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  • 251.
    Lundh, Dan
    et al.
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre.
    Coleman, Scott
    Motion and Sports Lab, Baylor University Medical Center, Dallas, TX, USA.
    Riad, Jacques
    Orthopaedic Department, Skaraborg Hospital Skövde, Sweden / Women's and Children's Health, Karolinska Institute, Stockholm, Sweden.
    Movement deviation and asymmetry assessment with three dimensional gait analysis of both upper- and lower extremity results in four different clinical relevant subgroups in unilateral cerebral palsy2014In: Clinical Biomechanics, ISSN 0268-0033, E-ISSN 1879-1271, Vol. 29, no 4, p. 381-386Article in journal (Refereed)
    Abstract [en]

    Background

    In unilateral cerebral palsy, movement pattern can be difficult to define and quantify. The aim was to assess the degree of deviation and asymmetry in upper and lower extremities during walking.

    Methods

    Forty-seven patients, 45 Gross Motor Function Classification Scale (GMFCS) I and 2 patients GMFCS II, mean age 17.1 years (range 13.1 to 24.0) and 15 matched controls were evaluated. Gait profile score (GPS) and arm posture score (APS) were calculated from three-dimensional gait analysis (GA). Asymmetry was the calculated difference in deviation between affected and unaffected sides.

    Findings

    The GPS was significantly increased compared to the control group on the affected side (6.93 (2.08) versus 4.23 (1.11) degrees) and on the unaffected side (6.67 (2.14)). The APS was also significantly increased on the affected side (10.39 (5.01) versus 5.52 (1.71) degrees) and on the unaffected side (7.13 (2.23)). The lower extremity asymmetry increased (significantly) in comparison with the control group (7.89 (3.82) versus 3.90 (1.01)) and correspondingly in the upper extremity (9.75 (4.62) versus 5.72 (1.84)). The GPS was not different between affected and unaffected sides, however the APS was different (statistically significant).

    Interpretation

    We calculated deviation and asymmetry of movement during walking in unilateral CP, identifying four important clinical groups: close to normal, deviations mainly in the leg, deviations mainly in the arm and those with deviation in the arm and leg. This method can be applied to any patient group, and aid in diagnosing, planning treatment, and prognosis.

  • 252.
    Lundh, Dan
    et al.
    University of Skövde, School of Life Sciences. University of Skövde, The Systems Biology Research Centre.
    Coleman, Scott
    Baylor University Medical Center, Dallas, USA.
    Riad, Jacques
    Ortopaedic, Skaraborgs Hospital Skövde, Skövde, Sweden.
    The relationship between arm posturing and gait deviation in teenagers and young adults with spastic unilateral cerebral palsy2012In: Gait & Posture, ISSN 0966-6362, E-ISSN 1879-2219, Vol. 36, no Supplement 1, p. S13-Article in journal (Refereed)
  • 253.
    Lundh, Dan
    et al.
    University of Skövde, School of Life Sciences. University of Skövde, The Systems Biology Research Centre.
    Hedelin, Hans
    Skaraborgs Sjukhus, Skövde , Sweden.
    Jonsson, Karin
    Kärnsjukhuset, Skövde , Sweden.
    Gifford, Mervyn
    University of Skövde, School of Life Sciences.
    Larsson, Dennis
    University of Skövde, School of Life Sciences. University of Skövde, The Systems Biology Research Centre.
    Assessing chronic pelvic pain syndrome patients: Blood plasma factors and cortisol saliva2013In: Scandinavian Journal of Urology, ISSN 2168-1813, Vol. 47, no 6, p. 521-528Article in journal (Refereed)
    Abstract [en]

    Objective. The aim of this study was to identify changes in inflammatory molecules in the blood (plasma) of patients with chronic prostatitis/chronic pelvic syndrome (CP/CPPS) compared with controls. Altered levels indicate a systemic component by possible involvement of the prostate and/or the inner pelvic floor musculature. Material and methods. In 32 patients with CP/CPPS and 37 controls, blood plasma levels of testosterone, macrophage migration inhibitory factor (MIF), tumour necrosis factor-alpha (TNF-alpha), TNF-beta, interleukin-2 (IL-2) and IL-1 beta were measured by enzyme-linked immunosorbent assay. Cortisol in saliva samples was measured in the morning and late evening. All participants answered a questionnaire regarding their health profile. Results. Significantly higher levels of MIF (p = 0.012) were detected in patients. The testosterone level was, contrary to other studies, little lower in patients (p = 0.014; age adjusted). When controls with health issues and patients with a parallel disease were excluded, the MIF and TNF-alpha levels were higher in the patients (p = 0.007, p = 0.016, respectively) than in controls, and the testosterone was slightly lower in patients (p = 0.047). Conclusions. The findings show an immune response extending to the circulatory system, in which MIF makes a significant contribution to CP/CPPS. This study also indicates TNF-alpha as a circulatory component when excluding subjects with concomitant diseases. Both MIF and TNF-alpha have previously been highlighted for other diseases related to chronic pain and here also for CP/CPPS. These results provide further insights into the immunological basis of CP/CPPS.

  • 254.
    Lundh, Dan
    et al.
    University of Skövde, School of Life Sciences. University of Skövde, The Systems Biology Research Centre.
    Hedelin, Hans
    Department of Research and Development, Skaraborgs Sjukhus, Skövde, Sweden.
    Larsson, Dennis
    University of Skövde, School of Life Sciences. University of Skövde, The Systems Biology Research Centre.
    Chronic prostatitis/chronic pelvic pain syndrome: Interplay of inflammatory mediators, "Beyond the Abstract"2013In: UroToday International Journal, ISSN 1939-4810Article in journal (Refereed)
  • 255.
    Lundh, Dan
    et al.
    University of Skövde, School of Life Sciences. University of Skövde, The Systems Biology Research Centre.
    Larsson, Dennis
    University of Skövde, School of Life Sciences. University of Skövde, The Systems Biology Research Centre.
    Nahar, Noor
    University of Skövde, School of Life Sciences. University of Skövde, The Systems Biology Research Centre.
    Mandal, Abul
    University of Skövde, School of Life Sciences. University of Skövde, The Systems Biology Research Centre.
    Arsenic accumulation in plants - Outlining strategies for developing improved variety of crops for avoiding arsenic toxicity in foods2010In: Journal of biological systems, ISSN 0218-3390, Vol. 18, no 1, p. 223-241Article in journal (Refereed)
    Abstract [en]

    Contamination of food with arsenics is a potential health risk for both humans and animals in many regions of the world, especially in Asia. Arsenics can be accumulated in humans, animals and plants for a longer period and a long-term exposure of humans to arsenics results in severe damage of kidney, lever, heart etc. and many other vascular diseases. Arsenic contamination in human may also lead to development of cancer. In this paper we report our results on data mining approach (an in silico analysis based on searching of the existing genomic databases) for identification and characterization of genes that might be responsible for uptake, accumulation or metabolism of arsenics. For these in silico analyses we have involved the model plant Arabidopsis thaliana in our investigation. By employing a system biology model (a kinetic model) we have studied the molecular mechanisms of these processes in this plant. This model contains equations for uptake, metabolism and sequestration of different types of arsenic; As(V), As(III), MMAA and DMAA. The model was then implemented in the software XPP. The model was also validated against the data existing in the literatures. Based on the results of these in silico studies we have developed some strategies that can be used for reducing arsenic contents in different parts of the plant. Data mining experiments resulted in identification of two candidate genes (ACR2, arsenate reductase 2 and PCS1, phytochelatin synthase 1) that are involved either in uptake, transport or cellular localization of arsenic in A. thaliana. However, our system biology model revealed that by increasing the level of arsenate reductase together with an increased rate of arsenite sequestration in the vacuoles (by involving an arsenite efflux pump MRP1/2), it is possible to reduce the amount of arsenics in the shoots of A. thaliana to 11–12%.

  • 256.
    Lundin, Anders
    et al.
    Discovery Sciences, IMED Biotech Unit, AstraZeneca, Mölndal, Sweden / Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden.
    Delsing, Louise
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre. Discovery Sciences, IMED Biotech Unit, AstraZeneca, Mölndal, Sweden / Institute of Neuroscience and Physiology, Department of Neurochemistry, the Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden.
    Clausen, Maryam
    Discovery Sciences, IMED Biotech Unit, AstraZeneca, Mölndal, Sweden.
    Ricchiuto, Piero
    Discovery Sciences, IMED Biotech Unit, AstraZeneca, Mölndal, Sweden.
    Sanchez, José
    Discovery Sciences, IMED Biotech Unit, AstraZeneca, Mölndal, Sweden.
    Sabirsh, Alan
    Pharmaceutical Sciences, IMED Biotech Unit, AstraZeneca, Mölndal, Sweden.
    Ding, Mei
    Discovery Sciences, IMED Biotech Unit, AstraZeneca, Mölndal, Sweden.
    Synnergren, Jane
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre.
    Zetterberg, Henrik
    Institute of Neuroscience and Physiology, Department of Neurochemistry, 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, UK / UK Dementia Research Institute at UCL, London, UK.
    Brolén, Gabriella
    Discovery Sciences, IMED Biotech Unit, AstraZeneca, Mölndal, Sweden.
    Hicks, Ryan
    Discovery Sciences, IMED Biotech Unit, AstraZeneca, Mölndal, Sweden.
    Herland, Anna
    Department of Micro and Nanosystems KTH Royal Institute of Technology, Stockholm, Sweden / Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden.
    Falk, Anna
    Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden.
    Human iPS-Derived Astroglia from a Stable Neural Precursor State Show Improved Functionality Compared with Conventional Astrocytic Models2018In: Stem Cell Reports, ISSN 2213-6711, Vol. 10, no 3, p. 1030-1045Article in journal (Refereed)
    Abstract [en]

    In vivo studies of human brain cellular function face challenging ethical and practical difficulties. Animal models are typically used but display distinct cellular differences. One specific example is astrocytes, recently recognized for contribution to neurological diseases and a link to the genetic risk factor apolipoprotein E (APOE). Current astrocytic in vitro models are questioned for lack of biological characterization. Here, we report human induced pluripotent stem cell (hiPSC)-derived astroglia (NES-Astro) developed under defined conditions through long-term neuroepithelial-like stem (ltNES) cells. We characterized NES-Astro and astrocytic models from primary sources, astrocytoma (CCF-STTG1), and hiPSCs through transcriptomics, proteomics, glutamate uptake, inflammatory competence, calcium signaling response, and APOE secretion. Finally, we assess modulation of astrocyte biology using APOE-annotated compounds, confirming hits of the cholesterol biosynthesis pathway in adult and hiPSC-derived astrocytes. Our data show large diversity among astrocytic models and emphasize a cellular context when studying astrocyte biology.

  • 257.
    Långsjö, Jaakko W.
    et al.
    Turku PET Centre, University of Turku and Turku University hospital, Finland / Intensive Care Unit, Tampere University Hospital, Central Hospital, Tampere, Finland.
    Revonsuo, Antti
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre. Department of Psychology, University of Turku, Finland.
    Scheinin, Harry
    Turku PET Centre, University of Turku and Turku University hospital, Finland / Department of Pharmacology, Drug Development and Therapeutics, University of Turku, Finland.
    Harnessing anaesthesia and brain imaging for the study of human consciousness2014In: Current pharmaceutical design, ISSN 1381-6128, E-ISSN 1873-4286, Vol. 20, no 26, p. 4211-4224Article in journal (Refereed)
  • 258.
    Lööf, Jasmine
    et al.
    University of Skövde, School of Life Sciences. University of Skövde, The Systems Biology Research Centre.
    Pfeifer, Daniella
    Linköping University.
    Ding, Zhenyu
    Linköping University.
    Sun, Xiao-Feng
    Linköping University.
    Zhang, Hong
    University of Skövde, School of Life Sciences. University of Skövde, The Systems Biology Research Centre.
    Effects of ΔNp73β on Cisplatin Treatment in Colon Cancer Cells2012In: Molecular Carcinogenesis, ISSN 0899-1987, E-ISSN 1098-2744, Vol. 51, no 8, p. 628-635Article in journal (Refereed)
    Abstract [en]

    p73 can activate transcription of p53-responsive genes, thereby inhibiting cell growth. An alternative promoter in the TP73 gene gives rise to an N-terminally truncated isoform of p73, DNp73, which lacks the transactivation domain of the full length TAp73 protein. TAp73 is considered pro-apoptotic, and DNp73 anti-apoptotic. In this study, we overexpressed DNp73β in p53 wild type and p53 mutant colon cancer cell lines and further exposed the cells to cancer therapeutic drug cisplatin. The results showed that cisplatin decreased the protein expression levels of DNp73β in a dose-dependent manner, and both TAp73 and p53 were upregulated after cisplatin treatment. Further, clonogenic potential and cell viability were decreased, and apoptotic cells increased, in p53 mutant and in p53 wild type cells. Cellular viability was significantly higher in DNp73β-cells than mock-transfected cells. However, DNp73β overexpression did not affect the cellular susceptibility to cisplatin. In conclusion, the overexpression of DNp73β increases viability in p53 wild type and p53 mutant colon cancer cells, and cisplatin induces the degradation of DNp73β in a dose-dependent manner.

  • 259.
    Lööf, Jasmine
    et al.
    University of Skövde, The Systems Biology Research Centre. University of Skövde, School of Life Sciences.
    Rosell, Johan
    Department of Oncology, Linköping University Hospital, S-58185 Linköping, Sweden.
    Bratthäll, Charlotte
    Department of Oncology, Linköping University Hospital, S-58185 Linköping, Sweden.
    Doré, Siv
    Department of Pathology, Linköping University, Linköping, Sweden.
    Starkhammar, Hans
    Department of Oncology, Linköping University Hospital, S-58185 Linköping, Sweden.
    Zhang, Hong
    University of Skövde, The Systems Biology Research Centre. University of Skövde, School of Life Sciences.
    Sun, Xiao-Feng
    Department of Oncology, Linköping University, Linköping, Sweden.
    Impact of PINCH expression on survival in colorectal cancer patients2011In: BMC Cancer, ISSN 1471-2407, E-ISSN 1471-2407, Vol. 11, p. Artikelnr 103-Article in journal (Refereed)
    Abstract [en]

    Background: The adaptor protein PINCH is overexpressed in the stroma of several types of cancer, and is an independent prognostic marker in colorectal cancer. In this study we further investigate the relationship of PINCH and survival regarding the response to chemotherapy in colorectal cancer. Results: Paraffin-embedded tissue sections from 251 primary adenocarcinomas, 149 samples of adjacent normal mucosa, 57 samples of distant normal mucosa and 75 lymph node metastases were used for immunohistochemical staining. Stromal staining for PINCH increased from normal mucosa to primary tumour to metastasis. Strong staining in adjacent normal mucosa was related to worse survival independently of sex, age, tumour location, differentiation and stage (p = 0.044, HR, 1.60, 95% Cl, 1.01-2.52). PINCH staining at the invasive margin tended to be related to survival (p = 0.051). In poorly differentiated tumours PINCH staining at the invasive margin was related to survival independently of sex, age and stage (p = 0.013, HR, 1.90, 95% Cl, 1.14-3.16), while in better differentiated tumours it was not. In patients with weak staining, adjuvant chemotherapy was related to survival (p = 0.010, 0.013 and 0.013 in entire tumour area, invasive margin and inner tumour area, respectively), but not in patients with strong staining. However, in the multivariate analysis no such relationship was seen. Conclusions: PINCH staining in normal adjacent mucosa was related to survival. Further, PINCH staining at the tumour invasive margin was related to survival in poorly differentiated tumours but not in better differentiated tumours, indicating that the impact of PINCH on prognosis was dependent on differentiation status.

  • 260.
    Mac Giolla, Erik
    et al.
    Department of psychology, University of Gothenburg.
    Kajonius, Petri J.
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre. Department of Psychology, University of Gothenburg, Gothenburg, Sweden / Department of Behavioral Sciences, University West, Trollhättan, Sweden.
    Sex differences in personality are larger in gender equal countries: Replicating and extending a surprising finding2018In: International Journal of Psychology, ISSN 0020-7594, E-ISSN 1464-066XArticle in journal (Refereed)
    Abstract [en]

    Sex differences in personality have been shown to be larger in more gender equal countries. We advance this researchby using an extensive personality measure, the IPIP-NEO-120, with large country samples (N > 1000), from 22countries. Furthermore, to capture the multidimensionality of personality we measure sex differences with a multivariateeffect size (Mahalanobis distance D). Results indicate that past research, using univariate measures of effect size, haveunderestimated the size of between-country sex differences in personality. Confirming past research, there was a strongcorrelation (r = .69) between a country’s sex differences in personality and their Gender Equality Index. Additionalanalyses showed that women typically score higher than men on all five trait factors (Neuroticism, Extraversion, Openness, Agreeableness and Conscientiousness), and that these relative differences are larger in more gender equal countries. Wespeculate that as gender equality increases both men and women gravitate towards their traditional gender roles.

  • 261.
    MacGregor, Oskar
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre.
    Trivial Love2015In: Cambridge Quarterly of Healthcare Ethics, ISSN 0963-1801, E-ISSN 1469-2147, Vol. 24, no 4, p. 497-500Article in journal (Refereed)
  • 262.
    MacGregor, Oskar
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre.
    WADA's Whereabouts Requirements and Privacy2015In: Routledge Handbook of Drugs and Sport / [ed] Verner Møller, Ivan Waddington & John M. Hoberman, London: Routledge, 2015, p. 310-321Chapter in book (Refereed)
  • 263.
    MacGregor, Oskar
    et al.
    University of Skövde, School of Humanities and Informatics. University of Skövde, The Systems Biology Research Centre.
    Griffith, Richard
    Swansea University, UK.
    Ruggiu, Daniele
    University of Padua, Italy.
    McNamee, Mike
    Swansea University, UK.
    Anti-doping, purported rights to privacy and WADA’s whereabouts requirements: A legal analysis2013In: Fair Play, ISSN 2014-9255, Vol. 1, no 2, p. 13-38Article in journal (Refereed)
    Abstract [en]

    Recent discussions among lawyers, philosophers, policy researchers and athletes have focused on thepotential threat to privacy posed by the World Anti-Doping Agency’s (WADA) whereaboutsrequirements. These requirements demand, among other things, that all elite athletes file theirwhereabouts information for the subsequent quarter on a quarterly basis and comprise data for onehour of each day when the athlete will be available and accessible for no advance notice testing at aspecified location of their choosing. Failure to file one’s whereabouts, or the non-availability fortesting at said location on three occasions within any 18-month period constitutes an anti-doping ruleviolation that is equivalent to testing positive to a banned substance, and may lead to a suspension ofthe athlete for a time period of between one and two years. We critically explore the extent to whichWADA’s whereabouts requirements are in tension with existing legislation on privacy, with respect toUK athletes, who are simultaneously protected by UK domestic and EU law. Both UK domestic andEU law are subject to the European Convention on Human Rights (ECHR) Article 8, whichestablishes a right to “respect for private and family life, home and correspondence”. We criticallydiscuss the centrality of the whereabouts requirements in relation to WADA’s aims, and the adoptionand implementation of its whereabouts rules. We conclude that as WADA’s whereabouts requirementsappear to be in breach of an elite athlete’s rights under European workers’ rights, health & safety anddata protection law they are also, therefore, in conflict with Article 8 of the ECHR and the UK HumanRights Act 1998. We call for specific amendments that cater for the exceptional case of elite sportslabour if the WADA requirements are to be considered legitimate.

  • 264.
    Magnusson, Lisa U.
    et al.
    Sahlgrenska Academy, University of Gothenburg.
    Lundqvist, Annika
    Sahlgrenska Academy, University of Gothenburg.
    Asp, Julia
    Sahlgrenska Academy, University of Gothenburg.
    Synnergren, Jane
    University of Skövde, The Systems Biology Research Centre. University of Skövde, School of Life Sciences.
    Thalén Johansson, Cecilia
    Sahlgrenska Academy, University of Gothenburg.
    Palmqvist, Lars
    Sahlgrenska Academy, University of Gothenburg.
    Jeppsson, Anders
    Sahlgrenska University Hospital.
    Mattsson Hultén, Lillemor
    Sahlgrenska Academy, University of Gothenburg.
    High expression of arachidonate 15-lipoxygenase and proinflammatory markers in human ischemic heart tissue2012In: Biochemical and Biophysical Research Communications - BBRC, ISSN 0006-291X, E-ISSN 1090-2104, Vol. 424, no 2, p. 327-330Article in journal (Refereed)
    Abstract [en]

    A common feature of the ischemic heart and atherosclerotic plaques is the presence of hypoxia (insufficient levels of oxygen in the tissue). Hypoxia has pronounced effects on almost every aspect of cell physiology, and the nuclear transcription factor hypoxia inducible factor-1α (HIF-1α) regulates adaptive responses to low concentrations of oxygen in mammalian cells. In our recent work, we observed that hypoxia increases the proinflammatory enzyme arachidonate 15-lipoxygenase (ALOX15B) in human carotid plaques. ALOX15 has recently been shown to be present in the human myocardium, but the effect of ischemia on its expression has not been investigated. Here we test the hypothesis that ischemia of the heart leads to increased expression of ALOX15, and found an almost 2-fold increase in HIF-1α mRNA expression and a 17-fold upregulation of ALOX15 mRNA expression in the ischemic heart biopsies from patients undergoing coronary bypass surgery compared with non ischemic heart tissue. To investigate the effect of low oxygen concentration on ALOX15 we incubated human vascular muscle cells in hypoxia and showed that expression of ALOX15 increased 22-fold compared with cells incubated in normoxic conditions. We also observed increased mRNA levels of proinflammatory markers in ischemic heart tissue compared with non-ischemic controls. In summary, we demonstrate increased ALOX15 in human ischemic heart biopsies. Furthermore we demonstrate that hypoxia increases ALOX15 in human muscle cells. Our results yield important insights into the underlying association between hypoxia and inflammation in the human ischemic heart disease.

  • 265.
    Mahfuz, Istiak
    et al.
    Uppsala University.
    Mandal, Abul
    University of Skövde, School of Life Sciences. University of Skövde, The Systems Biology Research Centre.
    RNA interference and its role in the inhibition and cure of HIV/AIDS2010In: Journal of Life and Earth Science, ISSN 1990-4827, Vol. 5, p. 1-10Article in journal (Refereed)
    Abstract [en]

    The HIV/AIDS epidemic kills about 2.1 million people around the world every year. Unfortunately, until now attempts to control and diminish further spread of the disorder have resulted in very limited success. Although highly active antiretroviral therapy (HAART) is now available as a treatment option, the rate of its success is limited because of drug resistance. In this context, a more efficient treatment is very much necessary to fight with this fatal disease. The RNA interference (RNAi) can be employed as one of the powerful methods for treatment of the disease as it can effectively silence gene expression in a sequence specific manner. The RNAi-mediated treatment is therefore a promising substitution for therapy of the global epidemic HIV/AIDS in the future. The main objective of this review is to focus on an in-depth analysis of RNAi and the principles underlying RNAi treatment, and it's also described the molecular mechanisms of HIV infection, current treatment facilities available to patients as well as therapeutic applications of RNAi along with their limitations as to why the options are inadequate to give a safe and sound cure of HIV/AIDS.

  • 266.
    Mandal, Abul
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre.
    Probiotic potential of lactic acid bacteria from fresh vegetables: Application in food preservation: PRESERVATIVE POTENTIAL PROBIOTIC LAB FROM VEGETABLES2019In: Indian Journal of Experimental Biology, Vol. 57, p. 825-838Article in journal (Refereed)
    Abstract [en]

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

  • 267.
    Mandal, Abul
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre. Högskolan i Skövde.
    Transgenic tobacco plants expressing ACR2 gene of Arabidopsis thaliana exhibit reduced accumulation of arsenics and increased tolerance to arsenate2015In: Transgenic tobacco plants expressing ACR2 gene of Arabidopsis thaliana exhibit reduced accumulation of arsenics and increased tolerance to arsenate, Omics International Conference , 2015, Vol. 2, p. 32-Conference paper (Refereed)
    Abstract [en]

    Transgenic tobacco plants expressing ACR2 gene of Arabidopsis thaliana exhibit reduced accumulation of arsenics and increased tolerance to arsenate.

    Toxic metals such as arsenics, lead, cadmium or chromium are the major environmental pollutants that severely contribute to contamination of the global food chain directly through their accumulation in the edible parts of the cultivated crops or indirectly via meat-milk pathway. Fortunately, plant genetic engineering has the potential for developing new crop cultivars for removal of the toxic substances from the polluted sources or for avoiding accumulation of these contaminants in the edible parts. Previously, we have identified and studied four key genes that are involved in accumulation of arsenics in plants (J Biol. Systems 2010, 18/1:1-19; J Mol. Modeling 2012, DOI 10.1007/s00894-012-1419 and J Mol. Modeling 2014, DOI 10.1007/s00894-014-2104). In this study, we have cloned and transformed the ACR2 gene (arsenic reductase 2) of Arabidopsis thaliana into tobacco plants (Nicotiana tabacum). Our results revealed that the transgenic tobacco plants are more tolerant to arsenic than the wild-type control plants. These plants can grow on medium containing 200 µM arsenate, whereas the non-transgenic plants can hardly survive under this condition. Furthermore, when exposed to 100 µM arsenate for 35 days accumulation of arsenics in shoots of the transgenic plants decreases significantly (28 µg/g d wt.) compared to that observed in the non-transgenic control plants (40 µg/g d wt.). This study shows that A. thaliana ACR2 gene is a potential candidate for genetic engineering of plants to develop new cultivars that can be grown on arsenic contaminated fields and can supply harmless foods containing no or significantly reduced amount of arsenics.

  • 268.
    Mandal, Abul
    et al.
    University of Skövde, School of Life Sciences. University of Skövde, The Systems Biology Research Centre.
    Lundh, Dan
    University of Skövde, School of Life Sciences. University of Skövde, The Systems Biology Research Centre.
    Nahar, Noor
    University of Skövde, School of Life Sciences. University of Skövde, The Systems Biology Research Centre.
    Bentol, Hoda
    University of Skövde, School of Life Sciences.
    Bari, Abdul
    University of Skövde, School of Life Sciences.
    Johnson-Brousseau, Sheila
    Department of Natural Sciences and Mathematics, Dominican University of California, San Rafael, United States.
    Ghosh, Sibdas
    Department of Natural Sciences and Mathematics, Dominican University of California, San Rafael, United States.
    Modeling Arsenic Accumulation in Plants2011In: Proceedings Second International Conference on Emerging Applications of Information Technology / [ed] Debasish Jana & Pinakpani Pal, IEEE Computer Society, 2011, p. 133-137Conference paper (Refereed)
    Abstract [en]

    Rice growing regions plagued by arsenic-contaminated soils and irrigation water do not have a viable option for producing arsenic-free crops. For instance, in Bangladesh every year more than 30 million people are affected from rice-derived arsenic contamination that contributes to arsenic levels known to cause health-related illnesses. Our strategy is to genetically-modify molecular mechanisms involved in the localization of arsenic to divert it to the non-edible parts of the plant. To identify viable candidate genes, we employed data mining, an in silico analysis based on searching existing genomic databases and in the genetic model plant Arabidopsis thaliana. To assist our investigation, we constructed a kinetic model to outline strategies for developing genetically-modified plants exhibiting a significant reduction in arsenic concentration in the edible parts (straw and grain). This model contains equations for uptake, metabolism and sequestration of different types of arsenic (As (V), As (III), MMAA and DMAA). The model was implemented using XPP and validated against existing data from the literature. From these analysis, we identified four candidate genes that are involved either in uptake, transport or cellular localization of arsenic in plants. But we found only one gene implicated in arsenic metabolism in rice. In parallel, we identified available T-DNA insertion mutants to determine the effects of these genes on arsenic accumulation. Results obtained from in silico data-mining, kinetic modeling, and assays with T-DNA insertion mutants will be used to design gene cloning experiments to study the target genes in yeast, E. coli and Arabidopsis heterologous systems. Upon confirmation of the effectiveness of these candidates, vectors containing the target genes will be constructed for transformation into rice. The new rice varieties produced will be tested under field conditions to assess their effectiveness at reducing or eliminating arsenic from the edible parts of the rice plant.

  • 269.
    Marcišauskas, Simonas
    et al.
    Division of Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.
    Ulfenborg, Benjamin
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre.
    Kristjansdottir, Björg
    Department of Obstetrics and Gynecology, Institute of Clinical Sciences, Sahlgrenska Cancer Center, University of Gothenburg, Gothenburg, Sweden.
    Waldemarson, Sofia
    Department of Immunotechnology, Lund University, Medicon Village, Lund, Sweden.
    Sundfeldt, Karin
    Department of Obstetrics and Gynecology, Institute of Clinical Sciences, Sahlgrenska Cancer Center, University of Gothenburg, Gothenburg, Sweden.
    Univariate and classification analysis reveals potential diagnostic biomarkers for early stage ovarian cancer Type 1 and Type 22019In: Journal of Proteomics, ISSN 1874-3919, E-ISSN 1876-7737, Vol. 196, p. 57-68Article in journal (Refereed)
    Abstract [en]

    Biomarkers for early detection of ovarian tumors are urgently needed. Tumors of the ovary grow within cysts and most are benign. Surgical sampling is the only way to ensure accurate diagnosis, but often leads to morbidity and loss of female hormones. The present study explored the deep proteome in well-defined sets of ovarian tumors, FIGO stage I, Type 1 (low-grade serous, mucinous, endometrioid; n = 9), Type 2 (high-grade serous; n = 9), and benign serous (n = 9) using TMT–LC–MS/MS. Data are available via ProteomeXchange with identifier PXD010939. We evaluated new bioinformatics tools in the discovery phase. This innovative selection process involved different normalizations, a combination of univariate statistics, and logistic model tree and naive Bayes tree classifiers. We identified 142 proteins by this combined approach. One biomarker panel and nine individual proteins were verified in cyst fluid and serum: transaldolase-1, fructose-bisphosphate aldolase A (ALDOA), transketolase, ceruloplasmin, mesothelin, clusterin, tenascin-XB, laminin subunit gamma-1, and mucin-16. Six of the proteins were found significant (p <.05) in cyst fluid while ALDOA was the only protein significant in serum. The biomarker panel achieved ROC AUC 0.96 and 0.57 respectively. We conclude that classification algorithms complement traditional statistical methods by selecting combinations that may be missed by standard univariate tests. Significance: In the discovery phase, we performed deep proteome analyses of well-defined histology subgroups of ovarian tumor cyst fluids, highly specified for stage and type (histology and grade). We present an original approach to selecting candidate biomarkers combining several normalization strategies, univariate statistics, and machine learning algorithms. The results from validation of selected proteins strengthen our prior proteomic and genomic data suggesting that cyst fluids are better than sera in early stage ovarian cancer diagnostics. 

  • 270.
    McBean, G. J.
    et al.
    School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Dublin, Ireland.
    López, M. G.
    Instituto Teófilo Hernando for Drug Discovery, Department of Pharmacology, School of Medicine, Universidad Autónoma de Madrid, Madrid, Spain.
    Wallner, Fredrik K.
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre. Redoxis AB.
    Redox-based therapeutics in neurodegenerative disease2017In: British Journal of Pharmacology, ISSN 0007-1188, E-ISSN 1476-5381, Vol. 174, no 12, p. 1750-1770Article in journal (Refereed)
    Abstract [en]

    This review describes recent developments in the search for effective therapeutic agents that target redox homeostasis in neurodegenerative disease. The disruption to thiol redox homeostasis in Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis and multiple sclerosis is discussed, together with the experimental strategies that are aimed at preventing, or at least minimizing, oxidative damage in these diseases. Particular attention is given to the potential of increasing antioxidant capacity by targeting the Nrf2 pathway, the development of inhibitors of NADPH oxidases that are likely candidates for clinical use, together with strategies to reduce nitrosative stress and mitochondrial dysfunction. We describe the shortcomings of compounds that hinder their progression to the clinic and evaluate likely avenues for future research.

  • 271. McLaughlin, Órla B.
    et al.
    Jonsson, Tomas
    University of Skövde, The Systems Biology Research Centre. University of Skövde, School of Life Sciences.
    Emmerson, Mark C.
    Temporal Variability in Predator - Prey Relationships of a Forest Floor Food Web2010In: Advances in Ecological Research, ISSN 0065-2504, E-ISSN 2163-582X, Vol. 42, p. 171-264Article in journal (Refereed)
    Abstract [en]

    Connectance webs represent the standard data description in food web ecology, but their usefulness is often limited in understanding the patterns and processes within ecosystems. Increasingly, efforts have been made to incorporate additional, biologically meaningful, data into food web descriptions, including the construction of food webs using data describing the body size and abundance of each species. Here, data from a terrestrial forest floor food web, sampled seasonally over a 1-year period, were analysed to investigate (i) how stable the body size–abundance and predator–prey relationships of an ecosystem are through time and (ii) whether there are system-specific differences in body size–abundance and predator–prey relationships between ecosystem types.

  • 272.
    Mohanta, Moni Krishno
    et al.
    University of Rajshahi, Bangladesh.
    Salam, M. A.
    University of Rajshahi, Bangladesh.
    Saha, A. K.
    University of Rajshahi, Bangladesh.
    Mandal, Abul
    University of Skövde, The Systems Biology Research Centre. University of Skövde, School of Life Sciences.
    Microbial Bioremediation of Effluents from Tanning Industry in Bangladesh2010In: International Journal on Environmental Sciences, ISSN 0976-4534, Vol. 1, no 2, p. 155-167Article in journal (Refereed)
    Abstract [en]

    Extensive use of chromium, cadmium and lead nitrate in tanning industry has caused substantial environmental pollution in Bangladesh. Bioremediation of tanning effluents with the help of bacteria was investigated. Samples of effluents with cadmium, chromium and lead nitrate (10mg/ml) were incubated in mineral salt medium at 37°C for 4 days and bacterial strain was isolated from the sample. Preliminary characterization of the organisms according to Bergey's manual suggests that the organisms may belong to Coccus species. The rate of reduction of these effluents was determined by using the flame Atomic Absorption Spectrophotometer (AAS). Out of 3 ppm concentration the rates of reduction were found to be 2.96 ppm for chromium; 2.92 ppm for cadmium and 2.46 ppm for lead nitrate. The isolated bacteria harboured three endogenous plasmids. All of the plasmids were lost when the organisms were treated with ethidium bromide (100mg/ml). Loss of the plasmids resulted in disability of the bacteria to grow on media containing chromium, cadmium and lead-nitrate. Phenotypic testing of wild type and cured strains revealed that the gene(s) responsible for chromium, cadmium and lead-nitrate degradation may reside upon the plasmids.

  • 273.
    Morrison, India
    et al.
    University of Skövde, School of Humanities and Informatics. University of Skövde, The Systems Biology Research Centre. Department of Clinical Neurophysiology, Sahlgrenska University Hospital, Gothenburg, Sweden / Institute of Neuroscience and Physiology, University of Gothenburg, Gothenburg, Sweden.
    Perini, Irene
    Department of Clinical Neurophysiology, Sahlgrenska University Hospital, Gothenburg, Sweden / Institute of Neuroscience and Physiology, University of Gothenburg, Gothenburg, Sweden.
    Dunham, James
    Division of Anaesthesia, University of Cambridge, Addenbrookes University Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK.
    Facets and mechanisms of adaptive pain behavior: predictive regulation and action2013In: Frontiers in Human Neuroscience, ISSN 1662-5161, E-ISSN 1662-5161, Vol. 7, p. 755-Article, review/survey (Refereed)
    Abstract [en]

    Neural mechanisms underlying nociception and pain perception are considered to serve the ultimate goal of limiting tissue damage. However, since pain usually occurs in complex environments and situations that call for elaborate control over behavior, simple avoidance is insufficient to explain a range of mammalian pain responses, especially in the presence of competing goals. In this integrative review we propose a Predictive Regulation and Action (PRA) model of acute pain processing. It emphasizes evidence that the nervous system is organized to anticipate potential pain and to adjust behavior before the risk of tissue damage becomes critical. Regulatory processes occur on many levels, and can be dynamically influenced by local interactions or by modulation from other brain areas in the network. The PRA model centers on neural substrates supporting the predictive nature of pain processing, as well as on finely-calibrated yet versatile regulatory processes that ultimately affect behavior. We outline several operational categories of pain behavior, from spinally-mediated reflexes to adaptive voluntary action, situated at various neural levels. An implication is that neural processes that track potential tissue damage in terms of behavioral consequences are an integral part of pain perception.

  • 274.
    Möllerström, Elin
    et al.
    University of Gothenburg.
    Delle, Ulla
    University of Gothenburg.
    Danielsson, Anna
    University of Gothenburg.
    Parris, Toshima
    University of Gothenburg.
    Olsson, Björn
    University of Skövde, The Systems Biology Research Centre. University of Skövde, School of Life Sciences.
    Karlsson, Per
    University of Gothenburg.
    Helou, Khalil
    University of Gothenburg.
    High-resolution genomic profiling to predict 10-year overall survival in node-negative breast cancer2010In: Cancer Genetics and Cytogenetics, ISSN 2210-7762, E-ISSN 2210-7770, Vol. 198, no 2, p. 79-89Article in journal (Refereed)
    Abstract [en]

    Women with clinically node-negative breast cancer have a better prognosis than do those with axillary lymph node metastasis. Nonetheless, ~20% of node-negative patients die within 15 years of diagnosis, and thus additional prognostic markers are greatly needed. To identify specific copy number alterations (CNAs) that differed in frequency between 10-year survivors and deceased patients with node-negative breast cancer, array comparative genomic hybridization (aCGH) was applied to 41 primary node-negative breast tumors. Fisher's exact test was used to identify significantly different CNAs between 10-year survivors and deceased patients. Losses at 8p21.2~p21.3, 8p23.1~p23.2, Xp21.3, and Xp22.31~p22.33 were significantly more common in tumors from deceased patients, suggesting that these alterations may contribute to tumor aggressiveness. Gains at 1q25.2~q25.3 and 1q31.3~q41 were more prevalent in tumors from survivors; specific gains at these genomic regions may inhibit further tumor progression, resulting in a less aggressive form of node-negative breast cancer. Evaluation of the identified CNAs in an independent external data set verified the prognistic potential of the 1q31.3~q41 region. Although further extensive validation is needed, the prognostic CNAs identified in this work may in time facilitate the clinical assessment of breast cancer.

  • 275.
    Nahar, Noor
    et al.
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre.
    Rahman, Aminur
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre.
    Moś, Maria
    Department of Plant Breeding and Seed Science, University of Agriculture in Krakow, Krakow, Poland.
    Warzecha, Tomasz
    Department of Plant Breeding and Seed Science, University of Agriculture in Krakow, Krakow, Poland.
    Ghosh, Sibdas
    School of Arts and Science, Iona College, New Rochelle, USA.
    Hossain, Khaled
    Department of Biochemistry and Molecular Biology, University of Rajshahi, Bangladesh.
    Nawani, Neelu N.
    Dr. D. Y. Patil Biotechnology and Bioinformatics Institute, Dr. D. Y. Patil Vidyapeeth University, Tathawade, Pune 411033, India.
    Mandal, Abul
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre.
    In silico and in vivo studies of molecular structures and mechanisms of AtPCS1 protein involved in binding arsenite and/or cadmium in plant cells2014In: Journal of Molecular Modeling, ISSN 1610-2940, E-ISSN 0948-5023, Vol. 20, no 3, article id 2104Article in journal (Refereed)
    Abstract [en]

    This paper reports a continuation of our previous research on the phytochelatin synthase1 (PCS1) gene involved in binding and sequestration of heavy metals or metalloids in plant cells. Construction of a 3D structure of the Arabidopsis thaliana PCS1 protein and prediction of gene function by employing iterative implementation of the threading assembly refinement (I-TASSER) revealed that PC ligands (3GC-gamma-glutamylcysteine) and Gln50, Pro53, Ala54, Tyr55, Cys56, Ile102, Gly161, His162, Phe163, Asp204 and Arg211 residues are essential for formation of chelating complex with cadmium (Cd²⁺) or arsenite (AsIII). This finding suggests that the PCS1 protein might be involved in the production of the enzyme phytochelatin synthase, which might in turn bind, localize, store or sequester heavy metals in plant cells. For validation of the in silico results, we included a T-DNA tagged mutant of Arabidopsis thaliana, SAIL_650_C12, (mutation in AtPCS1 gene) in our investigation. Furthermore, using reverse transcriptase PCR we confirmed that the mutant does not express the AtPCS1 gene. Mutant plants of SAIL_650_C12 were exposed to various amounts of cadmium (Cd²⁺) and arsenite (AsIII) and the accumulation of these toxic metals in the plant cells was quantified spectrophotometrically. The levels of Cd²⁺ and AsIII accumulation in the mutant were approximately 2.8 and 1.6 times higher, respectively, than that observed in the wild-type controlled plants. We confirmed that the results obtained in in silico analyses complement those obtained in in vivo experiments.

  • 276.
    Nahar, Noor
    et al.
    University of Skövde, The Systems Biology Research Centre. University of Skövde, School of Life Sciences.
    Rahman, Aminur
    University of Skövde, The Systems Biology Research Centre. University of Skövde, School of Life Sciences.
    Mós, Maria
    University of Agriculture in Krakow.
    Warzecha, Tomasz
    University of Agriculture in Krakow.
    Algerin, Maria
    University of Skövde, The Systems Biology Research Centre. University of Skövde, School of Life Sciences.
    Ghosh, Sibdas
    Dominican University of California.
    Johnson-Brousseau, Sheila
    Dominican University of California.
    Mandal, Abul
    University of Skövde, The Systems Biology Research Centre. University of Skövde, School of Life Sciences.
    In silico and in vivo studies of an Arabidopsis thaliana gene, ACR2, putatively involved in arsenic accumulation in plants2012In: Journal of Molecular Modeling, ISSN 1610-2940, E-ISSN 0948-5023, Vol. 18, no 9, p. 4249-4262Article in journal (Refereed)
    Abstract [en]

    Previously, our in silico analyses identified four candidate genes that might be involved in uptake and/or accumulation of arsenics in plants: arsenate reductase 2 (ACR2), phytochelatin synthase 1 (PCS1) and two multi-drug resistant proteins (MRP1 and MRP2) [Lund et al. (2010) J Biol Syst 18:223–224]. We also postulated that one of these four genes, ACR2, seems to play a central role in this process. To investigate further, we have constructed a 3D structure of the Arabidopsis thaliana ACR2 protein using the iterative implementation of the threading assembly refinement (I-TASSER) server. These analyses revealed that, for catalytic metabolism of arsenate, the arsenate binding-loop (AB-loop) and residues Phe-53, Phe-54, Cys-134, Cys-136, Cys-141, Cys-145, and Lys-135 are essential for reducing arsenate to arsenic intermediates (arsenylated enzyme-substrate intermediates) and arsenite in plants. Thus, functional predictions suggest that the ACR2 protein is involved in the conversion of arsenate to arsenite in plant cells. To validate the in silico results, we exposed a transfer-DNA (T-DNA)-tagged mutant of A. thaliana (mutation in the ACR2 gene) to various amounts of arsenic. Reverse transcriptase PCR revealed that the mutant exhibits significantly reduced expression of the ACR2 gene. Spectrophotometric analyses revealed that the amount of accumulated arsenic compounds in this mutant was approximately six times higher than that observed in control plants. The results obtained from in silico analyses are in complete agreement with those obtained in laboratory experiments.

  • 277.
    Nahar, Noor
    et al.
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre.
    Rahman, Aminur
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre.
    Nawani, Neelu N.
    Microbial Diversity Research Centre, Dr. D. Y. Patil Biotechnology and Bioinformatics Institute, Dr. D. Y. Patil Vidyapeeth, Tathawade, Pune, India.
    Ghosh, Sibdas
    School of Arts and Science, Iona College, New Rochelle, NY, USA.
    Mandal, Abul
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre.
    Phytoremediation of arsenic from the contaminated soil using transgenic tobacco plants expressing ACR2 gene of Arabidopsis thaliana2017In: Journal of plant physiology (Print), ISSN 0176-1617, E-ISSN 1618-1328, Vol. 218, p. 121-126Article in journal (Refereed)
    Abstract [en]

    We have cloned, characterized and transformed the AtACR2 gene (arsenic reductase 2) of Arabidopsis thaliana into the genome of tobacco (Nicotiana tabacum, var Sumsun). Our results revealed that the transgenic tobacco plants are more tolerant to arsenic than the wild type ones. These plants can grow on culture medium containing 200μM arsenate, whereas the wild type can barely survive under this condition. Furthermore, when exposed to 100μM arsenate for 35days the amount of arsenic accumulated in the shoots of transgenic plants was significantly lower (28μg/g d wt.) than that found in the shoots of non-transgenic controls (40μg/g d wt.). However, the arsenic content in the roots of transgenic plants was significantly higher (2400μg/g d. wt.) than that (2100μg/g d. wt.) observed in roots of wild type plants. We have demonstrated that Arabidopsis thaliana AtACR2 gene is a potential candidate for genetic engineering of plants to develop new crop cultivars that can be grown on arsenic contaminated fields to reduce arsenic content of the soil and can become a source of food containing no arsenic or exhibiting substantially reduced amount of this metalloid.

  • 278.
    Nahar, Nour
    et al.
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre.
    Rahman, Aminur
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre.
    Ghosh, Sibdas
    School of Arts and Science, Iona College, New Rochelle, NY, USA.
    Nawani, Neelu
    Microbial Diversity Research Centre, Dr. D. Y. Patil Biotechnology and Bioinformatics Institute, Dr. D. Y. Patil Vidyapeeth, Tathawade, Pune, India.
    Mandal, Abul
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre.
    Functional studies of AtACR2 gene putatively involved in accumulation, reduction and/or sequestration of arsenic species in plants2017In: Biologia (Bratislava), ISSN 0006-3088, E-ISSN 1336-9563, Vol. 72, no 5, p. 520-526Article in journal (Refereed)
    Abstract [en]

    Food-based exposure to arsenic is a human carcinogen and can severely impact human health resulting in many cancerous diseases and various neurological and vascular disorders. This project is a part of our attempts to develop new varieties of crops for avoiding arsenic contaminated foods. For this purpose, we have previously identified four key genes, and molecular functions of two of these, AtACR2 and AtPCSl, have been studied based on both in silico and in vivo experiments. In the present study, a T-DNA tagged mutant, (SALK-143282C with mutation in AtACR2 gene) of Arabidopsis thaliana was studied for further verification of the function of AtACR2 gene. Semi-quantitative RT-PCR analyses revealed that this mutant exhibits a significantly reduced expression of the AtACR2 gene. When exposed to 100 μM of arsenate (AsV) for three weeks, the mutant plants accumulated arsenic approximately three times higher (778 μg/g d. wt.) than that observed in the control plants (235 μg/g d. wt.). In contrast, when the plants were exposed to 100 μM of arsenite (AsIII), no significant difference in arsenic accumulation was observed between the control and the mutant plants (535 μg/g d. wt. and 498 μg/g d. wt., respectively). Also, when arsenate and arsenite was measured separately either in shoots or roots, significant differences in accumulation of these substances were observed between the mutant and the control plants. These results suggest that AtACR2 gene is involved not only in accumulation of arsenic in plants, but also in conversion of arsenate to arsenite inside the plant cells. © 2017 Institute of Molecular Biology, Slovak Academy of Sciences.

  • 279.
    Nawani, Neelu
    et al.
    Dr. D. Y. Patil Biotechnology and Bioinformatics Institute, India.
    Aigle, Bertrand
    Université de Lorraine, France / INRA, Dynamique des Genomes et Adaptation Microbienne, France.
    Mandal, Abul
    University of Skövde, The Systems Biology Research Centre. University of Skövde, School of Life Sciences.
    Bodas, Manish
    Dr. D. Y. Patil Biotechnology and Bioinformatics Institute, India.
    Ghorbel, Sofiane
    Laboratoire de Génie Enzymatique et de Microbiologie, Ecole Nationale D’Ingénieurs de Sfax, Tunisia.
    Prakash, Divya
    Dr. D. Y. Patil Biotechnology and Bioinformatics Institute, India.
    Actinomycetes: Role in Biotechnology and Medicine2013In: BioMed Research International, ISSN 2314-6133, E-ISSN 2314-6141, no 2013, p. 687190-Article in journal (Refereed)
    Abstract [en]

    Actinomycetes, one of the most diverse groups of filamentous bacteria, are well recognized for their metabolic versatility. The bioactive potential of these bacteria facilitates their survival even in distress and unfavourable ecological conditions. This special issue is dedicated to the importance of multitude of primary and secondary metabolites produced by actinomycetes. The importance of large repertory of enzymes from actinomycetes and their potential in replacing chemical catalysts is discussed.

  • 280.
    Nawani, Neelu
    et al.
    Microbial Diversity Research Centre, Dr D Y Patil Biotechnology and Bioinformatics Institute, Dr D Y Patil Vidyapeeth, Pune, India.
    Rahman, Aminur
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre.
    Nahar, Noor
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre.
    Saha, Anandakumar
    Department of Zoology, University of Rajshahi, Bangladesh.
    Kapadnis, Balasaheb
    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.
    Status of metal pollution in rivers flowing through urban settlements at Pune and its effect on resident microflora2016In: Biologia (Bratislava), ISSN 0006-3088, E-ISSN 1336-9563, Vol. 71, no 5, p. 494-507Article in journal (Refereed)
    Abstract [en]

    This study illustrates the sporadic distribution of metals in fluvial systems flowing from catchments to urban settlements. This is a detailed study prognosticating the deteriorating quality of rivers at specific locations due to metal pollution. Heavy metals like cadmium, lead, nickel and mercury are prominent in industrial sector. Contour plots derived using spatial and temporal data could determine the focal point of metal pollution and its gradation. Metal values recorded were cadmium 157 mg/L, lead 47 mg/L, nickel 61 mg/L and mercury 0.56 mg/L. Prokaryote diversity was less in polluted water and it harboured metal tolerant bacteria, which were isolated from these polluted sites. Actinomycetes like Streptomyces and several other bacteria like Stenotrophomonas and Pseudomonas isolated from the polluted river sites exhibited changes in morphology in presence of heavy metals. This stress response offered remedial measures as Streptomyces were effective in biosorption of cadmium, nickel and lead and Stenotrophomonas and Pseudomonas were effective in the bioaccumulation of lead and cadmium. The amount of 89 mg of lead and 106 mg of nickel could be adsorbed on one gram of Streptomyces biomass-based biosorbent. Such biological remedies can be further explored to remove metals from polluted sites and from metal contaminated industrial or waste waters.

  • 281.
    Nguyen, Duong T.
    et al.
    Cardiovascular, Renal and Metabolic Diseases, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Mölndal, Sweden.
    O'Hara, Matthew
    Cardiovascular, Renal and Metabolic Diseases, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Mölndal, Sweden.
    Granéli, Cecilia
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre. Discovery Sciences, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Mölndal, Sweden.
    Hicks, Ryan
    Discovery Sciences, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Mölndal, Sweden.
    Miliotis, Tasso
    Cardiovascular, Renal and Metabolic Diseases, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Mölndal, Sweden.
    Nyström, Ann-Christin
    Cardiovascular, Renal and Metabolic Diseases, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Mölndal, Sweden.
    Hansson, Sara
    Cardiovascular, Renal and Metabolic Diseases, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Mölndal, Sweden.
    Davidsson, Pia
    Cardiovascular, Renal and Metabolic Diseases, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Mölndal, Sweden.
    Gan, Li-Ming
    Early Clinical and Development, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Mölndal, Sweden.
    Magnone, Maria Chiara
    Cardiovascular, Renal and Metabolic Diseases, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Mölndal, Sweden.
    Althage, Magnus
    Cardiovascular, Renal and Metabolic Diseases, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Mölndal, Sweden.
    Heydarkhan-Hagvall, Sepideh
    Cardiovascular, Renal and Metabolic Diseases, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Mölndal, Sweden.
    Humanizing Miniature Hearts through 4-Flow Cannulation Perfusion Decellularization and Recellularization2018In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 8, article id 7458Article in journal (Refereed)
    Abstract [en]

    Despite improvements in pre-clinical drug testing models, predictability of clinical outcomes continues to be inadequate and costly due to poor evidence of drug metabolism. Humanized miniature organs integrating decellularized rodent organs with tissue specific cells are translational models that can provide further physiological understanding and evidence. Here, we evaluated 4-Flow cannulated rat hearts as the fundamental humanized organ model for cardiovascular drug validation. Results show clearance of cellular components in all chambers in 4-Flow hearts with efficient perfusion into both coronary arteries and cardiac veins. Furthermore, material characterization depicts preserved organization and content of important matrix proteins such as collagens, laminin, and elastin. With access to the complete vascular network, different human cell types were delivered to show spatial distribution and integration into the matrix under perfusion for up to three weeks. The feature of 4-Flow cannulation is the preservation of whole heart conformity enabling ventricular pacing via the pulmonary vein as demonstrated by noninvasive monitoring with fluid pressure and ultrasound imaging. Consequently, 4-Flow hearts surmounting organ mimicry challenges with intact complexity in vasculature and mechanical compliance of the whole organ providing an ideal platform for improving pre-clinical drug validation in addition to understanding cardiovascular diseases.

  • 282.
    Nolin, Lina
    et al.
    University of Skövde, The Systems Biology Research Centre. University of Skövde, School of Life Sciences.
    Larsolle, Anders
    Swedish University of Agricultural Sciences.
    Stenberg, Bo
    Swedish University of Agricultural Sciences.
    Söderström, Mats
    Swedish University of Agricultural Sciences.
    N-sensor measurements combined with model simulations to estimate variable nitrogen requirements in spring barley2010In: NJF Report, ISSN 1653-2015, Vol. 6, no 7, p. 26-27Article in journal (Refereed)
  • 283.
    Nolskog, Peter
    et al.
    Department of Communicable Disease Control and Prevention, Region of Västra Götaland, Skaraborg Hospital, Skövde, Sweden.
    Backhaus, Erik
    Department of Infectious Diseases, Skaraborg Hospital, Skövde, Sweden.
    Nasic, Salmir
    Research and Development Centre, Skaraborg Hospital, Skövde, Sweden.
    Enroth, Helena
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre. Clinical molecular microbiology, Laboratory Medicine, Unilabs, Skövde, Sweden.
    STI with Mycoplasma genitalium: More common than Chlamydia trachomatis in patients attending youth clinics in Sweden2019In: European Journal of Clinical Microbiology and Infectious Diseases, ISSN 0934-9723, E-ISSN 1435-4373, Vol. 38, no 1, p. 81-86Article in journal (Refereed)
    Abstract [en]

    The prevalence of Chlamydia trachomatis in Sweden is well known, whereas the prevalence of Mycoplasma genitalium is less well documented. Youth clinics offer free contraception advice, sexually transmitted infection (STI) testing and/or contact tracing for the age group 15–25 years. The main objective of this study was to determine the prevalence of STIs, the presence of symptoms and the role of contact tracing. From July 2013 to March 2014, 1001 persons, 509 women and 492 men, were included in this study of six youth clinics in the Region of Västra Götaland. Symptoms were registered and whether the patient was tested because of contract tracing. Collection of urine samples, testing, treatment and disease registration were performed according to clinical routines. Urine samples were analysed for C. trachomatis/N. gonorrhoeae on the Cobas 4800 system (Roche). M. genitalium was analysed by lab-developed PCR. Genital infection was present in 16.8%. The prevalence of M. genitalium was higher than for C. trachomatis (9.6% and 7.1%). Men with symptoms have a significantly higher relative risk for infection with M. genitalium or C. trachomatis compared to asymptomatic men, while there is no increase for women. Contact tracing is important since positive outcome has a high relative risk for both infections. The prevalence of M. genitalium was higher than C. trachomatis in this study population. Initial testing for both C. trachomatis and M. genitalium should at least be considered for young men presenting with symptoms of genital infection. In finding positive cases, contact tracing is of great importance. © 2018, Springer-Verlag GmbH Germany, part of Springer Nature.

  • 284.
    Norrström, Niclas
    University of Skövde, School of Life Sciences. University of Skövde, The Systems Biology Research Centre.
    Artificial neural networks in models of specialization and sympatric speciation2009Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    This thesis deals with specialization and how it is linked to sympatric speciation. The trait driving specialization is a cue recognition trait modelled with artificial neural networks that exploiters use to discriminate beneficial resources from detrimental resources based on the signals of the resources. Paper I investigates how haploid exploiters and the resources coevolve when the signals of the resources can evolve through mutations. We find that this coevolution can be a cyclic process with saltational changes between different stages and that evolution is only directional and the exploiters are only specialists in parts of this cycle. In simulations underlying Paper II the signals of the resources can not mutate but the exploiters have a diploid genome and the organisms reproduce sexually. We show that the disruptive selection stemming from exploiters specializing on different resources can overcome the homogenizing effect of sexual recombination when exploiters mate randomly and produce a functional genetic polymorphism with specialized exploiters. A functional genetic polymorphism removes the force of reinforcement but we run simulations where the exploiters have a mating gene determining if mating is random or if exploiters should mate assortatively in Paper III. We find that assortative invades the exploiter population and homozygote specialists evolve because the genetic polymorphism pays a cost by having some alleles being silenced (that is they do not contribute to the complete phenotype) in certain genotypes so a mutation in these silenced alleles is not selected against, which cause these alleles to accumulate deleterious mutations. The homozygote specialists, mating assortatively, are much more efficiently removing deleterious mutations from the population and hence can invade the population. Finally, in Paper IV we investigate the effects of resource and resource signal arrangements in the environment. We show that the environment can influence the evolution of specialization and sympatric speciation. By modelling a resource discrimination trait based on the interaction of epistatic genes we find a novel force promoting sympatric speciation over genetic polymorphisms.

  • 285.
    Norrström, Niclas
    et al.
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre.
    Casini, Michele
    Swedish University of Agricultural Sciences, Department of Aquatic Resources, Institute of Marine Research, Lysekil, Sweden.
    Holmgren, Noél M. A.
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre.
    Nash equilibrium can resolve conflicting maximum sustainable yields in multi-species fisheries management2017In: ICES Journal of Marine Science, ISSN 1054-3139, E-ISSN 1095-9289, Vol. 74, no 1, p. 78-90Article in journal (Refereed)
    Abstract [en]

    The current fisheries management goals set by the European Commission states that fish stocks should be harvested to deliver maximum sustainable yields (MSY) and simultaneously, management should take ecosystem considerations into account. This creates unsolved trade-offs for the management of the stocks. We suggest a definition of a multi-species-MSY (MS-MSY) where no alternative fishing mortality (F) can increase yield (long term) for any ecologically interacting stock, given that the other stocks are fished at constant efforts (Fs). Such a MS-MSY can be solved through the game theoretic concept of a Nash equilibrium and here we explore two solutions to this conflict in the Baltic Sea. We maximize the sustainable yield of each stock under two constraints: first, we harvest the other stocks at a fixed F (FNE); second, we keep the spawning stock biomasses of the other stocks fixed [biomass Nash equilibrium (BNE)]. As a case study, we have developed a multi-species interaction stochastic operative model (MSI-SOM), which contains a SOM for each of the three dominant species of the Baltic Sea, the predator cod (Gadus morhua), and its prey herring (Clupea harengus), and sprat (Sprattus sprattus). For our Baltic Sea case, MS-MSYs exist under both the FNE and the BNE, but there is no guarantee that point solutions exists. We found that the prey species’ spawning stock biomasses are additive in the cod growth function, which allowed for a point solution in BNE. In the FNE, the herring MSY was found to be relatively insensitive to the other species’ fishing mortalities (F), which facilitated a point solution. The MSY targets of the BNE and the FNE differ slightly where the BNE gives higher predator yields and lower prey yields.

  • 286.
    Norrström, Niclas
    et al.
    University of Skövde, School of Life Sciences. University of Skövde, The Systems Biology Research Centre.
    Getz, Wayne M.
    Department of Environmental Sciences, Policy and Management, University of California, Berkeley, California, United States of America / School of Mathematical Sciences, University of KwaZulu-Natal, Durban, South Africa.
    Holmgren, Noél M. A.
    University of Skövde, School of Life Sciences. University of Skövde, The Systems Biology Research Centre.
    Selection against Accumulating Mutations in Niche-Preference Genes Can Drive Speciation2011In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 6, no 12, p. 29487-Article in journal (Refereed)
    Abstract [en]

    Our current understanding of sympatric speciation is that it occurs primarily through disruptive selection on ecological genes driven by competition, followed by reproductive isolation through reinforcement-like selection against inferior intermediates/heterozygotes. Our evolutionary model of selection on resource recognition and preference traits suggests a new mechanism for sympatric speciation. We find speciation can occur in three phases. First a polymorphism of functionally different phenotypes is established through evolution of specialization. On the gene level, regulatory functions have evolved in which some alleles are conditionally switched off (i.e. are silent). These alleles accumulate harmful mutations that potentially may be expressed in offspring through recombination. Second mating associated with resource preference invades because harmful mutations in parents are not expressed in the offspring when mating assortatively, thereby dividing the population into two pre-zygotically isolated resource-specialist lineages. Third, silent alleles that evolved in phase one now accumulate deleterious mutations over the following generations in a Bateson-Dobzhansky-Muller fashion, establishing a post-zygotic barrier to hybridization.

  • 287.
    Nushair, Ali Mohammad
    et al.
    University of Rajshahi, Bangladesh.
    Saha, Ananda Kumar
    University of Rajshahi, Bangladesh.
    Mandal, Abul
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre.
    Rahman, Md. Anisur
    University of Rajshahi, Bangladesh.
    Mohanta, Moni Krishno
    University of Rajshahi, Bangladesh.
    Hasan, Md. Ariful
    University of Rajshahi, Bangladesh.
    Haque, Md. Fazlul
    University of Rajshahi, Bangladesh.
    Rhizobium sp.CCNWYC119: a single strain highly effective as biofertilizer for three different peas (Pigeon pea, Sweet pea and Chick pea)2018In: Legume Research An International Journal, ISSN 0250-5371, Vol. 41, no 5, p. 771-777, article id LR-389Article in journal (Refereed)
    Abstract [en]

    Rhizobium spp. was isolated from root nodules of Pigeon pea (Cajanus cajan L.), Sweet pea (Lathyrus sativus L.), Chickpea (Cicer arietinum L.). The isolates ware rod shaped, aerobic, gram negative, motile and non-spore forming. Isolates were positive to Catalase, Citrate utilization, Urea hydrolysis, Congored, Nitrification, Oxidase, Triple sugar iron and MacConkey agar test. The isolates can ferment all nine sugars. Then, the isolates identified as Rhizobium spp. Depending on above results were subjected to 16S rRNA sequencing for further confirmation and identification. Surprisingly, theisolates were same strain or member of same cluster of Rhizobium and identified as Rhizobium sp.CCNWYC119 strain based on 16S rRNA sequence (98% similarity). Then, different parameters of soil quality enrichment and plant growth viz.plant height; weight of pods and seeds; number, fresh and dry weight of nodules were studied to test the efficacy of the isolate as biofertilizer. Here, inoculant of Rhizobium sp. isolated from Pigeon pea was used as biofertilizer. The results showed the significant increase of nodulation, enrichment of soil of rhizosphere, plant growth and yield for all three types of inoculated peas as compared with non-inoculated control peas indicating that the isolated strain could be used as a common efficient biofertilizer for Pigeon pea, Sweet pea and Chick pea. It was also found that the isolate grew optimally at temperature 28°C and pH 7.0.Moreover, the isolate was sensitive to the higher concentration of NaCl (>1%) and to antibiotics- Mecillinam, Ciprofloxacin,Cotrimoxazole, Pefloxacin, Ceftazidime and Tetracycline.

  • 288.
    Nyberg, Per
    et al.
    Fiskeriverkets Sötvattenslaboratorium (nuvarande Institutionen för akvatiska resurser, SLU).
    Degerman, Erik
    Fiskeriverkets Sötvattenslaboratorium (nuvarande Institutionen för akvatiska resurser, SLU).
    Setzer, Malin
    University of Skövde, School of Life Sciences. University of Skövde, The Systems Biology Research Centre.
    Norrgård, Johnny
    Vätternvårdsförbundet.
    Jonsson, Tomas
    University of Skövde, School of Life Sciences. University of Skövde, The Systems Biology Research Centre. School of Bioscience, University of Skövde.
    Predation av fisk och signalkräfta på rödingrom - resultat från en fältstudie i Vättern2012Report (Other academic)
    Abstract [sv]

    Vätterns unika bestånd av storröding har minskat kraftigt de senaste decennierna och orsakerna till minskningen diskuteras livligt. Bland föreslagna orsaker nämns exvis konkurrens från inplanterad lax, överexploatering och klimatförändringar. Därutöver befaras även signalkräftan, via predation på rödingrom kunna ha en negativ inverkan på rödingens reproduktion. För att undersöka predationen på rödingrom från såväl fisk som signalkräfta utfördes 2009 ett fältförsök vid en känd lekplats i norra Vättern. I de använda försöksburarna var den uppskattade mortaliteten av ägg till följd av kräftpredation 5 gånger högre än den till följd av fiskpredation. Resultaten indikerar därmed att predationen på rödingrom från signalkräfta kan vara kraftigt underskattad och att den kan ha påverkat rödingbeståndets återhämtning i Vättern negativt.

  • 289.
    Nöremark, Maria
    et al.
    Department of Disease Control and Epidemiology, SVA, National Veterinary Institute / Swedish University of Agricultural Sciences, Department of Clinical Sciences.
    Håkansson, Nina
    University of Skövde, The Systems Biology Research Centre. University of Skövde, School of Life Sciences.
    Lindström, Tom
    IFM, Theory and Modelling, Linköpings Universitet.
    Wennergren, Uno
    IFM, Theory and Modelling, Linköpings Universitet.
    Sternberg Lewerin, Susanna
    Department of Disease Control and Epidemiology, SVA, National Veterinary Institute.
    Spatial and temporal investigations of reported movements, births and deaths of cattle and pigs in Sweden2009In: Acta Veterinaria Scandinavica, ISSN 1751-0147, E-ISSN 1751-0147, Vol. 51, article id 37Article in journal (Refereed)
    Abstract [en]

    Background: Livestock movements can affect the spread and control of contagious diseases and new data recording systems enable analysis of these movements. The results can be used for contingency planning, modelling of disease spread and design of disease control programs.

    Methods: Data on the Swedish cattle and pig populations during the period July 2005 until June 2006 were obtained from databases held by the Swedish Board of Agriculture. Movements of cattle and pigs were investigated from geographical and temporal perspectives, births and deaths of cattle were investigated from a temporal perspective and the geographical distribution of holdings was also investigated.

    Results: Most movements of cattle and pigs were to holdings within 100 km, but movements up to 1200 km occurred. Consequently, the majority of movements occurred within the same county or to adjacent counties. Approximately 54% of the cattle holdings and 45% of the pig holdings did not purchase any live animals. Seasonal variations in births and deaths of cattle were identified, with peaks in spring. Cattle movements peaked in spring and autumn. The maximum number of holdings within a 3 km radius of one holding was 45 for cattle and 23 for pigs, with large variations among counties. Missing data and reporting bias (digit preference) were detected in the data.

    Conclusion: The databases are valuable tools in contact tracing. However since movements can be reported up to a week after the event and some data are missing they cannot replace other methods in the acute phase of an outbreak. We identified long distance transports of cattle and pigs, and these findings support an implementation of a total standstill in the country in the case of an outbreak of foot-and-mouth disease. The databases contain valuable information and improvements in data quality would make them even more useful.

  • 290.
    Nöremark, Maria
    et al.
    SVA, National Veterinary Institute, Department of Disease Control and Epidemiology, 751 89 Uppsala, Sweden / Department of Clinical Sciences, Swedish University of Agricultural Sciences, Box 7054, 750 09 Uppsala, Sweden.
    Håkansson, Nina
    University of Skövde, School of Life Sciences. University of Skövde, The Systems Biology Research Centre.
    Sternberg Lewerin, Susanna
    SVA, National Veterinary Institute, Department of Disease Control and Epidemiology, 751 89 Uppsala, Sweden.
    Lindberg, Ann
    SVA, National Veterinary Institute, Department of Disease Control and Epidemiology, 751 89 Uppsala, Sweden.
    Jonsson, Annie
    University of Skövde, School of Life Sciences. University of Skövde, The Systems Biology Research Centre.
    Network analysis of cattle and pig movements in Sweden: Measures relevant for disease control and risk based surveillance2011In: Preventive Veterinary Medicine, ISSN 0167-5877, E-ISSN 1873-1716, Vol. 99, no 2-4, p. 78-90Article in journal (Refereed)
    Abstract [en]

    Registration ofcattle and pigmovements is mandatory in Sweden and all registered movements between farms in the years 2006–2008 were investigated using network analysis. The networks were analysed as monthly and yearly networks, separately per species and with the two species together. Measures that have been previously discussed in relation to outbreaks and disease control were calculated; moreover a measure of the ingoing infection chain was constructed.The ingoing infection chain captures in going contacts through other holdings, taking the temporal aspect and sequence of the movements into account. The distribution of the contacts among the holdings was skewed.Many farms had few or no contacts, while others had many, a pattern which has also been described from other countries. The cattle network and the combined network showed a recurring seasonal pattern, while this was not seen in the pig network.The in-degree was not equivalent to the ingoing infection chain; there were holdings with limited direct contacts, but a large number of indirect contacts.The ingoing infection chain could be a useful measure when setting up strategies for disease control and for risk based surveillance as it identifies holdings with many contacts through live animal movements and thus at potentially higher risk for introduction of contagious diseases.

  • 291.
    O'Gorman, Eoin J.
    et al.
    University College Cork.
    Jacob, Ute
    University College Cork.
    Jonsson, Tomas
    University of Skövde, The Systems Biology Research Centre. University of Skövde, School of Life Sciences.
    Emmerson, Mark C.
    University College Cork.
    Interaction strength, food web topology and the relative importance of species in food webs.2010In: Journal of Animal Ecology, ISSN 0021-8790, E-ISSN 1365-2656, Vol. 79, no 3, p. 682-692Article in journal (Refereed)
    Abstract [en]

    1. We established complex marine communities, consisting of over 100 species, in large subtidal experimental mesocosms. We measured the strength of direct interactions and the net strength of direct and indirect interactions between the species in those communities, using a combination of theoretical and empirical approaches.

    2. Theoretical predictions of interaction strength were derived from the interaction coefficient matrix, which was parameterised using allometric predator–prey relationships. Empirical estimates of interaction strength were quantified using the ln-ratio, which measures the change in biomass density of species A in the presence and absence of species B.

    3. We observed that highly connected species tend to have weak direct effects and net effects in our experimental food webs, whether we calculate interaction strength theoretically or empirically.

    4. We found a significant correlation between our theoretical predictions and empirical estimates of direct effects and net effects. The net effects correlation was much stronger, indicating that our experimental communities were dominated by a mixture of direct and indirect effects.

    5. Re-calculation of the theoretical predictions of net effects after randomising predator and prey body masses did not affect the negative relationship with connectance.

    6. These results suggest that food web topology, which in this system is constrained by body mass, is overwhelmingly important for the magnitude of direct and indirect interactions and hence species importance in the face of biodiversity declines.

  • 292.
    Olivé, Montse
    et al.
    Institute of Neuropathology, Department of Pathology and Neuromuscular Unit, Department of Neurology / CIBERNED, Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas, Instituto Carlos III, Barcelona, Spain.
    Abdul-Hussein, Saba
    Department of Pathology, University of Gothenburg, Sahlgrenska University Hospital, Gothenburg, Sweden.
    Oldfors, Anders
    Department of Pathology, University of Gothenburg, Sahlgrenska University Hospital, Gothenburg, Sweden.
    González-Costello, José
    Department of Cardiology, Barcelona, Spain.
    van der Ven, Peter F. M.
    Department of Molecular Cell Biology, Institute for Cell Biology, University of Bonn, Bonn, Germany.
    Fürst, Dieter O.
    Department of Molecular Cell Biology, Institute for Cell Biology, University of Bonn, Bonn, Germany.
    González, Laura
    Institute of Neuropathology, Department of Pathology and Neuromuscular Unit, Department of Neurology.
    Moreno, Dolores
    Institute of Neuropathology, Department of Pathology, Barcelona, Spain.
    Torrejón-Escribano, Benjamín
    Scientific and Technical Services Facility, Biology Unit, CCiTUB, IDIBELL-University of Barcelona, Barcelona, Spain.
    Alió, Josefina
    Department of Cardiology, Barcelona, Spain.
    Pou, Adolf
    Department of Neurology, Hospital del Mar, Barcelona, Spain.
    Ferrer, Isidro
    Institute of Neuropathology, Department of Pathology, Barcelona, Spain / CIBERNED, Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas, Instituto Carlos III, Barcelona, Spain.
    Tajsharghi, Homa
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre. Department of Pathology, University of Gothenburg, Sahlgrenska University Hospital, Gothenburg, Sweden / Department of Clinical and Medical Genetics, University of Gothenburg, Gothenburg, Sweden.
    New cardiac and skeletal protein aggregate myopathy associated with combined MuRF1 and MuRF3 mutations2015In: Human Molecular Genetics, ISSN 0964-6906, E-ISSN 1460-2083, Vol. 24, no 13, p. 3638-3650, article id 108Article in journal (Refereed)
    Abstract [en]

    Protein aggregate myopathies (PAMs) define muscle disorders characterized by protein accumulation in muscle fibres. We describe a new PAM in a patient with proximal muscle weakness and hypertrophic cardiomyopathy, whose muscle fibres contained inclusions containing myosin and myosin-associated proteins, and aberrant distribution of microtubules. These lesions appear as intact A- and M-bands lacking thin filaments and Z-discs. These features differ from inclusions in myosin storage myopathy (MSM), but are highly similar to those in mice deficient for the muscle-specific RING finger proteins MuRF1 and MuRF3. Sanger sequencing excluded mutations in the MSM-associated gene MYH7 but identified mutations in TRIM63 and TRIM54, encoding MuRF1 and MuRF3, respectively. No mutations in other potentially disease-causing genes were identified by Sanger and whole exome sequencing. Analysis of seven family members revealed that both mutations segregated in the family but only the homozygous TRIM63 null mutation in combination with the heterozygous TRIM54 mutation found in the proband caused the disease phenotype. Both MuRFs are microtubule-associated proteins localizing to sarcomeric M-bands and Z-discs. They are E3 ubiquitin ligases that play a role in degradation of sarcomeric proteins, stabilization of microtubules and myogenesis. Lack of ubiquitin and the 20S proteasome subunit in the inclusions found in the patient suggested impaired turnover of thick filament proteins. Disruption of microtubules in cultured myotubes was rescued by transient expression of wild-type MuRF1. The unique features of this novel myopathy point to defects in homeostasis of A-band proteins in combination with instability of microtubules as cause of the disease.

  • 293.
    Olivé, Montse
    et al.
    Institute of Neuropathology, Department of Pathology and Neuromuscular Unit, Department of Neurology, Barcelona, Spain / CIBERNED, Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas, Instituto Carlos III, Barcelona, Spain.
    Abdul-Hussein, Saba
    Department of Pathology, University of Gothenburg, Sahlgrenska University Hospital, Gothenburg, Sweden.
    Oldfors, Anders
    Department of Pathology, University of Gothenburg, Sahlgrenska University Hospital, Gothenburg, Sweden.
    González-Costello, José
    Department of Cardiology, Barcelona, Spain.
    van der Ven, Peter F. M.
    Department of Molecular Cell Biology, Institute for Cell Biology, University of Bonn, Bonn, Germany.
    Fürst, Dieter O.
    Department of Molecular Cell Biology, Institute for Cell Biology, University of Bonn, Bonn, Germany.
    González, Laura
    Institute of Neuropathology, Department of Pathology and Neuromuscular Unit, Department of Neurology.
    Moreno, Dolores
    Institute of Neuropathology, Department of Pathology, Barcelona, Spain.
    Torrejón-Escribano, Benjamín
    Scientific and Technical Services Facility, Biology Unit, CCiTUB, IDIBELL-University of Barcelona, Barcelona, Spain.
    Alió, Josefina
    Department of Cardiology, Barcelona, Spain.
    Pou, Adolf
    Department of Neurology, Hospital del Mar, Barcelona, Spain.
    Ferrer, Isidro
    Institute of Neuropathology, Department of Pathology, Barcelona, Spain / CIBERNED, Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas, Instituto Carlos III, Barcelona, Spain.
    Tajsharghi, Homa
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre.
    New cardiac and skeletal protein aggregate myopathy associated with combined MuRF1 and MuRF3 mutations: [Human Molecular Genetics, 24, 13, (2015) 3638-3650] DOI: 10.1093/hmg/ddv108 [Erratum]2015In: Human Molecular Genetics, ISSN 0964-6906, E-ISSN 1460-2083, Vol. 24, no 21, p. 6264-6264Article in journal (Refereed)
  • 294.
    Olsson, Björn E.
    et al.
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre.
    Korsakova, Ekaterina S.
    Institute of Ecology and Genetics of Microorganisms, Ural Branch of the Russian Academy of Sciences, Perm, Russia.
    Anan'ina, Lyudmila N.
    Institute of Ecology and Genetics of Microorganisms, Ural Branch of the Russian Academy of Sciences, Perm, Russia.
    Pyankova, Anna A.
    Institute of Ecology and Genetics of Microorganisms, Ural Branch of the Russian Academy of Sciences, Perm, Russia.
    Mavrodi, Olga V.
    Department of Biological Sciences, The University of Southern Mississippi, USA.
    Plotnikova, Elena G.
    Institute of Ecology and Genetics of Microorganisms, Ural Branch of the Russian Academy of Sciences, Perm, Russia.
    Mavrodi, Dmitri V.
    Department of Biological Sciences, The University of Southern Mississippi, USA.
    Draft genome sequences of strains Salinicola socius SMB35T, Salinicola sp. MH3R3–1 and Chromohalobacter sp. SMB17 from the Verkhnekamsk potash mining region of Russia2017In: Standards in Genomic Sciences, ISSN 1944-3277, E-ISSN 1944-3277, Vol. 12, no 39, p. 1-13Article in journal (Refereed)
    Abstract [en]

    Halomonads are moderately halophilic bacteria that are studied as models of prokaryotic osmoadaptation and sources of enzymes and chemicals for biotechnological applications. Despite the progress in understanding the diversity of these organisms, our ability to explain ecological, metabolic, and biochemical traits of halomonads at the genomic sequence level remains limited. This study addresses this gap by presenting draft genomes of Salinicola socius SMB35T, Salinicola sp. MH3R3-1 and Chromohalobacter sp. SMB17, which were isolated from potash mine tailings in the Verkhnekamsk salt deposit area of Russia. The analysis of these genomes confirmed the importance of ectoines and quaternary amines to the capacity of halomonads to tolerate osmotic stress and adapt to hypersaline environments. The study also revealed that Chromohalobacter and Salinicola share 75-90% of the predicted proteome, but also harbor a set of genus-specific genes, which in Salinicola amounted to approximately 0.5 Mbp. These genus-specific genome segments may contribute to the phenotypic diversity of the Halomonadaceae and the ability of these organisms to adapt to changing environmental conditions and colonize new ecological niches.

  • 295.
    Orio, Alessandro
    et al.
    SLU, Sweden.
    Nielsen, Anders
    DTU Aqua, Denmark.
    Luzenczyk, Anna
    Morski Instytut Rybacki, Poland.
    Berg, Casper
    DTU Aqua, Denmark.
    Ustups, Didzis
    BIOR, Latvia.
    Artemenkov, Dmitriy
    Russian Federal Research Institute of Fisheries and Oceanography, Russia.
    Schade, Franziska
    Thünen-Institut, Germany.
    Kornilovs, Georgs
    BIOR, Latvia.
    Degel, Henrik
    DTU Aqua, Denmark.
    Strehlow, Harry
    Thünen-Institut, Germany.
    Karpushevskiy, Igor
    AtlantNIRO, Russia.
    Horbowy, Jan
    Morski Instytut Rybacki, Poland.
    Raitaniemi, Jari
    Luke Natural Resources Institute, Finland.
    Boje, Jesper
    DTU Aqua, Denmark.
    Hjelm, Joakim
    SLU, Sweden.
    Lövgren, Johan
    SLU, Sweden.
    Pönni, Jukka
    Luke Natural Resources Institute, Finland.
    Hommik, Kristiina
    Öhman, Kristin
    SLU, Sweden.
    Eero, Margit
    DTU Aqua, Denmark.
    Storr-Paulsen, Marie
    DTU Aqua, Denmark.
    Plikshs, Maris
    BIOR, Latvia.
    Casini, Michele
    SLU, Sweden.
    Bergenius, Mikaela
    SLU, Sweden.
    Mosegaard, Henrik
    Holmgren, Noel
    SLU, Sweden.
    Norrström, Niclas
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre.
    Kaljuste, Olavi
    SLU, Sweden.
    Jounela, Pekka
    Luke Natural Resources Institute, Finland.
    Statkus, Romas
    Lithuania.
    Jonusas, Stanislovas
    European Commission.
    Neuenfeldt, Stefan
    DTU Aqua, Denmark.
    Stoetera, Sven
    Thünen-Institut, Germany.
    Raid, Tiit
    University of Tartu, Estonia.
    Mildenberger, Tobias
    DTU Aqua, Denmark.
    Gröhsler, Tomas
    Thünen-Institut, Germany.
    Krumme, Uwe
    Thünen-Institut, Germany.
    Amosova, Viktoriia
    AtlantNIRO, Russia.
    Grygiel, Wlodzimierz
    Morski Instytut Rybacki, Poland.
    Pekcan-Hekim, Zeynep
    SLU, Sweden.
    Mirny, Zuzanna
    Morski Instytut Rybacki, Poland.
    Report of the Baltic Fisheries AssessmentWorking Group (WGBFAS): 19-26 April 2017, Copenhagen, Denmark2017Report (Other academic)
    Abstract [en]

    The ICES Baltic Fisheries Assessment Working Group (WGBFAS) met 19-26 April 2017(Chair: Tomas Gröhsler, Germany and Co-chair: Michele Casini, Sweden), with 41 participants and 9 countries represented. The objective of WGBFAS was to assess the status of the following stocks: Sole in Division 3.a, SDs 20–24; Cod in Kattegat, Cod in SDs 22–24, Cod in SDs 25–32; Herring in SDs 25–27, 28.2, 29 and 32, Herring in SD 28.1 (Gulf of Riga), Herring in SDs 30-31 (Gulf of Bothnia); Sprat in SDs 22–32; Plaice in SDs 21–23, Plaice in SDs 24–25; Flounder in SDs 22–23, in SDs 24–25, in SDs 26+28 and SDs 27+29–32; Brill in SDs 22–32, Dab in SDs 22–32 and Turbot in SDs 22–32. WGBFAS also identified the data needed for next year’s data call with some suggestions for improvements in the data call, and stock-specific research needs.The report contains an introduction with the summary of other WGs relevant for the WGBFAS, the methods used, and ecosystem considerations. The results of the analytical stock assessment or survey trends for the species listed above are then presented with all the stocks with the same species in the same sections. The report ends with references, recommendations, links to Stock Annexes and list of Working Documents.The principle analytical models used for the stock assessments were XSA and SAM. For most flatfishes and cod in SDs 25–32 (data limited stocks), CPUE trends from bottomtrawl surveys were used in the assessment (except plaice in SDs 24–25 for which relative SSB from SAM was used). For the data limited stocks, reference points based on length-based indicators were estimated (except cod in SDs 25-32 for which relative reference points were estimated using the SPiCT model). For cod in SDs 25–32, intersessional work was planned to hopefully allow returning to an analytical stock assessment in the near future. Ecosystem changes have been analytically considered in the following stock assessments: Herring in SD 25–27, 28.2, 29 and 32, and Sprat in SD 22–32, in form of cod predation mortality.

  • 296.
    Owemyr, Ida
    et al.
    University of Skövde, The Systems Biology Research Centre. University of Skövde, School of Life Sciences.
    Enroth, Helena
    Unilabs AB, Skövde, Sweden.
    Ljungström, Lars
    Skaraborg Hospital, Skövde, Sweden.
    Jacobsson, Gunnar
    Skaraborgs Sjukhus, Skövde, Sweden.
    Pernestig, Anna-Karin
    University of Skövde, The Systems Biology Research Centre. University of Skövde, School of Life Sciences.
    Karlsson, Diana
    University of Skövde, The Systems Biology Research Centre. University of Skövde, School of Life Sciences.
    Evaluation of microarray-based assay for identification of bloodstream bacteria in patients with suspected sepsis2013Conference paper (Refereed)
  • 297.
    Owemyr, Ida
    et al.
    University of Skövde, The Systems Biology Research Centre. University of Skövde, School of Life Sciences.
    Enroth, Helena
    Unilabs AB, Skövde.
    Ljungström, Lars
    Kärnsjukhuset, Skövde.
    Pernestig, Anna-Karin
    University of Skövde, School of Life Sciences. University of Skövde, The Systems Biology Research Centre.
    Karlsson, Diana
    University of Skövde, School of Life Sciences. University of Skövde, The Systems Biology Research Centre.
    Utvärdering av microarray-baserad plattform för snabb identifiering av patogener hos patienter med misstänkt sepsis2012Conference paper (Refereed)
  • 298.
    Padvitski, Tsimafei
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre. CECAD University of Cologne.
    Integrative analysis of age-related changes in the transcriptome of Caenorhabditis elegans2015Independent thesis Advanced level (degree of Master (One Year)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Ageing is difficult to study because of the complexity and multi-factorial nature of traits that result from a combination of environmental, genetic, epigenetic and stochastic factors, each contributing to the overall phenotype. In light of this challenge, transcriptomic studies of aging organisms are of particular interest, since transcription is an intermediate step that links genotype and phenotype.

    In recent years microarrays have been widely used for elucidation of changes that occur with age in the transcriptome in Caenorhabditis elegans. However, different microarray studies of C. elegans report sets of differentially expressed genes of varying consistence, with different functional annotations. Failures to find a consistent set of transcriptomic alterations may reflect the absence of a specific genetic program that would guide age-related changes but may also, to some extent, be a consequence of a small sample sizes and a lack of study power in transcriptomic researches. To tackle this issue we analyzed RNA sequences of samples from a time-series experiment of normal aging of C. elegans, performing the first, to our knowledge, NGS-based study of such kind. As a result, evidences were collected that promote a union of two competing theories: the theory of DNA damage accumulation and the theory of programmed aging.

    Next, we applied two alternative methods, namely the Short Time-series Expression Mining and the Network Smoothing algorithm, in order to obtain and analyze sets of genes that represent distinct modules of age-related changes in the transcriptome. Besides characterization of age-related changes, we were also interested in assessment and validation of the Network Smoothing algorithm. Generally, results of clustering of smoothed scores are consistent with results of short time-series clustering, allowing robust elucidation of functions that are perturbed during aging.

    At the last phase of the project we questioned if observed changes in the transcriptome can be controlled by specific transcription factors. Thus we used Chip-seq data to predict plausible transcription factor regulators of gene sets obtained using time series clustering and Network smoothing. On the one hand, all predicted transcription factors had documented relevance to aging. On the other hand, we did not achieve gene set specific prediction of transcription factors. In fact, genes with the opposite dynamics were predicted to respond to the same transcription factors. 

    To summarize, we characterized in details age-related changes in the transcriptome of C. elegans, validated the performance of the Network Smoothing algorithm and showed that integration of gene expression with Chip-seq data allows to predict transcription factors that are capable to modulate the lifespan of C. elegans.

  • 299.
    Paltto, Heidi
    et al.
    University of Skövde, School of Life Sciences. University of Skövde, The Systems Biology Research Centre. Department of Plant and Environmental Sciences, Gothenburg University, Gothenburg, Sweden / Department of Plant and Environmental Sciences, Gothenburg University, Gothenburg, Sweden.
    Thomasson, Ingrid
    Department of Plant and Environmental Sciences, Gothenburg University, Gothenburg, Sweden.
    Nordén, Björn
    Department of Plant and Environmental Sciences, Gothenburg University, Gothenburg, Sweden.
    Multispecies and Multiscale Conservation Planning: Setting Quantitative Targets for Red-Listed Lichens on Ancient Oaks2010In: Conservation Biology, ISSN 0888-8892, E-ISSN 1523-1739, Vol. 24, no 3, p. 758-768Article in journal (Refereed)
    Abstract [en]

    Species occurrence in a habitat patch depends on local habitat and the amount of that habitat in the wider landscape. We used predictions from empirical landscape studies to set quantitative conservation criteria and targets in a multispecies and multiscale conservation planning effort. We used regression analyses to compare species richness and occurrence of five red-listed lichens on 50 ancient oaks (Quercus robur; 120–140 cm in diameter) with the density of ancient oaks in circles of varying radius from each individual oak. Species richness and the occurrence of three of the five species were best explained by increasing density of oaks within 0.5 km; one species was best explained by the density of oaks within 2 km, and another was best predicted by the density of oaks within 5 km. The minimum numbers of ancient oaks required for “successful conservation” was defined as the number of oaks required to obtain a predicted local occurrence of 50% for all species included or a predicted local occurrence of 80% for all species included. These numbers of oaks were calculated for two relevant landscape scales (1 km2 and 13 km2) that corresponded to various species responses, in such a way that calculations also accounted for local number of oaks. Ten and seven of the 50 ancient oaks surveyed were situated in landscapes that already fulfilled criteria for successful conservation when the 50% and 80% criteria, respectively, were used to define the level of successful conservation. For cost-efficient conservation, oak stands in the landscapes most suitable for successful conservation should be prioritized for conservation and management (e.g., grazing and planting of new oaks) at the expense of oak stands situated elsewhere.

  • 300.
    Parthemore, Joel
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre.
    A cognitive semiotic perspective on the nature and limitations of concepts andconceptual frameworks2016In: Meaning, Mind and Communication: Explorations in Cognitive Semiotics / [ed] Jordan Zlatev, Göran Sonesson, Piotr Konderak, Frankfurt am Main: Peter Lang Publishing Group, 2016, p. 47-68Chapter in book (Refereed)
    Abstract [en]

    Known under the potentially misleading rubric of “knowledge representation” in cognitive science, theories of concepts represent both a subfield within philosophy of mind and an application area for cognitive semiotics. They describe the properties of conceptual thought, typically through a listing of those properties: minimally taken to include systematicity, productivity, compositionality, intentionality, and endogenous control. Beyond that point, most things are up for grabs. Debate rages over such questions as whether concepts are representations or abilities; likewise unclear is whether they are essentially public or largely private, discrete or continuous, stable or dynamic, transparent or translucent or opaque. Cognitive semiotics helps clarify discussion over an inevitably abstract area in a number of key ways: through its grounding in semiotics, showing how concepts both are entwined with language (intrinsically public) and pull apart from it; through its roots in phenomenology, showing how concepts both are and are not representations; through its focus on meaning as a dynamic process, showing how concepts’ relative stability belies an underlying dynamics; through its deep resonance with enactive philosophy, showing how concepts impose seemingly sharp boundaries onto underlying continuities; through its bold refusal to shy away from apparent contradictions and paradox, revealing how concepts both reveal the world and simultaneously hide it from us. As a concrete example, I discuss the conceptual nature of metaphor from a cognitive semiotic perspective. I show how – given the problematic nature of so-called literal meaning – the crucial distinction is not between literal and metaphorical meanings, but between tertiary/novel meanings and primary/secondary ones: between meanings that call attention to themselves and those that do not, where only the former are appropriately termed “metaphors”. The lesson is not that all meaning is metaphorical but rather that the line between metaphor and non-metaphor is pragmatic rather than absolute, conceptual rather than ontological.

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