, School of Bioscience. Baghdad university.
    Optimizing the Fluorescence In situ hybridization technique for a more rapid inspection of Sepsis causative pathogens by employing DNA probes2014Independent thesis Advanced level (degree of Master (One Year)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Abstract

    Sepsis is a serious clinical condition that is characterized by a systemic inflammatory response syndrome resulting from a known or suspected infection. The major clinical symptoms involve an abnormal WBC count, elevated body temperature, respiration and pulse rate. Reported cases with high mortality rate range between 13 - 20 million. In order to treat Sepsis, the detection of bacteria in blood culture is extremely crucial. Treating patients with broad spectrum antibiotics is usually related to adverse effects, drug resistance, increased mortality, and high cost. In the past decades, researches had detected that E. coli and S. aureus are the major role players that cause sepsis. These microbes are molecularly tested by methods like MALDI TOF, FISH and Microarrays.  

    In this analysis, DNA fluorescence in situ hybridization (FISH) assessment for the identification of S. aureus, one of the most frequent blood pathogens, was optimized in the labs of Högskolan i Skövde. As a result, the growth of S. aureus was observed very carefully, optimizing the FISH procedure for gram positive bacteria was done and the sensitivity, stability and specificity of the DNA probe were examined under variant conditions like the continuous decrease in the bacteria cells number and utilizing a mixture of different types of bacteria cells. 

  • 4.
    Almgren, Ingrid
    University of Skövde, School of Bioscience. studingrid@gmail.com.
    Challenging the dual coding theory: Does Affective Information Play a Greater Role in Abstract Compared to Concrete Word Processing?2018Independent thesis Basic level (degree of Bachelor), 15 credits / 22,5 HE creditsStudent thesis
    Abstract [en]

    It has long been held that concrete material has a processing advantage over abstract material, as predicted by Dual Coding Theory (Paivio,1991), although this has been challenged. For example, based on evidence for behavioural and neuroscientific studies, Kousta,, Vigliocco, Vinson, & Del Campo, (2011) proposed that emotional valance had a greater influence in the processing of abstract words, and that under some circumstances there may be no concreteness effect and might even be an abstractness effect. This would not be predicted by DCT. In addition, Isen and Daubman (1984) have claimed that emotional valence, and particularly positive emotion can influence cognitive processing. Specifically, they demonstrated that positive emotion was associated with more inclusive categorization of ambiguous category members. This current study was a 2 x 2 between group design to investigate the effect of positive and negative valence on recognition memory for concrete and abstract words and on categorization. Contrary to what was predicted by Dual Coding Theory, abstract words were generally better recognized than concrete, with there being an additional interaction with valence. A significant interaction between word type and valence on categorization was also found. Results partially support Kousta et al. (2011).

  • 5.
    Alteryd, Olivia
    University of Skövde, School of Bioscience.
    Think your pain away: The neurochemistry of placebo analgesia2019Independent thesis Basic level (degree of Bachelor), 15 credits / 22,5 HE creditsStudent thesis
    Abstract [en]

    Placebo treatments are inert but are known to alleviate symptoms across numerous clinical conditions. One of the most studied placebo effects is placebo analgesia, which is a placebo effect limited to pain relief. This thesis aims to introduce the current state of research regarding the neuroscience of placebo analgesia and specifically to present research findings regarding the neurotransmission. Studies have demonstrated that placebo analgesia can be elicited through two separate processes interacting with each other; manipulation of expectations and through conditioning. These processes seem to affect neurotransmission in different ways. Many brain areas have been found to be correlated to placebo analgesia. Besides the pain-processing brain areas, studies point to that the prefrontal cortex can have a vital role in the placebo analgesic effect. Known neurotransmitters that have shown to be involved in placebo analgesia are endogenous opioids, cholecystokinin (CCK), and endocannabinoids. Studies point to that endogenous opioids are involved in the placebo analgesic effect when elicited by expectation or conditioned by an opioid drug. CCK act on placebo analgesia by affecting the release of endogenous opioids and endocannabinoids seem to be involved in placebo analgesia while it occurs due to conditioning with non-opioid drugs. Getting a better understanding of placebo analgesia and find ways to apply this knowledge in the clinical context could powerfully develop the whole medical society.

  • 6.
    Andersson, Christoffer
    University of Skövde, School of Humanities and Informatics.
    PELICAN: a PipELIne, including a novel redundancy-eliminating algorithm, to Create and maintain a topicAl family-specific Non-redundant protein database2005Independent thesis Advanced level (degree of Master (One Year))Student thesis
    Abstract [en]

    The increasing number of biological databases today requires that users are able to search more efficiently among as well as in individual databases. One of the most widespread problems is redundancy, i.e. the problem of duplicated information in sets of data. This thesis aims at implementing an algorithm that distinguishes from other related attempts by using the genomic positions of sequences, instead of similarity based sequence comparisons, when making a sequence data set non-redundant. In an automatic updating procedure the algorithm drastically increases the possibility to update and to maintain the topicality of a non-redundant database. The procedure creates a biologically sound non-redundant data set with accuracy comparable to other algorithms focusing on making data sets non-redundant

  • 7.
    Arif Jahangir, Chowdhury
    University of Skövde, School of Bioscience.
    Role of BACH1 in regulation of antioxidant mediated metastasis in lung cancer2018Independent thesis Advanced level (degree of Master (One Year)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Consumption of antioxidant supplements is widely popular worldwide mainly because of their supposed anticancer benefits. Though these benefits against cancer are highly advertised by supplement industry and a well stablished perception in general population, there are not enough studies to support those claims. In fact, several studies have pinpointed antioxidants’ role in promoting tumor proliferation and migration in multiple types of cancer. Nevertheless, the mechanisms behind how antioxidants are actually mediating these events is largely unknown. This study aims to investigate how antioxidants are affecting lung cancer cells migration and to decipher the involvement of the transcription factor BACH1 in it. In this study, effect of antioxidant supplementation on three human Non-small-cell lung carcinoma (NSCLC) cell lines were investigated. Antioxidant administration was found to increase cell migration and BACH1 expression in all of them. Effect of inactivation and over activation of BACH1 confirmed significant relation between antioxidant induced migration and BACH1 expression. Along with increased migration, antioxidants increased glycolysis in the cells in a Bach1 dependent manner. Activation of NRF2, the master regulator of endogenous antioxidant expression had also been found to increase migration through up regulation of BACH1. Overall findings of this study confirm Bach1’s role in antioxidant-induced migration in lung cancer from different directions and provides a broader understanding how redox status of cancer cells influence their metastatic ability.

  • 8.
    Arnesén, Lisa
    University of Skövde, School of Bioscience.
    Vems landskap ska förändras för att öka den biologiska mångfalden?: En studie av skillnaderna i odlingslandskapets konnektivitet med avseende på två skyddsvärda arter med olika preferenser2014Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    Organisms relevant for nature conservation dont follow administrative borders. Because of this there is a need for a landscape perspective within conservation and planning, and a need for the species of interest to have legal protection. Network analysis adapted for ecological purposes has grown to become a powerful tool for studying and communicating the relationships between species dispersion and access to habitat. In this study the following question is posed: How is the Osmoderma eremita and the Pernis apivorus dispersal possibilities in the small scale cultivated landscape of Borås affected by exploitation in respect to a) dispersal ability, b) habitat quality, c) position of habitat patches in a network? The analysis were based on municipal and regional nature conservation data, which in due to confidentiality is not accounted for in the report by maps, coordinates, etc. Several networks were established for both species to indicate how habitat patches are distributed today and how the species dispersal changes depending on which patches are excluded – this was done to imitate how exploitation can affect the species future survival and dispersion. The results showed that the O.e. is mainly inhibited by its poor dispersal abilities, followed by patch position, while the P.a. is the most affected by degrading habitat quality. The most important conclusions of the study were that the O.e. natural dispersal may be restricted but can be improved by linking small network components together and by maintaining the largest components. As for the P.a. it was concluded that a different type of analysis, focusing on its behaviour and need for different patches for different purposes, would generate more interesting results.

  • 9.
    Asker, Mohammed
    University of Skövde, School of Bioscience.
    Real-time measurement of locus coeruleus (LC) activity during eating and mild stress with fiber photometry2019Independent thesis Advanced level (degree of Master (Two Years)), 30 credits / 45 HE creditsStudent thesis
    Abstract [en]

    Stress has been always associated with a deviating than normal feeding behavior. Both over-eating and under-eating accompanied by altered food choice towards palatable food have been reported in response to stress. The neuronal pathways that link stress with eating are still unclear. Locus Coeruleus (LC) is the main endogenous norepinephrine (NE) secreting nucleus. It lies in the center of the stress response mediating arousal state. LC-NE nucleus with its widespread innervations throughout the brain can modulate brain mechanisms linked with motivation towards food. In this study, the aim was to study the activity of NE neurons in the LC in relation to stress and food intake. The hypothesis was that NE neurons are activated by mild stressors and that this activity drives food intake. Because the association between LC activity and food intake is observational by nature, it is not expected to demonstrate a causal link but to show findings consistent with this hypothesis. Another aim was to standardize the photometry measurements and an analysis paradigm. In response to a stressor, animals showed freezing behavior, with photometry recordings displaying a significant reduction in Ca+2 signals right after the distressing stimulus. When a stressor preceded food intake, LC-NE activity significantly decreased right after the first meal the effect that did not last to the second meal with no difference between chow and palatable food. These results highlight the involvement of LC-NE in modulating feeding behavior by integrating environmental cues and internal needs. Future investigations of distinct, projection-defined, LC-NE sub-populations may reveal more specific food and stress interactions.

  • 10.
    Backlöf, Kalle
    University of Skövde, School of Life Sciences.
    GROWTH CONDITIONS AND EXPERIMENTAL SETUP FOR BACTERIAL GROWTH AND THE FADING OF PHENOLPHTHALEIN IN ALKALINE SOLUTION2011Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    The whole project consisted of two different parts. The first subproject were running optical density measurements to assist in finding optimal growth conditions and experimental setup for use of E.coli BL21 (DE3) bacteria with the PYCARD gene transformed into them. The transformed bacteria will be used for generating data for modeling. Previous laboratory attempts had problems with timing of the exponential phase when several tests were performed simultaneously. The optimizations of a method for displaying growth include trying out using different medium but also different inoculation ratios between culture and medium to see the effects on growth rate. Results have shown that lysogeny broth together with an inoculation ratio of 1:25 results in rapid absorbance increase in the bacterial growth curves.The second part of the thesis project was to study the kinetics of fading of phenolphthalein in sodium hydroxide solution in order to provide a basis for experiments illustrating this in laboratory environment. Phenolphthalein is used in many different applications such as an active ingredient in some laxatives but the perhaps most common use is as an acid-base indicator of pH. The experiments were performed by mixing alkaline solutions of varying sodium hydroxide concentration together with sodium chloride, then after addition of phenolphthalein to study absorbance variations over time to illustrate the rate law which correlates the rate of color fade to sodium hydroxide concentration. The results have proven that they correspond directly so that increasing the concentration of sodium hydroxide raised the color fading rate just as much in percent.

  • 11.
    Backstrom, Tobias
    et al.
    Uppsala Univ, Dept Neurosci, Physiol Unit, Biomed Ctr BMC, SE-75123 Uppsala, Sweden / Uppsala Univ, Evolutionary Biol Ctr, SE-75236 Uppsala, Sweden .
    Pettersson, Andreas
    Swedish Univ Agr Sci, Dept Food Sci, SE-75007 Uppsala, Sweden.
    Johansson, Viktoria
    University of Skövde, School of Life Sciences.
    Winberg, Svante
    Uppsala Univ, Dept Neurosci, Physiol Unit, Biomed Ctr BMC, SE-75123 Uppsala, Sweden .
    CRF and urotensin I effects on aggression and anxiety-like behavior in rainbow trout2011In: Journal of Experimental Biology, ISSN 0022-0949, E-ISSN 1477-9145, Vol. 214, no 6, p. 907-914Article in journal (Refereed)
    Abstract [en]

    Corticotropin-releasing factor (CRF) is central in the stress response but also modulates several behaviors including anxiety-related behaviors and aggression. In this study, juvenile rainbow trout (Oncorhynchus mykiss) were tested for competitive ability, determined during dyadic fights for dominance, after intracerebroventricular (i.c.v.) administration of CRF, urotensin I (UI), the non-specific CRF antagonist alpha-helical RF(9-41) (ahCRF) or the CRF receptor subtype 1-specific antagonist antalarmin, when paired with a mass-matched con-specific injected with saline. In addition, isolated fish received the same substances. Plasma cortisol and brain monoamines were monitored in all fish. Most fish receiving CRF showed a conspicuous behavior consisting of flaring the opercula, opening the mouth and violent shaking of the head from side to side. When this occurred, the fish immediately forfeited the fight. Similar behavior was observed in most fish receiving UI but no effect on outcome of dyadic fights was noted. This behavior seems similar to non-ambulatory motor activity seen in rats and could be anxiety related. Furthermore, fish receiving CRF at a dose of 1000. ng became subordinate, whereas all other treatments had no effects on the outcome of dyadic fights. In addition, isolated fish receiving ahCRF had lower brain stem concentrations of 5-hydroxyindoleacetic acid, serotonin, 3,4-dihydroxyphenylacetic acid and dopamine. In conclusion, CRF seems to attenuate competitive ability, and both CRF and UI seem to induce anxiety-like behavior.

  • 12.
    Banks, H. T.
    et al.
    Center for Research in Scientific Computation North Carolina State University Raleigh, NC, USA.
    Banks, J. E.
    Undergraduate Research Opportunities Center (UROC) California State University, Monterey Bay Seaside, CA, USA.
    Bommarco, Riccardo
    Department of Ecology Swedish University of Agricultural Sciences Uppsala, Sweden.
    Curtsdotter, Alva
    Department of Ecology Swedish University of Agricultural Sciences Uppsala, Sweden.
    Jonsson, Tomas
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre. Department of Ecology Swedish University of Agricultural Sciences Uppsala, Sweden.
    Laubmeier, A. N.
    Center for Research in Scientific Computation North Carolina State University Raleigh, NC, USA.
    Parameter estimation for an allometric food web model2017In: International journal of pure and applied mathematics, ISSN 1311-8080, E-ISSN 1314-3395, Vol. 114, no 1, p. 143-160Article in journal (Refereed)
    Abstract [en]

    The application of mechanistic models to natural systems is of interest to ecological researchers. We use the mechanistic Allometric Trophic Network (ATN) model, whichis well-studied for controlled and theoretical systems, to describe the dynamics of the aphidRhopalosiphum padi in an agricultural field. We diagnose problems that arise in a first attemptat a least squares parameter estimation on this system, including formulation of the modelfor the inverse problem and information content present in the data. We seek to establishwhether the field data, as it is currently collected, can support parameter estimation for theATN model.

  • 13.
    Baxter, John
    University of Skövde, School of Bioscience.
    Evaluation of Oxford nanopore’s MinION: Use, functionality, and genome assembly2019Independent thesis Advanced level (degree of Master (Two Years)), 30 credits / 45 HE creditsStudent thesis
    Abstract [en]

    The rapid and reliable detection of pathogens is of utmost importance in healthcare settings to ensure the appropriate treatment thereby reducing morbidity and mortality for the patient. Current culturing, PCR based and NGS species detection methods are time consuming (Opota et al., 2015), limited in their detection (Buckley et al., 2015), or require specialist skills and are expensive (Basho and Eterovic., 2015). Oxford Technologies Nanopore devices could provide detailed genomic sequencing at a fraction of the cost and without the need for technical bioinformatic skills. This study evaluates the MinION device and analysis tools to suggest best practice. Classification and genotyping of 12 Klebsiella isolates were performed using EPI2ME automated workflows and manual de novo assembly.  Automated workflows using raw MinION reads provided clinically relevant information identified in ~6hrs. Manual de novo assembly and analysis used hybrid, and single source data took >24hrs. The inclusion of MinION long reads overcome problems assembling short reads. Hybrid genomes provided the most contiguous and highly detailed contigs. MinION only read assemblies contained more errors but still identified similar genotypic findings. Automated workflows are rapid and require minimal bioinformatic know-how. There should be a dialogue between clinicians and bioinformaticians to develop bespoke analysis tools.  Although challenges remain around compatible kits and vulnerable flowcells long read sequencing can be an effective tool for species detection and pathogen typing. Furthermore, hybrid assemblies have the potential to advance our genome detailing and discovery.

  • 14.
    Bedi, Abhishek
    University of Skövde, School of Bioscience.
    Impact of the new class of clinically relevant drugs: Imipridones on the migration of mantle cell Lymphoma cells2018Independent thesis Advanced level (degree of Master (One Year)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Mantle cell lymphoma (MCL)is a subtype of B-cell lymphoma characterized by chromosomal translocation t(11;14)(q13;q32), enhancing the expression of cyclin D1, resulting in alteration in cell cycle progression. The translocation is the key event for initiation of mantle cell lymphoma however is not sufficient for the development of the disease. Changes in the expression of the G-protein coupled receptors in different cancer types due to mutations and other regulating mechanisms can lead to changes in expression of proteins, resulting in defects in signalling pathways,favouring tumor dissemination. Growing evidences suggests that the disease progression in various B cell malignancies is due to the interactions between neoplastic B cells and stromal cells in tissue microenvironment. ONC201 is an imipridone, which is an antagonist to a type of G-protein coupled receptor: dopamine receptor D2. ONC201 has the property for inhibiting proliferation and inducing apoptosis. The objective of the project was to investigate the migration of MCL cells towards fetal bovine serum and by this, study the impact of ONC201 on the migration of mantle cell lymphoma cells using chemotaxis assay. Theapoptotic effect of the drug was examined by detection of activecaspase-3 and cleaved PARP proteins using western blotting. The chemotaxis assay and western blot demonstrated that ONC201 inhibited migration of the mantle cell lymphoma cell lines at the concentration-dependent manner without inducing apoptosis in the cells at the investigated time point. The expression of cyclin D1 in the cells treated with ONC201 was also investigated after incubation period of 24 hours and it was observed that ONC201 plays a role in reducing cyclin D1 expression in mantle cell lymphoma cells.

  • 15.
    Benediktsson, Elís Ingi
    University of Skövde, School of Humanities and Informatics.
    Detection and analysis of megasatellites in the human genome using in silico methods2005Independent thesis Advanced level (degree of Master (One Year))Student thesis
    Abstract [en]

    Megasatellites are polymorphic tandem repetitive sequences with repeat-units longer than or equal to 1000 base pairs. The novel algorithm Megasatfinder predicts megasatellites in the human genome. A structured method of analysing the algorithm is developed and conducted. The analysis method consists of six test scenarios. Scripts are created, which execute the algorithm using various parameter settings. Three nucleotide sequences are applied; a real sequence extracted from the human genome and two random sequences, generated using different base probabilities. Usability and accuracy are investigated, providing the user with confidence in the algorithm and its output. The results indicate that Megasatfinder is an excellent tool for the detection of megasatellites and that the generated results are highly reliable. The results of the complete analysis suggest alterations in the default parameter settings, presented as user guidelines, and state that artificially generated sequences are not applicable as models for real DNA in computational simulations.

  • 16.
    Berg Junker, Maria Constance
    University of Skövde, School of Bioscience.
    Neural correlates of romantic love and romantic attachment2018Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    In the field of neuroscience, being in love and feeling romantically attached to a partner is described as a dynamic process. Romantic love may be viewed as a motivational system, changing throughout time and place, fluctuating on the interest and motivation of the individual. Early memories and attachment towards a caregiver, lay the foundation for later attachment behavior, also known as attachment styles. In this thesis, an exploratory approach is present. The thesis aims to introduce and describe the neural correlates of romantic love and romantic attachment. Brain regions concerned with reward, emotion and thought processing, such as the reward circuitry network of the brain and the limbic system, are being investigated. So are other brain areas involved in romantic love and romantic attachment. Research findings suggest that brain areas responsible for affection, emotional control, learning, memory and social judgment are all involved in the complex processes of being in love and feeling romantically attached. These findings are represented by the involvement of the frontal lobe, cerebral cortex, limbic system, orbitofrontal cortex, and hippocampus, anterior cingulate cortex (ACC), ventral tegmental area (VTA), caudate tail, including the reward pathways of the brain. Distribution and regulation of neurotransmitters such as; vasopressin, oxytocin, dopamine, corticosterone and serotonin are all present in the state of romantic  attachment and romantic love. Overlapping evidence confirms the involvement of the reward circuitry network, together with the limbic system as crucial in the formation and maintenance of a romantic relationship.

  • 17.
    Berg, Sofia
    et al.
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre. Dept of Physics, Chemistry and Biology, Div. of Theoretical Biology, Linköping Univ., Linköping, Sweden.
    Pimenov, Aexander
    Weierstrass Inst., Berlin, Germany / Environmental Research Inst., Univ. College Cork, Cork, Ireland.
    Palmer, Catherine
    Weierstrass Inst., Berlin, Germany.
    Emmerson, Mark
    School of Biological Sciences, Queen's Univ. Belfast, Belfast, United Kingdom.
    Jonsson, Tomas
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre. Dept of Ecology, Swedish Univ. of Agricultural Sciences, Uppsala, Sweden.
    Ecological communities are vulnerable to realistic extinction sequences2015In: Oikos, ISSN 0030-1299, E-ISSN 1600-0706, Vol. 124, no 4, p. 486-496Article in journal (Refereed)
  • 18.
    Bergenius, Mikaela
    et al.
    Swedish University of Agricultural Sciences, Institute of Coastal Research, Öregrund.
    Holmgren, Noél
    University of Skövde, The Systems Biology Research Centre. University of Skövde, School of Life Sciences.
    Comparison of methods and results for the estimation of a sustainable harvest rate for the Bothnian Sea herring2012In: Report of the Benchmark Workshop on Pelagic Stocks (WKPELA 2012): 13–17 February 2012, Copenhagen, Denmark, International Council for the Exploration of the Sea (ICES) , 2012Chapter in book (Refereed)
  • 19.
    Bergkvist, Anders
    et al.
    Biochemistry and Biophysics, Department of Chemistry, Göteborg University, Sweden / Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, USA.
    Ejdebäck, Mikael
    University of Skövde, Department of Natural Sciences. Biochemistry and Biophysics, Department of Chemistry, Göteborg University, Sweden.
    Ubbink, Marcellus
    Leiden Institute of Chemistry, Leiden University, Gorlaeus Laboratories, The Netherlands.
    Karlsson, B. Göran
    Department of Molecular Biotechnology, Chalmers University of Technology, Göteborg, Sweden.
    Surface interactions in the complex between cytochrome f and the E43Q/D44N and E59K/E60Q plastocyanin double mutants as determined by (1)H-NMR chemical shift analysis2001In: Protein Science, ISSN 0961-8368, E-ISSN 1469-896X, Vol. 10, no 12, p. 2623-2626Article in journal (Refereed)
    Abstract [en]

    A combination of site-directed mutagenesis and NMR chemical shift perturbation analysis of backbone and side-chain protons has been used to characterize the transient complex of the photosynthetic redox proteins plastocyanin and cytochrome f. To elucidate the importance of charged residues on complex formation, the complex of cytochrome f and E43Q/D44N or E59K/E60Q spinach plastocyanin double mutants was studied by full analysis of the (1)H chemical shifts by use of two-dimensional homonuclear NMR spectra. Both mutants show a significant overall decrease in chemical shift perturbations compared with wild-type plastocyanin, in agreement with a large decrease in binding affinity. Qualitatively, the E43Q/D44N mutant showed a similar interaction surface as wild-type plastocyanin. The interaction surface in the E59K/E60Q mutant was distinctly different from wild type. It is concluded that all four charged residues contribute to the affinity and that residues E59 and E60 have an additional role in fine tuning the orientation of the proteins in the complex.

  • 20.
    Bergman, Jimmy
    University of Skövde, School of Life Sciences.
    Cellulär automat simulerar utbredning av Taraxacum2012Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [sv]

    I detta arbete undersöks vilken grad av inomartskonkurrens som ger upphov till ett observerat utbredningsmönster av maskrosor (Taraxacum sect. Ruderalia). Maskrosor har både fröspridning och vegetativ förökning. Studien hypotiserar att utbredningen kan beskrivas utifrån enkla regler för spridning och konkurrens. Dessa används i simuleringar med en binär cellulär automat där utveckling sker i deterministiska tidssteg. Modellen består av ett rutnät där en tom cell antingen kan förbli tom eller koloniseras, medan en upptagen cell antingen kan överleva eller dö ut. Reglerna efterliknar situationer med hög respektive låg känslighet för inomartskonkurrens. De mått på jämförelse mellan observation och simulering som används är mönstrets fraktala dimension, mönstrets tendens att aggregera och storleken på den enklaste algoritm som beskriver datan. Två olika initialvillkor används för att testa modellens robusthet. Den observerade utbredningen kontrolleras även mot slumpmässig fördelning. Resultaten visar att den observerade utbredningen är klusterartad. Simulering med en högre inomartskonkurrens beskriver utbredningen väl sett till aggregering och fraktal dimension. Lägre inomartskonkurrens beskriver dock maskrosornas verkliga utbredning sett till algoritmisk komplexitet, vilket tolkas som att individer kan leva närmare inpå varandra än vad regeln om högre inomartskonkurrens förutsätter. För vald klusterstorlek är simuleringarna ej känsliga för initialvillkoren, men då hela fördelningen av antal celler per klusterstorlek i stickprov på ett tidssteg analyseras har initialvillkoren fakstiskt betydelse. Sett till fördelningen av cell per klusterstorlek liknar ingen simulering den observerade utbredningen. Därmed kan modellen tänkas inrymma den vegetativa förökningen medan fröspridningen, som är stokastisk, ej inryms på samma vis.

  • 21.
    Bergström, Lena
    et al.
    Swedish University of Agricultural Sciences, Department of Aquatic Resources, Öregrund, Sweden.
    Blenckner, Thorsten
    Stockholm Recilience Centre, Stockholm University, Stockholm, Sweden.
    Frelat, Romain
    University of Hamburg, Institute of Hydrobiology and Fishery Science, Hamburg, Germany.
    Grimvall, Anders
    Swedish Institute for the Marine Environment, Gothenburg, Sweden.
    Haapasaari, Päivi
    University of Helsinki, Department of Environmental Sciences, Helsinki, Finland.
    Haas, Bianca
    University of Hamburg, Institute of Hydrobiology and Fishery Science, Hamburg Germany.
    Heikinheimo, Outi
    Natural Resources Institute Finland, Helsinki, Finland.
    Jernberg, Susanna
    Finnish Environment Institute, Marine Research Centre, Helsinki, Finland.
    Large, Scott
    ICES, Copenhagen, Denmark.
    Lindegren, Martin
    Centre for Ocean Life, DTU-Aqua, Charlottenlund, Denmark.
    Levin, Phil
    Northwest Fisheries Science Center, Seattle, USA.
    Lehikoinen, Annukka
    Helsinki University, Kotka Maritime Research Centre, Kotka, Finland.
    Möllmann, Christian
    University of Hamburg, Institute of Hydrobiology and Fishery Science, Hamburg, Germany.
    Nordström, Marie
    Åbo Akademi University, Environmental and Marine Biology, Åbo, Finland.
    Norrström, Niclas
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre.
    Otto, Saskia
    University of Hamburg, Institute of Hydrobiology and Fishery Science, Hamburg, Germany.
    Peltonen, Heikki
    Marine Research Centre, Finnish Environment Institute, Helsinki, Finland.
    Précuchét, Laurence
    Centre for Ocean Life, DTU-Aqua, Charlottenlund, Denmark.
    Putnis, Ivars
    Institute of Food Safety, Animal Health and Environment BIOR, Fish Resources Research Department, Riga, Latvia.
    Romakkaniemi, Atso
    Natural Resources Institute Finland, Oulun yliopisto, Finland.
    Suikkanen, Sanna
    Finnish Environment Institute, Marine Research Centre, Helsinki, Finland.
    Torres, Marian
    Swedish University of Agricultural Sciences, Department of Aquatic Resources, Öregrund, Sweden.
    Uusitalo, Laura
    Finnish Environment Institute, Marine Research Centre, Helsinki, Finland.
    Weigel, Benjamin
    Åbo Akademi University, Environmental and Marine Biology, Åbo, Finland.
    Wesslander, Karin
    Swedish Meteorological and Hydrological Institute, Marine Environment, Västra Frölunda, Sweden.
    Zagrodzka, Zuzanna
    University of Hamburg, Institute of Hydrobiology and Fishery Science, Hamburg, Germany.
    Interim Report of the ICES/HELCOM Working Group on Integrated Assessments of the Baltic Sea (WGIAB): 18-22 April 2016 Helsinki, Finland2016Report (Other academic)
    Abstract [en]

    The ICES/HELCOM Working Group on Integrated Assessments of the Baltic Sea (WGIAB) meeting was held in Helsinki (Finland), 18-22 April 2016. The meeting was attended by 26 participants from five countries and chaired by Laura Uusitalo, Fin-land, Saskia Otto, Germany, Martin Lindegren, Denmark, and Lena Bergström, Swe-den. This was the first year of the new three-year Terms of Reference (ToR) for WGIAB. The main working activities in 2016 were to A) develop the trait-based ap-proach of understanding the ecosystem function, and B) explore the social-ecological system, including indicator development, revising the conceptual model, and devel-oping case studies. As a primary outcome of the ToR A, we built on our previous work on integrated ecosystem assessments (IEAs) in the Baltic Sea, but extended it beyond considering changes in abundances of a few dominant species, to accounting for community-wide changes in a number of key traits across multiple trophic levels. These traits represent various ecosystem functions upon which we derive important ecosystem services. By investigating temporal changes in the community weighted mean traits of phyto-plankton, zooplankton, zoobenthos, and fish, we demonstrated whether trait reor-ganizations at the level of entire communities occurred in the Central Baltic Sea as a result of the 1980s regime shift. Using in total 29 traits combined for all groups we found indications of two breakpoints across all four taxonomic groups over the last decades, i.e. one around 1990 and one around 2000. Further work will focus on ex-ploring the nature of the changes in trait composition and on standardizing the num-ber of traits and data types (i.e. binary, continuous or categorical) across taxonomic group.In addition, we collected data on key functional groups and abiotic variables in all main sub-basins of the Baltic Sea, setting the stage for a cross-regional comparison of temporal patterns and trends in lower trophic level in the face of recent develop-ments in climate-related drivers.With reference to Tor B, to explore how social indicators could be used in parallel with biological indicators in an integrated assessment framework, we developed a conceptual model of interrelationships between ecosystem and society. We used the model as a basis for mapping factors to be accounted for in the ecosystem-based management using the Baltic salmon and clupeid species as case studies. The models depict 1) the structure of the foodweb relevant to the target species, 2) the key com-munity level and population traits that contribute to the state of the species, 3) main pressures affecting the foodweb and their effects on the species, 4) key management measures, and 5) benefits that the species can produce for society.To support the development of Ecosystem Overview the group members evaluated the probability of occurrence and the magnitude of the effect of 15 pressures occur-ring in the Baltic Sea. The top five pressures identified were input of nutrients, in-creased temperature, decreased salinity, input of hazardous substances, and input or spread of non-indigenous species.The work will continue intersessionally and the next meeting of WGIAB is planned to be held in Lisbon, Portugal, back-to-back with WGCOMEDA and WGEAWESS.

  • 22.
    Bertilsson, Ann
    et al.
    University of Skövde, The Systems Biology Research Centre. University of Skövde, School of Life Sciences.
    Jonsson, Annie
    University of Skövde, The Systems Biology Research Centre. University of Skövde, School of Life Sciences.
    Inventeringsmetodik med undervattensvideokamera för studier av stormusslors förekomst och tätheter vid vägbroar2012Report (Other academic)
  • 23.
    Bjerenius, Sara
    University of Skövde, School of Bioscience.
    RANKING AV EKOSYSTEMTJÄNSTER KOPPLADE TILL URBANA TRÄD: En avgränsad metodstudie i Skövde2019Independent thesis Basic level (degree of Bachelor), 20 credits / 30 HE creditsStudent thesis
    Abstract [sv]

    Människan är beroende av de ekosystemtjänster som naturen bidrar med, i staden är människan inte alltid medveten om dessa ekosystemtjänster och kan lätt förbise dessa. Träden i städerna förser stadsborna med fler ekosystemtjänster än de är medvetna om. Ekosystemtjänster som temperaturreglering och dagvattenhantering kan bli kostsamma att återskapa om alla naturliga element som bidrar med dessa helt gratis är borta. För att inte missa värdefulla naturmiljöer och därmed förlora pengar i planerad exploatering har ett verktyg för att ranka ekosystemtjänster kopplade till urbana träd tagits fram. För att på ett tydligt sätt kunna peka ut olika ekosystemtjänster i staden har en värderingsmatris för ranking av dessa skapats. Rankingvärdet en ekosystemtjänst inom ett område fått kan därpå multipliceras med egen inputdata, en egen värdering av ekosystemtjänsten. Resultatet av sammanställningen visas i form av kartbilder med graderade polygoner för att synliggöra vart ekosystemtjänsten finns i störst redundans. Så vitt författaren känner till, finns det ingen annan typ av kartläggning som kombinerar möjligheten med litteraturbaserad värdering och egen åsikt. Verktyget kan användas i två delar, den litteraturbaserade värderingsmatrisen kan användas enskilt och genererar ett resultat om vart det finns högst värde för ekosystemtjänster, eller gemensamt med egen input kan ett resultat visas i GIS. Metoden är unik och kan förhoppningsvis avvärja konflikter i t ex. planarbeten då ett visst område kan bli extra viktigt, även om olika ekosystemtjänster fått högst värde av de som använder verktyget. Olika åsikter om ekosystemtjänsters värdekan då ändå generera samma resultat.

  • 24.
    Blomstrand, Johanna
    University of Skövde, School of Life Sciences.
    Studie av kantzoner i Valleområdet och Varaslätten: Inventering av invertebrater, träd, mossor och lavar2013Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    Ecotones are areas where different ecosystems meet, and they vary in sharpness and range. The areas provide a great biological diversity since they are a mixture of the meeting areas and provide special microclimate. The biological diversity is affected by the width, length and structure of the ecotone and they have a biological significance in that they provide habitat, protection and food to many species. To demonstrate where in the landscape there are ecotones the tool GIS can be used. In this work GIS have been used to define which areas the work is concentrated on and to randomize out points for inventory in the ecotones in these areas. Inventory of the ecotones was made with the help of twenty 5x2 meters big inventory boxes, ten in the Valle area and ten on the Vara flat. Invertebrates, trees, mosses and lichens where inventoried in the boxes. The aim of this work was to see how the biological diversity in ecotones between forest and open land differ between the Valle area and the Vara flat. A study was also made to see whether the cardinal direction the ecotones lie in have an impact on the invertebrate fauna or not. None of the tests made showed any statistically significant difference between the Valle area and the Vara flat. Nor was there any statistically significant difference in invertebrate fauna depending on cardinal direction of the ecotone. Nevertheless, there are indications that the areas differ in invertebrate fauna and number of tree individuals. 

  • 25.
    Borghate, Vedant Subhash
    University of Skövde, School of Bioscience.
    Functional analysis of an arsB gene (gene-4251) presumably involved in accumulation of arsenics in Lysinibacillus sphaericus2017Independent thesis Advanced level (degree of Master (One Year)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Many regions of the world are facing the problem with arsenic toxicity. Arsenic contamination has become a considerable threat to the environment triggering various big health issues for every life in that contaminated environment. Lysinibacillus sphaericus (B1-CDA) is an arsenic tolerant strain of bacteria that has been reported and characterized before by the researchers of the University of Skövde, Sweden. The bacteria were found to contain many arsenic responsive genes such as arsB, arsC, and arsR which are responsible for arsenic tolerance in the bacterium. The main focus of the current study was to characterize one of the arsB genes (gene-4251) of Lysinibacillus sphaericus B1-CDA by in silico and in vitro analyses in order to determine the molecular function of this gene. The in silico studies conducted by using the Iterative Threading Assembly and Refinement (I-TASSER) server predicted the tertiary structure of the ArsB protein and suggested that this protein is an intrinsic component of the membrane which primarily helps in the binding of metal ions and liberation of metabolic energy. To validate this predictive results, several in vitro experiments were performed. For complementation studies, the arsB gene was cloned from L. sphaericus B1-CDA and transferred to an arsB knock-out mutant of Escherichia coli JW3469-1. Both, the transgenic and mutant strains were grown under the arsenic stress of 50 mM for 96 hrs followed by measuring their growth and arsenic tolerance after every 24 hrs. Statistical analysis confirmed that there was a significant difference in growth between the transgenic and the mutant E. coli strains. The ICP-MS (Inductive Coupled Plasma-Mass Spectroscopy) analysis revealed that after 24 hrs of culture, the arsenic content in the cell-free broth of transgenic strain was reduced from 50 mM to 9.10 mM (81.8%), whereas the reduction in arsenic content by the mutant strain was from 50 mM to 9.80 mM (80.2%). These results suggest that the arsB gene is partly involved in the accumulation of arsenic inside the cells and this feature could be used for a large scale removal of arsenic from the contaminated environment.

  • 26.
    Borgmästars, Emmy
    University of Skövde, School of Bioscience.
    Functional analysis of circulating microRNAs in pancreatic cancer2018Independent thesis Advanced level (degree of Master (One Year)), 20 credits / 30 HE creditsStudent thesis
    The full text will be freely available from 2020-01-30 12:27
  • 27.
    Borgmästars, Emmy
    et al.
    Department of Surgical and Perioperative Sciences, Umeå University, Umeå, Sweden.
    de Weerd, Hendrik Arnold
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre. Department of Physics, Chemistry and Biology, Bioinformatics, Linköping University, Linköping, Sweden.
    Lubovac-Pilav, Zelmina
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre.
    Sund, Malin
    Department of Surgical and Perioperative Sciences, Umeå University, Umeå, Sweden.
    miRFA: an automated pipeline for microRNA functional analysis with correlation support from TCGA and TCPA expression data in pancreatic cancer2019In: BMC Bioinformatics, ISSN 1471-2105, E-ISSN 1471-2105, Vol. 20, no 1, p. 1-17, article id 393Article in journal (Refereed)
    Abstract [en]

    BACKGROUND: MicroRNAs (miRNAs) are small RNAs that regulate gene expression at a post-transcriptional level and are emerging as potentially important biomarkers for various disease states, including pancreatic cancer. In silico-based functional analysis of miRNAs usually consists of miRNA target prediction and functional enrichment analysis of miRNA targets. Since miRNA target prediction methods generate a large number of false positive target genes, further validation to narrow down interesting candidate miRNA targets is needed. One commonly used method correlates miRNA and mRNA expression to assess the regulatory effect of a particular miRNA. The aim of this study was to build a bioinformatics pipeline in R for miRNA functional analysis including correlation analyses between miRNA expression levels and its targets on mRNA and protein expression levels available from the cancer genome atlas (TCGA) and the cancer proteome atlas (TCPA). TCGA-derived expression data of specific mature miRNA isoforms from pancreatic cancer tissue was used.

    RESULTS: Fifteen circulating miRNAs with significantly altered expression levels detected in pancreatic cancer patients were queried separately in the pipeline. The pipeline generated predicted miRNA target genes, enriched gene ontology (GO) terms and Kyoto encyclopedia of genes and genomes (KEGG) pathways. Predicted miRNA targets were evaluated by correlation analyses between each miRNA and its predicted targets. MiRNA functional analysis in combination with Kaplan-Meier survival analysis suggest that hsa-miR-885-5p could act as a tumor suppressor and should be validated as a potential prognostic biomarker in pancreatic cancer.

    CONCLUSIONS: Our miRNA functional analysis (miRFA) pipeline can serve as a valuable tool in biomarker discovery involving mature miRNAs associated with pancreatic cancer and could be developed to cover additional cancer types. Results for all mature miRNAs in TCGA pancreatic adenocarcinoma dataset can be studied and downloaded through a shiny web application at https://emmbor.shinyapps.io/mirfa/ .

  • 28.
    Borgström, Juliana
    University of Skövde, School of Bioscience.
    Cyclical Women: Menstrual Cycle Effects on Mood and Neuro-Cognitive Performance2019Independent thesis Basic level (degree of Bachelor), 15 credits / 22,5 HE creditsStudent thesis
    Abstract [en]

    During roughly forty years of a woman’s life-span, the fertile female human body prepares itself monthly for the possibility of pregnancy. Science has shown that the fluctuation of the sex steroids progesterone and estrogen have a crucial role in the female body's physiology, determining the menstrual cycle and its general phases. This biological dance of hormones governing the cycle influences a lot of physical, mental and cognitive aspects of life for a fertile ovulating woman. Although the question of whether these changes also affect women's cognitive performance is still unclear, some evidence has been gathered that could bring us closer to answers. Recent research findings show that this hormonal interplay might have a significant role in cognitive and psychological development - modulating brain activity, cognitive performance, higher cognition, emotional status, sensory processing, appetite and more. This thesis aims to uncover to what extent the menstrual cycle affects brain functions, neurobiology, mood, well-being and cognitive performance in menstruating cisgender women.

  • 29.
    Borrvall, Charlotta
    et al.
    Linköping University.
    Ebenman, Bo
    Linköping University.
    Jonsson, Tomas
    Linköping University.
    Biodiversity lessens the risk of cascading extinction in model food webs2000In: Ecology Letters, ISSN 1461-023X, E-ISSN 1461-0248, Vol. 3, p. 131-136Article in journal (Refereed)
  • 30.
    Budnjo, Almir
    University of Skövde, School of Bioscience.
    Gene expression of MAP2K1 and Cyclin D1 in BDII rat model of Endometrial cancer2016Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    Endometrial adenocarcinoma (EAC) is the most frequently diagnosed gynecological cancer of the female genital tract in the Western world. Research studies in EC is difficult to conduct on human tumor samples due to the complex nature of tumor arousal and genetic heterogeneousness in the human population. Therefore, inbred animal models can be promising tools to use in EC research due to similar histopathology and pathogenesis as humans. Studies performed on MAP2K1 and CCND1 has shown that their altered expression play a crucial role in carcinogenesis. CCND1 has been demonstrated to have oncogenic properties when overexpressed in human neoplasias.

    The aim of this study is to investigate gene expression levels of MAP2K1 and CCND1 in BDII rat model of endometrial adenocarcinoma cells. Quantitative real-time PCR was used to analyze expression levels of MAP2K1 and CCND1 genes in BDII/Han rat model of endometrial cancer cells using TaqMan approach. The differences in gene expression levels of MAP2K1 and CCND1 between pathologically EAC malignant and nonmalignant cells showed an upregulation of MAP2K1 and CCND1 in EAC malignant cells. The analyzed data presented observable mean differences between MAP2K1 and CCND1 in several endometrial cell lines that were examined.

    Although no statistical significance was reached, an alteration in gene expression levels in malignant and nonmalignant endometrial cells could be observed. Furthermore, this present study shows observable upregulation of MAP2K1 and CCND1 in endometrial carcinoma cells vs. nonmalignant endometrium cells and encourages further investigation of the role of CCND1 and MAP2K genes in endometrial carcinogenesis.

  • 31.
    Burnet, Phil W. J.
    et al.
    Department of Psychiatry, University of Oxford, Warneford Hospital.
    Eastwood, Sharon L.
    Department of Psychiatry, University of Oxford, Warneford Hospital.
    Bristow, Greg C.
    Department of Psychiatry, University of Oxford, Warneford Hospital.
    Godlewska, Beata R.
    Department of Psychiatry, University of Oxford, Warneford Hospital.
    Sikka, Pilleriin
    Department of Psychiatry, University of Oxford, Warneford Hospital.
    Walker, Mary
    Department of Psychiatry, University of Oxford, Warneford Hospital.
    Harrison, Paul J.
    Department of Psychiatry, University of Oxford, Warneford Hospital.
    D-amino acid oxidase activity and expression are increased in schizophrenia2008In: Molecular Psychiatry, ISSN 1359-4184, E-ISSN 1476-5578, Vol. 13, no 7, p. 658-660Article in journal (Refereed)
  • 32.
    Byström Mollstedt, Hannes
    University of Skövde, School of Bioscience.
    Laken i vänern – Populationsutveckling och potentiella påverkansfaktorer: Jämförande analyser av material från perioden 1973-20182019Independent thesis Basic level (degree of Bachelor), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    The burbot (Lota lota, Linnaeus 1758) is a benthic and predatory cod-relative that only occurs in fresh- and brackish water around the northern hemisphere. It has long been a common catch in Swedish lakes and rivers, but the species has seen a decline by over 20% since the mid 1980’s. This led to the burbot being red listed as nearly threatened (NT) in 2010. A decline of this magnitude might be alarming, the burbot is mostly declining in smaller lakes and rivers in southern Sweden and it’s still showing significant numbers in larger lakes such as Vänern – Sweden’s largest lake. Although recent monitoring of the burbot shows an erratic population that’s declining over several years, only to bounce back a couple of years later. This peculiar pattern made me interested in the historical aspects of the burbot population and its potential influencing factors in lake Vänern.

    In this study I compare data from the oldest known gillnet sampling done in lake Vänern that also contain burbot with more contemporary samplings (2010, 2011, 2012, 2015 and 2018).

    I manage to show that the number of large burbot caught were in line later years, but I also manage to show a decline by over 80% in the number of middle-sized burbot between 1973 and the later years. Furthermore, I produced results showing that the burbot seems to be aggregating deeper in later years compared to 1973.

    Finally, I correlate the population changes to environmental data and get statistically significant correlations showing that the declining numbers of fish and their decent into deeper areas of the lake are connected to the rising water temperatures.

    This result is in line with ecological studies that describes the burbot as cold-water dependent with a preferred temperature of around 10 – 14 °C. This study suggests that the burbot is affected by rising average water temperatures caused by climate change.

  • 33.
    Candelli, Tito
    University of Skövde, School of Life Sciences.
    NOVEL APPROACH TO STORAGE AND STORTING OF NEXT GENERATION SEQUENCING DATA FOR THE PURPOSE OF FUNCTIONAL ANNOTATION TRANSFER2012Independent thesis Advanced level (degree of Master (One Year)), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    The problem of functional annotation of novel sequences has been a sigfinicant issue for many laboratories that decided to apply next generation sequencing techniques to less studied species. In particular experiments such as transcriptome analysis heavily suer from this problem due to the impossibility of ascribing their results in a relevant biological context. Several tools have been proposed to solve this problem through homology annotation transfer. The principle behind this strategy is that homologous genes share common functions in dierent organisms, and therefore annotations are transferable between these genes. Commonly, BLAST reports are used to identify a suitable homologousgene in a well annotated species and the annotation is then transferred fromthe homologue to the novel sequence. Not all homologues, however, possess valid functional annotations. The aim of this project was to devise an algorithm to process BLAST reports and provide a criterion to discriminate between homologues with a biologically informative and uninformative annotation, respectively. In addition, all data obtained from the BLAST report isto be stored in a relational database for ease of consultation and visualization. In order to test the solidity of the system, we utilized 750 novel sequences obtained through application of next generation sequencing techniques to Avena sativa samples. This species particularly suits our needs as it represents the typical target for homology annotation transfer: lack of a reference genome and diculty in attributing functional annotation. The system was able to perform all the required tasks. Comparisons between best hits asdetermined by BLAST and best hits as determined by the algorithm showed a significant increase in the biological significance of the results when thealgorithm sorting system was applied.

  • 34.
    Carlsson, Veronica
    University of Skövde, School of Bioscience.
    Emotional attention: A cognitive neuroscience perspective2018Independent thesis Basic level (degree of Bachelor), 15 credits / 22,5 HE creditsStudent thesis
    Abstract [en]

    Attention is a cognitive mechanism that guides our perception in order to prioritize the limited resources to the most relevant information while ignoring distracting information. Attention can be voluntarily deployed to stimuli during tasks or goals, or the features of the stimulus can capture our attention either by being salient or being emotionally induced. Emotions affect multiple different cognitive processes such as attention because emotional stimuli can be relevant for defending or sustain life. This relationship between attention and emotion indicates that there should be interactive but distinct networks between these cognitive mechanisms as well as a modulative effect on perceptional and attentional systems. Emotions were in general demonstrating a facilitation affect on attentional and saccadic processes as well as broadening or narrowing the scope of attention. The reason behind emotions impact on attention was proposed to be for eliciting a change in the application of resources in order to solve the limited capacity problem and possibly to protect and sustain life. Inconsistent findings as well as limitations for emotional attention studies are discussed.

  • 35.
    Carrelli, Tove
    University of Skövde, School of Life Sciences.
    FÖRSTUDIE OM RESTAURERING AV VÄNGA MOSSE2012Independent thesis Advanced level (degree of Master (One Year)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Vänga bog is one of the six large peat bogs in the Borås municipality which all have high biodiversity. All of these bogs are threatened by encroachment of shrubs and trees. This report presents a study of how the shrubs and trees are invading Vänga bog, and what the possible causes might be.

    A comparison of vegetation via five aerial photos over Vänga bog from 1955, 1964, 1983, 1996 and 2007, was conducted using ArcGIS. Aerial photos are made up of pixels and the method used was to dived the pixels in two values (open ground and shrubs-trees) and then to calculate how the area of shrubs and trees has changed over time. The analysis shows that there was an increase in growth of 43.5% from 1955 to 2007 and that the annual growth varied considerably between the different periods.

    Four factors were examined to determine the possible cause of such changes, namely, temperature, precipitation, atmospheric nitrogen (nitrate and ammonium) and sulphur deposition. The analysis contained within this report shows that temperature, precipitation and nitrogen deposits have a positive correlation to the growth of shrubs and trees. However, sulphur deposition exhibited the strongest correlation, indicating an inhibiting effect on growth of shrubs and trees during the end of the last century. These are new results when sulphur deposition was assumed to be a potential cause of growth of shrubs and trees on bogs in southern Sweden.

  • 36.
    Chaudhari, Aditi
    et al.
    Wallenberg Laboratory, Department of Molecular and Clinical Medicine, University of Gothenburg, Sweden.
    Krumlinde, Daniel
    Wallenberg Laboratory, Department of Molecular and Clinical Medicine, University of Gothenburg, Sweden / Scientific Solutions, Stockholm, Sweden.
    Lundqvist, Annika
    Wallenberg Laboratory, Department of Molecular and Clinical Medicine, University of Gothenburg, Sweden.
    Akyurek, Levent M
    Department of Medical Chemistry and Cell Biology, University of Gothenburg, Sweden.
    Bandaru, Sashidhar
    Department of Medical Chemistry and Cell Biology, University of Gothenburg, Sweden.
    Skalen, Kristina
    Wallenberg Laboratory, Department of Molecular and Clinical Medicine, University of Gothenburg, Sweden.
    Stahlman, Marcus
    Wallenberg Laboratory, Department of Molecular and Clinical Medicine, University of Gothenburg, Sweden.
    Boren, Jan
    Wallenberg Laboratory, Department of Molecular and Clinical Medicine, University of Gothenburg, Sweden.
    Wettergren, Yvonne
    Department of Surgery, University of Gothenburg, Sweden.
    Ejeskär, Katarina
    University of Skövde, The Systems Biology Research Centre. University of Skövde, School of Health and Education. Department of Medical and Clinical Genetics, University of Gothenburg, Sweden.
    Sopasakis, Victoria Rotter
    Wallenberg Laboratory, Department of Molecular and Clinical Medicine, University of Gothenburg, Sweden.
    p110 alpha Hot Spot Mutations E545K and H1047R Exert Metabolic Reprogramming Independently of p110 alpha Kinase Activity2015In: Molecular and Cellular Biology, ISSN 0270-7306, Vol. 35, no 19, p. 3258-3273Article in journal (Refereed)
    Abstract [en]

    The phosphatidylinositol-4,5-bisphosphate 3-kinase (PI3K) catalytic subunit p110α is the most frequently mutated kinase in human cancer, and the hot spot mutations E542K, E545K, and H1047R are the most common mutations in p110α. Very little is known about the metabolic consequences of the hot spot mutations of p110α in vivo. In this study, we used adenoviral gene transfer in mice to investigate the effects of the E545K and H1047R mutations on hepatic and whole-body glucose metabolism. We show that hepatic expression of these hot spot mutations results in rapid hepatic steatosis, paradoxically accompanied by increased glucose tolerance, and marked glycogen accumulation. In contrast, wild-type p110α expression does not lead to hepatic accumulation of lipids or glycogen despite similar degrees of upregulated glycolysis and expression of lipogenic genes. The reprogrammed metabolism of the E545K and H1047R p110α mutants was surprisingly not dependent on altered p110α lipid kinase activity.

  • 37.
    Chawade, Aakash
    et al.
    Department of Cell and Molecular Biology, Göteborg University, Box 462, 403 20 Göteborg, Sweden.
    Bräutigam, Marcus
    Department of Cell and Molecular Biology, Göteborg University, Box 462, 403 20 Göteborg, Sweden.
    Lindlöf, Angelica
    University of Skövde, School of Humanities and Informatics.
    Olsson, Olof
    Department of Cell and Molecular Biology, Göteborg University, Box 462, 403 20 Göteborg, Sweden.
    Olsson, Björn
    University of Skövde, School of Humanities and Informatics.
    Putative cold acclimation pathways in Arabidopsis thaliana identified by a combined analysis of mRNA co-expression patterns, promoter motifs and transcription factors2007In: BMC Genomics, ISSN 1471-2164, E-ISSN 1471-2164, Vol. 8, p. 304-Article in journal (Refereed)
    Abstract [en]

    Background

    With the advent of microarray technology, it has become feasible to identify virtually all genes in an organism that are induced by developmental or environmental changes. However, relying solely on gene expression data may be of limited value if the aim is to infer the underlying genetic networks. Development of computational methods to combine microarray data with other information sources is therefore necessary. Here we describe one such method.

    Results

    By means of our method, previously published Arabidopsis microarray data from cold acclimated plants at six different time points, promoter motif sequence data extracted from ~24,000 Arabidopsis promoters and known transcription factor binding sites were combined to construct a putative genetic regulatory interaction network. The inferred network includes both previously characterised and hitherto un-described regulatory interactions between transcription factor (TF) genes and genes that encode other TFs or other proteins. Part of the obtained transcription factor regulatory network is presented here. More detailed information is available in the additional files.

    Conclusion

    The rule-based method described here can be used to infer genetic networks by combining data from microarrays, promoter sequences and known promoter binding sites. This method should in principle be applicable to any biological system. We tested the method on the cold acclimation process in Arabidopsis and could identify a more complex putative genetic regulatory network than previously described. However, it should be noted that information on specific binding sites for individual TFs were in most cases not available. Thus, gene targets for the entire TF gene families were predicted. In addition, the networks were built solely by a bioinformatics approach and experimental verifications will be necessary for their final validation. On the other hand, since our method highlights putative novel interactions, more directed experiments could now be performed.

  • 38.
    Chowdhury, Manjushree
    et al.
    Institute of Environmental Science, University of Rajshahi, Rajshahi, Bangladesh.
    Mostafa, M. G.
    Institute of Environmental Science, University of Rajshahi, Rajshahi, Bangladesh.
    Biswas, Tapan Kumar
    Department of Chemistry, University of Rajshahi, Rajshahi, Bangladesh.
    Mandal, Abul
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre.
    Saha, Ananda Kumar
    Department of Zoology, University of Rajshahi, Rajshahi, Bangladesh.
    Characterization of the effluents from leather processing industries2015In: Environmental Processes, ISSN 2198-7491, Vol. 2, no 1, p. 173-187Article in journal (Refereed)
  • 39.
    Cinarli, Pembe
    University of Skövde, School of Bioscience.
    Strategy to tag Actin II in Plasmodium berghei2018Independent thesis Advanced level (degree of Master (One Year)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Malaria is a disease that is caused by parasite called Plasmodium spp. and trasmitted by female Anopheles mosquitoes to the host. The disease has great impact around the world and there are half a million deaths and several hundred million infections every year. Studies revealed that there are two actin isoforms in the parasite, actin I and actin II. Absence of actin II has severe effect on the development of the parasite in the mosquito but the molecular function is still unknown. Identification of interacting proteins is of great importance to understand further the function of the protein. To achieve this goal actin II has to be enriched and this required a tagged version of the protein. In this project purification of the protein was to be achieved through biotinylation. In this method the protein of interest is biotinylated by BirA ligase in the cell and is then purified by , streptavidin. The project involved transfection of vector for Plasmodium berghei, containing the BirA gene and a stage-specific promoter (cdpk4). The construct was integrated in the chromosomal locus Sil6 and introduced to wild-type and actin II knock out parasites. Genotyping by PCR revealed integration of the insert in wild type parasites and phenotypic anaylsis showed no difference between BirA wild type and wild type control parasites. The expression of the BirA ligase in the parasite was investigated with Western blot but no signal was detected.

  • 40.
    Cohen, Joel
    et al.
    The Rockefeller University and Columbia University, New York, USA.
    Jonsson, Tomas
    The Rockefeller University, New York, USA.
    Carpenter, Stephen R.
    Center for Limnology, University of Wisconsin, Madison, USA.
    Ecological community description using the food web, species abundance, and body size2003In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 100, no 4, p. 1781-1786Article in journal (Refereed)
  • 41.
    Curtsdotter, Alva
    et al.
    University of Skövde, School of Bioscience. Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden / Department of Environmental Sciences, Emory University, Atlanta, GA, Georgia, United States.
    Banks, H. Thomas
    Center for Research in Scientific Computation, North Carolina State University, Raleigh, NC, United States.
    Banks, John E.
    Undergraduate Research Opportunities Center (UROC), California State University, Monterey Bay, Seaside, CA, United States.
    Jonsson, Mattias
    Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Jonsson, Tomas
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre. Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden .
    Laubmeier, Amanda N.
    Center for Research in Scientific Computation, North Carolina State University, Raleigh, NC, United States.
    Traugott, Michael
    Mountain Agriculture Research Unit, Institute of Ecology, University of Innsbruck, Innsbruck, Austria.
    Bommarco, Riccardo
    Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Ecosystem function in predator-prey food webs: confronting dynamic models with empirical data2019In: Journal of Animal Ecology, ISSN 0021-8790, E-ISSN 1365-2656, Vol. 88, no 2, p. 196-210Article in journal (Refereed)
    Abstract [en]

    Most ecosystem functions and related services involve species interactions across trophic levels, for example, pollination and biological pest control. Despite this, our understanding of ecosystem function in multitrophic communities is poor, and research has been limited to either manipulation in small communities or statistical descriptions in larger ones. Recent advances in food web ecology may allow us to overcome the trade-off between mechanistic insight and ecological realism. Molecular tools now simplify the detection of feeding interactions, and trait-based approaches allow the application of dynamic food web models to real ecosystems. We performed the first test of an allometric food web model's ability to replicate temporally nonaggregated abundance data from the field and to provide mechanistic insight into the function of predation. We aimed to reproduce and explore the drivers of the population dynamics of the aphid herbivore Rhopalosiphum padi observed in ten Swedish barley fields. We used a dynamic food web model, taking observed interactions and abundances of predators and alternative prey as input data, allowing us to examine the role of predation in aphid population control. The inverse problem methods were used for simultaneous model fit optimization and model parameterization. The model captured >70% of the variation in aphid abundance in five of ten fields, supporting the model-embodied hypothesis that body size can be an important determinant of predation in the arthropod community. We further demonstrate how in-depth model analysis can disentangle the likely drivers of function, such as the community's abundance and trait composition. Analysing the variability in model performance revealed knowledge gaps, such as the source of episodic aphid mortality, and general method development needs that, if addressed, would further increase model success and enable stronger inference about ecosystem function. The results demonstrate that confronting dynamic food web models with abundance data from the field is a viable approach to evaluate ecological theory and to aid our understanding of function in real ecosystems. However, to realize the full potential of food web models, in ecosystem function research and beyond, trait-based parameterization must be refined and extended to include more traits than body size. © 2018 The Authors. Journal of Animal Ecology © 2018 British Ecological Society

  • 42.
    Dahl-Halvarsson, Martin
    et al.
    University of Gothenburg, Gothenburg, Sweden.
    Olive, Montse
    Institut Investigació Biomèdica de Bellvitge – Hospital de Bellvitge, Hospitalet de Llobregat, Barcelona, Spain.
    Pokrzywa, Malgorzata
    University of Gothenburg, Gothenburg, Sweden.
    Ejeskär, Katarina
    University of Skövde, School of Health and Education. University of Skövde, Health and Education.
    Palmer, Ruth H.
    University of Gothenburg, Gothenburg, Sweden.
    Uv, Anne Elisabeth
    University of Gothenburg, Gothenburg, Sweden.
    Tajsharghi, Homa
    University of Skövde, School of Health and Education. University of Skövde, Health and Education.
    Drosophila model of myosin myopathy rescued by overexpression of a TRIM-protein family member2018In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 115, no 28, p. E6566-E6575Article in journal (Refereed)
    Abstract [en]

    Myosin is a molecular motor indispensable for body movement and heart contractility. Apart from pure cardiomyopathy, mutations in MYH7 encoding slow/β-cardiac myosin heavy chain also cause skeletal muscle disease with or without cardiac involvement. Mutations within the α-helical rod domain of MYH7are mainly associated with Laing distal myopathy. To investigate the mechanisms underlying the pathology of the recurrent causative MYH7 mutation (K1729del), we have developed a Drosophila melanogaster model of Laing distal myopathy by genomic engineering of the Drosophila Mhc locus. Homozygous MhcK1728del animals die during larval/pupal stages, and both homozygous and heterozygous larvae display reduced muscle function. Flies expressing only MhcK1728del in indirect flight and jump muscles, and heterozygous MhcK1728del animals, were flightless, with reduced movement and decreased lifespan. Sarcomeres of MhcK1728del mutant indirect flight muscles and larval body wall muscles were disrupted with clearly disorganized muscle filaments. Homozygous MhcK1728del larvae also demonstrated structural and functional impairments in heart muscle, which were not observed in heterozygous animals, indicating a dose-dependent effect of the mutated allele. The impaired jump and flight ability and the myopathy of indirect flight and leg muscles associated with MhcK1728del were fully suppressed by expression of Abba/Thin, an E3-ligase that is essential for maintaining sarcomere integrity. This model of Laing distal myopathy in Drosophila recapitulates certain morphological phenotypic features seen in Laing distal myopathy patients with the recurrent K1729del mutation. Our observations that Abba/Thin modulates these phenotypes suggest that manipulation of Abba/Thin activity levels may be beneficial in Laing distal myopathy.

  • 43.
    Das Burman, Anindita
    University of Skövde, School of Life Sciences.
    TGF-β (BETA) AND PERIOSTIN MODULATE EACH OTHER’S EXPRESSION IN BOTH BREAST STROMA AND TUMOR CELLS2013Independent thesis Advanced level (degree of Master (One Year)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Breast cancer is the most common cancer in female population worldwide. In addition to mutations, the breast tumor microenvironment especially the tumor cell - stroma interactions through extracellular matrix components and multiple growth factors have been shown to promote tumor progression. Among those, increases in both TGF-β (transforming growth factor beta) activities and periostin expression were associated with tumor cell survival, proliferation and metastasis. TGF-β role in breast cancer progression including its ability to promote periostin expression has been extensively studied. In contrast, the role of periostin in cancer progression remains to be fully understood. Thus, the present study aimed to determine whether TGF-β and periostin have effect on each other’s expressions in breast tumor and stroma cells using in vitro cell models. Through Western blot analyses and ELISAs, the periostin and TGF-β expressions of both stroma and tumor cells were analyzed following TGF-β and periostin treatments, respectively. The results indicate that TGF-β treatments led to significant increase in periostin expression in fibroblasts (p<0.05). In addition, periostin was differentially expressed by human breast cancer cells following TGF-β1 treatment. The TGF-β activities involved activation of pSMAD2 in both L929 fibroblasts and MCF10A mammary cells. Taken together, all experimental data indicate that within the breast tumor TGF-β and periostin likely participate in a regulation loop. Whether this putative regulation loop is critical to metastasis remains to be determined. Should periostin play a critical role in breast cancer progression, it could become a specific target in the preventive and/or therapeutic development of breast cancer patients.

  • 44.
    Dave, Vivek Priy
    et al.
    Technical University of Denmark, Lyngby, Denmark.
    Ngo, Tien Anh
    Technical University of Denmark, Lyngby, Denmark.
    Pernestig, Anna-Karin
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre.
    Tilevik, Diana
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre.
    Kanit, Krishna
    Technical University of Denmark, Lyngby, Denmark.
    Nguyen, Trieu
    Technical University of Denmark, Lyngby, Denmark.
    Wolff, Anders
    Technical University of Denmark, Lyngby, Denmark.
    Bang, Dang Duong
    Technical University of Denmark, Lyngby, Denmark.
    MicroRNA amplification and detection technologies: opportunities and challenges for point of care diagnostics2018In: Laboratory Investigation, ISSN 0023-6837, E-ISSN 1530-0307, Vol. 99, no 4, p. 452-469Article, review/survey (Refereed)
    Abstract [en]

    The volume of point of care (POC) testing continues to grow steadily due to the increased availability of easy-to-use devices, thus making it possible to deliver less costly care closer to the patient site in a shorter time relative to the central laboratory services. A novel class of molecules called microRNAs have recently gained attention in healthcare management for their potential as biomarkers for human diseases. The increasing interest of miRNAs in clinical practice has led to an unmet need for assays that can rapidly and accurately measure miRNAs at the POC. However, the most widely used methods for analyzing miRNAs, including Northern blot-based platforms, in situ hybridization, reverse transcription qPCR, microarray, and next-generation sequencing, are still far from being used as ideal POC diagnostic tools, due to considerable time, expertize required for sample preparation, and in terms of miniaturizations making them suitable platforms for centralized labs. In this review, we highlight various existing and upcoming technologies for miRNA amplification and detection with a particular emphasis on the POC testing industries. The review summarizes different miRNA targets and signals amplification-based assays, from conventional methods to alternative technologies, such as isothermal amplification, paper-based, oligonucleotide-templated reaction, nanobead-based, electrochemical signaling-based, and microfluidic chip-based strategies. Based on critical analysis of these technologies, the possibilities and feasibilities for further development of POC testing for miRNA diagnostics are addressed and discussed.

  • 45.
    Deo, Ameya
    University of Skövde, School of Life Sciences.
    Normalization of microRNA expression levels in Quantitative RT-PCR arrays2010Independent thesis Advanced level (degree of Master (One Year)), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    Background: Real-time quantitative Reverse Transcriptase Polymerase Chain Reaction (qRT-PCR) is recently used for characterization and expression analysis of miRNAs. The data from such experiments need effective analysis methods to produce reliable and high-quality data. For the miRNA prostate cancer qRT-PCR data used in this study, standard housekeeping normalization method fails due to non-stability of endogenous controls used. Therefore, identifying appropriate normalization method(s) for data analysis based on other data driven principles is an important aspect of this study.

    Results: In this study, different normalization methods were tested, which are available in the R packages Affy and qpcrNorm for normalization of the raw data. These methods reduce the technical variation and represent robust alternatives to the standard housekeeping normalization method. The performance of different normalization methods was evaluated statistically and compared against each other as well as with the standard housekeeping normalization method. The results suggest that qpcrNorm Quantile normalization method performs best for all methods tested.

    Conclusions: The qpcrNorm Quantile normalization method outperforms the other normalization methods and standard housekeeping normalization method, thus proving the hypothesis of the study. The data driven methods used in this study can be applied as standard procedures in cases where endogenous controls are not stable.

  • 46.
    Deo, Ameya
    et al.
    University of Skövde, The Systems Biology Research Centre. University of Skövde, School of Life Sciences.
    Carlsson, Jessica
    University of Skövde, The Systems Biology Research Centre. University of Skövde, School of Life Sciences.
    Lindlof, Angelica
    University of Skövde, The Systems Biology Research Centre. University of Skövde, School of Life Sciences.
    HOW TO CHOOSE A NORMALIZATION STRATEGY FOR MIRNA QUANTITATIVE REAL-TIME (QPCR) ARRAYS2011In: Journal of Bioinformatics and Computational Biology, ISSN 0219-7200, E-ISSN 1757-6334, Vol. 9, no 6, p. 795-812Article in journal (Refereed)
    Abstract [en]

    Low-density arrays for quantitative real-time PCR (qPCR) are increasingly being used as an experimental technique for miRNA expression profiling. As with gene expression profiling using microarrays, data from such experiments needs effective analysis methods to produce reliable and high-quality results. In the pre-processing of the data, one crucial analysis step is normalization, which aims to reduce measurement errors and technical variability among arrays that might have arisen during the execution of the experiments. However, there are currently a number of different approaches to choose among and an unsuitable applied method may induce misleading effects, which could affect the subsequent analysis steps and thereby any conclusions drawn from the results. The choice of normalization method is hence an important issue to consider. In this study we present the comparison of a number of data-driven normalization methods for TaqMan low-density arrays for qPCR and different descriptive statistical techniques that can facilitate the choice of normalization method. The performance of the normalization methods was assessed and compared against each other as well as against standard normalization using endogenous controls. The results clearly show that the data-driven methods reduce variation and represent robust alternatives to using endogenous controls.

  • 47.
    Derveni, Eleni
    University of Skövde, School of Bioscience.
    Isolaion and characteization of an arsC generesponsible (gene ID: 2889) for arsenicsequestration in Lysinibacillus sphaericus2018Independent thesis Advanced level (degree of Master (One Year)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Many inhabited regions in the world, especially in the South‐East Asia, are suffering from heavy metalpollution in the soil, the ground water and in the corps. During the previous decades chemical methodswere being used to collect the pollutants from the environment, especially the arsenic, but during the lastyears bioremediation has gained ground, using microorganisms. Lysinibacillus sphaericus is one of thenumerous bacterial species that can be used for this purpose. It is a Gram+ bacterium that contains all theimportant genes for arsenic uptake and accumulation inside the cells. One of these genes it the arsenicreductase, arsC (gene ID: 2889). The aim of this study was to characterize thestructure of the ArsC proteinin order to determine the function of the gene. The prediction of the structure was conducted by usingthe online server I‐TASSER, which proposed a 3D model for the protein and predicted its role as anarsenate reductase. For verification of its function numerous laboratory techniques were used. The genewas isolated by PCR amplification using custom primers designed just for this project. The next step wasthe cloning of the gene into the pGEMT‐Easy vector and transformation of a mutant arsC‐ strain of E. coliOP50 with this vector containing the insert. After the transformation, the transformed colonies wereselected based on blue‐white screening and exposed to LB medium containing 50 mM sodium arsenate(As5+). The results obtained so far were not concluding, as no bacterial growth was observed in presenceof arsenate.

  • 48.
    Desale, Prithviraj
    et al.
    Dr. D. Y. Patil Biotechnology and Bioinformatics Institute, India.
    Kashyap, Deboleena
    Dr. D. Y. Patil Biotechnology and Bioinformatics Institute, India.
    Nawani, Neelu
    Dr. D. Y. Patil Biotechnology and Bioinformatics Institute, India.
    Nahar, Noor
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre.
    Rahman, Aminur
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre.
    Kapadnis, Balasaheb
    University of Pune, India.
    Mandal, Abul
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre.
    Biosorption of nickel by Lysinibacillus sp. BA2 native to bauxite mine2014In: Ecotoxicology and Environmental Safety, ISSN 0147-6513, E-ISSN 1090-2414, Vol. 107, p. 260-268Article in journal (Refereed)
    Abstract [en]

    The current scenario of environmental pollution urges the need for an effective solution for toxic heavy metal removal from industrial wastewater. Bioremediation is the most cost effective process employed by the use of microbes especially bacteria resistant to toxic metals. In this study, Lysinibacillus sp. BA2, a nickel tolerant strain isolated from bauxite mine was used for the biosorption of Ni(II). Lysinibacillus sp. BA2 biomass had isoelectric point (pI) of 3.3. The maximum negative zeta potential value (−39.45) was obtained at pH 6.0 which was highly favourable for Ni(II) biosorption. 238.04 mg of Ni(II) adsorbed on one gram of dead biomass and 196.32 mg adsorbed on one gram of live biomass. The adsorption of Ni(II) on biomass increased with time and attained saturation after 180 min with rapid biosorption in initial 30 min. The Langmuir and Freundlich isotherms could fit well for biosorption of Ni(II) by dead biomass while Langmuir isotherm provided a better fit for live biomass based on correlation coefficient values. The kinetic studies of Ni(II) removal, using dead and live biomass was well explained by second-order kinetic model. Ni(II) adsorption on live biomass was confirmed by SEM-EDX where cell aggregation and increasing irregularity of cell morphology was observed even though cells were in non-growing state. The FTIR analysis of biomass revealed the presence of carboxyl, hydroxyl and amino groups, which seem responsible for biosorption of Ni(II). The beads made using dead biomass of Lysinibacillus sp. BA2 could efficiently remove Ni(II) from effluent solutions. These microbial cells can substitute expensive methods for treating nickel contaminated industrial wastewaters.

  • 49.
    Dnyansagar, Rohit
    University of Skövde, School of Life Sciences.
    Investigation of phylogenetic relationships using microRNA sequences and secondary structures2010Independent thesis Advanced level (degree of Master (One Year)), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    MicroRNAs are important biomolecules for regulating biological processes. Moreover, the secondary structure of microRNA is important for its activity and has been used previously as a mean for finding unknown microRNAs. A phylogenetic study of the microRNA secondary structure reveals more information than its primary sequence, because the primary sequence can undergo mutations that give rise to different phylogenetic relationships, whereas the secondary structure is more robust against mutations and therefore sometimes  more informative.

    Here we constructed a phylogenetic tree entirely based on microRNA secondary structures using tools PHYLIP (Felsenstein, 1995) and RNAforester (Matthias Höchsmann, 2003, Hochsmann et al., 2004), and compared the overall topology and clusters with the phylogenetic tree constructed using microRNA sequence. The purpose behind this comparison was to investigate the sequence and structure similarity in phylogenetic context and also to investigate if functionally similar microRNA genes are closer in their structure-derived phylogenetic tree.

    Our phylogenetic comparison shows that the sequence similarity has hardly any effect on the structure similarity in the phylogenetic tree. MicroRNAs that have similar function are closer in the phylogenetic tree based on secondary structure than its respective sequence phylogeny. Hence, this approach can be very useful in predicting the functions of the new microRNAs whose function is yet to be known, since the function of the miRNAs heavily relies on its secondary structure.

     

  • 50.
    Donaldson, Chad
    University of Skövde, School of Bioscience.
    Analyzing Factors Influencing Reproductive Success of the Mountain Chicken: Nordens Ark Captive Breeding Program2019Independent thesis Basic level (degree of Bachelor), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Amphibians globally are declining with roughly a third facing extinction due primarily to threats linked to human impacts. One way in which this is being combated is by captive breeding programs. Nordens Ark in Sweden, in collaboration with other organizations, is attempting to breed one of the most threatened frogs for future reintroduction to the wild. The mountain chicken (Leptodactylus fallax) has unique characteristics related to its reproduction which make it challenging to breed successful offspring. Using Nordens Ark’s data on environmental conditions within breeding enclosures, this study attempts to determine which extrinsic factors are having the most influence on reproduction, in order to increase the success of the captive breeding program.

    Multiple linear regression analysis and model simplification using Stepwise regression and Akaike information criterion (AIC) were performed in order to determine which explanatory variables had the most influence in relation to foam nests.

    A reduced model with significant values for explanatory variables was deemed the best model based on the dataset. Of the 14 environmental variables tested, minimum temperature after nest construction had the most influence on foam nest length. When compared to wild habitats, temperatures within enclosures may be too high or lack seasonal cyclical patterns. Barometric pressure and humidity also had influence on foam nests, but the relationships between these environmental conditions is difficult to parse. Food supplements were also a significant factor and suggest that lack of vitamins or nutrients can have a negative effect on reproductive success. Ensuring the optimal conditions can be difficult for captive breeding programs, especially as amphibians are under-represented and face biases in conservation and research.

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