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  • 351.
    Revonsuo, Antti
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre. Department of Psychology and Center for Cognitive Neuroscience, University of Turku, Finland.
    Hard to See the Problem?2015In: Journal of consciousness studies, ISSN 1355-8250, E-ISSN 2051-2201, Vol. 22, no 3-4, p. 52-67Article in journal (Refereed)
  • 352.
    Revonsuo, Antti
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre.
    The future of consciousness science: From empirical correlations to theoretical explanation2015In: The Constitution of Phenomenal Consciousness: Toward a science and theory / [ed] Steven M. Miller, John Benjamins Publishing Company, 2015, p. 260-270Chapter in book (Refereed)
  • 353.
    Revonsuo, Antti
    et al.
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre. Turun yliopisto, Turku, Finland.
    Tuominen, Jarno
    Turun yliopisto, Turku, Finland.
    Valli, Katja
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre. Turun yliopisto, Turku, Finland.
    The Avatars in the Machine: Dreaming as a Simulation of Social Reality2016In: Open MIND: Philosophy and the Mind Sciences in the 21st Century / [ed] Thomas Metzinger & Jennifer M. Windt, MIT Press, 2016, p. 1295-1322Chapter in book (Refereed)
  • 354.
    Revonsuo, Antti
    et al.
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre. Turun yliopisto, Turku, Finland.
    Tuominen, Jarno
    Turun yliopisto, Turku, Finland.
    Valli, Katja
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre. Turun yliopisto, Turku, Finland.
    The Simulation Theories of Dreaming: How to Make Theoretical Progress in Dream Science2016In: Open MIND: Philosophy and the Mind Sciences in the 21st Century / [ed] Thomas Metzinger & Jennifer M. Windt, MIT Press, 2016, p. 1341-1348Chapter in book (Refereed)
  • 355.
    Riad, Jacques
    et al.
    Department of Orthopedics, Skaraborgs Hospital, 541 42 Skövde, Sweden / Department of Woman and Child Health, Karolinska Institutet, 171 76 Stockholm, Sweden.
    Coleman, Scott
    Motion and Sports Lab, Baylor University Medical Center, 411 N. Washington Ave Suite 2100, Dallas, TX 752 46, United States.
    Lundh, Dan
    University of Skövde, The Systems Biology Research Centre. University of Skövde, School of Life Sciences.
    Broström, Eva
    Department of Woman and Child Health, Karolinska Institutet, 171 76 Stockholm, Sweden.
    Arm posture score and arm movement during walking: A comprehensive assessment in spastic hemiplegic cerebral palsy2011In: Gait & Posture, ISSN 0966-6362, E-ISSN 1879-2219, Vol. 33, no 1, p. 48-53Article in journal (Refereed)
    Abstract [en]

    Patients with hemiplegic cerebral palsy often have noticeably deviant arm posture and decreased arm movement. Here we develop a comprehensive assessment method for the upper extremity during walking.

    Arm posture score (APS), deviation of shoulder flexion/extension, shoulder abduction/adduction, elbow flexion/extension and wrist flexion/extension were calculated from three-dimensional gait analysis. The APS is the root mean square deviation from normal, similar to Baker's Gait Profile Score (GPS)[1].

    The total range of motion (ROM) was defined as the difference between the maximum and minimum position in the gait cycle for each variable. The arm symmetry, arm posture index (API) was calculated by dividing the APS on the hemiplegic side by that on the non-involved side, and the range of motion index (ROMI) by dividing the ROM on the hemiplegic side by that on the non-involved side.

    Using the APS, two groups were defined. Group 1 had minor deviations, with an APS under 9.0 and a mean of 6.0 (95% CI 5.0–7.0). Group 2 had more pronounced deviations, with an APS over 9.0 and a mean of 13.1 (CI 10.8–15.5) (p=0.000). Total ROM was 60.6 in group 1 and 46.2 in group 2 (p=0.031). API was 0.89 in group 1 and 1.70 in group 2 (p<0.001). ROMI was 1.15 in group 1 and 0.69 in group 2 (p=0.003).

    APS describes the amount of deviation, ROM provides additional information on movement pattern and the indices the symmetry. These comprehensive objective and dynamic measurements of upper extremity abnormality can be useful in following natural progression, evaluating treatment and making prognoses in several categories of patients.

  • 356.
    Riede, Jens O.
    et al.
    J.F. Blumenbach Institute of Zoology and Anthropology, Systemic Conservation Biology Group, Georg-August University Goettingen, 37073 Goettingen, Germany.
    Brose, Ulrich
    J.F. Blumenbach Institute of Zoology and Anthropology, Systemic Conservation Biology Group, Georg-August University Goettingen, 37073 Goettingen, Germany.
    Ebenman, Bo
    IFM Theory and Modelling, Division of Theoretical Biology, Linköping University, S-581 83 Linköping, Sweden.
    Jacob, Ute
    Institute for Hydrobiology and Fisheries Science, University Hamburg, 22767 Hamburg, Germany.
    Thompson, Ross
    School of Biological Sciences, Monash University, Bld 18, Vic. 3800, Australia.
    Townsend, Colin R.
    Department of Zoology, University of Otago, Dunedin 9054, New Zealand.
    Jonsson, Tomas
    University of Skövde, School of Life Sciences. University of Skövde, The Systems Biology Research Centre.
    Stepping in Elton's footprints: a general scaling model for body masses and trophic levels across ecosystems2011In: Ecology Letters, ISSN 1461-023X, E-ISSN 1461-0248, Vol. 14, no 2, p. 169-178Article in journal (Refereed)
    Abstract [en]

    Despite growing awareness of the significance of body-size and predator–prey body-mass ratios for the stability of ecological networks, our understanding of their distribution within ecosystems is incomplete. Here, we study the relationships between predator and prey size, body-mass ratios and predator trophic levels using body-mass estimates of 1313 predators (invertebrates, ectotherm and endotherm vertebrates) from 35 food-webs (marine, stream, lake and terrestrial). Across all ecosystem and predator types, except for streams (which appear to have a different size structure in their predator–prey interactions), we find that (1) geometric mean prey mass increases with predator mass with a power-law exponent greater than unity and (2) predator size increases with trophic level. Consistent with our theoretical derivations, we show that the quantitative nature of these relationships implies systematic decreases in predator–prey body-mass ratios with the trophic level of the predator. Thus, predators are, on an average, more similar in size to their prey at the top of food-webs than that closer to the base. These findings contradict the traditional Eltonian paradigm and have implications for our understanding of body-mass constraints on food-web topology, community dynamics and stability.

  • 357.
    Riquelme Medina, Ignacio
    et al.
    University of Skövde, The Systems Biology Research Centre.
    Lubovac-Pilav, Zelmina
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre.
    Gene Co-Expression Network Analysis for Identifying Modules and Functionally Enriched Pathways in Type 1 Diabetes2016In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 11, no 6, article id e0156006Article in journal (Refereed)
    Abstract [en]

    Type 1 diabetes (T1D) is a complex disease, caused by the autoimmune destruction of the insulin producing pancreatic beta cells, resulting in the body?s inability to produce insulin. While great efforts have been put into understanding the genetic and environmental factors that contribute to the etiology of the disease, the exact molecular mechanisms are still largely unknown. T1D is a heterogeneous disease, and previous research in this field is mainly focused on the analysis of single genes, or using traditional gene expression profiling, which generally does not reveal the functional context of a gene associated with a complex disorder. However, network-based analysis does take into account the interactions between the diabetes specific genes or proteins and contributes to new knowledge about disease modules, which in turn can be used for identification of potential new biomarkers for T1D. In this study, we analyzed public microarray data of T1D patients and healthy controls by applying a systems biology approach that combines network-based Weighted Gene Co-Expression Network Analysis (WGCNA) with functional enrichment analysis. Novel co-expression gene network modules associated with T1D were elucidated, which in turn provided a basis for the identification of potential pathways and biomarker genes that may be involved in development of T1D.

  • 358.
    Riveiro, Maria
    et al.
    University of Skövde, School of Informatics. University of Skövde, The Informatics Research Centre.
    Lebram, Mikael
    University of Skövde, School of Informatics. University of Skövde, The Informatics Research Centre.
    Andersson, Christian X.
    Takara Bio Europe, Gothenburg, Sweden.
    Sartipy, Peter
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre. Astra Zeneca, Mölndal, Sweden.
    Synnergren, Jane
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre.
    Interactive visualization of large-scale gene expression data2016In: Information Visualisation: Computer Graphics, Imaging and Visualisation / [ed] Ebad Banissi, Mark W. McK. Bannatyne, Fatma Bouali, Remo Burkhard, John Counsell, Urska Cvek, Martin J. Eppler, Georges Grinstein, Wei Dong Huang, Sebastian Kernbach, Chun-Cheng Lin, Feng Lin, Francis T. Marchese, Chi Man Pun, Muhammad Sarfraz, Marjan Trutschl, Anna Ursyn, Gilles Venturini, Theodor G. Wyeld, and Jian J. Zhang, IEEE Computer Society, 2016, p. 348-354Conference paper (Refereed)
    Abstract [en]

    In this article, we present an interactive prototype that aids the interpretation of large-scale gene expression data, showing how visualization techniques can be applied to support knowledge extraction from large datasets. The developed prototype was evaluated on a dataset of human embryonic stem cell-derived cardiomyocytes. The visualization approach presented here supports the analyst in finding genes with high similarity or dissimilarity across different experimental groups. By using an external overview in combination with filter windows, and various color scales for showing the degree of similarity, our interactive visual prototype is able to intuitively guide the exploration processes over the large amount of gene expression data.

  • 359.
    Roubinet, Eve
    et al.
    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.
    Malsher, Gerard
    Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Staudacher, Karin
    Mountain Agriculture Research Unit, Institute of Ecology, University of Innsbruck, Innsbruck, Austria.
    Traugott, Michael
    Mountain Agriculture Research Unit, Institute of Ecology, University of Innsbruck, Innsbruck, Austria.
    Ekbom, Barbara
    Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Jonsson, Mattias
    Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden.
    High Redundancy as well as Complementary Prey Choice Characterize Generalist Predator Food Webs in Agroecosystems2018In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 8, article id 8054Article in journal (Refereed)
    Abstract [en]

    Food web structure influences ecosystem functioning and the strength and stability of associated ecosystem services. With their broad diet, generalist predators represent key nodes in the structure of many food webs and they contribute substantially to ecosystem services such as biological pest control. However, until recently it has been difficult to empirically assess food web structure with generalist predators. We utilized DNA-based molecular gut-content analyses to assess the prey use of a set of generalist invertebrate predator species common in temperate agricultural fields. We investigated the degree of specialization of predator-prey food webs at two key stages of the cropping season and analysed the link temperature of different trophic links, to identify non-random predation. We found a low level of specialization in our food webs, and identified warm and cool links which may result from active prey choice or avoidance. We also found a within-season variation in interaction strength between predators and aphid pests which differed among predator species. Our results show a high time-specific functional redundancy of the predator community, but also suggest temporally complementary prey choice due to within-season succession of some predator species.

  • 360.
    Saha, Ananda Kumar
    et al.
    Department of Zoology, University of Rajshahi, Rajshahi-6205, Bangladesh.
    Sultana, Nahida
    Department of Zoology, University of Rajshahi, Rajshahi-6205, Bangladesh.
    Mohanta, Moni Krishno
    Department of Zoology, University of Rajshahi, Rajshahi-6205, Bangladesh.
    Mandal, Abul
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre.
    Haque, Fazlul
    Identification and Characterization of Azo Dye Decolourizing Bacterial Strains, Alcaligenes faecalis E5.Cd and A. faecalis Fal.3 Isolated from Textile Effluents2017In: American Scientific Research Journal for Engineering, Technology, and Sciences (ASRJETS), ISSN 2313-4410, Vol. 31, no 1, p. 163-175Article in journal (Refereed)
    Abstract [en]

    The study was designed for isolation and characterization of azo dye decolourizing bacteria which is a prerequisite for developing a microorganism-facilitated treatment of polluting dyes. In this study nine types of bacteria which were able to decolourize three types of azo dyes (Blue H/C, Red 3B and Yellow 3R dye) were isolated from textile effluents collected from Gazipur industrial area in Bangladesh. Depending on 16S rDNA analysis, the most efficient decolourizing bacterium for the Blue H/C and the Red 3B dye was identified as Alcaligenesfaecalis strain E5.Cd while that for the Yellow 3R dye was identified as Alcaligenesfaecalis strain Fal.3. After characterization, both A. faecalis E5.Cdand A. faecalis Fal.3 were found to grow optimally at 35 0 C and at pH 7 and pH 8, respectively. Both of these strains were sensitive to all antibiotics studied except for Bacitracin. Also, both strains showed maximum decolourization activities after 96 hours incubation in MS media at pH 7 (up to 93%) and pH 8 (up to 94%), at 35 0 C temperature ( up to 91%), at 50 ppm initial dye concentration (up to 92%), at 20% inoculum size (up to 93%), and at supplementation of 1% co-substrate (up to 93%).

  • 361.
    Salgaonkar, Neeta A.
    et al.
    Microbial Diversity Research Centre, Dr D Y Patil Biotechnology and Bioinformatics Institute, Dr D Y Patil Vidyapeeth, Pune, India.
    Thakare, Prasad M.
    Microbial Diversity Research Centre, Dr D Y Patil Biotechnology and Bioinformatics Institute, Dr D Y Patil Vidyapeeth, Pune, India.
    Junnarkar, Manisha V.
    Microbial Diversity Research Centre, Dr D Y Patil Biotechnology and Bioinformatics Institute, Dr D Y Patil Vidyapeeth, Pune, India.
    Kapadnis, Balasaheb P.
    Department of Microbiology, Savitribai Phule University of Pune, Pune, India.
    Mandal, Abul
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre.
    Eriksson, Cecilia
    University of Skövde, School of Health and Education. University of Skövde, Health and Education.
    Neelu, Nawani N.
    Microbial Diversity Research Centre, Dr D Y Patil Biotechnology and Bioinformatics Institute, Dr D Y Patil Vidyapeeth, Pune, India.
    Use of N,N-diacetylchitobiose in decreasing toxic effects of indoor air pollution by preventing oxidative DNA damage2016In: Biologia (Bratislava), ISSN 0006-3088, E-ISSN 1336-9563, Vol. 71, no 5, p. 505-515Article in journal (Refereed)
    Abstract [en]

    Indoor air pollution occurs due to hazardous pollutants, such as tobacco smoke, pesticides and carbon oxides, sulphur oxides and nitrogen oxides arising from combustion of biomass fuels. Exposure to these pollutants results in respiratory conditions like asthma, chronic obstructive pulmonary disease, lung cancer, pneumonia and other lower respiratory infections. Several of these infections are a result of inflammation and oxidative stress. Here we demonstrate the ability of N,N-diacetylchitobiose in preventing oxidative DNA damage in peripheral blood mononuclear cells exposed to biomass smoke extracts and cigarette smoke extract. The cytotoxic effect of these pollutants was determined by trypan blue exclusion assay in peripheral blood mononuclear cells, where cytotoxicity in decreasing order was  garette > wood > sawdust > cowdung. Cytotoxicity could be due to single- and double-strand breaks in the DNA as a result of oxidative stress. Comet assay measures the extent of DNA damage in the cells exposed to toxic agents. When mononuclear cells were treated with N,N-diacetylchitobiose and later exposed to smoke extracts, the extent of DNA damage decreased by 44.5% and 57.5% as compared to untreated cells. The protection offered by N,N-diacetylchitobiose towards oxidative DNA damage was at par with quercetin, a popular herbal medicine. Glutathione-S-transferase activity was determined in mononuclear cells exposed to smoke extracts, where oxidative stress in cells exposed to cigarette smoke extract was maximum. The present study demonstrates for the first time the ability of N,N -diacetylchitobiose to alleviate the harmful effects of indoor air pollutants.

  • 362.
    Salminen-Vaparanta, Niina
    et al.
    University of Turku, Finland.
    Koivisto, Mika
    University of Turku, Finland.
    Vorobyev, Victor
    University of Turku, Finland.
    Alakurtti, Kati
    University of Turku, Turku, Finland.
    Revonsuo, Antti
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre. University of Turku, Finland.
    Does TMS on V3 block conscious visual perception?2019In: Neuropsychologia, ISSN 0028-3932, E-ISSN 1873-3514, ISSN 000493910900026, Vol. 128, p. 223-231Article in journal (Refereed)
    Abstract [en]

    Primary visual cortex (V1) and extrastriate V2 are necessary for the emergence of visual consciousness, but the effects of involvement of extrastriate V3 on visual consciousness is unclear. The objective of this study was to examine the causal role of V3 in visual consciousness in humans. We combined neuronavigated transcranial magnetic stimulation (TMS) with a computational model of the TMS-induced electric field to test whether or not the intact processing of visual input in V3, like in V1 and V2, is necessary for conscious visual perception. We targeted the stimulation both to V2 and to V3. If TMS of V3 blocks conscious visual perception of stimuli, then activation in V3 is a causally necessary prerequisite for conscious perception of stimuli. According to the alternative hypothesis, TMS of V3 will not block the conscious visual perception of stimuli, because the pathways from V1 to the higher cortical areas that go around V3 provide sufficient visual input for the emergence of conscious visual perception. The results showed that TMS interfered with conscious perception of features, detection of stimulus presence and the ability to discriminate the letter stimuli both when TMS was targeted either to V3 or to V2. For the conscious detection of stimulus presence, the effect was significantly stronger when V2 was stimulated than when V3 was stimulated. The results of the present study suggest that in addition to the primary visual cortex and V2, also V3 causally contributes to the generation of the most basic form of visual consciousness. Importantly, the results also indicate that V3 is necessary for visual perception in general, not only for visual consciousness.

  • 363.
    Salminen-Vaparanta, Niina
    et al.
    Centre for Cognitive Neuroscience, University of Turku, Finland / Department of Psychology, University of Turku, Finland.
    Vanni, Simo
    Advanced Magnetic Imaging Centre, Aalto University School of Science, Finland / Brain Research Unit, O.V. Lounasmaa Laboratory, Aalto University School of Science, Finland.
    Noreika, Valdas
    Centre for Cognitive Neuroscience, University of Turku, Finland / Department of Psychology, University of Turku, Finland.
    Valiulis, Vladas
    Department of Neurobiology and Biophysics, Vilnius University, Lithuania.
    Moro, Levente
    Centre for Cognitive Neuroscience, University of Turku, Finland / Department of Psychology, University of Turku, Finland.
    Revonsuo, Antti
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre. Centre for Cognitive Neuroscience, University of Turku, Finland / Department of Psychology, University of Turku, Finland.
    Subjective characteristics of TMS-induced phosphenes originating in human V1 and V22014In: Cerebral Cortex, ISSN 1047-3211, E-ISSN 1460-2199, Vol. 24, no 10, p. 2751-2760Article in journal (Refereed)
  • 364.
    Samrani, George
    et al.
    Karolinska Institute / Stockholm University.
    Marklund, Petter
    Stockholm University.
    Engström, Lisa
    University of Skövde.
    Broman, Daniel
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre. Dalarna University.
    Persson, Jonas
    Karolinska Institute / Stockholm University.
    Behavioral facilitation and increased brain responses from a high interference working memory context2018In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 8, no 1, article id 15308Article in journal (Refereed)
    Abstract [en]

    Many real-life situations require flexible behavior in changing environments. Evidence suggests that anticipation of conflict or task difficulty results in behavioral and neural allocation of task-relevant resources. Here we used a high- and low-interference version of an item-recognition task to examine the neurobehavioral underpinnings of context-sensitive adjustment in working memory (WM). We hypothesized that task environments that included high-interference trials would require participants to allocate neurocognitive resources to adjust to the more demanding task context. The results of two independent behavioral experiments showed enhanced WM performance in the high-interference context, which indicated that a high-interference context improves performance on non-interference trials. A third behavioral experiment showed that when WM load was increased, this effect was no longer significant. Neuroimaging results further showed greater engagement of inferior frontal gyrus, striatum, parietal cortex, hippocampus, and midbrain in participants performing the task in the high- than in the low-interference context. This effect could arise from an active or dormant mode of anticipation that seems to engage fronto-striatal and midbrain regions to flexibly adjust resources to task demands. Our results extend the model of conflict adaptation beyond trial-to-trial adjustments by showing that a high interference context affects both behavioral and biological aspects of cognition.

  • 365.
    Samuelson, Emma
    et al.
    Sahlgrenska Academy, University of Gothenburg.
    Karlsson, Sara
    Sahlgrenska Academy, University of Gothenburg.
    Partheen, Karolina
    University of Gothenburg.
    Nilsson, Staffan
    Chalmers University of Technology.
    Szpirer, Claude
    Université Libre de Bruxelles.
    Behboudi, Afrouz
    University of Skövde, The Systems Biology Research Centre. University of Skövde, School of Life Sciences.
    BAC CGH-array identified specific small-scale genomic imbalances in diploid DMBA-induced rat mammary tumors2012In: BMC Cancer, ISSN 1471-2407, E-ISSN 1471-2407, Vol. 12, p. artikelnummer 352-Article in journal (Refereed)
    Abstract [en]

    Background: Development of breast cancer is a multistage process influenced by hormonal and environmental factors as well as by genetic background. The search for genes underlying this malignancy has recently been highly productive, but the etiology behind this complex disease is still not understood. In studies using animal cancer models, heterogeneity of the   genetic background and environmental factors is reduced and thus analysis and identification of genetic aberrations in tumors may become easier. To identify chromosomal regions   potentially involved in the initiation and progression of mammary cancer, in the present   work we subjected a subset of experimental mammary tumors to cytogenetic and molecular   genetic analysis.

    Methods: Mammary tumors were induced with DMBA (7,12-dimethylbenz[a]anthrazene) in female rats from the susceptible SPRD-Cu3 strain and from crosses and backcrosses between this strain and the resistant WKY strain. We first produced a general overview of chromosomal aberrations in the tumors using conventional kartyotyping (G-banding) and Comparative Genome Hybridization (CGH) analyses. Particular chromosomal changes were then analyzed in more details using an in-house developed BAC (bacterial artificial chromosome) CGH-array platform.

    Results: Tumors appeared to be diploid by conventional karyotyping, however several sub-microscopic chromosome gains or losses in the tumor material were identified by BAC CGH-array analysis. An oncogenetic tree analysis based on the BAC CGH-array data suggested gain of rat chromosome (RNO) band 12q11, loss of RNO5q32 or RNO6q21 as the earliest events in the development of these mammary tumors.

    Conclusions: Some of the identified changes appear to be more specific for DMBA-induced mammary tumors and some are similar to those previously reported in ACI rat model for estradiol-induced mammary tumors. The later group of changes is more interesting, since they may represent anomalies that involve genes with a critical role in mammary tumor development. Genetic changes identified in this work are at very small scales and thus may provide a more feasible basis for the identification of the target gene(s). Identification of the genes underlying these chromosome changes can provide new insights to the mechanisms   of mammary carcinogenesis.

  • 366.
    Sandman, Nils
    et al.
    Genomics and Biomarkers Unit, National Institute for Health and Welfare, Helsinki, Finland / Department of Psychology and Speech Language Pathology, Centre for Cognitive Neuroscience, Turku Brain and Mind Centre, University of Turku, Turku, Finland.
    Merikanto, Ilona
    Department of Health, National Institute for Health and Welfare, Helsinki, Finland / Department of Biosciences, University of Helsinki, Helsinki, Finland.
    Määttänen, Hanna
    Department of Psychology and Speech Language Pathology, Centre for Cognitive Neuroscience, Turku Brain and Mind Centre, University of Turku, Turku, Finland.
    Valli, Katja
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre. Department of Psychology and Speech Language Pathology, Centre for Cognitive Neuroscience, Turku Brain and Mind Centre, University of Turku, Turku, Finland.
    Kronholm, Erkki
    Department of Health, National Institute for Health and Welfare, Turku, Finland.
    Laatikainen, Tiina
    Department of Health, National Institute for Health and Welfare, Helsinki, Finland / Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland / Hospital District of North Karelia, Joensuu, Finland .
    Partonen, Timo
    Department of Health, National Institute for Health and Welfare, Helsinki, Finland.
    Paunio, Tiina
    Genomics and Biomarkers Unit, National Institute for Health and Welfare, Helsinki, Finland / Department of Psychiatry, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland.
    Winter is coming: nightmares and sleep problems during seasonal affective disorder2016In: Journal of Sleep Research, ISSN 0962-1105, E-ISSN 1365-2869, Vol. 25, no 5, p. 612-619Article in journal (Refereed)
    Abstract [en]

    Sleep problems, especially nightmares and insomnia, often accompany depression. This study investigated how nightmares, symptoms of insomnia, chronotype and sleep duration associate with seasonal affective disorder, a special form of depression. Additionally, it was noted how latitude, a proxy for photoperiod, and characteristics of the place of residence affect the prevalence of seasonal affective disorder and sleep problems. To study these questions, data from FINRISK 2012 study were used. FINRISK 2012 consists of a random population sample of Finnish adults aged 25–74 years (n = 4905) collected during winter from Finnish urban and rural areas spanning the latitudes of 60°N to 66°N. The Seasonal Pattern Assessment Questionnaire was used to assess symptoms of seasonal affective disorder. Participants with symptoms of seasonal affective disorder had significantly increased odds of experiencing frequent nightmares and symptoms of insomnia, and they were more often evening chronotypes. Associations between latitude, population size and urbanicity with seasonal affective disorder symptoms and sleep disturbances were generally not significant, although participants living in areas bordering urban centres had less sleep problems than participants from other regions. These data show that the prevalence of seasonal affective disorder was not affected by latitude. 

  • 367.
    Sandman, Nils
    et al.
    National Institute for Health and Welfare, Public Health Genomics Unit and Institute for Molecular Medicine FIMM, Helsinki, Finland / University of Turku, Centre for Cognitive Neuroscience, Department of Psychology, Turku, Finland.
    Valli, Katja
    University of Skövde, School of Humanities and Informatics. University of Skövde, The Systems Biology Research Centre. University of Turku, Centre for Cognitive Neuroscience, Department of Psychology, Turku, Finland.
    Kronholm, Erkki
    National Institute for Health and Welfare, Department of Chronic Disease Prevention, Finland.
    Ollila, Hanna M.
    National Institute for Health and Welfare, Public Health Genomics Unit and Institute for Molecular Medicine FIMM, Helsinki, Finland.
    Revonsuo, Antti
    University of Skövde, School of Humanities and Informatics. University of Skövde, The Systems Biology Research Centre. University of Turku, Centre for Cognitive Neuroscience, Department of Psychology, Turku, Finland.
    Laatikainen, Tiina
    National Institute for Health and Welfare, Department of Chronic Disease Prevention, Finland / University of Eastern Finland, Institute for Public Health and Clinical Nutrition.
    Paunio, Tiina
    National Institute for Health and Welfare, Public Health Genomics Unit and Institute for Molecular Medicine FIMM, Helsinki, Finland / Helsinki University Hospital, Department of Psychiatry, Helsinki, Finland.
    Nightmares: Prevalence among the Finnish General Adult Population and War Veterans during 1972-20072013In: Sleep, ISSN 0161-8105, E-ISSN 1550-9109, Vol. 36, no 7, p. 1041-1050Article in journal (Refereed)
    Abstract [en]

    Study Objectives: To investigate the prevalence of nightmares among the Finnish general adult population during 1972-2007 and the association between nightmare prevalence and symptoms of insomnia, depression, and anxiety in World War II veterans. Design: Eight independent cross-sectional population surveys of the National FINRISK Study conducted in Finland in 1972, 1977, 1982, 1987, 1992, 1997, 2002, and 2007. Setting: Epidemiologic. Participants: A total of 69,813 people (33,811 men and 36,002 women) age 25-74 years. Interventions: N/A. Measurements and Results: The investigation of nightmare prevalence and insomnia, depression, and anxiety symptoms was based on questionnaires completed by the participants. Among the whole sample, 3.5% of the men and 4.8% of the women reported frequent nightmares (P < 0.0001 for sex difference), but the prevalence was affected by the age of participants and the year of the survey. Nightmare prevalence increased with age, particularly among the men. The number of people reporting occasional nightmares increased roughly by 20% for both sexes from 1972 to 2007 (P < 0.0001). Participants with war experiences reported more frequent nightmares and symptoms of insomnia, depression, and anxiety than participants without such experiences (P < 0.0001). Conclusions: Prevalence of nightmares was affected by the sex and age of the participants, and occasional nightmares have become more common in Finland. Exposure to war elevates nightmare prevalence as well as insomnia, depression, and anxiety symptoms even decades after the war; large numbers of war veterans can affect nightmare prevalence on population level.

  • 368.
    Sandman, Nils
    et al.
    National Institute for Health and Welfare, Public Health Genomics Unit and Institute for Molecular Medicine FIMM, Helsinki, Finland / University of Turku, Centre for Cognitive Neuroscience, Turku Brain and Mind Center, Department of Psychology, Turku, Finland.
    Valli, Katja
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre. University of Turku, Centre for Cognitive Neuroscience, Turku Brain and Mind Center, Department of Psychology, Turku, Finland.
    Kronholm, Erkki
    National Institute for Health and Welfare, Department of Health, Unit of Chronic Disease Prevention, Turku, Finland.
    Revonsuo, Antti
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre. University of Turku, Centre for Cognitive Neuroscience, Turku Brain and Mind Center, Department of Psychology, Turku, Finland.
    Laatikainen, Tiina
    National Institute for Health and Welfare, Department of Health, Unit of Chronic Disease Prevention, Turku, Finland / University of Eastern Finland, Institute of Public Health and Clinical Nutrition, Kuopio, Finland / Hospital District of North Karelia, Joensuu, Finland.
    Paunio, Tiina
    National Institute for Health and Welfare, Public Health Genomics Unit and Institute for Molecular Medicine FIMM, Helsinki, Finland / Helsinki University and University Hospital, Department of Psychiatry, Helsinki, Finland.
    Nightmares: Risk factors among the Finnish general adult population2015In: Sleep, ISSN 0161-8105, E-ISSN 1550-9109, Vol. 38, no 4, p. 507-514Article in journal (Refereed)
    Abstract [en]

    STUDY OBJECTIVES: To identify risk factors for experiencing nightmares among the Finnish general adult population. The study aimed to both test whether previously reported correlates of frequent nightmares could be reproduced in a large population sample and to explore previously unreported associations.

    DESIGN: Two independent cross-sectional population surveys of the National FINRISK Study.

    SETTING: Age- and sex-stratified random samples of the Finnish population in 2007 and 2012.

    PARTICIPANTS: A total of 13,922 participants (6,515 men and 7,407 women) aged 25-74 y.

    INTERVENTIONS: N/A.

    MEASUREMENTS AND RESULTS: Nightmare frequency as well as several items related to socioeconomic status, sleep, mental well-being, life satisfaction, alcohol use, medication, and physical well-being were recorded with a questionnaire. In multinomial logistic regression analysis, a depression-related negative attitude toward the self (odds ratio [OR] 1.32 per 1-point increase), insomnia (OR 6.90), and exhaustion and fatigue (OR 6.86) were the strongest risk factors for experiencing frequent nightmares (P < 0.001 for all). Sex, age, a self-reported impaired ability to work, low life satisfaction, the use of antidepressants or hypnotics, and frequent heavy use of alcohol were also strongly associated with frequent nightmares (P < 0.001 for all).

    CONCLUSIONS: Symptoms of depression and insomnia were the strongest predictors of frequent nightmares in this dataset. Additionally, a wide variety of factors related to psychological and physical well-being were associated with nightmare frequency with modest effect sizes. Hence, nightmare frequency appears to have a strong connection with sleep and mood problems, but is also associated with a variety of measures of psychological and physical well-being.

  • 369.
    Sandman, Nils
    et al.
    Center for Cognitive Neuroscience, Turku Brain and Mind Center, Department of Psychology and Speech-Language Pathology, University of Turku, Finland / Genomics and Biomarkers Unit, National Institute for Health and Welfare, Finland.
    Valli, Katja
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre. Center for Cognitive Neuroscience, Turku Brain and Mind Center, Department of Psychology and Speech-Language Pathology, University of Turku, Finland.
    Kronholm, Erkki
    Department of Health, National Institute for Health and Welfare, Turku, Finland.
    Vartiainen, Erkki
    Department of Health, National Institute for Health and Welfare, Helsinki, Finland.
    Laatikainen, Tiina
    Department of Health, National Institute for Health and Welfare, Finland / Institute of Public Health and Clinical Nutrition, University of Eastern Finland / Hospital District of North Karelia, Finland.
    Paunio, Tiina
    Genomics and Biomarkers Unit, National Institute for Health and Welfare, Finland / Department of Psychiatry, University of Helsinki and Helsinki University Central Hospital, Finland.
    Nightmares as predictors of suicide: an extension study including war veterans2017In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 7, article id 44756Article in journal (Refereed)
    Abstract [en]

    Nightmares are intensive dreams with negative emotional tone. Frequent nightmares can pose a serious clinical problem and in 2001, Tanskanen et al. found that nightmares increase the risk of suicide. However, the dataset used by these authors included war veterans in whom nightmare frequency -and possibly also suicide risk -is elevated. Therefore, re-examination of the association between nightmares and suicide in these data is warranted. We investigated the relationship between nightmares and suicide both in the general population and war veterans in Finnish National FINRISK Study from the years 1972 to 2012, a dataset overlapping with the one used in the study by Tanskanen et al. Our data comprise 71,068 participants of whom 3139 are war veterans. Participants were followed from their survey participation until the end of 2014 or death. Suicides (N = 398) were identified from the National Causes of Death Register. Frequent nightmares increase the risk of suicide: The result of Tanskanen et al. holds even when war experiences are controlled for. Actually nightmares are not significantly associated with suicides among war veterans. These results support the role of nightmares as an independent risk factor for suicide instead of just being proxy for history of traumatic experiences.

  • 370.
    Sartipy, P.
    et al.
    Cellartis AB, Arvid Wallgrens Backe 20, SE-413 46 Göteborg, Sweden.
    Olsson, Björn
    University of Skövde, The Systems Biology Research Centre. University of Skövde, School of Life Sciences.
    Hyllner, J.
    Cellartis AB, Arvid Wallgrens Backe 20, SE-413 46 Göteborg, Sweden.
    Synnergren, Jane
    University of Skövde, The Systems Biology Research Centre. University of Skövde, School of Life Sciences.
    Regulation of 'stemness' and stem cell differentiation by microRNAs2009In: IDrugs. The Investigational Drugs Journal, ISSN 1369-7056, E-ISSN 2040-3410, Vol. 12, no 8, p. 492-496Article, review/survey (Refereed)
    Abstract [en]

    Pluripotency and cellular differentiation are intricate biological processes that are coordinately regulated by a complex set of factors and epigenetic regulators. Human pluripotent stem cell lines can be generated from surplus fertilized eggs or, as demonstrated more recently, from the reprogramming of somatic cells. Standardized culture conditions for the long-term maintenance and propagation of undifferentiated human pluripotent stem cells have also been developed. An objective of current research is to increase the understanding of the molecular mechanisms that regulate stem cell differentiation. The differentiation of human pluripotent stem cells may enable the generation of large quantities of specialized cells that can be used as in vitro tools for drug development, as well as for future applications in regenerative medicine. However, most of the currently used differentiation protocols yield inefficient stem cell quantities and low purity of the final cell preparations. The discovery of microRNAs (miRNAs) and their role as important transcriptional regulators may provide a new means of manipulating stem cell fate. This article provides an overview of some recent advancements made in the fields of both stem cell biology and miRNA.

  • 371.
    Sartipy, Peter
    et al.
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre. Cellectis AB, Göteborg, Sweden.
    Björquist, Petter
    Cellectis AB, Göteborg, Sweden / NovaHep AB, Göteborg, Sweden.
    Employment of the Triple Helix concept for development of regenerative medicine applications based on human pluripotent stem cells2014In: Clinical and translational medicine, ISSN 2001-1326, Vol. 3, p. 1-7, article id 9Article in journal (Refereed)
    Abstract [en]

    Using human pluripotent stem cells as a source to generate differentiated progenies for regenerative medicine applications has attracted substantial interest during recent years. Having the capability to produce large quantities of human cells that can replace damaged tissue due to disease or injury opens novel avenues for relieving symptoms and also potentially offers cures for many severe human diseases. Although tremendous advancements have been made, there is still much research and development left before human pluripotent stem cell derived products can be made available for cell therapy applications. In order to speed up the development processes, we argue strongly in favor of cross-disciplinary collaborative efforts which have many advantages, especially in a relatively new field such as regenerative medicine based on human pluripotent stem cells. In this review, we aim to illustrate how some of the hurdles for bringing human pluripotent stem cell derivatives from bench-to-bed can be effectively addressed through the establishment of collaborative programs involving academic institutions, biotech industries, and pharmaceutical companies. By taking advantage of the strengths from each organization, innovation and productivity can be maximized from a resource perspective and thus, the chances of successfully bringing novel regenerative medicine treatment options to patients increase.

  • 372.
    Sartipy, Peter
    et al.
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre.
    Holmgren, Gustav
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre.
    Synnergren, Jane
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre.
    Andersson, Christian
    Takara Bio, Gothenburg, Sweden.
    Lindahl, Anders
    University of Gothenburg, Sweden.
    Visual integration of multiple omics data from human pluripotent stem cell-derived cardiomyocytes2017Conference paper (Refereed)
  • 373.
    Scheinin, Annalotta
    et al.
    University of Turku, Finland / Hospital District of Southwest Finland, Turku, Finland / Turku University Hospital, Finland.
    Kallionpää, Roosa E.
    Turku University Hospital, Finland / University of Turku, Finland.
    Li, Duan
    University of Michigan Medical School, Ann Arbor, Michigan.
    Kallioinen, Minna
    Turku University Hospital, Finland.
    Kaisti, Kaike
    University of Turku, Finland / Hospital District of Southwest Finland, Turku, Finland / Oulu University Hospital, Finland.
    Långsjö, Jaakko
    University of Turku, Finland / Hospital District of Southwest Finland, Turku, Finland / Tampere University Hospital, Finland.
    Maksimow, Anu
    University of Turku, Finland / Hospital District of Southwest Finland, Turku, Finland / Turku University Hospital, Finland.
    Vahlberg, Tero
    University of Turku, Finland / Turku University Hospital, Finland.
    Valli, Katja
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre. University of Turku, Finland.
    Mashour, George A.
    University of Michigan Medical School, Ann Arbor, Michigan.
    Revonsuo, Antti
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre. University of Turku, Finland.
    Scheinin, Harry
    University of Turku, Finland / Hospital District of Southwest Finland, Turku, Finland / Turku University Hospital, Finland.
    Differentiating Drug-related and State-related Effects of Dexmedetomidine and Propofol on the Electroencephalogram2018In: Anesthesiology, ISSN 0003-3022, E-ISSN 1528-1175, Vol. 129, no 1, p. 22-36Article in journal (Refereed)
    Abstract [en]

    BACKGROUND

    Differentiating drug-related changes and state-related changes on the electroencephalogram during anesthetic-induced unconsciousness has remained a challenge. To distinguish these, we designed a rigorous experimental protocol with two drugs known to have distinct molecular mechanisms of action. We hypothesized that drug- and state-related changes can be separated.

    METHODS: 

    Forty-seven healthy participants were randomized to receive dexmedetomidine (n = 23) or propofol (n = 24) as target-controlled infusions until loss of responsiveness. Then, an attempt was made to arouse the participant to regain responsiveness while keeping the drug infusion constant. Finally, the concentration was increased 1.5-fold to achieve presumable loss of consciousness. We conducted statistical comparisons between the drugs and different states of consciousness for spectral bandwidths, and observed how drug-induced electroencephalogram patterns reversed upon awakening. Cross-frequency coupling was also analyzed between slow-wave phase and alpha power.

    RESULTS: 

    Eighteen (78%) and 10 (42%) subjects were arousable during the constant drug infusion in the dexmedetomidine and propofol groups, respectively (P = 0.011 between the drugs). Corresponding with deepening anesthetic level, slow-wave power increased, and a state-dependent alpha anteriorization was detected with both drugs, especially with propofol. Negative phase-amplitude coupling before and during loss of responsiveness frontally and positive coupling during the highest drug concentration posteriorly were observed in the propofol but not in the dexmedetomidine group.

    CONCLUSIONS: 

    Electroencephalogram effects of dexmedetomidine and propofol are strongly drug- and state-dependent. Changes in slow-wave and alpha activity seemed to best detect different states of consciousness.

  • 374.
    Scholtes, Rosalie A.
    et al.
    Diabetes Centre, Department of Internal Medicine, Amsterdam University Medical Centres, location VUmc, Amsterdam, Netherlands.
    van Raalte, Daniël H.
    Diabetes Centre, Department of Internal Medicine, Amsterdam University Medical Centres, location VUmc, Amsterdam, Netherlands.
    Correa-Rotter, Ricardo
    Nephrology and Mineral Metabolism, National Medical Science and Nutrition Institute Salvador Zubirán, Mexico City, Mexico.
    Toto, Robert D.
    University of Texas Southwestern Medical Center, Dallas, TX, United States.
    Heerspink, Hiddo J. L.
    Clinical Pharmacy and Pharmacology, University of Groningen, University Medical Center Groningen, Netherlands.
    Cain, Valerie
    Bogier Clinical and IT Solutions Inc., Raleigh, NC, United States.
    Sjöström, C. David
    AstraZeneca, Gothenburg, Sweden.
    Sartipy, Peter
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre. AstraZeneca, Gothenburg, Sweden.
    Stefánsson, Bergur V.
    AstraZeneca, Gothenburg, Sweden.
    The effects of dapagliflozin on cardio-renal risk factors in patients with type 2 diabetes with or without renin-angiotensin system inhibitor treatment: a post hoc analysis2019In: Diabetes, obesity and metabolism, ISSN 1462-8902, E-ISSN 1463-1326Article in journal (Refereed)
    Abstract [en]

    Aims: Renin-angiotensin system inhibitors (RASi) are the most effective treatments for diabetic kidney disease but significant residual renal risk remains, possibly because of other mechanisms of kidney disease progression unrelated to RAS that may be present. Sodium-glucose co-transporter-2 inhibitors reduce albuminuria and may complement RASi by offering additional renal protection. This post hoc analysis investigated the effects of dapagliflozin on cardio-renal risk factors in patients with type 2 diabetes (T2D) with increased albuminuria treated with or without RASi at baseline. Materials and methods: We evaluated the effects of dapagliflozin 10 mg/day over 12–24 weeks across 13 placebo-controlled studies in patients with T2D with a urinary albumin-to-creatinine ratio (UACR) ≥30 mg/g at baseline. Patients were divided into two subgroups based on treatment with or without RASi at baseline. Results: Compared with patients with RASi at baseline (n = 957), patients without RASi (n = 302) were younger, had a shorter duration of diabetes (7 vs. 12 years), higher estimated glomerular filtration rate (eGFR) and lower UACR, serum uric acid (sUA), body weight and systolic blood pressure. Placebo-adjusted treatment effects of dapagliflozin on UACR, eGFR, glycated haemoglobin and haematocrit over 24 weeks were similar across groups. Mean reductions in body weight and sUA were more distinct in patients without RASi treatment at baseline. Conclusions: Treatment with dapagliflozin over 24 weeks provides similar clinically relevant improvements in metabolic and haemodynamic parameters, and similar reductions in UACR, in patients with T2D with elevated albuminuria treated with or without RASi at baseline. © 2019 The Authors. Diabetes, Obesity and Metabolism published by John Wiley & Sons Ltd.

  • 375.
    Sedghi, Maryam
    et al.
    Medical Genetics Laboratory, Alzahra University Hospital, Isfahan University of Medical Sciences, Isfahan, Iran.
    Salari, Mehri
    Department of Neurology, Shahid Beheshti University of Medical Science, Tehran, Iran.
    Moslemi, Ali-Reza
    Department of Pathology, University of Gothenburg, Sahlgrenska University Hospital, Sweden.
    Kariminejad, Ariana
    Kariminejad-Najmabadi Pathology and Genetics Center, Tehran, Iran.
    Davis, Mark
    Department of Diagnostic Genomics, Pathwest, QEII Medical Centre, Australia.
    Goullée, Hayley
    Centre for Medical Research, University of Western Australia / Harry Perkins Institute for Medical Research, Nedlands, Australia.
    Olsson, Björn
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre.
    Laing, Nigel
    Centre for Medical Research, University of Western Australia / Harry Perkins Institute for Medical Research, Nedlands, Australia.
    Tajsharghi, Homa
    University of Skövde, School of Health and Education. University of Skövde, Health and Education. Centre for Medical Research, University of Western Australia / Harry Perkins Institute for Medical Research, Nedlands, Australia.
    Ataxia-telangiectasia-like disorder in a family deficient for MRE11A, caused by a MRE11 variant2018In: Neurology: Genetics, ISSN 2376-7839, Vol. 4, no 6, article id e295Article in journal (Refereed)
    Abstract [en]

    Objective We report 3 siblings with the characteristic features of ataxia-telangiectasia-like disorder associated with a homozygous MRE11 synonymous variant causing nonsense-mediated mRNA decay (NMD) and MRE11A deficiency. Methods Clinical assessments, next-generation sequencing, transcript and immunohistochemistry analyses were performed. Results The patients presented with poor balance, developmental delay during the first year of age, and suffered from intellectual disability from early childhood. They showed oculomotor apraxia, slurred and explosive speech, limb and gait ataxia, exaggerated deep tendon reflex, dystonic posture, and mirror movement in their hands. They developed mild cognitive abilities. Brain MRI in the index case revealed cerebellar atrophy. Next-generation sequencing revealed a homozygous synonymous variant in MRE11 (c.657C>T, p.Asn219=) that we show affects splicing. A complete absence of MRE11 transcripts in the index case suggested NMD and immunohistochemistry confirmed the absence of a stable protein. Conclusions Despite the critical role of MRE11A in double-strand break repair and its contribution to the Mre11/Rad50/Nbs1 complex, the absence of MRE11A is compatible with life. 

  • 376.
    Sellman, Stefan
    et al.
    Linköping University, Sweden.
    Jonsson, Annie
    University of Skövde, School of Life Sciences. University of Skövde, The Systems Biology Research Centre.
    Algers, Bo
    Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Flisberg, Patrik
    Linköping University, Sweden.
    Henningsson, Mathias
    Linköping University, Sweden.
    Håkansson, Nina
    University of Skövde, School of Life Sciences. University of Skövde, The Systems Biology Research Centre.
    Rönnqvist, Mikael
    Norwegian School of Economics, Bergen, Norway.
    Wennergren, Uno
    Linköping University, Sweden.
    Reducing the amount of slaughter transports in modern Swedish cattle production systems2012In: Tackling the Future Challenges of Organic Animal Husbandry: 2nd Organic Animal Husbandry Conference, Hamburg, Trenthorst, 12-14 September, 2012 / [ed] Gerold Rahmann, Denise Godinho, Braunschweig: Johann Heinrich von Thünen-Institut , 2012, p. 262-265Conference paper (Refereed)
    Abstract [en]

    Two methods that can help to reduce the distances involved in transportation of cattle to slaughter are presented, route optimization and spatial redistribution of slaughter capacities. In a comparison ot three route optimization techniques we show that RuttOpt is the most effective and that the number of stops on routes can be reduced compared to what is the case today. We also find that transport distances can be reduced by 40 % compared to the real transports of 2008 if animals are sent to the closest available facilities. We believe that the metods highlighted here can help improve the sustainability and animal health in both organic and conventional farming.

  • 377.
    Setzer, Malin
    University of Skövde, The Systems Biology Research Centre. University of Skövde, School of Life Sciences.
    The decline of great Arctic charr in Lake Vättern: empirical and theoretical analyses of suggested causes2012Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Human activity is affecting species and ecosystems all over the world. In aquatic systems negative trends can be seen for many fish stocks and potential consequences of this, for ecosystem structure and functions, are of particular concern. Overexploitation is often suggested as a major driver behind these changes but other factors such as acidification, habitat destruction, eutrophication, pollution, introduction of alien species and climate change are also considered important. Fisheries biologist are now faced with the challenge of finding suitable management for affected fish stocks but the task is difficult because the causal connections tend to be complex, involving many factors and synergistic effects as well as interactions among species that may lead to cascades of indirect effects within communities. Thus, to fully understand, ameliorate and predict the complex effects of disturbances and environmental change on ecosystems, knowledge of species and how they interact with each other and the environment is required. This has led to an increased demand for multispecies management of fisheries and ecosystem-based management and food webs are central to both these approaches. This thesis is an attempt to use a food web approach to increase our understanding of an endangered fish stock in Europe’s sixth, and Sweden’s second largest lake: Lake Vättern.

    Lake Vättern is a deep, oligotrophic lake in south-central Sweden that harbours some 30 species of fish, among these a large-bodied form of Arctic charr: great Arctic charr (Salvelinus umbla). The stock of great Arctic charr in Lake Vättern used to be of great importance for the commercial fisheries but today the stock is considered critically endangered. Suggested causes for the decline and/or problems for the stock to recover include overexploitation, decreased nutrient loading, climate change and introduction of Salmon (Salmo salar) and signal crayfish (Pacifastacus leniusculus). The focus of this thesis is great Arctic charr in Lake Vättern and the dramatic decline of this important fish stock during the second part of the 20th century. In a series of papers we combine field experiments, analyses of climate, commercial harvest and stock survey data, stomach content analyses and model simulations to study several of the suggested causes for the decline of the stock of great Arctic charr and discuss implications of the results for future management of the stock.

    In Paper I we investigate the potential effect of the introduced signal crayfish on the stock of great Arctic charr, using a controlled field experiment. More precisely, we investigate the extent of predation on eggs of great Arctic charr. We are able to partition the total loss rate of eggs into background mortality, predation mortality from introduced crayfish and predation from native fish. It has earlier been suggested that predation on eggs of great Arctic charr by fish is more important than by crayfish. However, we find that the mortality rate due to signal crayfish in our experiment is more than five times that because of native fish. We thereby conclude that crayfish predation are at least of the same magnitude, or even greater, than fish predation and that high abundance of signal crayfish on spawning sites could impair the recovery of the stock of great Arctic charr in Lake Vättern. Thus, suggests that targeted reductions of signal crayfish on selected spawning grounds are potential management options that should be considered.

    In Paper II we use survey data from 2006-2010 of the stock of great Arctic charr to first estimate the selection curves for the gillnets used in the survey and subsequently estimate the size-frequency distribution and relative abundance of the stock. We begin by analyzing some of the assumptions behind the so called SELECT-model, which is used to estimate selection curves, and suggest how data can be treated to better conform to these assumptions. We show that by removing potentially nonmeshed fish from the data and taking non-isometric growth into account, our approach results in narrower and less asymmetric selection curves with a significantly better model fit. Next, using the obtained selection curves, we estimate the size frequency distribution and relative abundance of great Arctic charr in different years and find that mortality of medium-sized fish have decreased and abundance of fish is increasing slightly. Likely causes for this are the new fishery regulations that were implemented in 2007. Generally speaking, our study demonstrates an approach that is expected to increase the accuracy of estimates of fish size-distributions from survey data and more specifically, this is expected to lead to better understanding the dynamics of the endangered stock of great Arctic charr in Lake Vättern.

    Paper III uses records of commercial catch data since 1914 to analyse the potential effects of climate change on great Arctic charr in Lake Vättern. We find that there is a positive effect of winters with ice on the stock of Arctic charr that can be seen as increasing commercial catches that peak four years after an ice-winter. Furthermore, the positive effect increases with the duration of the ice winter. It is unclear however, if this is a direct or indirect effect of ice on the stock of great Arctic charr. To analyze this, the date of different development stages in hatching for eggs of great Arctic charr is estimated using water temperature data since 1955. The results show that there is a positive correlation between the predicted date of fully consumed yolk sac and standardized catches six years later. This suggests that warmer winters, which result in early hatching of eggs and early date for when the yolk sack is consumed, will affect survival of fry and subsequent recruitment to older size classes negatively. Thus, lending support for a strong possibility for a trophic mismatch. Our study show that climate do appear to affect the stock of great Arctic charr in several ways and underscore the fear that future climate change will have negative consequences for the stock.

    Paper IV uses stomach content analysis to (i) describe the diets of fish and thus identify and quantify links in the pelagic food web in present day Lake Vättern, and (ii) compare the results with older diet data to see if observed changes in Lake Vättern in the last 30-40 years have led to any changes in the trophic interactions between the species. Overall, we conclude that the investigated food web structure of Lake Vättern has remained largely intact and stable during the last 50 years even if there have been introductions of non-native species and environmental changes in Lake Vättern. However, when comparing the old and new data there appear to have been some diet shifts for some species. For example, the diets during summer for both great Arctic charr and Atlantic salmon in our study suggest a possible shift to a diet dominated by three-spined stickleback, thus, indicating support that an increased interspecific competition between these species may have occurred.

    Finally, Paper V develops and analyzes a size-structured model of the pelagic food web of Lake Vättern. The aim is to analyze the combined effects of some of the suggested causes for the decline of the stock of great Arctic charr in Lake Vättern. We incorporate results from preceding papers to quantify trophic links in the food web and define a realistic starting size distribution of great Arctic charr. In the model we vary the stocking of salmon, the fishing pressure and the abundance of signal crayfish and study the effects on different size classes of great Arctic charr. We find that a decrease in salmon stocking into the lake has the greatest positive impact on large great Arctic charr while a decrease in fishing intensity has the greatest positive impact on smaller sizes of great Arctic charr.

  • 378.
    Setzer, Malin
    et al.
    University of Skövde, School of Life Sciences. University of Skövde, The Systems Biology Research Centre.
    Norrgård, Johnny R.
    Management and Ecology of River Resources, Department of Biology, Karlstad University, Karlstad, Sweden.
    Jonsson, Tomas
    University of Skövde, School of Life Sciences. University of Skövde, The Systems Biology Research Centre.
    An invasive crayfish affects egg survival and the potential recovery of an endangered population of Arctic charr2011In: Freshwater Biology, ISSN 0046-5070, E-ISSN 1365-2427, Vol. 56, no 12, p. 2543-2553Article in journal (Refereed)
    Abstract [en]

    Summary

    1. Many fish stocks have declined, because of overharvesting, habitat destruction and introduced species. Despite efforts to rehabilitate some of these stocks, not all are responding or are recovering only slowly.

    2. In freshwater systems, introduced crayfish are often problematic, and it has been suggested that their egg predation could reduce recruitment in depleted stocks of native fish.

    3. Here, we report the results of a field experiment, using experimental cages, on the extent of predation on eggs of great Arctic charr (Salvelinus umbla) in Lake Vättern, Europe’s fifth largest lake. Here, the great Arctic charr has declined dramatically and is listed as critically endangered.

    4. We were able to partition the total loss rate of eggs into background mortality, predation by introduced signal crayfish (Pacifastacus leniusculus) and predation by native fish. The mortality rate of charr eggs because of crayfish was estimated at more than five times that because of native fish. Of the total loss of eggs, 80% is believed to be caused by crayfish and 14% by fish, with 6% being natural background mortality.

    5. In a worst case scenario, our data infer that only 25% of the original number of eggs would survive, compared with 75% in the absence of crayfish. This could impair recovery of the stock of the endangered great Arctic charr in Lake Vättern.

    6. Contrary to earlier claims that crayfish predation on eggs of great Arctic charr is insignificant, our results indicate that crayfish predation may exceed fish predation and suggest that the abundance of signal crayfish on the spawning sites of great Arctic charr should be managed.

  • 379.
    Shamloo-Dashtpagerdi, Roohollah
    et al.
    Shiraz University, Iran.
    Razi, Hooman
    Shiraz University, Iran.
    Aliakbari, Massumeh
    Shiraz University, Iran.
    Lindlöf, Angelica
    University of Skövde, The Systems Biology Research Centre. University of Skövde, School of Bioscience.
    Ebrahimi, Mahdi
    Alumnus from Saarland University, Germany.
    Ebrahimie, Esmaeil
    Shiraz University, Iran / The University of Adelaide, Australia.
    A novel pairwise comparison method for in silico discovery of statistically significant cis-regulatory elements in eukaryotic promoter regions: Application to Arabidopsis: Application to Arabidopsis2015In: Journal of Theoretical Biology, ISSN 0022-5193, Vol. 364, p. 364-376Article in journal (Refereed)
    Abstract [en]

    Cis regulatory elements (CREs), located within promoter regions, play a significant role in the blueprint for transcriptional regulation of genes. There is a growing interest to study the combinatorial nature of CREs including presence or absence of CREs, the number of occurrences of each CRE, as well as of their order and location relative to their target genes. Comparative promoter analysis has been shown to be a reliable strategy to test the significance of each component of promoter architecture. However, it remains unclear what level of difference in the number of occurrences of each CRE is of statistical significance in order to explain different expression patterns of two genes. In this study, we present a novel statistical approach for pairwise comparison of promoters of Arabidopsis genes in the context of number of occurrences of each CRE within the promoters. First, using the sample of 1000 Arabidopsis promoters, the results of the goodness of fit test and non-parametric analysis revealed that the number of occurrences of CREs in a promoter sequence is Poisson distributed. As a promoter sequence contained functional and non-functional CREs, we addressed the issue of the statistical distribution of functional CREs by analyzing the ChIP-seq datasets. The results showed that the number of occurrences of functional CREs over the genomic regions was determined as being Poisson distributed. In accordance with the obtained distribution of CREs occurrences, we suggested the Audic and Claverie (AC) test to compare two promoters based on the number of occurrences for the CREs. Superiority of the AC test over Chi-square (2 2) and Fisher’s exact tests was also shown, as the AC test was able to detect a higher number of significant CREs. The two case studies on the Arabidopsis genes were performed in order to biologically verify the pairwise test for promoter comparison. Consequently, a number of CREs with significantly different occurrences was identified between the promoters. The results of the pairwise comparative analysis together with the expression data for the studied genes revealed the biological significance of the identified CREs. 

  • 380.
    Shamloo-Dashtpagerdi, Roohollah
    et al.
    Shiraz University, Iran.
    Razi, Hooman
    Shiraz University, Iran.
    Lindlöf, Angelica
    University of Skövde, School of Life Sciences. University of Skövde, The Systems Biology Research Centre.
    Niazi, Ali
    Shiraz University, Iran.
    Dadkhodaie, Ali
    Shiraz University, Iran.
    Ebrahimie, Esmaeil
    University of Adelaide, Australia.
    Comparative analysis of expressed sequence tags (ESTs) from Triticum monococcum shoot apical meristem at vegetative and reproductive stages2013In: Genes and Genomics, ISSN 1976-9571, Vol. 35, no 3, p. 365-375Article in journal (Refereed)
    Abstract [en]

    Triticum monococcum has recently drawn the attention of biologists to discover and utilize novel genes and alleles. To explore the molecular features of the genetic network governing floral transition in shoot apical meristem (SAM) of spring growth habit T. monococcum, two expressed sequence tag (EST) libraries containing 3,031 ESTs from vegetative SAM (VS) and 2,647 ESTs from early reproductive SAM (RS) were analyzed. Assembly of ESTs resulted in 2,303 unigenes for VS library (368 contigs and 1,935 singletons) and 1,890 unigenes (337 contigs and 1,553 singletons) for RS library. The 67.05 % of VS unigenes and 66.30 % of RS unigenes showed significant similarity with genes of known, putative and or unknown function, whereas the remaining 32.95 % of the VS unigenes and 33.7 % of RS unigenes displayed no significant match with the public protein database. The 1,064 and 866 unigenes of VS and RS libraries were assigned to functional categories using Pageman ontology tool. Further analysis revealed that the switch from VS to RS caused significant changes in the abundance of unigenes assigned to some functional categories. A total of 37 genes were identified which were significantly differentially expressed between vegetative and reproductive stages of T. monococcum SAM. Investigation of the differentially expressed genes revealed the importance of the genes involved in energy metabolism, ubiquitin/26S proteasome system, polyamines biosynthesis and signaling of reactive oxygen species in SAM differentiation towards floral transition in T. monococcum.

  • 381.
    Shamloo-Dashtpagerdia, Roohollah
    et al.
    Department of Agriculture and Natural Resources, Higher Education Center of Eghlid, Iran.
    Lindlöf, Angelica
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre.
    Niazi, Ali
    Institute of Biotechnology, Shiraz University, Iran.
    Pirasteh-Anosheh, Hadi
    National Salinity Research Center, Agricultural Research, Education and Extension Organization, Yazd, Iran.
    LOS2 gene plays a potential role in barley (Hordeum vulgare L.) salinity tolerance as a hub gene2019In: Molecular breeding, ISSN 1380-3743, E-ISSN 1572-9788, Vol. 39, no 8, article id 119Article in journal (Refereed)
    Abstract [en]

    Understanding how plants respond to salinity stress is essential for developing tolerant genotypes, to keep human food secure since it is threaten by climate changes and increasing population worldwide. Barley (Hordeum vulgare) is a crop that possesses various salinity tolerance mechanisms that remain to be explored. In this study, data from an RNA-Seq experiment in barley was analyzed to identify changes in genome activities as well as differentially expressed genes (DEGs) in response to salinity stress. A gene network was predicted among identified DEGs and was subjected to network topology analysis, which resulted in the prediction of a hub gene, namely low expression of osmotically responsive gene 2 (LOS2). LOS2 and its two hierarchical downstream genes, salt-tolerant zinc finger (ZAT10) and ascorbate peroxidase 1 (APX1), were used in a genome-wide association (GWA) survey to confirm their importance. A field experiment was conducted to recognize susceptible and tolerant genotypes among 10 different barley genotypes based on the principle component analysis (PCA) of stress-related indices. In a separate salinity experiment, two of the genotypes were assessed to assign their physiological and biochemical responses as well as to identify expression profiles of LOS2, ZAT10, and APX1. From the results, the activity of the barley genome was significantly altered toward response to stress. In total, 5692 DEGs were identified and the gene network derived from these genes contained 131 nodes and 257 edges. The identified genotypes clearly showed the difference in water status, osmolyte accumulation, cell membrane damages, and ion homeostasis as well as in expression profiles for studied genes during salinity stress. Our results suggest that LOS2 along with the ZAT10 and APX1 genes may serve as an important part of barley salinity stress tolerance pathways. To our knowledge, this is the first report on the role(s) of LOS2 in barley salinity stress tolerance in a gene network system.

  • 382.
    Shen, Yang-Mei
    et al.
    Department of Oncology, Institute of Biomedicine and Surgery, University of Linköping, S-581 85 Linköping, Sweden / Department of Pathology, West China Second University Hospital, Sichuan University, Chengdu, P.R. China.
    Arbman, Gunnar
    Department of Surgery, Vrinnevi Hospital, Norrköping, Sweden.
    Sandström, Per
    Department of Surgery, Institute of Biomedicine and Surgery, University of Linköping, S-581 85 Linköping, Sweden.
    Gullstrand, Per
    Department of Surgery, Institute of Biomedicine and Surgery, University of Linköping, S-581 85 Linköping, Sweden.
    Wei, Yu-Quan
    State Key laboratory of Biotherapy of Human Diseases, West China University Hospital, Sichuan University, Chengdu, P.R. China.
    Zhang, Hong
    University of Skövde, The Systems Biology Research Centre. University of Skövde, School of Life Sciences.
    Rosell, Johan
    Department of Oncology, Institute of Biomedicine and Surgery, University of Linköping, S-581 85 Linköping, Sweden.
    Olsson, Birgit
    Department of Oncology, Institute of Biomedicine and Surgery, University of Linköping, S-581 85 Linköping, Sweden.
    Peng, Feng
    State Key laboratory of Biotherapy of Human Diseases, West China University Hospital, Sichuan University, Chengdu, P.R. China.
    Yang, Han-Shuo
    State Key laboratory of Biotherapy of Human Diseases, West China University Hospital, Sichuan University, Chengdu, P.R. China.
    Wang, Chun-Ting
    State Key laboratory of Biotherapy of Human Diseases, West China University Hospital, Sichuan University, Chengdu, P.R. China.
    Sun, Xiao-Feng
    Department of Oncology, Institute of Biomedicine and Surgery, University of Linköping, S-581 85 Linköping, Sweden / Department of Gastrointestinal Surgery, West China Hospital, Sichuan University, Chengdu, P.R. China.
    Novel gene hBiot2 is an independent prognostic factor in colorectal cancer patients2012In: Oncology Reports, ISSN 1021-335X, E-ISSN 1791-2431, Vol. 27, no 2, p. 376-382Article in journal (Refereed)
    Abstract [en]

    The present study investigated the expression of the novel gene hBiot2 in colorectal cancer (CRC) and its relationships with clinicopathological variables in CRC patients. The expression of hBiot2 in 163 primary CRCs together with the corresponding normal mucosa, 36 liver metastases and 5 colon cancer cell lines was examined using real-time PCR. In situ hybridization (ISH) was performed to evaluate the localization of hBiot2 expression in CRC and normal mucosa. hBiot2 expression at the RNA level was localized in the nucleus of tumor cells and normal epithelial cells. The mean expression of hBiot2 in the CRCs (243.571 +/- 564.569) was higher compared to the normal mucosa (107.252 +/- 413.635, P<0.0001) and liver metastasis samples (42.002 +/- 40.809, P=0.0002). hBiot2 expression was increased from stages I + II to III (P=0.047), and no difference in the expression was found in stages III and IV (P=0.452). A high value of hBiot2 was associated with a poorer prognosis compared with a low value independently of gender, age, tumor site, stage and differentiation (P=0.007, RR 7.519, 95% Cl 1.729-32.704). Liver metastasis, smaller tumors, non-local recurrence and primary liver surgery alone were associated with a higher value of hBiot2 compared to larger tumors, local recurrence and repeated liver surgery (P=0.003, 0.044 and 0.026, respectively). An inverse relationship was found between hBiot2 expression and the metastatic potential of the colon cancer cell lines. Thus, increased expression of hBiot2 may be an early and interim event in the development of CRC. A higher expression of hBiot2 in primary CRC patients independently indicates a poorer prognosis.

  • 383.
    Shumkova, E. S.
    et al.
    A N Bach Institute of Biochemistry, RAS, Moscow, Russia / Perm State National Research University, Perm, Russia.
    Olsson, Björn E.
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre. Perm State National Research University, Perm, Russia.
    Plotnikova, E. G.
    Perm State National Research University, Perm, Russia / Institute of Ecology and Genetics of Microorganisms, UB RAS, Perm, Russia.
    Organization of Biphenyl and Polychlorinated Biphenyls Destruction Genes in Rhodococcus ruber P252015In: Russian Journal of Immunology, ISSN 1028-7221, Vol. 9, no 2, p. 624-626Article in journal (Refereed)
  • 384.
    Shumkova, Ekaterina
    et al.
    A.N. Bach Institute of Biochemistry, Russian Academy of Sciences, Moscow, Russia a/ Perm State University, Perm, Russia.
    Olsson, Björn
    University of Skövde, The Systems Biology Research Centre. University of Skövde, School of Bioscience.
    Kudryavtseva, Anna
    Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.
    Plotnikova, Elena
    Perm State University, Perm, Russia / Institute of Ecology and Genetics of Microorganisms, Ural Branch of the Russian Academy of Sciences, Perm, Russia.
    Draft Genome Sequence of Rhodococcus ruber Strain P25: an Active Polychlorinated Biphenyl Degrader2015In: Genome Announcements, ISSN 2169-8287, E-ISSN 2169-8287, Vol. 3, no 5, article id e00990-15Article in journal (Refereed)
    Abstract [en]

    We report the 5,728,255-bp draft genome sequence of Rhodococcus ruber P25, isolated from a soil polluted with halogenated aromatic compounds in the city of Perm, Russia. The strain degrades polychlorinated biphenyls and a broad range of aromatic compounds. It possesses genes that mediate the degradation of biphenyls/polychlorinated biphenyls, naphthalene, and monoaromatic compounds.

  • 385.
    Sikka, Pilleriin
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre. Centre for Cognitive Neuroscience, Department of Psychology, University of Turku, Finland.
    How to Study Dream Experiences2019In: Dreams: Understanding Biology, Psychology, and Culture Volume 1 / [ed] Robert J. Hoss, Katja Valli, Robert P. Gongloff, Santa Barbara, CA: Greenwood, an Imprint of ABC-CLIO, LLC , 2019, 1, p. 153-166Chapter in book (Refereed)
    Abstract [en]

    In the scientific study of dreams, as in the scientific study of any other topic, it is important to first clearly define the phenomenon one is investigating. The definition determines what exactly is being studied. Then, the methods for collecting and analyzing data regarding this phenomenon need to be chosen. These methods determine what kind of results are obtained, to what extent the results reflect the phenomenon of interest, and whether the results can be trusted. This chapter gives an overview of how dream experiences are scientifically studied: how dreams and dreaming are defined, what kinds of methods are used to collect and analyze dream data, and what aspects need to be considered when conducting and reading studies that investigate dream experiences (see also Kahan & Horton, 2012, and Zadra & Domhoff, 2017).

  • 386.
    Sikka, Pilleriin
    et al.
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre. Centre for Cognitive Neuroscience, Department of Psychology, University of Turku, Finland.
    Feilhauer, Diana
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre.
    Valli, Katja
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre. Centre for Cognitive Neuroscience, Department of Psychology, University of Turku, Finland.
    Revonsuo, Antti
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre. Centre for Cognitive Neuroscience, Department of Psychology, University of Turku, Finland.
    How You Measure Is What You Get: Differences in Self- and External Ratings of Emotional Experiences in Home Dreams2017In: American Journal of Psychology, ISSN 0002-9556, E-ISSN 1939-8298, Vol. 130, no 3, p. 367-384Article in journal (Refereed)
    Abstract [en]

    This study demonstrates that different methods for measuring emotional experiences in dreams — self-ratings of dreams using emotion rating scales versus external ratings in the form of content analysis of narrative dream reports — can lead to strikingly different results and contradicting conclusions about the emotional content of home dreams. During 3 consecutive weeks, every morning upon awakening, 44 participants (16 men, 28 women, average age 26.9± 5.1 years) reported their dreams and rated their emotional experiences in those dreams using the modified Differential Emotions Scale. Two external judges rated emotional experiences inthe same 552 (M = 12.55 ± 5.72) home dream reports using the same scale. Comparison of the 2 methods showed that with self-ratings dreams were rated as more emotional and more positive than with external ratings. Moreover, whereas with self-ratings the majority of dreams was rated as positively valenced, with external ratings the majority of dream reports was rated as negatively valenced. Although self- and external ratings converge, at least partially, in the measurement of negative emotional experiences, they diverge greatly in the measurement of positive emotional experiences. On one hand, this discrepancy may result from different biases inherent in the 2 measurement methods highlighting the need to develop better methods for measuring emotional experiences. On the other hand, self- and external ratings may capture different phenomena and should thus be considered complementary and used concurrently. Nevertheless, results suggest that negative emotional experiences can be measured in a more valid and reliable manner than positive emotional experiences.

  • 387.
    Sikka, Pilleriin
    et al.
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre. Department of Psychology and Speech-Language Pathology, Turku Brain and Mind Center, University of Turku, Turku, Finland.
    Pesonen, Henri
    Department of Mathematics and Statistics, University of Turku, Turku, Finland / Department of Computer Science, Aalto University, Helsinki, Finland.
    Revonsuo, Antti
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre. Department of Turku Brain and Mind Center, University of Turku, Finland.
    Peace of mind and anxiety in the waking state are related to the affective content of dreams2018In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 8, article id 12762Article in journal (Refereed)
    Abstract [en]

    Waking mental well-being is assumed to be tightly linked to sleep and the affective content of dreams. However, empirical research is scant and has mostly focused on ill-being by studying the dreams of people with psychopathology. We explored the relationship between waking well-being and dream affect by measuring not only symptoms of ill-being but also different types and components of well-being. Importantly, this is the first time peace of mind was investigated as a distinct aspect of well-being in a Western sample and in relation to dream content. Healthy participants completed a well-being questionnaire, followed by a three-week daily dream diary and ratings of dream affect. Multilevel analyses showed that peace of mind was related to positive dream affect, whereas symptoms of anxiety were related to negative dream affect. Moreover, waking measures were better related to affect expressed in dream reports rather than participants’ self-ratings of dream affect. We propose that whereas anxiety may reflect affect dysregulation in waking and dreaming, peace of mind reflects enhanced affect regulation in both states of consciousness. Therefore, dream reports may possibly serve as markers of mental health. Finally, our study shows that peace of mind complements existing conceptualizations and measures of well-being.

  • 388.
    Sikka, Pilleriin
    et al.
    University of Skövde, The Systems Biology Research Centre. University of Skövde, School of Bioscience. Department of Psychology, University of Turku, Finland.
    Revonsuo, Antti
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre. Department of Psychology, University of Turku, Finland.
    Noreika, Valdas
    Department of Psychology, University of Cambridge, UK.
    Valli, Katja
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre. Department of Psychology, University of Turku, Finland.
    EEG Frontal Alpha Asymmetry and Dream Affect: Alpha Oscillations Over the Right Frontal Cortex During REM Sleep and Pre-Sleep Wakefulness Predict Anger in REM Sleep Dreams2019In: Journal of Neuroscience, ISSN 0270-6474, E-ISSN 1529-2401, Vol. 39, no 24, p. 4775-4784, article id 2884-18Article in journal (Refereed)
    Abstract [en]

    Affective experiences are central not only to our waking life but also to rapid eye movement(REM) sleep dreams. Despite our increasing understanding of the neural correlates of dreaming, we know little about the neural correlates of dream affect. Frontal alpha asymmetry (FAA) is considered a marker of affective states and traits as well as affect regulation in the waking state. Here, we explored whether FAA during REM sleep and during evening resting wakefulness is related to affective experiences in REM sleep dreams. EEG recordings were obtained from 17humanparticipants (7men)whospent 2 nights in the sleep laboratory. Participants were awakened 5minafter the onset of everyREMstage after which they provided a dream report and rated their dream affect. Two-minute preawakening EEG segments were analyzed. Additionally, 8 min of evening presleep and morning postsleep EEG were recorded during resting wakefulness. Mean spectral power in the alpha band (8 –13 Hz and correspondingFAAwere calculated over the frontal (F4-F3) sites. Results showed that FAA during REM sleep, and during evening resting wakefulness, predicted ratings of dream anger. This suggests that individuals with greater alpha power in the right frontal hemisphere may be less able to regulate (i.e., inhibit) strong affective states, such as anger, in dreams. Additionally, FAA was positively correlated across wakefulness and REM sleep. Together, these findings imply that FAA may serve as a neural correlate of affect regulation not only in the waking but also in the dreaming state.

  • 389.
    Sikka, Pilleriin
    et al.
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre. Centre for Cognitive Neuroscience, Department of Psychology, University of Turku, Finland.
    Revonsuo, Antti
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre. Centre for Cognitive Neuroscience, Department of Psychology, University of Turku, Finland.
    Sandman, Nils
    Centre for Cognitive Neuroscience, Department of Psychology, University of Turku, Finland / The Genomics and Biomarkers Unit, National Institute for Health and Welfare, Finland.
    Tuominen, Jarno
    Centre for Cognitive Neuroscience, Department of Psychology, University of Turku, Finland.
    Valli, Katja
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre. Centre for Cognitive Neuroscience, Department of Psychology, University of Turku, Finland.
    Dream emotions: a comparison of home dream reports with laboratory early and late REM dream reports2018In: Journal of Sleep Research, ISSN 0962-1105, E-ISSN 1365-2869, Vol. 27, no 2, p. 206-214Article in journal (Refereed)
    Abstract [en]

    The aim of this study was to compare the emotional content of dream reports collected at home upon morning awakenings with those collectedin the laboratory upon early and late rapid eye movement (REM) sleep awakenings. Eighteen adults (11 women, seven men; mean age = 25.89 ± 4.85) wrote down their home dreams every morning immediately upon awakening during a 7-day period. Participants also spent two non-consecutive nights in the sleep laboratory where they were awoken 5 min into each continuous REM sleep stage, upon which they gave a verbal dream report. The content of a total of 151 home and 120 laboratory dream reports was analysed by two blind judges using the modified Differential Emotions Scale. It was found that: (1) home dream reports were more emotional than laboratory early REM dream reports, but not more emotional than laboratory late REM dream reports; (2) home dream reports contained a higher density of emotions than laboratory (early or late REM) dream reports; and (3) home dream reports were more negative than laboratory dream reports, but differences between home and early REM reports were larger than those between home and late REM reports. The results suggest that differences between home and laboratory dream reports in overall emotionality may be due to the time of night effect. Whether differences in the density of emotions and negative emotionality are due to sleep environment or due to different reporting procedures and time spent in a sleep stage, respectively, remains to be determined in future studies.

  • 390.
    Sikka, Pilleriin
    et al.
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre. Centre for Cognitive Neuroscience, Department of Psychology, University of Turku, Finland.
    Revonsuo, Antti
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre. University of Turku, Finland.
    Valli, Katja
    Methodological Issues in Measuring Dream Emotions2016Conference paper (Refereed)
    Abstract [en]

    Emotions are central in dreams, specifically in rapid eye movement sleep dreams. Despite a wealth of research on the emotional content of dreams, there is little consensus about the overall emotionality and predominant valence of dreams or about the prevailing specific emotions in dreams. Previous contradictory findings are arguably due to unresolved methodological issues. However, studies that have directly investigated these methodological issues are scarce. In this presentation three studies that investigated the effect of study methodology on the frequency, valence and phenomenological content of dream emotions are discussed. The studies demonstrate that the use of different methods for rating dream emotions (participants who experience the dream vs external judges who analysed the respective dream report) and for collecting dream reports (home vs laboratory setting) leads to very different results and conclusions about the emotional content of dreams. As such, these studies highlight the importance of carefully considering study methodology when conducting and interpreting dream (emotional) content studies.

  • 391.
    Sikka, Pilleriin
    et al.
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre. Centre for Cognitive Neuroscience, Department of Psychology, University of Turku, Finland.
    Valli, Katja
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre. Centre for Cognitive Neuroscience, Department of Psychology, University of Turku, Finland.
    Virta, Tiina
    Centre for Cognitive Neuroscience, Department of Psychology, University of Turku, Finland.
    Revonsuo, Antti
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre.
    I know how you felt last night, or do I?: Self- and external ratings of emotions in REM dreams2014In: Consciousness and Cognition, ISSN 1053-8100, E-ISSN 1090-2376, Vol. 25, p. 51-66Article in journal (Refereed)
    Abstract [en]

    We investigated whether inconsistencies in previous studies regarding emotional experiencesin dreams derive from whether dream emotions are self-rated or externally evaluated.Seventeen subjects were monitored with polysomnography in the sleep laboratoryand awakened from every rapid eye movement (REM) sleep stage 5 min after the onsetof the stage. Upon awakening, participants gave an oral dream report and rated their dreamemotions using the modified Differential Emotions Scale, whereas external judges rated theparticipants’ emotions expressed in the dream reports, using the same scale. The twoapproaches produced diverging results. Self-ratings, as compared to external ratings,resulted in greater estimates of (a) emotional dreams; (b) positively valenced dreams;(c) positive and negative emotions per dream; and (d) various discrete emotions representedin dreams. The results suggest that this is mostly due to the underrepresentationof positive emotions in dream reports. Possible reasons for this discrepancy are discussed.

  • 392.
    Singh, Neha
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre.
    Breakthrough insight into HPV infection as an emerging risk factor in prostate cancer2015In: Onkologi i Sverige, ISSN 1653-1582, no 3, p. 76-77Article in journal (Other (popular science, discussion, etc.))
  • 393.
    Singh, Neha
    et al.
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre. Department of Biotechnology, Panjab University, Chandigarh, India.
    Hussain, Showket
    Division of Molecular Oncology, Institute of Cytology and Preventive Oncology (ICMR), NOIDA, India.
    Kakkar, Nandita
    Department of Histopathology, Post Graduate Institute of Medical Education and Research, Chandigarh, India.
    Singh, Shrawan K.
    Department of Urology, Post Graduate Institute of Medical Education and Research, Chandigarh, India.
    Sobti, Ranbir C.
    Department of Biotechnology, Panjab University, Chandigarh, India.
    Bharadwaj, Mausumi
    Division of Molecular Oncology, Institute of Cytology and Preventive Oncology (ICMR), NOIDA, India.
    Implication of high risk Human papillomavirus HR-HPV infection in prostate cancer in Indian population- A pioneering case-control analysis2015In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 5, article id 7822Article in journal (Refereed)
    Abstract [en]

    Prostate cancer is the second most common cancer with sexual history as a consistent risk factor. This is the pioneering study that evaluates the frequency of HPV infection in prostate cancer in India. Ninety five (95) histopathologically confirmed cancer and fifty five (55) BPH from Indian population were analyzed for HPV infection using a pair of consensus sequence primer followed by type specific PCRs for both high-risk and low-risk HPV types. The data demonstrate HPV infection in 41% of prostate tumor biopsies and 20% in BPH. Subsequent PCR- based HPV typing using type - specific primers revealed 32% were infected with HPV type 16 whereas 6% were found to be positive for HPV type 18, while in BPH controls only 5% of the BPH controls were infected with HPV 16 and this difference was highly significant (p = 0.0004). Significant proportion of HPV infected (74%) cases belonged to stage III and IV (p < 0.001) with a high Gleason score ≥8 (p = 0.003). The study represents for the first time the incidence of HPV infection in prostate cancer in Indian population and strengthens the hypothesis that HPV infection could be one of the co factor associated with progression of prostate cancer.

  • 394.
    Singh, Neha
    et al.
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre. Department of Biotechnology, Panjab University, Chandigarh, India.
    Hussain, Showket
    Division of Molecular Oncology, Institute of Cytology and Preventive Oncology (ICMR), Noida, India.
    Sharma, Upma
    Division of Molecular Genetics and Biochemistry, Institute of Cytology and Preventive Oncology (ICMR), Noida, India.
    Suri, Vanita
    Department of Obstetrics and Gynecology, Post Graduate Institute of Medical Education and Research, Chandigarh, India.
    Nijhawan, Raje
    Department of Cytology & Gynae. Pathology, Post Graduate Institute of Medical Education and Research, Chandigarh, India.
    Bharadwaj, Mausumi
    Division of Molecular Genetics and Biochemistry, Institute of Cytology and Preventive Oncology (ICMR), Noida, India.
    Sobti, R. C.
    Department of Biotechnology, Panjab University, Chandigarh, India / Vice Chancellor BBA (Central) University, Lucknow, India.
    The protective role of the -1306C>T functional polymorphism in matrix metalloproteinase-2 gene is associated with cervical cancer: implication of human papillomavirus infection2016In: Tumor Biology, ISSN 1010-4283, E-ISSN 1423-0380, Vol. 37, no 4, p. 5295-5303Article in journal (Refereed)
  • 395.
    Sivertsson, Louise
    et al.
    Section of Pharmacogenetics, Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden.
    Synnergren, Jane
    University of Skövde, School of Life Sciences. University of Skövde, The Systems Biology Research Centre.
    Jensen, Janne
    Cellectis Stem Cells, Cellartis AB, Göteborg, Sweden.
    Björquist, Petter
    Cellectis Stem Cells, Cellartis AB, Göteborg, Sweden.
    Ingelman-Sundberg, Magnus
    Section of Pharmacogenetics, Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden.
    Hepatic differentiation and maturation of human embryonic stem cells cultured in a perfused three-dimensional bioreactor2013In: Stem Cells and Development, ISSN 1547-3287, E-ISSN 1557-8534, Vol. 22, no 4, p. 581-594Article in journal (Refereed)
    Abstract [en]

    Drug-induced liver injury is a serious and frequently occurring adverse drug reaction in the clinics and is hard to predict during preclinical studies. Today, primary hepatocytes are the most frequently used cell model for drug discovery and prediction of toxicity. However, their use is marred by high donor variability regarding drug metabolism and toxicity, and instable expression levels of liver-specific genes such as cytochromes P450. An in vitro model system based on human embryonic stem cells (hESC), with their unique properties of pluripotency and self-renewal, has potential to provide a stable and unlimited supply of human hepatocytes. Much effort has been made to direct hESC toward the hepatic lineage, mostly using 2-dimensional (2D) cultures. Although the results are encouraging, these cells lack important functionality. Here, we investigate if hepatic differentiation of hESC can be improved by using a 3-dimensional (3D) bioreactor system. Human ESCs were differentiated toward the hepatic lineage using the same cells in either the 3D or 2D system. A global transcriptional analysis identified important differences between the 2 differentiation regimes, and we identified 10 pathways, highly related to liver functions, which were significantly upregulated in cells differentiated in the bioreactor compared to 2D control cultures. The enhanced hepatic differentiation observed in the bioreactor system was also supported by immunocytochemistry. Taken together, our results suggest that hepatic differentiation of hESC is improved when using this 3D bioreactor technology as compared to 2D culture systems. © Copyright 2013, Mary Ann Liebert, Inc. 2013.

  • 396.
    Skillbäck, Tobias
    et al.
    Department of Neurochemistry, Institute of Neuroscience and Physiology, the Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden / Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden.
    Delsing, Louise
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre. Department of Neurochemistry, Institute of Neuroscience and Physiology, the Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden.
    Synnergren, Jane
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre.
    Mattsson, Niklas
    Clinical Memory Research Unit, Department of Clinical Sciences Malmö, Lund University, Malmö, Sweden / Department of Neurology, Skåne University Hospital, Lund, Sweden.
    Janelidze, Shorena
    Clinical Memory Research Unit, Department of Clinical Sciences Malmö, Lund University, Malmö, Sweden.
    Nägga, Katarina
    Clinical Memory Research Unit, Department of Clinical Sciences Malmö, Lund University, Malmö, Sweden.
    Kilander, Lena
    Department of Public Health and Caring Sciences/Geriatrics, Uppsala University, Uppsala, Sweden.
    Hicks, Ryan
    Discovery Sciences, IMED Biotech Unit, AstraZeneca, Mölndal, Sweden.
    Wimo, Anders
    Centre for Research and Development, Uppsala University/County Council of Gävleborg, Gävle, Sweden / Division for Neurogeriatrics, Department of Neurobiology, Care Sciences, and Society (NVS), Center for Alzheimer Research, Karolinska Institutet, Huddinge, Sweden.
    Winblad, Bengt
    Division for Neurogeriatrics, Department of Neurobiology, Care Sciences, and Society (NVS), Center for Alzheimer Research, Karolinska Institutet, Huddinge, Sweden / Department Geriatric Medicine, Karolinska University Hospital, Huddinge, Sweden.
    Hansson, Oskar
    Clinical Memory Research Unit, Department of Clinical Sciences Malmö, Lund University, Malmö, Sweden / Department of Neurology, Skåne University Hospital, Lund, Sweden.
    Blennow, Kaj
    Department of Neurochemistry, Institute of Neuroscience and Physiology, the Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden / Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden.
    Eriksdotter, Maria
    Department Geriatric Medicine, Karolinska University Hospital, Huddinge, Sweden / Division of Clinical Geriatrics, Department of Neurobiology, Care Sciences, and Society (NVS), Center for Alzheimer Research, Karolinska Institutet, Huddinge, Sweden.
    Zetterberg, Henrik
    Department of Neurochemistry, Institute of Neuroscience and Physiology, the Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden / Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden / Department of Molecular Neuroscience, UCL Institute of Neurology, London, United Kingdom / UK Dementia Research Institute at UCL, London, United Kingdom.
    CSF/serum albumin ratio in dementias: a cross-sectional study on 1861 patients2017In: Neurobiology of Aging, ISSN 0197-4580, E-ISSN 1558-1497, Vol. 59, p. 1-9Article in journal (Refereed)
    Abstract [en]

    A connection between dementias and blood-brain barrier (BBB) dysfunction has been suggested, but previous studies have yielded conflicting results. We examined cerebrospinal fluid (CSF)/serum albumin ratio in a large cohort of patients diagnosed with Alzheimer's disease (AD, early onset [EAD, n = 130], late onset AD [LAD, n = 666]), vascular dementia (VaD, n = 255), mixed AD and VaD (MIX, n = 362), Lewy body dementia (DLB, n = 50), frontotemporal dementia (FTD, n = 56), Parkinson's disease dementia (PDD, n = 23), other dementias (other, n = 48), and dementia not otherwise specified (NOS, n = 271). We compared CSF/serum albumin ratio to 2 healthy control groups (n = 292, n = 20), between dementia diagnoses, and tested biomarker associations. Patients in DLB, LAD, VaD, MIX, other, and NOS groups had higher CSF/serum albumin ratio than controls. CSF/serum albumin ratio correlated with CSF neurofilament light in LAD, MIX, VaD, and other groups but not with AD biomarkers. Our data show that BBB leakage is common in dementias. The lack of association between CSF/serum albumin ratio and AD biomarkers suggests that BBB dysfunction is not inherent to AD but might represent concomitant cerebrovascular pathology.

  • 397.
    Sogaard, Peter
    et al.
    University of Skövde, The Systems Biology Research Centre. University of Skövde, School of Life Sciences.
    Szekeres, Ferenc
    Karolinska Institutet.
    Garcia-Roves, Pablo M.
    Karolinska Institutet.
    Larsson, Dennis
    University of Skövde, The Systems Biology Research Centre. University of Skövde, School of Life Sciences.
    Chibalin, Alexander V.
    Karolinska Institutet.
    Zierath, Juleen R.
    Karolinska Institutet.
    Spatial Insulin Signalling in Isolated Skeletal Muscle Preparations2010In: Journal of Cellular Biochemistry, ISSN 0730-2312, E-ISSN 1097-4644, Vol. 109, no 5, p. 943-949Article in journal (Refereed)
    Abstract [en]

    During in vitro incubation in the absence or presence of insulin, glycogen depletion occurs in the inner core of the muscle specimen, concomitant with increased staining of hypoxia-induced-factor-1-alpha and caspase-3, markers of hypoxia and apoptosis, respectively. The aim of this study was to determine whether insulin is able to diffuse across the entire muscle specimen in sufficient amounts to activate signalling cascades to promote glucose uptake and glycogenesis within isolated mouse skeletal muscle. Phosphoprotein multiplex assay on lysates from muscle preparation was performed to detect phosphorylation of insulin-receptor on Tyr1146, Akt on Ser473 and glycogen-synthases-kinase-3 on Ser21/Ser9. To address the spatial resolution of insulin signalling, immunohistochemistry studies on cryosections were performed. Our results provide evidence to suggest that during the in vitro incubation, insulin sufficiently diffuses into the centre of tubular mouse muscles to promote phosphorylation of these signalling events. Interestingly, increased insulin signalling was observed in the core of the incubated muscle specimens, correlating with the location of oxidative fibres. In conclusion, insulin action was not restricted due to insufficient diffusion of the hormone during in vitro incubation in either extensor digitorum longus or soleus muscles from mouse under the specific experimental settings employed in this study. Hence, we suggest that the glycogen depleted core as earlier observed is not due to insufficient insulin action.

  • 398.
    Song, Gang
    et al.
    Cancer Research Center, Medical College, Xiamen University, Xiamen 361005, China.
    Guo, Shiguang
    Cancer Research Center, Medical College, Xiamen University, Xiamen 361005, China.
    Wang, Weiwei
    Cancer Research Center, Medical College, Xiamen University, Xiamen 361005, China.
    Hu, Chun
    Cancer Research Center, Medical College, Xiamen University, Xiamen 361005, China.
    Mao, Yubing
    Department of Basic Medical Sciences, Medical College, Xiamen University, Xiamen 361005, China.
    Zhang, Bing
    Department of Basic Medical Sciences, Medical College, Xiamen University, Xiamen 361005, China.
    Zhang, Hong
    University of Skövde, School of Life Sciences. University of Skövde, The Systems Biology Research Centre. Cancer Research Center, Medical College, Xiamen University, Xiamen 361005, China.
    Hu, Tianhui
    Cancer Research Center, Medical College, Xiamen University, Xiamen 361005, China.
    Intestinal Metabolite Compound K of Ginseng Saponin Potently Attenuates Metastatic Growth of Hepatocellular Carcinoma by Augmenting Apoptosis via a Bid-Mediated Mitochondrial Pathway2010In: Journal of Agricultural and Food Chemistry, ISSN 0021-8561, E-ISSN 1520-5118, Vol. 58, no 24, p. 12753-12760Article in journal (Refereed)
    Abstract [en]

    It was recently shown that compound K (CK), an intestinal bacterial metabolite of ginseng saponin, exhibits antihepatocellular carcinoma (HCC) activity, and Bid is a potential drug target for HCC therapy. This paper reports a novel mechanism of CK-induced apoptosis of HCC cells via Bid-mediated mitochondrial pathway. OK dramatically inhibited HCC cells growth in concentration- and time-dependent manners, and a high dose of OK could induce HCC cell apoptotic cell death. Furthermore, the effective dose of CK potently attenuated the subcutaneous tumor growth and spontaneous HOC metastasis in vivo. At the molecular level, immunohistochemical staining revealed that Bid expression in subcutaneous tumor and liver metastasis tissues decreased dramatically in OK-treated groups compared to untreated controls, which also implies that Bid may play a critical role in the growth and progression of HCC. Further study shows that translocation of full-length Bid to the mitochondria from nuclei during cytotoxic apoptosis was associated with the release of cytochrome c from mitochondria, indicating that full-length Bid is sufficient for the activation of mitochondrial cell death pathways in response to CK treatment in HCC cells. Taken together, the results not only reveal a Bid-mediated mitochondrial pathway in HCC cells induced by CK but also suggest that OK may become a potential cytotoxic drug targeting Bid in the prevention and treatment of HCC.

  • 399.
    Srivasta, Amrita
    et al.
    Botany Department, University of Pune, Pune, India.
    Mehta, Sameet
    Centre for modeling and Simulation, University of Pune, Pune, India.
    Lindlöf, Angelica
    University of Skövde, The Systems Biology Research Centre. University of Skövde, School of Life Sciences.
    Bhargava, Sujata
    Botany Department, University of Pune, Pune, India.
    Over-represented promoter motifs in abiotic stress-induced DREB genes of rice and sorghum and their probable role in regulation of gene expression2010In: Plant Signalling & Behavior, ISSN 1559-2316, E-ISSN 1559-2324, Vol. 5, no 7, p. 775-784Article in journal (Refereed)
    Abstract [en]

    Genes coding for drought response element binding (DREB) proteins regulate transcription of a large number of downstream genes involved in the plant response to abiotic stresses. However the regulation of DREB genes themselves is not well understood. Using a bioinformatics approach, we identified the over-represented motifs in promoters of DREB genes of sorghum and rice as compared to all the other promoters in their genomes. Aligned orthologous promoter pairs of sorghum and rice DREBs were then used to identify co-localized motifs from among the over-represented ones, assuming that such motifs were likely to play a regulatory role. Finally the motifs over-represented in sorghum DREBs in comparison to their rice orthologs were identified. Results indicated over-representation of motifs pertaining to calcium, light, sugar, and hormone signaling in the DREB promoters. The co-localized motifs in DREB promoters were mainly those involved in abscisic acid-, light- and calcium-mediated regulation. These motifs along with others pertaining to ethylene signaling were over-represented in sorghum DREB promoters as compared to their orthologs from rice and could possibly contribute to its drought tolerance.  Besides calcium, an integration of abscisic acid, ethylene, auxin and methyl jasmonate signaling was probably involved in regulating expression of the drought response through DREB transcription factors.

  • 400.
    Stangeland, Biljana
    et al.
    University of Oslo.
    Rosenhave, E. Maryann
    University of Oslo.
    Winge, Per
    Norwegian University of Science and Technology.
    Berg, Anita
    University of Oslo.
    Amundsen, Silja S.
    University of Oslo.
    Karabeg, Mirela
    University of Oslo.
    Mandal, Abul
    University of Skövde, The Systems Biology Research Centre. University of Skövde, School of Life Sciences.
    Bones, Atle M.
    Norwegian University of Science and Technology.
    Grini, Paul E.
    University of Oslo.
    Aalen, Reidunn B.
    University of Oslo.
    AtMBD8 is involved in control of flowering time in the C24 ecotype of Arabidopsis thaliana2009In: Physiologia Plantarum: An International Journal for Plant Biology, ISSN 0031-9317, E-ISSN 1399-3054, Vol. 136, no 1, p. 110-126Article in journal (Refereed)
    Abstract [en]

    The Arabidopsis thaliana accession C24 is a vernalization-responsive, moderately late flowering ecotype. We report that a mutation in AtMBD8, which encodes a protein with a putative Methyl-CpG-Binding Domain (MBD), in C24 background, results in a delay in flowering time during both long and short days. The atmbd8-1 mutant responded to vernalization as wild type (wt) plants. Consistent with a role in modulation of flowering time, an AtMBD8::GUS-reporter construct was expressed in the shoot meristem region and developing leaves. Full-genome transcriptional profiling revealed very few changes in gene expression between atmbd8-1 and wt plants. The expression level of FLC, the major repressor of transition to flowering, was unchanged in atmbd8-1, and in accordance with that, genes upstream of FLC were unaffected by the mutation. The expression level of CONSTANS, involved in photoperiodic control of flowering, was very similar in atmbd8-1 and wt plants. In contrast, the major promoters of flowering, FT, and SOC1, were both downregulated. As FT is a regulator of SOC1, we conclude that AtMBD8 is a novel promotor of flowering that acts upstream of FT in the C24 accession. In contrast to atmbd8-1, the Colombia (Col) SALK T-DNA insertion line, atmbd8-2, did not display a delayed transition to flowering. Transcriptional profiling revealed that a substantial number of genes were differentially expressed between C24 and Col wt seedlings. Several of these genes are also differentially expressed in late flowering mutants. We suggest that these differences contribute to the contrasting effect of a mutation in AtMBD8 in the two ecotypes.

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