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  • 1.
    Bergman, Monica
    et al.
    University of Skövde, School of Bioscience. University of Skövde, Systems Biology Research Environment. University of Turku, Finland.
    MacGregor, Oskar
    University of Skövde, School of Bioscience. University of Skövde, Systems Biology Research Environment.
    Olkoniemi, Henri
    University Turku, Finland.
    Owczarski, Wojciech
    University of Gdańsk, Poland.
    Revonsuo, Antti
    University of Skövde, School of Bioscience. University of Skövde, Systems Biology Research Environment.
    Valli, Katja
    University of Skövde, School of Bioscience. University of Skövde, Systems Biology Research Environment. University of Turku, Finland.
    The Holocaust as a Lifelong Nightmare: Posttraumatic Symptoms and Dream Content in Polish Auschwitz Survivors 30 Years After World War II2020In: American Journal of Psychology, ISSN 0002-9556, E-ISSN 1939-8298, Vol. 133, no 2, p. 143-167Article in journal (Refereed)
    Abstract [en]

    Posttraumatic symptoms, including nightmares, are more prevalent in World War II survivors than in the general population, but how war experiences have affected subsequent dream content in specific survivor populations remains less explored. In the present study, we used self -reports collected in 1973 from Polish Auschwitz survivors (N = 150; 45 women) to investigate the prevalence of posttraumatic symptoms, classified according to the DSM-5 diagnostic criteria for posttraumatic stress disorder (PTSD). Furthermore, we classified main themes, central emotions, and threatening events in the dreams (N = 632) of the survivors, comparing dreams recalled from before, during, and after the war. Of the respondents, 12.7% described experiencing all diagnostic criteria for PTSD. War-related themes were less common in dreams dreamt before than during the war but were most common after the war. Themes related to family and freedom were most likely to appear in dreams dreamt during than before or after the war. The most often occurring emotion was fear, and dreams from after the war were likely to contain more negative and less positive emotions than dreams dreamt during the war. The likelihoods of reporting threatening events and threats involving aggression were higher in dreams dreamt during than before the war and in dreams dreamt after than during the war. In conclusion, PTSD symptoms were common in Polish Auschwitz survivors 30 years after World War II, and the themes, emotions, and threatening events in their dreams seem to reflect lifelong posttraumatic dreaming. We interpret the results as lending support for the threat simulation theory of dreaming.

  • 2.
    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, Systems Biology Research Environment. 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

  • 3.
    de Weerd, Hendrik A.
    et al.
    University of Skövde, School of Bioscience. University of Skövde, Systems Biology Research Environment. Department of Physics, Chemistry and Biology, Linköping University, Linköping, Sweden.
    Badam, Tejaswi V. S.
    University of Skövde, School of Bioscience. University of Skövde, Systems Biology Research Environment. Department of Physics, Chemistry and Biology, Linköping University, Linköping, Sweden.
    Martínez-Enguita, David
    Department of Physics, Chemistry and Biology, Linköping University, Linköping, Sweden.
    Åkesson, Julia
    University of Skövde, School of Bioscience. University of Skövde, Systems Biology Research Environment. Department of Physics, Chemistry and Biology, Linköping University, Linköping, Sweden.
    Muthas, Daniel
    Translational Science & Experimental Medicine, Early Respiratory, Inflammation and Autoimmunity, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden.
    Gustafsson, Mika
    Department of Physics, Chemistry and Biology, Linköping University, Linköping, Sweden.
    Lubovac-Pilav, Zelmina
    University of Skövde, School of Bioscience. University of Skövde, Systems Biology Research Environment.
    MODifieR: an ensemble R package for inference of disease modules from transcriptomics networks2020In: Bioinformatics, ISSN 1367-4803, E-ISSN 1367-4811Article in journal (Refereed)
    Abstract [en]

    MOTIVATION: Complex diseases are due to the dense interactions of many disease-associated factors that dysregulate genes that in turn form so-called disease modules, which have shown to be a powerful concept for understanding pathological mechanisms. There exist many disease module inference methods that rely on somewhat different assumptions, but there is still no gold standard or best performing method. Hence, there is a need for combining these methods to generate robust disease modules.

    RESULTS: We developed MODule IdentiFIER (MODifieR), an ensemble R package of nine disease module inference methods from transcriptomics networks. MODifieR uses standardized input and output allowing the possibility to combine individual modules generated from these methods into more robust disease-specific modules, contributing to a better understanding of complex diseases.

    AVAILABILITY: MODifieR is available under the GNU GPL license and can be freely downloaded from https://gitlab.com/Gustafsson-lab/MODifieR and as a Docker image from https://hub.docker.com/r/ddeweerd/modifier.

    SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

  • 4.
    Ekelund Ugge, Gustaf Magnus Oskar
    et al.
    University of Skövde, School of Bioscience. University of Skövde, Systems Biology Research Environment. Department of Biology, Lund University, Sweden.
    Jonsson, Annie
    University of Skövde, School of Bioscience. University of Skövde, Systems Biology Research Environment.
    Olsson, Björn
    University of Skövde, School of Bioscience. University of Skövde, Systems Biology Research Environment.
    Sjöback, Robert
    TATAA Biocenter, Gothenburg, Sweden.
    Berglund, Olof
    Department of Biology, Lund University, Sweden.
    Transcriptional and biochemical biomarker responses in a freshwater mussel (Anodonta anatina) under environmentally relevant Cu exposure2020In: Environmental Science and Pollution Research, ISSN 0944-1344, E-ISSN 1614-7499, Vol. 27, no 9, p. 9999-10010Article in journal (Refereed)
    Abstract [en]

    Molecular biomarkers, like gene transcripts or enzyme activities, are potentially powerful tools for early warning assessment of pollution. However, a thorough understanding of response and baseline variation is required to distinguish actual effects from pollution. Here, we assess the freshwater mussel Anodonta anatina as a biomarker model species for freshwater ecosystems, by testing responses of six transcriptional (cat, gst, hsp70, hsp90, mt, and sod) and two biochemical (AChE and GST) biomarkers to environmentally relevant Cu water concentrations. Mussels (n = 20), collected from a stream free from point source pollution, were exposed in the laboratory, for 96 h, to Cu treatments (< 0.2 mu g/L, 0.77 +/- 0.87 mu g/L, and 6.3 +/- 5.4 mu g/L). Gills and digestive glands were extracted and analyzed for transcriptional and biochemical responses. Biological and statistical effect sizes from Cu treatments were in general small (mean log(2) fold-change <= 0.80 and Cohen's f <= 0.69, respectively), and no significant treatment effects were observed. In contrast, four out of eight biomarkers (cat, gst, hsp70, and GST) showed a significant sex:tissue interaction, and additionally one (sod) showed significant overall effects from sex. Specifically, three markers in gills (cat, mt, GST) and one in digestive gland (AChE) displayed significant sex differences, independent of treatment. Results suggest that sex or tissue effects might obscure low-magnitude biomarker responses and potential early warnings. Thus, variation in biomarker baselines and response patterns needs to be further addressed for the future use of A. anatina as a biomarker model species.

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  • 5.
    Förster, Jona
    et al.
    University of Skövde, School of Bioscience. University of Skövde, Systems Biology Research Environment.
    Koivisto, Mika
    Department of Psychology, University of Turku, Finland / Turku Brain and Mind Centre, University of Turku, Finland.
    Revonsuo, Antti
    University of Skövde, School of Bioscience. University of Skövde, Systems Biology Research Environment. Department of Psychology, University of Turku, Finland / Turku Brain and Mind Centre, University of Turku, Finland.
    ERP and MEG correlates of visual consciousness: The second decade2020In: Consciousness and Cognition, ISSN 1053-8100, E-ISSN 1090-2376, Vol. 80, article id 102917Article in journal (Refereed)
    Abstract [en]

    The first decade of event-related potential (ERP) research had established that the most consistent correlates of the onset of visual consciousness are the early visual awareness negativity (VAN), a posterior negative component in the N2 time range, and the late positivity (LP), an anterior positive component in the P3 time range. Two earlier extensive reviews ten years ago had concluded that VAN is the earliest and most reliable correlate of visual phenomenal consciousness, whereas LP probably reflects later processes associated with reflective/access consciousness. This article provides an update to those earlier reviews. ERP and MEG studies that have appeared since 2010 and directly compared ERPs between aware and unaware conditions are reviewed, and important new developments in the field are discussed. The result corroborates VAN as the earliest and most consistent signature of visual phenomenal consciousness, and casts further doubt on LP as an ERP correlate of phenomenal consciousness. 

  • 6.
    Gerafi, Joel
    et al.
    University of Skövde, School of Bioscience. University of Skövde, Systems Biology Research Environment. Faculty of Social Sciences, Department of Psychology, University of Gothenburg, Sweden / Department of Clinical Neuroscience, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at University of Gothenburg, Sweden / The Skaraborg Institute for Research and Development, Skövde, Sweden.
    Samuelsson, Hans
    Faculty of Social Sciences, Department of Psychology, University of Gothenburg, Sweden / Department of Clinical Neuroscience, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at University of Gothenburg, Sweden.
    Viken, Jo I.
    Faculty of Social Sciences, Department of Psychology, University of Gothenburg, Sweden / Department of Clinical Neuroscience, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at University of Gothenburg, Sweden.
    Jern, Christina
    Department of Laboratory Medicine, Institute of Biomedicine, The Sahlgrenska Academy at University of Gothenburg, Sweden.
    Blomstrand, Christian
    Department of Clinical Neuroscience, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at University of Gothenburg, Sweden.
    Jood, Katarina
    Department of Clinical Neuroscience, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at University of Gothenburg, Sweden / Department of Neurology, The Sahlgrenska University Hospital, Gothenburg, Sweden.
    The presence and prediction of lateralized inattention 7 years post-stroke2020In: Acta Neurologica Scandinavica, ISSN 0001-6314, E-ISSN 1600-0404, Vol. 141, no 5, p. 423-430Article in journal (Refereed)
    Abstract [en]

    Objective: Lateralized inattention is a typical sign of neglect and related to poor functional outcome. Knowledge of the long-term course of this phenomenon is limited. The purpose of this study was to investigate presence and predictors for signs of lateralized inattention 7 years after stroke. Methods: From a cohort of acute ischemic stroke patients, aged 18-69 years (n = 297), a consecutive series of 188 survivors without recurrent stroke at follow-up 7 years later were included. Within the first week after stroke onset, stroke severity was assessed according to the Scandinavian Stroke Scale. Target omissions, asymmetry of omissions, and perceptual speed according to Star- and Letter Cancellation Tests were also assessed. Presence of lateralized inattention at the 7-year follow-up was investigated with the Star- and Letter Cancellation Tests and with the neglect item in the National Institutes of Health Stroke Scale. Results: At the follow-up, 22 (11.7%) participants had lateralized inattention and the multivariable regression showed that independent significant baseline predictors were total omissions in target cancellations (P <.001) and inferior baseline performance on visual processing speed (P =.008). Conclusion: About one of ten individuals exhibited signs of lateralized inattention 7 years after stroke. Baseline performance in perceptual processing speed and target omissions independently predicted presence of late signs of lateralized inattention. This is the first time processing speed is recognized as a significant predictor of lateralized inattention several years after the stroke incidence, indicating that the longitudinal course of processing speed following stroke is a critical subject for future research. © 2020 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd

  • 7.
    Ghosheh, Nidal
    et al.
    University of Skövde, School of Bioscience. University of Skövde, Systems Biology Research Environment.
    Küppers-Munther, Barbara
    Takara Bio Europe AB, Gothenburg, Sweden.
    Asplund, Annika
    Takara Bio Europe AB, Gothenburg, Sweden.
    Andersson, Christian X.
    Takara Bio Europe AB, Gothenburg, Sweden.
    Björquist, Petter
    VeriGraft AB, Gothenburg, Sweden.
    Andersson, Tommy B.
    Cardiovascular Renal and Metabolism, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Mölndal, Sweden / Department of Physiology and Pharmacology, Section of Pharmacogenetics, Karolinska Institutet, Stockholm, Sweden.
    Carén, Helena
    Sahlgrenska Cancer Center, Department of Pathology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Sweden.
    Simonsson, Stina
    Institute of Biomedicine, Department of Clinical Chemistry and Transfusion Medicine, Sahlgrenska Academy, University of Gothenburg, Sweden.
    Sartipy, Peter
    University of Skövde, School of Bioscience. University of Skövde, Systems Biology Research Environment. Late Stage Cardiovascular, Renal, and Metabolism, R&D BioPharmaceuticals, AstraZeneca, Mölndal, Sweden.
    Synnergren, Jane
    University of Skövde, School of Bioscience. University of Skövde, Systems Biology Research Environment.
    Human Pluripotent Stem Cell-Derived Hepatocytes Show Higher Transcriptional Correlation with Adult Liver Tissue than with Fetal Liver Tissue2020In: ACS Omega, ISSN 2470-1343, Vol. 5, no 10, p. 4816-4827Article in journal (Refereed)
    Abstract [en]

    Human pluripotent stem cell-derived hepatocytes (hPSC-HEP) display many properties of mature hepatocytes, including expression of important genes of the drug metabolizing machinery, glycogen storage, and production of multiple serum proteins. To this date, hPSC-HEP do not, however, fully recapitulate the complete functionality of in vivo mature hepatocytes. In this study, we applied versatile bioinformatic algorithms, including functional annotation and pathway enrichment analyses, transcription factor binding-site enrichment, and similarity and correlation analyses, to datasets collected from different stages during hPSC-HEP differentiation and compared these to developmental stages and tissues from fetal and adult human liver. Our results demonstrate a high level of similarity between the in vitro differentiation of hPSC-HEP and in vivo hepatogenesis. Importantly, the transcriptional correlation of hPSC-HEP with adult liver (AL) tissues was higher than with fetal liver (FL) tissues (0.83 and 0.70, respectively). Functional data revealed mature features of hPSC-HEP including cytochrome P450 enzymes activities and albumin secretion. Moreover, hPSC-HEP showed expression of many genes involved in drug absorption, distribution, metabolism, and excretion. Despite the high similarities observed, we identified differences of specific pathways and regulatory players by analyzing the gene expression between hPSC-HEP and AL. These findings will aid future intervention and improvement of in vitro hepatocyte differentiation protocol in order to generate hepatocytes displaying the complete functionality of mature hepatocytes. Finally, on the transcriptional level, our results show stronger correlation and higher similarity of hPSC-HEP to AL than to FL. In addition, potential targets for further functional improvement of hPSC-HEP were also identified. 

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  • 8.
    Irani Shemirani, Mahnaz
    et al.
    University of Skövde, School of Bioscience. University of Skövde, Systems Biology Research Environment. Göteborg Universitet.
    Tilevik, Andreas
    University of Skövde, School of Bioscience. University of Skövde, Systems Biology Research Environment.
    Tilevik, Diana
    University of Skövde, School of Bioscience. University of Skövde, Systems Biology Research Environment.
    Pernestig, Anna-Karin
    University of Skövde, School of Bioscience. University of Skövde, Systems Biology Research Environment.
    Enroth, Helena
    University of Skövde, School of Bioscience. University of Skövde, Systems Biology Research Environment. Department of Clinical Microbiology, Unilabs AB, Skövde.
    Comparison of Whole Genome Sequencing Pipelines for Analysis of Staphylococcus aureus Isolates from Sepsis Patients2019Conference paper (Refereed)
  • 9.
    Jonsson, Tomas
    et al.
    University of Skövde, School of Bioscience. University of Skövde, Systems Biology Research Environment. Department of ecology, Swedish university of agricultural sciences, Sweden / Department of physics, chemistry and biology, Division of theoretical biology, Linköping university, Sweden.
    Berg, Sofia
    University of Skövde, School of Bioscience. University of Skövde, Systems Biology Research Environment. Department of physics, chemistry and biology, Division of theoretical biology, Linköping university, Sweden.
    Säterberg, Torbjörn
    Department of physics, chemistry and biology, Division of theoretical biology, Linköping university, Sweden.
    Hauzy, Céline
    Department of physics, chemistry and biology, Division of theoretical biology, Linköping university, Sweden / UPMC, Ecologie et evolution, France INRA, USC 2031 Ecologie des populations et communautés, France.
    Ebenman, Bo
    Department of physics, chemistry and biology, Division of theoretical biology, Linköping university, Sweden.
    Rare but Important: Perturbations to Uncommon Species Can Have a Large Impact on the Structure of Ecological Communities2017In: Adaptive Food Webs: Stability and Transitions of Real and Model Ecosystems / [ed] John C. Moore, Peter C. de Ruiter, Kevin S. McCann, Volkmar Wolters, Cambridge University Press, 2017, p. 324-341Chapter in book (Refereed)
  • 10.
    Junnarkar, Manisha
    et al.
    Microbial Diversity Research Centre, Dr D Y Patil Biotechnology and Bioinformatics Institute, Dr D Y Patil Vidyapeeth, Tathawade, Maharashtra, India.
    Pawar, Sarika
    Microbial Diversity Research Centre, Dr D Y Patil Biotechnology and Bioinformatics Institute, Dr D Y Patil Vidyapeeth, Tathawade, Maharashtra, India.
    Gaikwad, Swapnil
    Microbial Diversity Research Centre, Dr D Y Patil Biotechnology and Bioinformatics Institute, Dr D Y Patil Vidyapeeth, Tathawade, Maharashtra, India.
    Mandal, Abul
    University of Skövde, School of Bioscience. University of Skövde, Systems Biology Research Environment.
    Jass, Jana
    The Life Science Centre, School of Science and Technology, Örebro University, Örebro, Sweden.
    Nawani, Neelu
    Microbial Diversity Research Centre, Dr D Y Patil Biotechnology and Bioinformatics Institute, Dr D Y Patil Vidyapeeth, Tathawade, Maharashtra, India.
    Probiotic potential of lactic acid bacteria from fresh vegetables: Application in food preservation2019In: Indian Journal of Experimental Biology, ISSN 0019-5189, E-ISSN 0975-1009, Vol. 57, p. 825-838Article in journal (Refereed)
    Abstract [en]

    Fresh vegetables are potential source of lactic acid bacteria (LAB). In the present study, LAB were isolated from the fresh vegetables from Pune region. Total 266 LAB were isolated from the edible parts of fresh vegetables viz. cauliflower, gherkins, cluster beans, fenugreek, cow pea, bitter gourd, french beans, tomato, ridged gourd, cucumber and bottle gourd. On phenotypic and molecular characterization predominant genera obtained were Lactobacillus, Enterococcus and Weissella. Twenty one isolates exhibited tolerance to bile salt, acidic pH and pancreatin. Cellular extracts of several isolates with ability to survive in artificial intestinal condition additionally showed antioxidant potential and cell free supernatants xhibited antibacterial potential against selected plant and human pathogens. Bacteriocin and bacteriocin like substances (BLS) substances secreted by these isolates can be used for food preservation.

  • 11.
    Kajonius, Petri J.
    et al.
    University of Skövde, School of Bioscience. University of Skövde, Systems Biology Research Environment. Department of Social and Behavioral Studies, University West, Sweden / Department of Psychology, University of Gothenburg, Sweden.
    Björkman, Therese
    Department of Social and Behavioral Studies, University West, Sweden.
    Individuals with dark traits have the ability but not the disposition to empathize2020In: Personality and Individual Differences, ISSN 0191-8869, E-ISSN 1873-3549, Vol. 155, article id 109716Article in journal (Refereed)
    Abstract [en]

    Empathy is fundamental to social cognition and societal values. Empathy is theorized as having both the ability as well as the disposition to imagine the content of other peoples minds. We tested whether the notorious low empathy in dark personalities (Machiavellianism, psychopathy, and narcissism; the Dark Triad) is best characterized by a lack of capacity (ability) or lack of disposition (trait). Data was collected for 278 international participants through an anonymous online survey shared on the online platform LinkedIn, consisting of trait-based Dark Triad personality (SD3) and empathy (IRI), and cognitive ability (ICAR16) and ability-based empathy (MET). Dark personality traits had no relationship with ability-based empathy, but strongly so with trait-based empathy (beta = -0.47). Instead, cognitive ability explained ability-based empathy (beta = 0.31). The finding is that dark personalities in a community sample is normally cognizant to empathize but has a low disposition to do so. This finding may help shed further light on how personality is interlinked with ability.

  • 12.
    Kallioinen, Minna
    et al.
    Department of Perioperative Services, Intensive Care and Pain Medicine, Turku University Hospital, Finland.
    Scheinin, Annalotta
    Department of Perioperative Services, Intensive Care and Pain Medicine, Turku University Hospital, Finland / Turku PET Centre, University of Turku and Turku University Hospital, Finland.
    Maksimow, Mikael
    Medicity Research Laboratory, University of Turku, Finland.
    Långsjö, Jaakko
    Turku PET Centre, University of Turku and Turku University Hospital, Finland / Department of Intensive Care, Tampere University Hospital, Finland.
    Kaisti, Kaike
    Turku PET Centre, University of Turku and Turku University Hospital, Finland / Department of Anesthesiology and Intensive Care, Oulu University Hospital, Finland.
    Takala, Riikka
    Department of Perioperative Services, Intensive Care and Pain Medicine, Turku University Hospital, Finland.
    Vahlberg, Tero
    Department of Clinical Medicine, Biostatistics, University of Turku and Turku University Hospital, Finland.
    Valli, Katja
    University of Skövde, School of Bioscience. University of Skövde, Systems Biology Research Environment. Department of Psychology and Speech-Language Pathology, and Turku Brain and Mind Centre, University of Turku, Finland.
    Salmi, Marko
    Medicity Research Laboratory, University of Turku, Finland / Institute of Biomedicine, University of Turku, Finland.
    Scheinin, Harry
    Department of Perioperative Services, Intensive Care and Pain Medicine, Turku University Hospital, Finland / Turku PET Centre, University of Turku and Turku University Hospital, Finland / Integrative Physiology and Pharmacology, Institute of Biomedicine, University of Turku, Finland.
    Maksimow, Anu
    Department of Perioperative Services, Intensive Care and Pain Medicine, Turku University Hospital, Finland.
    The influence of dexmedetomidine and propofol on circulating cytokine levels in healthy subjects2019In: BMC Anesthesiology, ISSN 1471-2253, E-ISSN 1471-2253, Vol. 19, no 1, p. 1-8, article id 222Article in journal (Refereed)
    Abstract [en]

    Background: Surgery and diseases modify inflammatory responses and the immune system. Anesthetic agents also have effects on the human immune system but the responses they induce may be altered or masked by the surgical procedures or underlying illnesses. The aim of this study was to assess how single-drug dexmedetomidine and propofol anesthesia without any surgical intervention alter acute immunological biomarkers in healthy subjects. Methods: Thirty-five healthy, young male subjects were anesthetized using increasing concentrations of dexmedetomidine (n = 18) or propofol (n = 17) until loss of responsiveness (LOR) was detected. The treatment allocation was randomized. Multi-parametric immunoassays for the detection of 48 cytokines, chemokines and growth factors were used. Concentrations were determined at baseline and at the highest drug concentration for each subject. Results: The changes in the concentration of eotaxin (decrease after dexmedetomidine) and platelet-derived growth factor (PDGF, increase after propofol) were statistically significantly different between the groups. Significant changes were detected within both groups; the concentrations of monocyte chemotactic protein 1, chemokine ligand 27 and macrophage migration inhibitory factor were lower in both groups after the drug administration. Dexmedetomidine decreased the concentration of eotaxin, interleukin-18, interleukin-2Ra, stem cell factor, stem cell growth factor and vascular endothelial growth factor, and propofol decreased significantly the levels of hepatocyte growth factor, IFN-.-induced protein 10 and monokine induced by IFN-gamma, and increased the levels of interleukin-17, interleukin-5, interleukin-7 and PDGF. Conclusions: Dexmedetomidine seemed to have an immunosuppressive effect on the immune system whereas propofol seemed to induce mixed pro- and anti-inflammatory effects on the immune system. The choice of anesthetic agent could be relevant when treating patients with compromised immunological defense mechanisms. Trial registration: Before subject enrollment, the study was registered in the European Clinical Trials database (EudraCT number 2013-001496-21, The Neural Mechanisms of Anesthesia and Human Consciousness) and in ClinicalTrials.gov (Principal Investigator: Harry Scheinin, number NCT01889004, The Neural Mechanisms of Anesthesia and Human Consciousness, Part 2, on the 23rd of June 2013).

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  • 13.
    Keane, Simon
    et al.
    University of Skövde, School of Health Sciences. University of Skövde, Digital Health Research (DHEAR).
    Améen, Sophie
    University of Skövde, School of Health Sciences. University of Skövde, Digital Health Research (DHEAR).
    Lindlöf, Angelica
    University of Skövde, School of Bioscience. University of Skövde, Systems Biology Research Environment.
    Ejeskär, Katarina
    University of Skövde, School of Health Sciences. University of Skövde, Digital Health Research (DHEAR).
    Low DLG2 gene expression, a link between 11q-deleted and MYCN-amplified neuroblastoma, causes forced cell cycle progression, and predicts poor patient survival2020In: Cell Communication and Signaling, ISSN 1478-811X, E-ISSN 1478-811X, Vol. 18, no 1, article id 65Article in journal (Refereed)
    Abstract [en]

    BACKGROUND: Neuroblastoma (NB) is a childhood neural crest tumor. There are two groups of aggressive NBs, one with MYCN amplification, and another with 11q chromosomal deletion; these chromosomal aberrations are generally mutually exclusive. The DLG2 gene resides in the 11q-deleted region, thus makes it an interesting NB candidate tumor suppressor gene. METHODS: We evaluated the association of DLG2 gene expression in NB with patient outcomes, stage and MYCN status, using online microarray data combining independent NB patient data sets. Functional studies were also conducted using NB cell models and the fruit fly. RESULTS: Using the array data we concluded that higher DLG2 expression was positively correlated to patient survival. We could also see that expression of DLG2 was inversely correlated with MYCN status and tumor stage. Cell proliferation was lowered in both 11q-normal and 11q-deleted NB cells after DLG2 over expression, and increased in 11q-normal NB cells after DLG2 silencing. Higher level of DLG2 increased the percentage of cells in the G2/M phase and decreased the percentage of cells in the G1 phase. We detected increased protein levels of Cyclin A and Cyclin B in fruit fly models either over expressing dMyc or with RNAi-silenced dmDLG, indicating that both events resulted in enhanced cell cycling. Induced MYCN expression in NB cells lowered DLG2 gene expression, which was confirmed in the fly; when dMyc was over expressed, the dmDLG protein level was lowered, indicating a link between Myc over expression and low dmDLG level. CONCLUSION: We conclude that low DLG2 expression level forces cell cycle progression, and that it predicts poor NB patient survival. The low DLG2 expression level could be caused by either MYCN-amplification or 11q-deletion. Video Abstract.

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  • 14.
    Kokkonen, Alexander
    et al.
    University of Skövde, School of Bioscience. University of Skövde, Systems Biology Research Environment. Unilabs AB.
    Tilevik, Diana
    University of Skövde, School of Bioscience. University of Skövde, Systems Biology Research Environment.
    Pernestig, Anna-Karin
    University of Skövde, School of Bioscience. University of Skövde, Systems Biology Research Environment.
    Tilevik, Andreas
    University of Skövde, School of Bioscience. University of Skövde, Systems Biology Research Environment.
    Fagerlind, Magnus
    University of Skövde, School of Bioscience. University of Skövde, Systems Biology Research Environment.
    Enroth, Helena
    University of Skövde, School of Bioscience. University of Skövde, Systems Biology Research Environment. Department of Clinical Microbiology, Unilabs AB, Skövde.
    Clinical use of 16SrRNA Ion TorrentNext-generation sequencing and bioinformatics pipeline2019Conference paper (Other academic)
  • 15.
    Leidenberger, Sonja
    et al.
    University of Skövde, School of Bioscience. University of Skövde, Systems Biology Research Environment.
    Berntsson, Ann-Charlotte
    Nordens ark.
    Niklasson, Mats
    Swedish University of Agricultural Sciences.
    Nordiskt honungsbi studeras på Nordens ark2019In: Yrfän, ISSN 2002-1151, no 3, p. 22-25Article in journal (Other (popular science, discussion, etc.))
  • 16.
    Leidenberger, Sonja
    et al.
    University of Skövde, School of Bioscience. University of Skövde, Systems Biology Research Environment.
    Boström, Sven
    Naturhistoriska riksmuseet.
    Diversitet hos hakmaskar – tarmparasiter hos gråsälar i Östersjön2019In: Fauna och flora : populär tidskrift för biologi, ISSN 0014-8903, Vol. 114, no 2, p. 35-39Article in journal (Other (popular science, discussion, etc.))
    Abstract [sv]

    Döda gråsälar i Östersjön har insamlats och undersökts genom obduktion på Naturhistoriska riksmuseet sedan 1970-talet. En relativt stor andel av de obducerade sälarna har haft sår i tarmarna,och troligen kan perforerade tarmsår vara en av orsakerna till att de har dött. Tarmsåren förorsakas av tre arter av hakmaskar i släktet Corynosoma, och dessa har blivit föremål för ingående morfologiska och ekologiska studier.

  • 17.
    Leidenberger, Sonja
    et al.
    University of Skövde, School of Bioscience. University of Skövde, Systems Biology Research Environment.
    Boström, Sven
    Swedish Museum of Natural History, Department of Zoology, Stockholm, Sweden.
    Wayland, Matthew Thomas
    University of Cambridge, United Kingdom.
    Host records and geographical distribution of Corynosoma magdaleni, C. semerme and C. strumosum (Acanthocephala: Polymorphidae)2020In: Biodiversity Data Journal, ISSN 1314-2836, E-ISSN 1314-2828, Vol. 8, article id e50500Article in journal (Refereed)
    Abstract [en]

    A literature survey was conducted to investigate the host and geographical distribution patterns of three Corynosoma species (Acanthocephala: Polymorphidae), viz. C. magdaleni, C. semerme and C. strumosum. All three species appear to be restricted to the Northern Hemisphere. Occurrence records of C. magdaleni are limited to the Northern Atlantic coasts, while C. semerme has a circumpolar distribution. The geographical range of Corynosoma strumosum encompasses the distributions of the other two species, but also extends into warmer southern regions. Some Corynosoma populations are living with their definitive hosts in very isolated locations, such as in the brackish Baltic Sea or different freshwater lakes (e.g. Lake Saimaa). All three species have a heteroxenous life cycle, comprising a peracaridan intermediate host, a fish paratenic host and a mammalian definitive host. Occasionally, an acanthocephalan may enter an accidental host, from which it is unable to complete its life cycle. The host records reported here are categorised by type, i.e. intermediate, paratenic, definitive or accidental. While most of the definitive hosts are shared amongst the three Corynosoma species, C. strumosum showed the broadest range of paratenic hosts, which reflects its more extensive geographical distribution. One aim of this study and extensive literature summary is to guide future sampling efforts therewith contribute to throw more light on the on-going species and morphotype discussion for this interesting parasite species.

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  • 18.
    Leidenberger, Sonja
    et al.
    University of Skövde, School of Bioscience. University of Skövde, Systems Biology Research Environment.
    Jonsson, Annie
    University of Skövde, School of Bioscience. University of Skövde, Systems Biology Research Environment.
    Bourlat, Sarah
    Centre for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, Bonn, Germany.
    End biodiversity loss through improved tracking of marine threatened invertebrates2019Conference paper (Refereed)
  • 19.
    Leidenberger, Sonja
    et al.
    University of Skövde, School of Bioscience. University of Skövde, Systems Biology Research Environment.
    Niklasson, Mats
    Nordens ark.
    Berntsson, AnnCharlotte
    Nordens ark.
    BIstånd till nordiska bin – en resurs för framtidens ekosystemtjänster2019In: NordBi-Aktuellt, no 1, p. 5-6Article in journal (Other (popular science, discussion, etc.))
  • 20.
    Leidenberger, Sonja
    et al.
    University of Skövde, School of Bioscience. University of Skövde, Systems Biology Research Environment.
    Norrström, Niclas
    University of Skövde, School of Bioscience. University of Skövde, Systems Biology Research Environment.
    Lägesrapport inom INTERREG-projektet: BIstånd till nordiska bin2019In: NordBi-Aktuellt, no 2, p. 5-6Article in journal (Other (popular science, discussion, etc.))
  • 21.
    Lycke, Maria
    et al.
    Department of Obstetrics and Gynecology, Institute of Clinical Science, Sahlgrenska Academy, University of Gothenburg and Region Västra Götaland, Sahlgrenska University Hospital, Gothenburg, Sweden.
    Ulfenborg, Benjamin
    University of Skövde, School of Bioscience. University of Skövde, Systems Biology Research Environment.
    Kristjansdottir, Björg
    Department of Obstetrics and Gynecology, Institute of Clinical Science, Sahlgrenska Academy, University of Gothenburg and Region Västra Götaland, Sahlgrenska University Hospital, Gothenburg, Sweden.
    Sundfeldt, Karin
    Department of Obstetrics and Gynecology, Institute of Clinical Science, Sahlgrenska Academy, University of Gothenburg and Region Västra Götaland, Sahlgrenska University Hospital, Gothenburg, Sweden.
    Increased Diagnostic Accuracy of Adnexal Tumors with A Combination of Established Algorithms and Biomarkers2020In: Journal of clinical medicine, ISSN 2077-0383, Vol. 9, no 2, article id E299Article in journal (Refereed)
    Abstract [en]

    Ovarian cancer is the most lethal gynecologic cancer. Pre-diagnostic testing lacks sensitivity and specificity, and surgery is often the only way to secure the diagnosis. Exploring new biomarkers is of great importance, but the rationale of combining validated well-established biomarkers and algorithms could be a more effective way forward. We hypothesized that we can improve differential diagnostics and reduce false positives by combining (a) risk of malignancy index (RMI) with serum HE4, (b) risk of ovarian malignancy algorithm (ROMA) with a transvaginal ultrasound score or (c) adding HE4 to CA125 in a simple algorithm. With logistic regression modeling, new algorithms were explored and validated using leave-one-out cross validation. The analyses were performed in an existing cohort prospectively collected prior to surgery, 2013-2016. A total of 445 benign tumors and 135 ovarian cancers were included. All presented models improved specificity at cut-off compared to the original algorithm, and goodness of fit was significant (p < 0.001). Our findings confirm that HE4 is a marker that improves specificity without hampering sensitivity or diagnostic accuracy in adnexal tumors. We provide in this study "easy-to-use" algorithms that could aid in the triage of women to the most appropriate level of care when presenting with an unknown ovarian cyst or suspicious ovarian cancer.

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  • 22.
    Noreika, Valdas
    et al.
    Department of Psychology, University of Cambridge, United Kingdom / Department of Psychology and Speech-Language Pathology, University of Turku, Finland.
    Windt, Jennifer M.
    Department of Philosophy, Monash University, Clayton, VIC, Australia.
    Kern, Markus
    Translational Neurotechnology Lab, University of Freiburg, Germany.
    Valli, Katja
    University of Skövde, School of Bioscience. University of Skövde, Systems Biology Research Environment. Department of Psychology and Speech-Language Pathology, University of Turku, Finland.
    Salonen, Tiina
    Department of Psychology and Speech-Language Pathology, University of Turku, Finlan.
    Parkkola, Riitta
    Department of Radiology, University and University Hospital of Turku, Finland.
    Revonsuo, Antti
    University of Skövde, School of Bioscience. University of Skövde, Systems Biology Research Environment.
    Karim, Ahmed A.
    Department of Psychiatry and Psychotherapy, University of Tübingen, Germany / Department of Psychology and Neuroscience, Jacobs University, Bremen, Germany / Department of Health Psychology and Neurorehabilitation, SRH Mobile University, Riedlingen, Germany.
    Ball, Tonio
    Translational Neurotechnology Lab, University of Freiburg, Germany.
    Lenggenhager, Bigna
    Department of Psychology, University of Zurich, Switzerland.
    Modulating dream experience: Noninvasive brain stimulation over the sensorimotor cortex reduces dream movement2020In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 10, no 1, article id 6735Article in journal (Refereed)
    Abstract [en]

    Recently, cortical correlates of specific dream contents have been reported, such as the activation of the sensorimotor cortex during dreamed hand clenching. Yet, despite a close resemblance of such activation patterns to those seen during the corresponding wakeful behaviour, the causal mechanisms underlying specific dream contents remain largely elusive. Here, we aimed to investigate the causal role of the sensorimotor cortex in generating movement and bodily sensations during REM sleep dreaming. Following bihemispheric transcranial direct current stimulation (tDCS) or sham stimulation, guided by functional mapping of the primary motor cortex, naive participants were awakened from REM sleep and responded to a questionnaire on bodily sensations in dreams. Electromyographic (EMG) and electroencephalographic (EEG) recordings were used to quantify physiological changes during the preceding REM period. We found that tDCS, compared to sham stimulation, significantly decreased reports of dream movement, especially of repetitive actions. Other types of bodily experiences, such as tactile or vestibular sensations, were not affected by tDCS, confirming the specificity of stimulation effects to movement sensations. In addition, tDCS reduced EEG interhemispheric coherence in parietal areas and affected the phasic EMG correlation between both arms. These findings show that a complex temporal reorganization of the motor network co-occurred with the reduction of dream movement, revealing a link between central and peripheral motor processes and movement sensations of the dream self. tDCS over the sensorimotor cortex interferes with dream movement during REM sleep, which is consistent with a causal contribution to dream experience and has broader implications for understanding the neural basis of self-experience in dreams. © 2020, The Author(s).

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  • 23.
    Roje, Blanka
    et al.
    Laboratory for Cancer Research, University of Split School of Medicine, Croatia.
    Elek, Anamaria
    Bioinformatics Group, Division of Molecular Biology, Department of Biology, Faculty of Science, University of Zagreb, Croatia.
    Palada, Vinko
    Department of Physiology and Pharmacology, Karolinska Institute, Solna, Sweden.
    Bom, Joana
    Instituto Gulbenkian de Ciência, Oeiras, Portugal.
    Iljazović, Aida
    Helmholtz Institute for Infection Research, Braunschweig, Germany.
    Šimić, Ana
    Laboratory for Cancer Research, University of Split School of Medicine, Croatia.
    Sušak, Lana
    Laboratory for Cancer Research, University of Split School of Medicine, Croatia.
    Vilović, Katarina
    Department of Pathology, University Hospital Split, Croatia.
    Strowig, Till
    Helmholtz Institute for Infection Research, Braunschweig, Germany.
    Vlahoviček, Kristian
    University of Skövde, School of Bioscience. University of Skövde, Systems Biology Research Environment. Bioinformatics Group, Division of Molecular Biology, Department of Biology, Faculty of Science, University of Zagreb, Croatia.
    Terzić, Janos
    Laboratory for Cancer Research, University of Split School of Medicine, Croatia.
    Microbiota alters urinary bladder weight and gene expression2020In: Microorganisms, E-ISSN 2076-2607, Vol. 8, no 3, article id 421Article in journal (Refereed)
    Abstract [en]

    We studied the effect of microbiota on the transcriptome and weight of the urinary bladder by comparing germ-free (GF) and specific pathogen-free (SPF) housed mice. In total, 97 genes were differently expressed (fold change > ±2; false discovery rate (FDR) p-value < 0.01) between the groups, including genes regulating circadian rhythm (Per1, Per2 and Per3), extracellular matrix (Spo1, Spon2), and neuromuscular synaptic transmission (Slc18a3, Slc5a7, Chrnb4, Chrna3, Snap25). The highest increase in expression was observed for immunoglobulin genes (Igkv1-122, Igkv4-68) of unknown function, but surprisingly the absence of microbiota did not change the expression of the genes responsible for recognizing microbes and their products. We found that urinary bladder weight was approximately 25% lighter in GF mice (p = 0.09 for males, p = 0.005 for females) and in mice treated with broad spectrum of antibiotics (p = 0.0002). In conclusion, our data indicate that microbiota is an important determinant of urinary bladder physiology controlling its gene expression and size.

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  • 24.
    Sandström, Alfred
    et al.
    Department of Aquatic Resources, Institute of Freshwater Research, Swedish University of Agricultural Sciences (SLU), Drottningholm, Sweden.
    Norrgård, Johnny
    Lake Vättern Society of Water Conservation, Jönköping, Sweden.
    Axenrot, Thomas
    Department of Aquatic Resources, Institute of Freshwater Research, Swedish University of Agricultural Sciences (SLU), Drottningholm, Sweden.
    Setzer, Malin
    University of Skövde, School of Bioscience. University of Skövde, Systems Biology Research Environment. Lake Vättern Society of Water Conservation, Jönköping, Sweden.
    Jonsson, Tomas
    University of Skövde, School of Bioscience. University of Skövde, Systems Biology Research Environment. Department of Ecology, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden.
    Getting Choosy About Whitefish in Lake Vättern: Using Participatory Approaches to Improve Fisheries Selectivity2020In: Collaborative Research in Fisheries / [ed] Peter Holm, Maria Hadjimichael, Sebastian Linke, Steven Mackinson, Cham: Springer, 2020, p. 43-59Chapter in book (Refereed)
    Abstract [en]

    Our case study was channeled through a comanagement group and initiated by fishermen. The aim was to develop the selectivity of the fisheries in Lake Vättern through a collaboration of fishermen, regional managers, and scientists. The case study was planned collectively within the fisheries co-management group and through workshops with participating fishermen. Fishermen were given special permits to test various strategies adapted to their own experiences and the properties of their local fishing grounds. First, the population structure of the focal species, whitefish, was investigated in a joint study utilizing fishermen’s experiential knowledge and genetic analyses of whitefish. The results showed that the population is divided into at least two unique stocks that ideally should be managed separately. Second, the results from studies on by-catch in different areas, seasons, and gears indicated a substantial potential to increase the selectivity in this fishery, particularly by targeting whitefish aggregations adjacent to spawning areas. Our study highlights the potential of the participatory approach when facilitating solutions to problems related to small-scale fisheries management. Nevertheless, we also identify some factors that might jeopardize the long-term success and dissemination of results from this case study. The recent discovery of high levels of dioxins and dioxin-like PCBs in muscle tissue of whitefish might make it harder for fishermen to sell their catch. Moreover, since the comanagement group only has an advisory function, the Swedish national authority needs to take the initiative and first implement the suggested changes in management.

  • 25.
    Shamloo-Dashtpagerdi, Roohollah
    et al.
    Department of Agriculture and Natural Resources, Higher Education Center of Eghlid, Eghlid, Iran.
    Lindlöf, Angelica
    University of Skövde, School of Bioscience. University of Skövde, Systems Biology Research Environment.
    Aliakbari, Massume
    Department of Crop Production and Plant Breeding, Shiraz University, Shiraz, Iran.
    Pirasteh-Anosheh, Hadi
    National Salinity Research Center, Agricultural Research, Education and Extension Organization, Yazd, Iran.
    Plausible association between drought stress tolerance of barley (Hordeum vulgare L.) and programmed cell death via MC1 and TSN1 genes2020In: Physiologia Plantarum: An International Journal for Plant Biology, ISSN 0031-9317, E-ISSN 1399-3054Article in journal (Refereed)
    Abstract [en]

    Studying the drought-responsive transcriptome is of high interest as it can serve as a blueprint for stress adaptation strategies. Despite extensive studies in this area, there are still many details to be uncovered, such as the importance of each gene involved in the stress response as well as the relationship between these genes and the physiochemical processes governing stress tolerance. This study was designed to address such important details and to gain insights into molecular responses of barley (Hordeum vulgare L.) to drought stress. To that, we combined RNA-seq data analysis with field and greenhouse drought experiments in a systems biology approach. RNA-sequence analysis identified a total of 665 differentially expressed genes (DEGs) belonging to diverse functional categories. A gene network was derived from the DEGs, which comprised of a total of 131 nodes and 257 edges. Gene network topology analysis highlighted two programmed cell death (PCD) modulating genes, MC1 (metacaspase 1) and TSN1 (Tudor-SN 1), as important (hub) genes in the predicted network. Based on the field trial, a drought-tolerant and a drought-susceptible barley genotype was identified from eight tested cultivars. Identified genotypes exhibited different physiochemical characteristics, including proline content, chlorophyll concentration, percentage of electrolyte leakage and malondialdehyde content as well as expression profiles of MC1 and TSN1 genes. Machine learning and correspondence analysis revealed a significant relationship between drought tolerance and measured characteristics in the context of PCD. Our study provides new insights which bridge barley drought tolerance to PCD through MC1 and TSN1 pathway.

  • 26.
    Shi, Lei
    et al.
    Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.
    Derouiche, Abderahmane
    Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.
    Pandit, Santosh
    Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.
    Rahimi, Shadi
    Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.
    Kalantari, Aida
    Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.
    Futo, Momir
    Laboratory of Evolutionary Genetics, Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia.
    Ravikumar, Vaishnavi
    The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark.
    Jers, Carsten
    The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark.
    Mokkapati, Venkata R.S.S.
    Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.
    Vlahoviček, Kristian
    University of Skövde, School of Bioscience. University of Skövde, Systems Biology Research Environment. Bioinformatics group, Division of Molecular Biology, Department of Biology, Faculty of Science, University of Zagreb, Croatia.
    Mijakovic, Ivan
    Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden / The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark.
    Evolutionary Analysis of the Bacillus subtilis Genome Reveals New Genes Involved in Sporulation2020In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719Article in journal (Refereed)
    Abstract [en]

    Bacilli can form dormant, highly resistant, and metabolically inactive spores to cope with extreme environmental challenges. In this study, we examined the evolutionary age of Bacillus subtilis sporulation genes using the approach known as genomic phylostratigraphy. We found that B. subtilis sporulation genes cluster in several groups that emerged at distant evolutionary time-points, suggesting that the sporulation process underwent several stages of expansion. Next, we asked whether such evolutionary stratification of the genome could be used to predict involvement in sporulation of presently uncharacterized genes (y-genes). We individually inactivated a representative sample of uncharacterized genes that arose during the same evolutionary periods as the known sporulation genes and tested the resulting strains for sporulation phenotypes. Sporulation was significantly affected in 16 out of 37 (43%) tested strains. In addition to expanding the knowledge base on B. subtilis sporulation, our findings suggest that evolutionary age could be used to help with genome mining.

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  • 27.
    Sikka, Pilleriin
    University of Skövde, School of Bioscience. University of Skövde, Systems Biology Research Environment. Department of Psychology and Speech-Language Pathology, University of Turku, Turku, Finland.
    Dream affect: Conceptual and Methodological Issues in the Study of Emotions and Moods Experienced in Dreams2020Doctoral thesis, monograph (Other academic)
    Abstract [en]

    We experience affect—emotions and mood—not only when we are awake but alsoduring dreaming. Despite considerable research, existing theories and empiricalfindings disagree about the frequency, nature, and correlates of dream affect. In thisthesis, I discuss the conceptual and methodological issues that underlie thesediscrepancies. I present five empirical studies, the overall aim of which was toinvestigate the phenomenology and correlates of dream affect and how resultsregarding these are influenced by study methodology. Studies I–III focusedspecifically on methodological issues, by comparing self- and external ratings ofdream affect (Studies I–II) or the affective content of home and laboratory dreamreports (Study III). Studies IV and V investigated the waking well-being and neuralcorrelates of dream affect, respectively. These studies show that results andconclusions regarding dream affect are very different, even contradictory, dependingon whether dream reports have been collected using sleep laboratory awakenings orhome dream diaries (Study III) or whether dream affect has been measured usingself- or external ratings (Studies I–II). Self- and external ratings of dream affect arealso differently correlated with waking well-being (Study IV). Together, theseresults caution against making broad generalizations about affective dreamexperiences from findings obtained with one type of methodology only. The studiesalso demonstrate that dream affect is related to aspects of waking well-being and illbeing(Study IV) and that certain affective states experienced in dreams, specificallyanger, rely on similar neural processes as in wakefulness (Study V). These findingssuggest that the phenomenology and neural correlates of affective experiences are,at least to some extent, continuous across sleep and wakefulness. Overall, this thesisshows how the conceptual and methodological issues in the study of dream affectmay limit the validity, generalizability, and replicability of findings and,consequently, pose challenges to theory building and theory testing. It contributes todream research by highlighting the need, and suggesting ways, to enhance theconceptual clarity and methodological rigour of research on dream affect. Due to theinterdisciplinary nature of the thesis, the theoretical discussion and novel empiricalfindings also have implications for emotion research, sleep research, well-beingresearch, consciousness research, and affective neuroscience.

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  • 28.
    Synnergren, Jane
    et al.
    University of Skövde, School of Bioscience. University of Skövde, Systems Biology Research Environment.
    Vukusic, Kristina
    Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Sweden.
    Dönnes, Pierre
    SciCross AB, Sweden.
    Jonsson, Marianne
    Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Sweden.
    Lindahl, Anders
    Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Sweden.
    Dellgren, Göran
    Department of Cardiothoracic Surgery, Sahlgrenska University Hospital Gothenburg, Sweden and Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Sweden.
    Jeppsson, Anders
    Department of Cardiothoracic Surgery, Sahlgrenska University Hospital Gothenburg, Sweden and Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Sweden.
    Asp, Julia
    Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Sweden / Department of Clinical Chemistry, Sahlgrenska University Hospital, Gothenburg, Sweden.
    Transcriptional sex and regional differences in paired human atrial and ventricular cardiac biopsies collected in vivo2020In: Physiological Genomics, ISSN 1094-8341, E-ISSN 1531-2267, Vol. 52, no 2, p. 110-120Article in journal (Refereed)
    Abstract [en]

    Transcriptional studies of the human heart provide insight into physiological and pathophysiological mechanisms, essential for understanding the fundamental mechanisms of normal cardiac function and how they are altered by disease. To improve the understanding of why men and women may respond differently to the same therapeutic treatment it is crucial to learn more about sex-specific transcriptional differences. In this study the transcriptome of right atrium and left ventricle was compared across sex and regional location. Paired biopsies from five male and five female patients undergoing aortic valve replacement or coronary artery bypass grafting were included. Gene expression analysis identified 620 differentially expressed transcripts in atrial and ventricular tissue in men and 471 differentially expressed transcripts in women. In total 339 of these transcripts overlapped across sex but notably, 281 were unique in the male tissue and 162 in the female tissue, displaying marked sex differences in the transcriptional machinery. The transcriptional activity was significantly higher in atrias than in ventricles as 70% of the differentially expressed genes were upregulated in the atrial tissue. Furthermore, pathway- and functional annotation analyses performed on the differentially expressed genes showed enrichment for a more heterogeneous composition of biological processes in atrial compared with the ventricular tissue, and a dominance of differentially expressed genes associated with infection disease was observed. The results reported here provide increased insights about transcriptional differences between the cardiac atrium and ventricle but also reveal transcriptional differences in the human heart that can be attributed to sex.

  • 29.
    Tilevik, Diana
    et al.
    University of Skövde, School of Bioscience. University of Skövde, Systems Biology Research Environment.
    Pernestig, Anna-Karin
    University of Skövde, School of Bioscience. University of Skövde, Systems Biology Research Environment.
    Ljungström, Lars
    Department of Infectious Diseases, Skaraborg Hospital, Skövde, Sweden.
    Clinical routine biomarkers in combination for early identification of patients with bacterial sepsis2019Conference paper (Refereed)
  • 30.
    Tilevik, Diana
    et al.
    University of Skövde, School of Bioscience. University of Skövde, Systems Biology Research Environment.
    Saxenborn, Patricia
    University of Skövde, School of Bioscience. University of Skövde, Systems Biology Research Environment.
    Tilevik, Andreas
    University of Skövde, School of Bioscience. University of Skövde, Systems Biology Research Environment.
    Fagerlind, Magnus
    University of Skövde, School of Bioscience. University of Skövde, Systems Biology Research Environment.
    Lubovac-Pilav, Zelmina
    University of Skövde, School of Bioscience. University of Skövde, Systems Biology Research Environment.
    Pernestig, Anna-Karin
    University of Skövde, School of Bioscience. University of Skövde, Systems Biology Research Environment.
    Enroth, Helena
    Department of Clinical Microbiology, Unilabs AB, Skövde, Sweden.
    Using next-generation sequencing to study biodiversity in Klebsiella spp. isolated from patients with suspected sepsis2019Conference paper (Refereed)
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