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  • 1.
    Anders, Gianluca
    University of Skövde, School of Health and Education.
    Analysis of the effects of LIN7A and LIN7C upregulation and knockdown in neuroblastoma cells2018Independent thesis Basic level (degree of Bachelor), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Background: LIN7 are a group of proteins that play a pivotal role in membrane protein localization and are thus important for cell adhesion and polarity. LIN7 proteins are shown to be important in neuroblastoma outcome, possibly through interactions with Disc-Large proteins (DLG). DLG2 has been shown to directly affect the regulation of LIN7A. Previous studies into the role of LIN7 have given conflicting results as to its nature.

    Methods: In this study we transfected LIN7A and LIN7C in SK-N-AS cells through the use of plasmids for upregulation and siRNA for knockdown of these genes. We also evaluated the expression levels of specific genes related to pathways such as PI3K, autophagy/lysosomal activity, AKT, etc., both independently and related to LIN7 expression through the R2 platform. Genes of interest were selected and then analyzed through qPCR.

    Results: Many of the genes that were significantly correlated when compared to LIN7A/C through R2 showed no significant expression correlation after experimentation. Some more functionally close genes to LIN7 were affected in a more predictable way such as CASK being upregulated after LIN7 knockdown, PTEN being downregulated upon LIN7 plasmid transfection while others such as FOXO3 also showed significant alterations.

    Conclusion: Many of the pathways discussed in this study are better studied through protein analysis due to the nature of the function of LIN7 proteins, however some downstream transcript changes were analyzed. Unexpectedly, the knockdown of both LIN7A and LIN7C displayed similar behavior to upregulation of LIN7A or LIN7C, possibly meaning that extreme expression differences have similar regulatory outcomes for some affected genes.

  • 2.
    Bergsten, Niklas
    University of Skövde, School of Life Sciences.
    PDIA3 and Prostate Cancer: Do changes in nucleotidesequence correspond tomalignancy?2012Independent thesis Advanced level (degree of Master (One Year)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    PDIA3 interacts with the lectin chaperons; calnexin and calreticulin to surveythe folding of newly synthesized glycoproteins by the addition of N-linkedglycans. PDIA3 is also involved in transcaltachia signaling cascades andimmunogenicity. The purpose was to determine if there were any changespresent in the nucleotide sequence of the Pdia3 gene. To study this, fourprostate cell lines were examined by Sanger sequencing, two malignant(LNCaP, PC3) and two normal (PNT1A, PNT2). These were to be compared tothe nucleotide sequence from nine formalin fixed paraffin-embedded (FFPE)samples of different Gleason score and the sequence from three FFPE samplesof normal prostate tissue chosen from the Örebro Radical Cohort. The obtainedsequences were then analysed with several bioinformatics tools to determine ifthere were any changes present. The nucleotide sequence obtained from thesequencing indicated that none of the cell lines expressed the most redundantisofrom; CRA_c, but instead CRA_a and CRA_b. Surprisingly, the two normalcell lines (PNT1A and PNT2) produced similar scores in BLAST search forboth the CRA_a and the CRA_b isoforms. Software analysis of the translatedsequences predicted that LNCaP expressed a membrane bound form PDIA3while PC3 expressed a cytoplasmic variant of the protein. To confirm this,another sequencing reaction was performed. The second results indicated thatall cell lines expressed the same isoform, but that the isoforms were localizedto different intracellular compartments.

  • 3.
    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.

  • 4.
    Claesson, Cim
    University of Skövde, School of Life Sciences.
    Is Multiplex Ligation-dependent Probe Amplification a good method for screening formalin fixed paraffin embedded neuroblastoma tumors?2011Independent thesis Basic level (degree of Bachelor), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Neuroblastoma is one of the most enigmatic solid tumors for scientists and pediatric oncologists. Neuroblastoma is primary a childhood form of cancer, consisting of neuroectodermal cells that originate from the neural crest and is destined for the  adrenal medulla and sympathetic nervous system. The Neuroblastoma group at The University of Gothenburg received formalin-fixed paraffin-embedded  tumor samples from Vietnam and this project was to examine if the quality of the DNA from, is good enough to run comparative genome hybridization array experiment  on by using a cheaper technique Multiplex  Ligation-dependent Probe Amplification   technique. Multiplex Ligation-dependent Probe Amplification (MRC Holland) is a multiplex PCR method that can detect abnormalities such as deletions and amplifications. By using probes consisting of one short synthetic arm with a PCR primer sequence Y at the 3´end, and one long probe with a stuffer sequence, and a PCR primer sequence X at the 5´end that can hybridize and ligate. If these probes ligate it is possible to amplify them by PCR just using specific primers for the X and Y sequences. The resulting amplification products can then be analyzed bycapillary electrophoresis. These patient that the DNA was derived from had all stage 4  neuroblastoma, and that is why they all present many aberrations. Among the fascinating data from this experiment, there are many patients with both 11q  deletions and has an extreme amplification of MYCN. In Sweden only a few cases has been discovered. In this material even though all patients are stage 4 patients, 16 have this combination.   

  • 5.
    Eduardo Venson, José
    et al.
    Institute of Informatics – INF, Universidade Federal do Rio Grande do Sul – UFRGS, Av. Bento Gonçalves, Porto Alegre, RS, Brazil / Animati - Computação aplicada à Saúde, Santa Maria, RS, Brazil.
    Bevilacqua, Fernando
    University of Skövde, School of Informatics. University of Skövde, The Informatics Research Centre. Universidade Federal da Fronteira Sul – UFFS, Chapecó, SC, Brazil.
    Onuki, Fabio
    Medvia Diagnósticos, Porto Alegre, RS, Brazil.
    Cordeiro d’Ornellas, Marcos
    Laboratory for Applied Computing – LaCA, Universidade Federal de Santa Maria – UFSM, Santa Maria, RS, Brazil.
    Anderson, Maciel
    Institute of Informatics – INF, Universidade Federal do Rio Grande do Sul – UFRGS, Av. Bento Gonçalves, Porto Alegre, RS, Brazil.
    Efficient medical image access in diagnostic environments with limited resources2016In: Research on Biomedical Engineering, ISSN 2446-4732, Vol. 32, no 4, p. 347-357Article in journal (Refereed)
    Abstract [en]

    Introduction

    A medical application running outside the workstation environment has to deal with several constraints, such as reduced available memory and low network bandwidth. The aim of this paper is to present an approach to optimize the data flow for fast image transfer and visualization on mobile devices and remote stationary devices.

    Methods

    We use a combination of client- and server-side procedures to reduce the amount of information transferred by the application. Our approach was implemented on top of a commercial PACS and evaluated through user experiments with specialists in typical diagnosis tasks. The quality of the system outcome was measured in relation to the accumulated amount of network data transference and the amount of memory used in the host device. Besides, the system's quality of use (usability) was measured through participants’ feedback.

    Results

    Contrarily to previous approaches, ours keeps the application within the memory constraints, minimizing data transferring whenever possible, allowing the application to run on a variety of devices. Moreover, it does that without sacrificing the user experience. Experimental data point that over 90% of the users did not notice any delays or degraded image quality, and when they did, they did not impact on the clinical decisions.

    Conclusion

    The combined activities and orchestration of our methods allow the image viewer to run on resource-constrained environments, such as those with low network bandwidth or little available memory. These results demonstrate the ability to explore the use of mobile devices as a support tool in the medical workflow.

  • 6.
    Enroth, Helena
    et al.
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre. Department of Clinical Microbiology, Unilabs AB, Skövde, Sweden.
    Retz, Karolina
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre. Department of Clinical Microbiology, Unilabs AB, Skövde, Sweden.
    Andersson, Sofie
    Department of Clinical Microbiology, Unilabs AB, Skövde, Sweden.
    Andersson, Carl
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre. Department of Clinical Microbiology, Unilabs AB, Skövde, Sweden.
    Svensson, Kristina
    Department of Clinical Microbiology, Unilabs AB, Skövde, Sweden.
    Ljungström, Lars
    Department of Infectious Diseases, Skaraborg Hospital, Skövde, Sweden.
    Tilevik, Diana
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre.
    Pernestig, Anna-Karin
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre.
    Evaluation of QuickFISH and maldi Sepsityper for identification of bacteria in bloodstream infection2019In: Infectious Diseases, ISSN 2374-4235, E-ISSN 2374-4243, Vol. 51, no 4, p. 249-258Article in journal (Refereed)
    Abstract [en]

    Background: Early detection of bacteria and their antibiotic susceptibility patterns are critical to guide therapeutic decision-making for optimal care of septic patients. The current gold standard, blood culturing followed by subculture on agar plates for subsequent identification, is too slow leading to excessive use of broad-spectrum antibiotic with harmful consequences for the patient and, in the long run, the public health. The aim of the present study was to assess the performance of two commercial assays, QuickFISH® (OpGen) and Maldi Sepsityper™ (Bruker Daltonics) for early and accurate identification of microorganisms directly from positive blood cultures.

    Materials and methods: During two substudies of positive blood cultures, the two commercial assays were assessed against the routine method used at the clinical microbiology laboratory, Unilabs AB, at Skaraborg Hospital, Sweden.

    Results: The Maldi Sepsityper™ assay enabled earlier microorganism identification. Using the cut-off for definite species identification according to the reference method (>2.0), sufficiently accurate species identification was achieved, but only among Gram-negative bacteria. The QuickFISH®assay was time-saving and showed high concordance with the reference method, 94.8% (95% CI 88.4–98.3), when the causative agent was covered by the QuickFISH® assay.

    Conclusions: The use of the commercial assays may shorten the time to identification of causative agents in bloodstream infections and can be a good complement to the current clinical routine diagnostics. Nevertheless, the performance of the commercial assays is considerably affected by the characteristics of the causative agents.

  • 7.
    Etezadi Amoli, Mahmood Reza
    University of Skövde, School of Life Sciences.
    Evaluation of different modifications of TRIzol Reagent method for total RNA isolation from bull spermatozoa2013Independent thesis Advanced level (degree of Master (One Year)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Transcriptional profile of spermatozoa can be used to assess male fertility; differences in spermatozoa attributes require adjustment of protocols for RNA isolation. Ten RNA precipitation modifications of heated TRIzol protocol were applied to total RNA extraction form bull spermatozoa. Motile spermatozoa were isolated from cryopreserved semen straws prepared from an ejaculate of a fertile bull. To evaluate total RNA purity and quantity, Ribogreen RNA detection system and Nanodrop 2000 were used. In RiboGreen assay, a consistent standard curve was not obtained, thus the measurements were ignored. Total RNA purity and concentrations also were assessed using Nanodrop. The A260/280 ratio obtained from Nanodrop showed a good range in the isolated total RNA samples (1.9±0.4). However, all RNA samples presented very low A260/230 ratios (≥1.26). It might be the effect of low concentration of the isolated total RNA. Statistical analysis of total RNA concentrations showed using manufacturer standard protocol had the highest concentration yield. Using either ethanol or Isopropanol as RNA precipitant and changing the incubation temperature had not significant effect on RNA concentration yields. However incubating samples in freezer overnight lowered the total RNA concentration. Using glycogen as a RNA carrier increased the total RNA precipitation yield. In other similar studies the highest total RNA concentration was obtained by using RNA carrier. Validating these findings by qRT-PCR and Bioanalyser might be helpful to enhance the total RNA extraction yield from bull sperm as well as for subsequent genomic studies of bull fertility.

  • 8.
    Fontes, Andre
    University of Skövde, School of Health and Education. iMM, Portugal.
    Dynamics and differentiation patterns of careg-expressing ependymal cells in the spinal cord of transgenic zebrafish; the role of senescence in caudal fin regeneration2018Independent thesis Basic level (degree of Bachelor), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Spinal cord injury (SCI) is a severe CNS injury with irreversible recovery of functions in mammalian species and consequent detrimental of social and psychological condition. It accounts for major economic resources in healthcare and current therapies of engrafting transplantation of in vitro neural cultures do not lead to functional recovery. Senescence has been shown as a dormant state where cells secrete several factors into the environment before they become phagocytized and cleared. These senescence-associated secretory phenotype (SASP) factors have been shown as crucial in the development and regeneration processes, and therefore new studies are taking place to understand if inducing the cellular senescence program is therapeutically beneficial at lesion sites. Here, we analysed the regeneration of the caudal fin of the zebrafish, which is a vertebrate model capable of regenerating tissue leading to full recovery. By quantifying proportion of senescent cells through several time points of caudal fin regeneration, through SA-β-gal staining, we assessed if there are differences between normal non-injured tissue and the regenerating and full regenerated tissue. It was revealed that the number of senescent cells increase during the regeneration process, but they become effectively cleared upon the fin is almost full regenerated. Although this confirms that there is in fact a development-programmed senescence (DPS) during regeneration, the proportion of cells after regeneration was lower than the non-injured tissue, which may be interest for the study of age-related senescence.

  • 9.
    Jahic, Sani
    University of Skövde, School of Bioscience.
    Functional investigation of the potential therapeutic target gene DLG2 in an11q-deleted neuroblastoma cell line and effects of 1,25 vitamin D3 and retinoic acid combination treatments2016Independent thesis Advanced level (degree of Master (One Year)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Neuroblastoma as a pediatric tumor develops in the sympathetic nervous system. DLG2 is a gene that encodes a member of the membrane-associated guanylate kinase (MAGUK) family and it resides in the chromosome region 11q. SK-N-AS is a neuroblastoma cell line with 11q deletion and consequently only one copy of the potential tumor suppressor gene DLG2. This study investigated synergistic effect by a combination treatment with 1,25(OH)2D3 and the vitamin A metabolite, retinoic acid.  Separately, SK-N-AS cells was transfected with expression vector pcDNA3.1+‐DYK that contained the DLG2-gene, followed by monitoring cell proliferation and qPCR, investigating the expression of the genes DLG2, DLG3, DLG4, VDR and PDIA3. Simultaneously, effects of knocked-down of DLG2, by siRNA transfection was monitored.  Transfection of expression plasmid with the DLG2 gene increased significantly gene expression in SK-N-AS cells with significant inhibition of the proliferation rate. Furthermore, silencing of DLG2 gene had no effect on the cell growth as well. Slower cell growth showed in combination treatment with 1,25(OH)2D3 (1nM) and 9-cis RA after 48 hours of treatment. Down-regulated VDR and possible missing RARRES3 could be the reason why SK-N-AS cell line showed resistance to the combination treatment with vitamin metabolites. All these results raised the question if another vitamin D synthetic analog could be a better choice for the future study of SK-N-AS cells. Moreover, overexpression of NAIP, large amounts of IGF-II, or not responsive RXR-VDR heterodimer to 1,25(OH)2D3 could be a potential explanation for the SK-N-AS cell unresponsiveness to the treatment.

  • 10.
    Kralj, Andrea
    University of Skövde, School of Bioscience.
    The neurobiology underlying personality traits and conflict behavior: Examining the similarities in brain regions between agreeableness, aggression and dominating conflict style2018Independent thesis Basic level (degree of Bachelor), 15 credits / 22,5 HE creditsStudent thesis
    Abstract [en]

    Conflicts are part of our everyday life and the field of psychology describes how specific personality traits relate to specific conflict styles. However, the question remaining is why these relations exist? Recently, personality neuroscience has begun pinning down the neurobiology of personality traits, providing a deeper understanding of the human behavior. The present thesis utilizes the Five Factor Model (FFM; Costa & McCrae, 1990) of personality to investigate the neurobiology underlying the inverse relation between the specific personality trait of Agreeableness and dominating conflict style (a conflict management style characterized by aggressiveness, authoritarianism and/or need for dominance). Agreeableness overlaps both empathy and aggression which can work as each other’s opposites in explaining conflict behaviors. The goal of the thesis was to investigate whether the inverse relation between Agreeableness and dominating conflict style can be explained by brain regions. Brain regions such as the medial prefrontal cortex and regions involving anterior cingulate appear to be the most prominent neurobiology describing the relation. Serotonin is the neural substance involved in most cortical and subcortical brain structures and it also regulates the suppression of aggression, making it an important substance both within Agreeableness and the preference for dominating conflict style. The thesis will sum up with a discussion including some limitations within the research and further aspects such the consequences of the findings will be discussed.

  • 11.
    Olson, Nasrine
    et al.
    Swedish School of Library and Information Science (SSLIS), University of Borås, Borås, Sweden.
    Bae, Juhee
    University of Skövde, School of Informatics. University of Skövde, The Informatics Research Centre.
    Biosensors-Publication Trends and Knowledge Domain Visualization2019In: Sensors, ISSN 1424-8220, E-ISSN 1424-8220, Vol. 19, no 11, article id 2615Article in journal (Refereed)
    Abstract [en]

    The number of scholarly publications on the topic of biosensors has increased rapidly; as a result, it is no longer easy to build an informed overview of the developments solely by manual means. Furthermore, with many new research results being continually published, it is useful to form an up-to-date understanding of the recent trends or emergent directions in the field. This paper utilizes bibliometric methods to provide an overview of the developments in the topic based on scholarly publications. The results indicate an increasing interest in the topic of biosensor(s) with newly emerging sub-topics. The US is identified as the country with highest total contribution to this area, but as a collective, EU countries top the list of total contributions. An examination of trends over the years indicates that in recent years, China-based authors have been more productive in this area. If research contribution per capita is considered, Singapore takes the top position, followed by Sweden, Switzerland and Denmark. While the number of publications on biosensors seems to have declined in recent years in the PubMed database, this is not the case in the Web of Science database. However, there remains an indication that the rate of growth in the more recent years is slowing. This paper also presents a comparison of the developments in publications on biosensors with the full set of publications in two of the main journals in the field. In more recent publications, synthetic biology, smartphone, fluorescent biosensor, and point-of-care testing are among the terms that have received more attention. The study also identifies the top authors and journals in the field, and concludes with a summary and suggestions for follow up research.

  • 12.
    Svensson, Andreas
    University of Skövde, Health and Education.
    In vitro study of the antiproliferative properties of Digitoxin glycosides and Keytruda on BxPC-3 pancreatic cancer2019Independent thesis Basic level (degree of Bachelor), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    In the early 1900s, cancer patients were often treated by inducing a bacterial infection that stimulated an immune response which lead to a spontaneous passive cancer regression. This discovery lead to today’s modern cancer immunotherapy – an approach in which medical interventions stimulate the body’s own immune system to fight cancer cells. Digitoxin glycosides, a sodium pump inhibitor used mainly to treat heart-related diseases has been reviewed in clinical trials for its anti-tumor like properties. Moreover, A new drug to aid in the war against progressive inoperable metastatic cancers was approved 2014 by FDA. Keytruda was the first monoclonal non-chimeric human IgG4 antibody drug to restore the immune response to activated T-cells by interfering with the tumours’ programmed death ligands (PD-L1) and (PD-L2). Cancer cells express an increased level of reactive oxygen species (ROS) that promote cancer cell proliferation and development. However, in too low or high levels, ROS promote oxidative damage in favour of anti-tumor properties. This study evaluated Digitoxin glycosides and Keytruda as potential anti-tumor therapies and any eventual synergic effects. Digitoxin, as mono-therapy, promoted apoptotic behaviour in pancreatic cancer cells when administrated in the mid- to high-end dosage range. Respectively, this study suggests a combination-therapy using a sub-physiological Keytruda-concentration together with a relatively high Digitoxin concentration produce a significant antiproliferative effect.

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