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  • 1.
    Aarts, B.
    et al.
    Netherlands Forensic Institute, Biological Traces and DNA, The Hague, Netherlands.
    Kokshoorn, B.
    Netherlands Forensic Institute, Biological Traces and DNA, The Hague, Netherlands.
    Mc Kenna, L.G.
    Forensic Science Ireland, DNA department, Dublin, Ireland.
    Drotz, W.
    Swedish National Forensic Centre, DNA department, Linköping, Sweden.
    Ansell, Ricky
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering. Swedish National Forensic Centre, DNA department, Linköping, Sweden.
    van Oorschot, R.A.
    Office of the Chief Forensic Scientist, Victoria Police Forensic Services Department, Macleod- Victoria, Australia.
    Kloosterman, A.D.
    Netherlands Forensic Institute, Biological Traces and DNA, The Hague, Netherlands.
    DNActivity: International cooperation in activity level interpretation of forensic DNA evidence.2015In: Abstract book, 7th European Academy of Forensic Science, EAFS, Prag, Tjeckien, 2015., 2015, p. 555-Conference paper (Other academic)
    Abstract [en]

    Questions posed to expert witnesses by the legal community and the courts are expanding to include not just those relating to source level (i.e. ‘who is the donor of the trace?’) but also those relating to activitity level (i.e. ‘how did the DNA get there?’). The answers to these questions are usually formulated as the probability of the evidence under alternative scenarios. As activity level questions are part of investigative and legal considerations it is of paramount importance that expert witnesses are provided with knowledge and tools to address these questions.

    To answer such questions within a probabilistic framework, empirical data is needed to estimate probabilities of transfer, persistence and recovery of DNA as well as background levels of DNA on everyday objects. There is a paucity of empirical data on these topics, but the number of studies is increasing both through in-house experiments and experimental data published in international scientific journals.

    Laboratories that conduct such studies all use different experimental setups, trace recovery strategies and techniques and DNA analysis systems and equipment. It is essential for the forensic genetics community in general to establish whether the data generated by different labs are in concordance, and can therefore be readily used by the forensic community.

    Moreover, if existing data and data generated from future experiments are made available to the (forensic) community, knowledge is needed on the key factors that underlie potential interlaboratory variation.

    The aims and objectives of this ENFSI Monopoly 2013 project are to conduct a study of methodologies and data from different laboratories and to assess the comparability of the scientific data on transfer, persistence and recovery of DNA. This comparison will allow us to identify key factors that underlie potential variation. This information will be used to setup guidelines to enable sharing and database-storage of relevant scientific

    data. This will improve the ability of forensic scientists and other professionals of the Criminal Justice System to give evidence-based answers to questions that relate to the activity level of the crime under investigation.

  • 2.
    Abbey-Lee, Robin
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering. Max Planck Inst Ornithol, Germany.
    Araya-Ajoy, Yimen G.
    Norwegian Univ Sci and Technol, Norway.
    Mouchet, Alexia
    Max Planck Inst Ornithol, Germany.
    Moiron, Maria
    Max Planck Inst Ornithol, Germany.
    Stuber, Erica F.
    Univ Nebraska Lincoln, NE USA.
    Kempenaers, Bart
    Max Planck Inst Ornithol, Germany.
    Dingemanse, Niels J.
    Max Planck Inst Ornithol, Germany; Ludwig Maximilians Univ Munchen, Germany.
    Does perceived predation risk affect patterns of extra-pair paternity? A field experiment in a passerine bird2018In: Functional Ecology, ISSN 0269-8463, E-ISSN 1365-2435, Vol. 32, no 4, p. 1001-1010Article in journal (Refereed)
    Abstract [en]

    Non-consumptive predator effects have been shown to influence a wide range of behavioural, life history and morphological traits. Extra-pair reproduction is widespread among socially monogamous birds and may incur predation costs. Consequently, altered rates of extra-pair reproduction are expected in circumstances characterized by increased adult perceived predation risk. In addition, extra-pair reproduction is expected to be most affected for birds with phenotypes that generally increase predation risk (such as more active individuals). In two consecutive years, perceived predation risk was manipulated for great tits Parus major breeding in 12 nest-box plots by broadcasting sounds of their main predator (European sparrowhawk Accipiter nisus; six plots). As a control treatment, sounds of a sympatric, avian non-predator species were broadcast (Eurasian blackbird Turdus merula; six plots). Levels of extra-pair paternity did not differ between plots with different predation risk treatments. Males that moved more in a novel environment (more active or faster exploring) tended to have offspring with fewer partners, but this effect did not vary with predation risk treatment. From an adaptive viewpoint, predation costs associated with extra-pair reproduction may be small and may not outweigh the benefits of extra-pair behaviour. Research on a broader range of taxa with different mating strategies is now needed to confirm the generality of our findings.

  • 3.
    Abbey-Lee, Robin N.
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Uhrig, Emily J.
    Department of Zoology, Stockholm University, 10691 Stockholm, Sweden.
    Zidar, Josefina
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Favati, Anna
    Department of Zoology, Stockholm University, 10691 Stockholm, Sweden.
    Almberg, Johan
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Dahlblom, Josefin
    Department of Neuroscience, Uppsala Biomedical Centre BMC, Uppsala University, Uppsala, Sweden.
    Winberg, Svante
    Department of Neuroscience, Uppsala Biomedical Centre BMC, Uppsala University, Uppsala, Sweden.
    Løvlie, Hanne
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    The influence of rearing on behavior, brain monoamines and gene expression in three-spined sticklebacks2018Data set
    Abstract [en]
    1. The causes of individual variation in behavior are often not well understood, and potential underlying mechanisms include both intrinsic and extrinsic factors, such as early environmental, physiological, and genetic differences.
    2. In an exploratory laboratory study, we raised three-spined sticklebacks (Gasterosteus aculeatus) under 4 different environmental conditions (simulated predator environment, complex environment, variable social environment, and control). We investigated how these manipulations related to behavior, brain physiology and gene expression later in life, with focus on brain dopamine and serotonin levels, turnover rates, and gene expression.
    3. The different rearing environments influenced behavior and gene expression, but did not alter monoamine levels or metabolites. Specifically, compared to control fish, fish exposed to a simulated predator environment tended to be less aggressive, more exploratory, and more neophobic; and fish raised in both complex and variable social environments tended to be less neophobic. Exposure to a simulated predator environment tended to lower expression of dopamine receptor DRD4A, a complex environment increased expression of dopamine receptor DRD1B, while a variable social environment tended to increase serotonin receptor 5-HTR2B and increased serotonin transporter SLC6A4A expression. Despite both behavior and gene expression varying with early environment, there was no evidence that gene expression mediated the relationship between early environment and behavior.
    4. Our results confirm that environmental conditions early in life can affect phenotypic variation. However, the mechanistic pathway of the monoaminergic systems translating early environmental variation into observed behavioral responses was not detected.
  • 4.
    Abbey-Lee, Robin N.
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Uhrig, Emily
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Zidar, Josefina
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Favati, A.
    Department of Zoology, Stockholm University, Stockholm, Sweden.
    Almberg, J.
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Dahlbom, J.
    Department of Neuroscience, Uppsala Biomedical Centre BMC, Uppsala University, Uppsala, Sweden.
    Winberg, S.
    Department of Neuroscience, Uppsala Biomedical Centre BMC, Uppsala University, Uppsala, Sweden.
    Løvlie, Hanne
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    The Influence of Rearing on Behavior, Brain Monoamines, and Gene Expression in Three-Spined Sticklebacks2018In: Brain, behavior, and evolution, ISSN 0006-8977, E-ISSN 1421-9743, Vol. 91, no 4, p. 201-213Article in journal (Refereed)
    Abstract [en]

    The causes of individual variation in behavior are often not well understood, and potential underlying mechanisms include both intrinsic and extrinsic factors, such as early environmental, physiological, and genetic differences. In an exploratory laboratory study, we raised three-spined sticklebacks <i>(Gasterosteus aculeatus)</i> under 4 different environmental conditions (simulated predator environment, complex environment, variable social environment, and control). We investigated how these manipulations related to behavior, brain physiology, and gene expression later in life, with focus on brain dopamine and serotonin levels, turnover rates, and gene expression. The different rearing environments influenced behavior and gene expression, but did not alter monoamine levels or metabolites. Specifically, compared to control fish, fish exposed to a simulated predator environment tended to be less aggressive, more exploratory, and more neophobic; and fish raised in both complex and variable social environments tended to be less neophobic. Exposure to a simulated predator environment tended to lower expression of dopamine receptor DRD4A, a complex environment increased expression of dopamine receptor DRD1B, while a variable social environment tended to increase serotonin receptor 5-HTR2B and serotonin transporter SLC6A4A expression. Despite both behavior and gene expression varying with early environment, there was no evidence that gene expression mediated the relationship between early environment and behavior. Our results confirm that environmental conditions early in life can affect phenotypic variation. However, the mechanistic pathway of the monoaminergic systems translating early environmental variation into observed behavioral responses was not detected.

  • 5.
    Abbey-Lee, Robin
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Uhrig, Emily
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering. Southern Oregon Univ, OR 97520 USA.
    Garnham, Laura
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Lundgren, Kristoffer
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Child, Sarah
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering. Univ Manchester, England.
    Lovlie, Hanne
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Experimental manipulation of monoamine levels alters personality in crickets2018In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 8, article id 16211Article in journal (Refereed)
    Abstract [en]

    Animal personality has been described in a range of species with ecological and evolutionary consequences. Factors shaping and maintaining variation in personality are not fully understood, but monoaminergic systems are consistently linked to personality variation. We experimentally explored how personality was influenced by alterations in two key monoamine systems: dopamine and serotonin. This was done using ropinirole and fluoxetine, two common human pharmaceuticals. Using the Mediterranean field cricket (Gryllus bimaculatus), we focused on the personality traits activity, exploration, and aggression, with confirmed repeatability in our study. Dopamine manipulations explained little variation in the personality traits investigated, while serotonin manipulation reduced both activity and aggression. Due to limited previous research, we created a dose-response curve for ropinirole, ranging from concentrations measured in surface waters to human therapeutic doses. No ropinirole dose level strongly influenced cricket personality, suggesting our results did not come from a dose mismatch. Our results indicate that the serotonergic system explains more variation in personality than manipulations of the dopaminergic system. Additionally, they suggest that monoamine systems differ across taxa, and confirm the importance of the mode of action of pharmaceuticals in determining their effects on behaviour.

  • 6.
    Abdelfattah, Ahmed
    et al.
    Univ Mediterranea Reggio Calabria, Italy.
    Malacrinò, Antonino
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Wisniewski, Michael
    USDA ARS, WV 25430 USA.
    Cacciola, Santa O.
    Univ Catania, Italy.
    Schena, Leonardo
    Univ Mediterranea Reggio Calabria, Italy.
    Metabarcoding: A powerful tool to investigate microbial communities and shape future plant protection strategies2018In: Biological control (Print), ISSN 1049-9644, E-ISSN 1090-2112, Vol. 120Article in journal (Refereed)
    Abstract [en]

    Microorganisms are the main drivers shaping the functioning and equilibrium of all ecosystems, contributing to nutrient cycling, primary production, litter decomposition, and multi-trophic interactions. Knowledge about the microbial assemblies in specific ecological niches is integral to understanding the assemblages interact and function the function, and becomes essential when the microbiota intersects with human activities, such as protecting crops against pests and diseases. Metabarcoding has proven to be a valuable tool and has been widely used for characterizing the microbial diversity of different environments and has been utilized in many research endeavors. Here we summarize the current status of metabarcoding technologies, the advantages and challenges in utilizing this technique, and how this pioneer approach is being applied to studying plant diseases and pests, with a focus on plant protection and biological control. Current and future developments in this technology will foster a more comprehensive understanding of microbial ecology, and the development of new, innovative pest control strategies.

  • 7.
    Agnvall, Beatrix
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Early domestication?: Phenotypic alterations of Red Junglefowl selected for divergent fear of humans2016Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Domestication is the process through which animals adapt to conditions provided by humans. The domesticated phenotype differs from wild ancestors in a number of traits relating to physiology, morphology and behaviour. One of the most striking differences is the animals’ fear response towards humans, and reduced fear of humans is assumed to have been an early prerequisite for the success of domestication. The early alterations seen in the domesticated phenotype may be traits developed as a correlated selection response due to tameness rather than selected upon one by one.

    This thesis summarizes a project where Red Junglefowl were selected for divergent fear of humans during six generations. In every generation, fear response to human was assessed in a standardized test and, according to fear score, the animals were bred for either high fear of humans (H) or low fear of humans (L). The animals were, above that of the standardized selection test, behaviourally phenotyped in different tests in each generation mainly focusing on fear, exploration and social behaviour. In addition to behaviour, the animals were phenotyped for body weight, egg weight, metabolism, feed intake, plumage condition, blood plasma corticosterone and peripheral serotonin. After culling, vital organs and brains were harvested and weighed.

    In paper I, we demonstrated that the selection trait has a significant genetic heritability and is genetically correlated with other behavioural responses associated with fearfulness and exploration. In paper II, we concluded that animals from the L strain had better plumage condition, higher weight, laid larger eggs and also generated larger offspring. Furthermore, when tested in a social dominance test with a limited resource, they received less and performed more aggression regardless of whether the restricted source was edible or not. In paper III, we revealed that animals from the L strain had higher basal metabolic rate as chicks, gained more weight in relation to feed intake and were bolder in a Novel Object test. Furthermore, the L males had higher plasma levels of peripheral serotonin, but the corticosterone after a restraint stress test did not differ. In paper IV and V, we concluded the project by comparing brain and organ weights as well as behaviour of the parental generation (P0) with the fifth selected generation (S5). The absolute brain weight as well as the weight specific brain weight were larger in the animals selected on H than in the L-animals. The relative weight of telencephalon was significantly higher in H whereas relative weight of cerebellum was significantly lower. Heart, liver, spleen and testes were all relatively heavier in H animals than in L. Interestingly, the behaviours assessed in P0 and S5 seemed to be rather resilient to the selection with only small differences in S5.

    To summarize, the selection on divergent tameness in Red Junglefowl has affected several phenotypic traits associated with the domesticated phenotype. The results of this project indicate that tameness in Red Junglefowl could be an underlying factor driving trait modifications towards the domesticated phenotype.

    List of papers
    1. Heritability and Genetic Correlations of Fear-Related Behaviour in Red Jungelfowl -Possible Implications for Early Domestication
    Open this publication in new window or tab >>Heritability and Genetic Correlations of Fear-Related Behaviour in Red Jungelfowl -Possible Implications for Early Domestication
    2012 (English)In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 7, no 4, p. e35162-Article in journal (Refereed) Published
    Abstract [en]

    Domesticated species differ from their wild ancestors in a number of traits, generally referred to as the domesticated phenotype. Reduced fear of humans is assumed to have been an early prerequisite for the successful domestication of virtually all species. We hypothesized that fear of humans is linked to other domestication related traits. For three generations, we selected Red Junglefowl (ancestors of domestic chickens) solely on the reaction in a standardized Fear of Human-test. In this, the birds were exposed for a gradually approaching human, and their behaviour was continuously scored. This generated three groups of animals, high (H), low (L) and intermediate (I) fearful birds. The birds in each generation were additionally tested in a battery of behaviour tests, measuring aspects of fearfulness, exploration, and sociality. The results demonstrate that the variation in fear response of Red Junglefowl towards humans has a significant genetic component and is genetically correlated to behavioural responses in other contexts, of which some are associated with fearfulness and others with exploration. Hence, selection of Red Junglefowl on low fear for humans can be expected to lead to a correlated change of other behavioural traits over generations. It is therefore likely that domestication may have caused an initial suite of behavioural modifications, even without selection on anything besides tameness.

    National Category
    Natural Sciences
    Identifiers
    urn:nbn:se:liu:diva-76833 (URN)10.1371/journal.pone.0035162 (DOI)000305336200026 ()
    Available from: 2012-04-20 Created: 2012-04-20 Last updated: 2017-12-07
    2. Red Junglefowl (Gallus gallus) selected for low fear of humans are larger, more dominant and produce larger offspring
    Open this publication in new window or tab >>Red Junglefowl (Gallus gallus) selected for low fear of humans are larger, more dominant and produce larger offspring
    2014 (English)In: animal, ISSN 1751-7311, Vol. 8, no 9, p. 1498-1505Article in journal (Refereed) Published
    Abstract [en]

    Many traits associated with domestication are suggested to have developed as correlated responses to reduced fear of humans. Tameness may have reduced the stress of living in human proximity and improved welfare in captivity. We selected Red Junglefowl (ancestors of all domestic chickens) for four generations on high or low fear towards humans, mimicking an important aspect of the earliest period of domestication, and tested birds from the third and fourth generation in three different social tests. Growth and plumage condition, as well as size of eggs and offspring were also recorded, as indicators of some aspects of welfare. Birds selected for low fear had higher weight, laid larger eggs and generated larger offspring, and had a better plumage condition. In a social dominance test they also performed more aggressive behaviour and received less of the same, regardless of whether the restricted resource was feed or not. Hence, dominance appeared to increase as a consequence of reduced fear of humans. Furthermore, egg size and the weight of the offspring were larger in the less fearful birds, and plumage condition better, which could be interpreted as the less fearful animals being better adapted to the environment in which they were selected.

    Place, publisher, year, edition, pages
    Cambridge University Press, 2014
    Keywords
    Red Junglefowl, domestication, fearfulness, selection, social behaviour
    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:liu:diva-109499 (URN)10.1017/S1751731114001426 (DOI)000342219000013 ()24910136 (PubMedID)
    Available from: 2014-08-20 Created: 2014-08-20 Last updated: 2016-11-17
    3. Is domestication driven by reduced fear of humans? Boldness, metabolism and serotonin levels in divergently selected red junglefowl (Gallus gallus)
    Open this publication in new window or tab >>Is domestication driven by reduced fear of humans? Boldness, metabolism and serotonin levels in divergently selected red junglefowl (Gallus gallus)
    2015 (English)In: Biology Letters, ISSN 1744-9561, E-ISSN 1744-957X, Vol. 11, no 9, article id 20150509Article in journal (Refereed) Published
    Abstract [en]

    Domesticated animals tend to develop a coherent set of phenotypic traits. Tameness could be a central underlying factor driving this, and we therefore selected red junglefowl, ancestors of all domestic chickens, for high or low fear of humans during six generations. We measured basal metabolic rate (BMR), feed efficiency, boldness in a novel object (NO) test, corticosterone reactivity and basal serotonin levels (related to fearfulness) in birds from the fifth and sixth generation of the high- and low-fear lines, respectively (44-48 individuals). Corticosterone response to physical restraint did not differ between selection lines. However, BMR was higher in low-fear birds, as was feed efficiency. Low-fear males had higher plasma levels of serotonin and both low-fear males and females were bolder in an NO test. The results show that many aspects of the domesticated phenotype may have developed as correlated responses to reduced fear of humans, an essential trait for successful domestication.

    Place, publisher, year, edition, pages
    ROYAL SOC, 2015
    Keywords
    genetics; domestication; stress
    National Category
    Zoology Evolutionary Biology
    Identifiers
    urn:nbn:se:liu:diva-123162 (URN)10.1098/rsbl.2015.0509 (DOI)000364772300009 ()26382075 (PubMedID)
    Note

    Funding Agencies|research council Formas; ERC [322206]

    Available from: 2015-12-07 Created: 2015-12-04 Last updated: 2017-12-01Bibliographically approved
    4. Effects of Divergent Selection for Fear of Humans on Behaviour in Red Junglefowl
    Open this publication in new window or tab >>Effects of Divergent Selection for Fear of Humans on Behaviour in Red Junglefowl
    2016 (English)In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 11, no 11, p. 1-12Article in journal (Refereed) Published
    Abstract [en]

    Domestication has caused a range of similar phenotypic changes across taxa, relating to physiology, morphology and behaviour. It has been suggested that this recurring domesticated phenotype may be a result of correlated responses to a central trait, namely increased tameness. We selected Red Junglefowl, the ancestors of domesticated chickens, during five generations for reduced fear of humans. This caused a marked and significant response in tameness, and previous studies have found correlated effects on growth, metabolism, reproduction, and some behaviour not directly selected for. Here, we report the results from a series of behavioural tests carried out on the initial parental generation (P0) and the fifth selected generation (S5), focusing on behaviour not functionally related to tameness, in order to study any correlated effects. Birds were tested for fear of humans, social reinstatement tendency, open field behaviour at two different ages, foraging/exploration, response to a simulated aerial predator attack and tonic immobility. In S5, there were no effects of selection on foraging/exploration or tonic immobility, while in the social reinstatement and open field tests there were significant interactions between selection and sex. In the aerial predator test, there were significant main effects of selection, indicating that fear of humans may represent a general wariness towards predators. In conclusion, we found only small correlated effects on behaviours not related to the tameness trait selected for, in spite of them showing high genetic correlations to fear of humans in a previous study on the same population. This suggests that species-specific behaviour is generally resilient to changes during domestication.

    Place, publisher, year, edition, pages
    PLOS, 2016
    National Category
    Developmental Biology Genetics
    Identifiers
    urn:nbn:se:liu:diva-132742 (URN)10.1371/journal.pone.0166075 (DOI)000387909300035 ()27851792 (PubMedID)
    Note

    European Research Council [322206]; FORMAS [221-2007-838]; Vetenskapsradet [621-2008-5437]

    Available from: 2016-11-22 Created: 2016-11-22 Last updated: 2017-11-29Bibliographically approved
  • 8.
    Agnvall, Beatrix
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, The Institute of Technology.
    Ali, A.
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, The Institute of Technology.
    Olby, S.
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, The Institute of Technology.
    Jensen, Per
    Linköping University, Department of Physics, Chemistry and Biology, Biology.
    Red Junglefowl (Gallus gallus) selected for low fear of humans are larger, more dominant and produce larger offspring2014In: animal, ISSN 1751-7311, Vol. 8, no 9, p. 1498-1505Article in journal (Refereed)
    Abstract [en]

    Many traits associated with domestication are suggested to have developed as correlated responses to reduced fear of humans. Tameness may have reduced the stress of living in human proximity and improved welfare in captivity. We selected Red Junglefowl (ancestors of all domestic chickens) for four generations on high or low fear towards humans, mimicking an important aspect of the earliest period of domestication, and tested birds from the third and fourth generation in three different social tests. Growth and plumage condition, as well as size of eggs and offspring were also recorded, as indicators of some aspects of welfare. Birds selected for low fear had higher weight, laid larger eggs and generated larger offspring, and had a better plumage condition. In a social dominance test they also performed more aggressive behaviour and received less of the same, regardless of whether the restricted resource was feed or not. Hence, dominance appeared to increase as a consequence of reduced fear of humans. Furthermore, egg size and the weight of the offspring were larger in the less fearful birds, and plumage condition better, which could be interpreted as the less fearful animals being better adapted to the environment in which they were selected.

  • 9.
    Agnvall, Beatrix
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Bélteky, Johan
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Jensen, Per
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Brain size is reduced by selectionfor tameness in Red Junglefowl–correlated effects in vital organs2017In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 7, article id 3306Article in journal (Refereed)
    Abstract [en]

    During domestication animals have undergone changes in size of brain and other vital organs. We hypothesize that this could be a correlated effect to increased tameness. Red Junglefowl (ancestors of domestic chickens) were selected for divergent levels of fear of humans for five generations. The parental (P0) and the fifth selected generation (S5) were culled when 48–54 weeks old and the brains were weighed before being divided into telencephalon, cerebellum, mid brain and optic lobes. Each single brain part as well as the liver, spleen, heart and testicles were also weighed. Brains of S5 birds with high fear scores (S5 high) were heavier both in absolute terms and when corrected for body weight. The relative weight of telencephalon (% of brain weight) was significantly higher in S5 high and relative weight of cerebellum was lower. Heart, liver, testes and spleen were all relatively heavier (% of body weight) in S5 high. Hence, selection for tameness has changed the size of the brain and other vital organs in this population and may have driven the domesticated phenotype as a correlated response.

  • 10.
    Agnvall, Beatrix
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Bélteky, Johan
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Katajamaa, Rebecca
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Jensen, Per
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Is evolution of domestication driven by tameness? A selective review with focus on chickens2018In: Applied Animal Behaviour Science, ISSN 0168-1591, E-ISSN 1872-9045, Vol. 205, p. 227-233Article in journal (Refereed)
    Abstract [en]

    Domestication of animals offers unique possibilities to study evolutionary changes caused by similar selection pressures across a range of species. Animals from separate genera tend to develop a suite of phenotypic alterations referred to as "the domesticated phenotype". This involves changes in appearance, including loss of pigmentation, and alterations in body size and proportions. Furthermore, effects on reproduction and behaviour are typical. It is hypothesized that this recurring phenotype may be secondary effects of the increased tameness that is an inevitable first step in the domestication of any species. We first provide a general overview of observations and experiments from different species and then review in more detail a project attempting to recreate the initial domestication of chickens. Starting from an outbred population of Red Junglefowl, ancestors of all modem chickens, divergent lines were selected based on scores in a standardized fear-of-human test applied to all birds at 12 weeks of age. Up to the eighth selected generation, observations have been made on correlated effects of this selection on various phenotypes. The fear score had a significant heritability and was genetically correlated to several other behavioural traits. Furthermore, low-fear birds were larger at hatch, grew faster, laid larger eggs, had a modified metabolism and increased feed efficiency, had modified social behaviour and reduced brain size. Selection affected gene expression and DNA-methylation in the brains, but the genetic and epigenetic effects were not specifically associated with stress pathways. Further research should be focused on unraveling the genetic and epigenetic mechanisms underlying the correlated side-effects of reduced fear of humans.

  • 11.
    Agnvall, Beatrix
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Jensen, Per
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Effects of Divergent Selection for Fear of Humans on Behaviour in Red Junglefowl2016In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 11, no 11, p. 1-12Article in journal (Refereed)
    Abstract [en]

    Domestication has caused a range of similar phenotypic changes across taxa, relating to physiology, morphology and behaviour. It has been suggested that this recurring domesticated phenotype may be a result of correlated responses to a central trait, namely increased tameness. We selected Red Junglefowl, the ancestors of domesticated chickens, during five generations for reduced fear of humans. This caused a marked and significant response in tameness, and previous studies have found correlated effects on growth, metabolism, reproduction, and some behaviour not directly selected for. Here, we report the results from a series of behavioural tests carried out on the initial parental generation (P0) and the fifth selected generation (S5), focusing on behaviour not functionally related to tameness, in order to study any correlated effects. Birds were tested for fear of humans, social reinstatement tendency, open field behaviour at two different ages, foraging/exploration, response to a simulated aerial predator attack and tonic immobility. In S5, there were no effects of selection on foraging/exploration or tonic immobility, while in the social reinstatement and open field tests there were significant interactions between selection and sex. In the aerial predator test, there were significant main effects of selection, indicating that fear of humans may represent a general wariness towards predators. In conclusion, we found only small correlated effects on behaviours not related to the tameness trait selected for, in spite of them showing high genetic correlations to fear of humans in a previous study on the same population. This suggests that species-specific behaviour is generally resilient to changes during domestication.

  • 12.
    Agnvall, Beatrix
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, The Institute of Technology.
    Jöngren, Markus
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, The Institute of Technology.
    Strandberg, Erling
    Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Jensen, Per
    Linköping University, Department of Physics, Chemistry and Biology, Zoology. Linköping University, The Institute of Technology.
    Heritability and Genetic Correlations of Fear-Related Behaviour in Red Jungelfowl -Possible Implications for Early Domestication2012In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 7, no 4, p. e35162-Article in journal (Refereed)
    Abstract [en]

    Domesticated species differ from their wild ancestors in a number of traits, generally referred to as the domesticated phenotype. Reduced fear of humans is assumed to have been an early prerequisite for the successful domestication of virtually all species. We hypothesized that fear of humans is linked to other domestication related traits. For three generations, we selected Red Junglefowl (ancestors of domestic chickens) solely on the reaction in a standardized Fear of Human-test. In this, the birds were exposed for a gradually approaching human, and their behaviour was continuously scored. This generated three groups of animals, high (H), low (L) and intermediate (I) fearful birds. The birds in each generation were additionally tested in a battery of behaviour tests, measuring aspects of fearfulness, exploration, and sociality. The results demonstrate that the variation in fear response of Red Junglefowl towards humans has a significant genetic component and is genetically correlated to behavioural responses in other contexts, of which some are associated with fearfulness and others with exploration. Hence, selection of Red Junglefowl on low fear for humans can be expected to lead to a correlated change of other behavioural traits over generations. It is therefore likely that domestication may have caused an initial suite of behavioural modifications, even without selection on anything besides tameness.

  • 13.
    Agnvall, Beatrix
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Katajamaa, Rebecca
    Linköping University, Department of Physics, Chemistry and Biology, Biology.
    Altimiras, Jordi
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Jensen, Per
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Is domestication driven by reduced fear of humans? Boldness, metabolism and serotonin levels in divergently selected red junglefowl (Gallus gallus)2015In: Biology Letters, ISSN 1744-9561, E-ISSN 1744-957X, Vol. 11, no 9, article id 20150509Article in journal (Refereed)
    Abstract [en]

    Domesticated animals tend to develop a coherent set of phenotypic traits. Tameness could be a central underlying factor driving this, and we therefore selected red junglefowl, ancestors of all domestic chickens, for high or low fear of humans during six generations. We measured basal metabolic rate (BMR), feed efficiency, boldness in a novel object (NO) test, corticosterone reactivity and basal serotonin levels (related to fearfulness) in birds from the fifth and sixth generation of the high- and low-fear lines, respectively (44-48 individuals). Corticosterone response to physical restraint did not differ between selection lines. However, BMR was higher in low-fear birds, as was feed efficiency. Low-fear males had higher plasma levels of serotonin and both low-fear males and females were bolder in an NO test. The results show that many aspects of the domesticated phenotype may have developed as correlated responses to reduced fear of humans, an essential trait for successful domestication.

  • 14.
    Ahlrot, Ulrica
    Linköping University, Department of Physics, Chemistry and Biology, Biology.
    Welfare in zoo kept felids: A study of resource usage2016Independent thesis Advanced level (degree of Master (Two Years)), 40 credits / 60 HE creditsStudent thesis
    Abstract [en]

    Due to a large number of felid species being endangered they are subjects of conservation projects both in situ and ex situ. Keeping felids in zoos are problematic with stereotypic behaviours such as pacing and reproduction difficulties often occurring. The aim of this study was to review research and zoo husbandry knowledge about which resources are most important for the welfare of zoo kept felids, and in addition perform behavioural observations in seven felid species in four Swedish zoos to try to find an order of priority of resources. Observations were performed during opening hours in 36 sessions per species and zoo. The results showed that studies of felid resource usage are missing. Zoo husbandry practice is probably based mainly on traditions and anecdotal knowledge. The observations showed that except for minor differences felids behave similarly regardless of species but the use of resources varies. Small felid species seems to be hiding rather than pacing as a way of coping. Elevated resources and areas as well as numerous hiding places are important to felids but many factors might affect the choice of resting places. Therefore it is important to provide the felids with multiple choices. It is also important to evaluate both species and individuals when designing enclosures and providing resources. More multi-institutional studies with large number of individuals of all zoo kept felid species are needed to gather knowledge about felids needs and preferences of resources.

  • 15.
    Ahlsén, Hanna
    Linköping University, Department of Physics, Chemistry and Biology, Biology.
    The Effects of Abiotic Stress on Alternative Splicing in Non-specific Lipid Transfer Proteins in Marchantia polymorpha2018Independent thesis Basic level (degree of Bachelor), 10,5 credits / 16 HE creditsStudent thesis
    Abstract [en]

    Due to global warming, our planet will experience more extreme weather conditions. Plants can protect themselves against these abiotic stress conditions with their stress response, which includes alternative splicing of certain genes. Alternative splicing is a post-transcriptional process where a single gene gives rise to different mRNAs, which in turn produces different proteins. In plants, this is usually done by intron retention. One type of protein that may be involved in this stress response are the non-specific lipid transfer proteins (LTPs). Indeed, evidence of intron retention has been found in the LTP genes in the liverwort Marchantia polymorpha, called MpLTPd. To investigate whether this alternative splicing is caused by abiotic stress or not, I subjected the moss to two different types of stress trials, drought and cold, and compared the general expression of the intron in MpLTPd2 and MpLTPd3 from the stressed samples to samples from a moss grown under normal conditions. I found that the expression of the intron did change in the stressed moss, but none of the differences were significant. This suggests that alterative splicing in MpLTPd2 and MpLTPd3 is not caused by cold and drought and that the intron-containing protein plays no role in the protection of M. polymorpha against abiotic stress.

  • 16.
    Albinsson, L.
    et al.
    Swedish National Forensic Centre - NFC, Linköping, Sweden.
    Hedman, J.
    Swedish National Forensic Centre - NFC, Linköping, Sweden.
    Ansell, Ricky
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering. Swedish National Forensic Centre - NFC, Linköping, Sweden.
    Mixed DNA profiles from single-donors2015In: Abstract book, 7th European Academy of Forensic Science, EAFS, Prag, Tjeckien, 2015, 2015, p. 538-Conference paper (Other academic)
    Abstract [en]

    Mosaicism and chimerism in individuals can complicate the interpretation and even lead to misinterpretation of DNA profiles in forensic casework. If a person has different DNA profiles in different tissue types, i.e. a true chimaera, wrongful exclusions can be made. Additionally, mixed chimaeras can have DNA profiles that may be mistaken for mixtures. We have set-up automatic DNA databasing processes to handle atypical single-donor DNA profiles, i.e. profiles having one or several “extra” alleles.

    Studying all reference samples analysed at NFC from 2006 until spring 2014, 2‰ of the samples showed atypical DNA profiles. To be able to set routines for handling these DNA profiles, each one was manually searched in CODIS with adjusted settings, to evaluate the frequency of false-positive hits. To tag these profiles in LIMS a new result status was implemented. Additionally, all such DNA profiles must be confirmed by analysing at least two discrete samples. In LIMS, the results are manually recorded to compose of all alleles from the samples from a suspect, i.e. containing most possible genetic information. LIMS automatically categorises the atypical DNA profiles with a special CODIS index, called “Multi-allelic offender”. The first time an atypical profile is searched, the matches are manually investigated. If a match is false, its disposition will be set to “no match” to prevent this from occurring in future searches. Automatic searches will then be performed in every day routine with moderate stringency, allowing the atypical DNA profile to match either a genotype or a mixture. If the match is true, a match-report will be created and sent to the police from the LIMS.

     

  • 17.
    Alonso-Magdalena, Paloma
    et al.
    Departamento de Biología Aplicada, Universidad Miguel Hernández.
    Rivera, Fransisco J.
    Laboratory of Stem Cells and Neurogeneration, Institute of Anatomy, Histology and Pathology, Facultu of Medicine and Center for INterdiciplinary Studies on the Nervous System (CISNe), Universitad Austral de Chile; Institute for Molecular Regenerative MEdicine and Spinal Cord Injury and Tissue Regeneration Center Salzburg (SCI-TReCS), Paracelsus University, Salzburg, Austira.
    Guerrero Bosagna, Carlos
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Bisphenol-A and metabolic diseases: epigenetic developmental and transgenerational basis2016In: Environmental Epigenetics, ISSN 2058-5888, Vol. 2, no 3, p. 1-10Article in journal (Refereed)
    Abstract [en]

    Exposure to environmental toxicants is now accepted as a factor contributing to the increasing incidence of obesity and metabolic diseases around the world. Such environmental compounds are known as ‘obesogens’. Among them, bisphenol-A (BPA) is the most widespread and ubiquitous compound affecting humans and animals. Laboratory animal work has provided conclusive evidence that early-life exposure to BPA is particularly effective in predisposing individuals to weight gain. Embryonic exposure to BPA is reported to generate metabolic disturbances later in life, such as obesity and diabetes. When BPA administration is combined with a high-fat diet, there is an exacerbation in the development of metabolic disorders. Remarkably, upon BPA exposure of gestating females, metabolic disturbances have been found both in the offspring and later in life in the mothers themselves. When considering the metabolic effects generated by an early developmental exposure to BPA, one of the questions that arises is the role of precursor cells in the etiology of metabolic disorders. Current evidence shows that BPA and other endocrine disruptors have the ability to alter fat tissue development and growth by affecting the capacity to generate functional adipocytes, as well as their rate of differentiation to specific cell types. Epigenetic mechanisms seem to be involved in the BPA-induced effects related to obesity, as they have been described in both in vitro and in vivo models. Moreover, recent reports also show that developmental exposure to BPA generates abnormalities that can be transmitted to future generations, in a process called as transgenerational epigenetic inheritance.

  • 18.
    Altimiras, Jordi
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Anderson, W. Gary
    University of Manitoba, Canada.
    Ecophysiology methods: Refining the old, validating the new and developing for the future2016In: Comparative Biochemistry and Physiology A, ISSN 1095-6433, E-ISSN 1531-4332, Vol. 202Article in journal (Other academic)
    Abstract [en]

    n/a

  • 19.
    Altimiras, Jordi
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Lindgren, Isa
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Giraldo-Deck, Lina Maria
    University of Mayor San Andres, Bolivia.
    Matthei, Alberto
    Tinamou Chile SL, Chile.
    Garitano-Zavala, Alvaro
    University of Mayor San Andres, Bolivia.
    Aerobic performance in tinamous is limited by their small heart. A novel hypothesis in the evolution of avian flight2017In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 7, article id 15964Article in journal (Refereed)
    Abstract [en]

    Some biomechanical studies from fossil specimens suggest that sustained flapping flight of birds could have appeared in their Mesozoic ancestors. We challenge this idea because a suitable musculoskeletal anatomy is not the only requirement for sustained flapping flight. We propose the "heart to fly" hypothesis that states that sustained flapping flight in modern birds required an enlargement of the heart for the aerobic performance of the flight muscles and test it experimentally by studying tinamous, the living birds with the smallest hearts. The small ventricular size of tinamous reduces cardiac output without limiting perfusion pressures, but when challenged to fly, the heart is unable to support aerobic metabolism (quick exhaustion, larger lactates and post-exercise oxygen consumption and compromised thermoregulation). At the same time, cardiac growth shows a crocodilian-like pattern and is correlated with differential gene expression in MAPK kinases. We integrate this physiological evidence in a new evolutionary scenario in which the ground-up, short and not sustained flapping flight displayed by tinamous represents an intermediate step in the evolution of the aerobic sustained flapping flight of modern birds.

  • 20.
    Ammenberg, Jonas
    et al.
    Linköping University, Department of Management and Engineering, Environmental Technology and Management. Linköping University, The Institute of Technology. Linköping University, Biogas Research Center.
    Svensson, Bo
    Linköping University, Department of Thematic Studies, Tema Environmental Change. Linköping University, Faculty of Arts and Sciences. Linköping University, Biogas Research Center.
    Karlsson, Magnus
    Linköping University, Department of Management and Engineering, Energy Systems. Linköping University, Biogas Research Center.
    Svensson, Niclas
    Linköping University, Department of Management and Engineering, Environmental Technology and Management. Linköping University, The Institute of Technology. Linköping University, Biogas Research Center.
    Björn, Annika
    Linköping University, Department of Thematic Studies, Tema Environmental Change. Linköping University, Faculty of Arts and Sciences. Linköping University, Biogas Research Center.
    Karlsson, Martin
    Linköping University, Department of Physics, Chemistry and Biology, Chemistry. Linköping University, The Institute of Technology. Linköping University, Biogas Research Center.
    Tonderski, Karin
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, The Institute of Technology. Linköping University, Biogas Research Center.
    Eklund, Mats
    Linköping University, Department of Management and Engineering, Environmental Technology and Management. Linköping University, The Institute of Technology. Linköping University, Biogas Research Center.
    Biogas Research Center, BRC: Slutrapport för etapp 12015Report (Other academic)
    Abstract [en]

    Biogas Research Center (BRC) is a center of excellence in biogas research funded by the Swedish Energy Agency, Linköping University and a number of external organizations with one-third each. BRC has a very broad interdisciplinary approach, bringing together biogas-related skills from several areas to create interaction on many levels:

    • between industry, academia and society,
    • between different perspectives, and
    • between different disciplines and areas of expertise.

    BRC’s vision is:

    BRC contributes to the vision by advancing knowledge and technical development, as well as by facilitating development, innovation and business. Resource efficiency is central, improving existing processes and systems as well as establishing biogas solutions in new sectors and enabling use of new substrates.

    For BRC phase 1, the first two year period from 2012-2014, the research projects were organized in accordance with the table below showing important challenges for biogas producers and other stakeholders, and how these challenges were tackled in eight research projects. Five of the projects had an exploratory nature, meaning that they were broader, more future oriented and, for example, evaluated several different technology paths (EP1-5). Three projects focused more on technology and process development (DP6-8).

    This final report briefly presents the background and contains some information about competence centers in general. Thereafter follows more detailed information about BRC, for example, regarding the establishment, relevance, organization, vision, corner stones and development. The participating organizations are presented, both the research groups within Linköping University and the partners and members. Further on, there is a more detailed introduction to and description of the challenges mentioned in the table above and a short presentation from each of the research projects, followed by some sections dealing with fulfillment of objectives and an external assessment of BRC. Detailed, listed information is commonly provided in the appendices.

    Briefly, the fulfillment of objectives is good and it is very positive that so many scientific articles have been published (or are to be published) from the research projects and also within the wider center perspective. Clearly, extensive and relevant activities are ongoing within and around BRC. In phase 2 it essential to increase the share of very satisfied partners and members, where now half of them are satisfied and the other half is very satisfied. For this purpose, improved communication, interaction and project management are central. During 2015, at least two PhD theses are expected, to a large extent based on the research from BRC phase 1.

    In the beginning of 2014 an external assessment of BRC was carried out, with the main purpose to assess how well the center has been established and to review the conditions for a future, successful competence center. Generally, the outcome was very positive and the assessors concluded that BRC within a short period of time had been able to establish a well-functioning organization engaging a large share of the participants within relevant areas, and that most of the involved actors look upon BRC as a justifiable and well working investment that they plan to continue to support. The assessment also contributed with several relevant tips of improvements and to clarify challenges to address.

    This report is written in Swedish, but for each research project there will be reports and/or scientific papers published in English.

    The work presented in this report has been financed by the Swedish Energy Agency and the participating organizations.

  • 21.
    Andersson, Elin
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, The Institute of Technology. IFM.
    Dogs´understanding of human pointing gestures2014Independent thesis Basic level (degree of Bachelor), 10,5 credits / 16 HE creditsStudent thesis
    Abstract [en]

    To investigate the ability for animals to understand human communication signals and the communication between animals and humans, scientists often investigate the understanding of human gestural cues. Dogs (Canis lupus familiaris) which have a long history of co-evolution with humans have been shown to make good use of human gestural cues. In the present study I investigated whether dogs in general understand a human pointing gesture and if there are differences between sex, age or breeds. In total 46 dogs of different breeds participated in the study. The study was carried out in a dog center in Linköping, Hundens och djurens beteendecenter. To test if dogs understand human pointing gestures, a two-way object choice test were used, where an experimenter pointed at a baited bowl at a distance of three meter from the dog. The results showed that dogs in general can understand human pointing gestures. However, no significant differences were found for sex, age or breeds. As a conclusion, I found that dogs in general can understand human pointing gestures, but sex, age or breed did not affect the ability.

  • 22.
    Andersson, Erika
    Linköping University, Department of Physics, Chemistry and Biology, Biology.
    Is there genetic variation in VicJ, which can be associated with protein content in pea (Pisum sativum L.)?2018Independent thesis Basic level (degree of Bachelor), 10,5 credits / 16 HE creditsStudent thesis
    Abstract [en]

    Today, the livestock sector accounts for 18 % of greenhouse gas emissions. To prevent negative environmental effects, dietary changes are required. Locally cultivated legumes with high protein content can be used in order to produce plant-based protein, which can replace animal-based protein. In Sweden, pea (Pisum sativum L.) has been cultivated for centuries and been a valuable protein source for both human consumption and animal feed. VicJ, a gene in pea, has previously been associated with variation in protein content. In the present study, a primarily Swedish material of 31 accessions from different improvement stages were analysed for differences in protein content. It was also tested if genetic variation of VicJ was associated with variation in protein content. The result showed no differences in protein content between various improvement stages, which indicated that selection on the trait has not occurred. No genetic variation associated with variation in protein content in VicJ was detected either. However a stop codon in VicJ, known to be associated with reduced protein content was missing in the material, suggesting that the accessions studied may be suitable for breeding to increase protein content in pea.

  • 23.
    Andersson, Klas
    et al.
    Swedish University of Agricultural Sciences, Alnarp, Sweden.
    Bergman, Karl-Olof
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, The Institute of Technology.
    Andersson, Fredrik
    Mid Sweden University, Sundsvall, Sweden.
    Hedenström, Erik
    Mid Sweden University, Sundsvall, Sweden.
    Jansson, Nicklas
    Linköping University, Department of Physics, Chemistry and Biology, Ecology. Linköping University, The Institute of Technology.
    Burman, Joseph
    Swedish University of Agricultural Sciences, Alnarp, Sweden.
    Winde, Inis
    Swedish University of Agricultural Sciences, Alnarp, Sweden.
    Larsson, Mattias C.
    Swedish University of Agricultural Sciences, Alnarp, Sweden.
    Milberg, Per
    Linköping University, Department of Physics, Chemistry and Biology, Ecology. Linköping University, The Institute of Technology.
    High-accuracy sampling of saproxylic diversity indicators at regionalscales with pheromones: The case of Elater ferrugineus (Coleoptera, Elateridae)2014In: Biological Conservation, ISSN 0006-3207, E-ISSN 1873-2917, Vol. 171, p. 156-166Article in journal (Refereed)
    Abstract [en]

    The rare beetle Elater ferrugineus was sampled at 47 sites in the county of Östergötland, Sweden by meansof pheromone-baited traps to assess its value as an indicator species for hollow oak stands rich in raresaproxylic beetle species. In addition, Osmoderma eremita was also sampled with pheromone baits. Thesedata were then compared against species survey data collected at the same sites by pitfall and windowtraps. Both species co-occur with many Red Listed saproxylic beetles, with E. ferrugineus being a somewhatbetter indicator for the rarest species. The conservation value of a site (measured as Red List pointsor number of Red Listed species) increased with the number of specimens of E. ferrugineus and O. eremitacaught. Accuracy of sampling by means of pheromone trapping turned out to be radically different for thetwo model species. E. ferrugineus traps put out during July obtained full accuracy after only 6 days,whereas O. eremita traps needed to be out from early July to mid-August in order to obtain full accuracywith one trap per site. By using E. ferrugineus, or preferably both species, as indicator species, accuracywould increase and costs decrease for saproxylic biodiversity sampling, monitoring and identificationof hotspots.

  • 24.
    Andersson, Rebecca
    Linköping University, Department of Physics, Chemistry and Biology, Biology.
    An Evaluation of Two Presumptive Blood Tests and Three Methods to Visualise Blood2017Independent thesis Basic level (degree of Bachelor), 10,5 credits / 16 HE creditsStudent thesis
    Abstract [en]

    The aim of this study was to validate the two presumptive blood tests LMG, LCV and the three visualising blood methods Bluestar Forensics, Lumiscene and the Ruhoff method. The methods’ sensitivity, durability, matrices effects, false positive results and the methods effect on subsequent DNA analysis were studied. DNA analyses were also performed to assess the detection limit of the forensic DNA analysis. Drops of diluted blood were applied on different absorptive matrices and the sensitivity was investigated. The solutions were also placed under different conditions to investigate the durability of the solutions. The solutions were applied upon panels using different chemicals and materials and the false positive results were studied. The DNA analyses were performed by diluting the blood with Bluestar Forensics, the hydrogen peroxide method, the Ruhoff method and deionised water. The study showed that the LMG with a 3 % H2O2 concentration performs the best and it is suited for practical casework. The positive results of LMG was easier to interpret than those of LCV, this is probably due to the fixative agent of the used LCV solution. Bluestar Forensics and Lumiscene did perform similar on the different matrices tested, but the Lumiscene solution had a slightly higher durability. The results strongly indicate that the Ruhoff method can be used without luminol, hence only as a hydrogen peroxide solution (the hydrogen peroxide method). All three visualising blood methods decreases chances of retrieving a positive DNA profile, however the visualising blood methods could be used if the blood cannot be found in any other way. A DNA profile was obtained from the one blood sample analysed at dilution of 1:256 in deionized water.

  • 25.
    Angelstam, Per
    et al.
    Swedish University of Agricultural Sciences, Skinnskatteberg, Sweden .
    Roberge, Jean-Michel
    Swedish University of Agricultural Sciences, Umeå, Sweden .
    Axelsson, Robert
    Swedish University of Agricultural Sciences, Skinnskatteberg, Sweden .
    Elbakidze, Marine
    Swedish University of Agricultural Sciences, Skinnskatteberg, Sweden .
    Bergman, Karl-Olof
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, The Institute of Technology.
    Dahlberg, Anders
    Swedish University of Agricultural Sciences, Uppsala, Sweden .
    Degerman, Erik
    Institute of Freshwater Research, Örebro, Sweden .
    Eggers, Sönke
    Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Essen, Per-Anders
    Umeå University, Sweden .
    Hjältén, Joakim
    Swedish University of Agricultural Sciences, Umeå, Sweden .
    Johansson, Therese
    Swedish University of Agricultural Sciences, Umeå, Sweden .
    Müller, Jörg
    National Park Bavarian Forest, Grafenau, Germany.
    Paltto, Heidi
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, The Institute of Technology.
    Snäll, Tord
    Swedish University of Agricultural Sciences, Uppsala, Sweden .
    Solovity, Ihor
    Ukrainian National Forestry University, Lviv, Ukraine .
    Törnblom, Johan
    Swedish University of Agricultural Sciences, Skinnskatteberg, Sweden .
    Evidence-Based Knowledge Versus Negotiated Indicators for Assessment of Ecological Sustainability: The Swedish Forest Stewardship Council Standard as a Case Study2013In: Ambio, ISSN 0044-7447, E-ISSN 1654-7209, Vol. 42, no 2, p. 229-240Article in journal (Refereed)
    Abstract [en]

    Assessing ecological sustainability involves monitoring of indicators and comparison of their states with performance targets that are deemed sustainable. First, a normative model was developed centered on evidence-based knowledge about (a) forest composition, structure, and function at multiple scales, and (b) performance targets derived by quantifying the habitat amount in naturally dynamic forests, and as required for presence of populations of specialized focal species. Second, we compared the Forest Stewardship Council (FSC) certification standards’ ecological indicators from 1998 and 2010 in Sweden to the normative model using a Specific, Measurable, Accurate, Realistic, and Timebound (SMART) indicator approach. Indicator variables and targets for riparian and aquatic ecosystems were clearly under-represented compared to terrestrial ones. FSC’s ecological indicators expanded over time from composition and structure towards function, and from finer to coarser spatial scales. However, SMART indicators were few. Moreover, they poorly reflected quantitative evidence-based knowledge, a consequence of the fact that forest certification mirrors the outcome of a complex social negotiation process.

  • 26.
    Ansell, Ricky
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering. Nationellt forensiskt center, Linköping, Sverige.
    Dna-möte på NFC2015In: KriminalteknikArticle in journal (Other (popular science, discussion, etc.))
  • 27.
    Ansell, Ricky
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, The Institute of Technology. Statens kriminaltekniska laboratorium, SKL, Linköping.
    Forensiska uppslag - Spaningsinformation från SKL2012In: Kriminalteknik, ISSN 1653-6169, no 4, p. 12-13Article in journal (Other (popular science, discussion, etc.))
  • 28.
    Ansell, Ricky
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, The Institute of Technology. SKL, The Swedish National Laboratory of Forensic Science, Linköping, Sweden .
    Internal quality control in forensic DNA analysis2013In: Accreditation and Quality Assurance, ISSN 0949-1775, E-ISSN 1432-0517, Vol. 18, no 4, p. 279-289Article in journal (Refereed)
    Abstract [en]

    The trail from initial evidence examination to a DNA profile reported to match a suspect is long and complex. The different nature and great variability in the biological and DNA evidence to be recovered and analyzed, add to this complexity. Internal quality controls play an important role in maintaining a high-quality performance in daily forensic biology and DNA profiling practice. In many cases are empirical rather than analytical approaches adopted. Obviously, despite the fact of being necessary, the internal quality controls performed still need to be kept rational at a limited, yet acceptable level. Quality control from a forensic biology and DNA profiling horizon has a wider context and does not only concern obvious fit-for-purpose verifications of analytical processes, chemicals, or reagents in daily routine practice. It also includes control on computerized laboratory management and expert systems, laboratory environmental DNA monitoring, and the use of elimination DNA databases. In addition, a structured recording and handling of non-conformances and “near failures” is essential. Proper management of the non-conformances supports continuous quality improvements by learning from the errors occurring in daily practice. High transparency of non-conformances is important not only for internal improvements, but also for the criminal justice system as well as to maintain public confidence and trust. Together the quality controls used aim at maintaining evidence and DNA sample integrity and to accomplish correct results and interpretations by verifying that methods used data transfers and interpretations made are correct and performed according to validated and accredited conditions.

  • 29.
    Ansell, Ricky
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, The Institute of Technology. Statens Kriminaltekniska Laboratorium (SKL), Linköping.
    Kvalitetsmöte med Forensic Science Regulator2014In: Kriminalteknik, ISSN 1653-6169, no 1, p. 22-23Article in journal (Other academic)
  • 30.
    Ansell, Ricky
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, The Institute of Technology. Statens kriminaltekniska laboratorium - SKL, Linköping.
    Nytt på dna-området2013Other (Other (popular science, discussion, etc.))
  • 31.
    Ansell, Ricky
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, The Institute of Technology.
    Pilotstudie om forensiska uppslag2014In: KriminalteknikArticle in journal (Other (popular science, discussion, etc.))
  • 32.
    Ansell, Ricky
    Linköping University, Department of Physics, Chemistry and Biology, Biology.
    Utveckling av arbetsmetoderna vid utredning av våldtäkter2014In: Kriminalteknik, Vol. 4, p. 10-11Article in journal (Other (popular science, discussion, etc.))
  • 33.
    Ansell, Ricky
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, The Institute of Technology. Statens Kriminaltekniska Laboratorium (SKL), Linköping.
    Eriksson, Helena
    Statens Kriminaltekniska Laboratorium (SKL), Linköping.
    Centrum för genetisk identifiering2014In: Kriminalteknik, ISSN 1653-6169, no 1, p. 21-Article in journal (Other academic)
  • 34.
    Ansell, Ricky
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, The Institute of Technology. Statens Kriminaltekniska Laboratorium (SKL), Linköping.
    Hedman, Johannes
    Statens Kriminaltekniska Laboratorium (SKL), Linköping.
    Snabbanalysinstrumentet RapidHIT på SKL2014In: Kriminalteknik, ISSN 1653-6169, no 1, p. 18-19Article in journal (Other academic)
    Abstract [sv]

     

  • 35.
    Ansell, Ricky
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering. Polismyndigheten - Nationellt Forensiskt Centrum.
    Nordgaard, Anders
    Linköping University, Department of Computer and Information Science, Statistics. Linköping University, Faculty of Arts and Sciences. Polismyndigheten - Nationellt Forensiskt Centrum.
    Hedell, Ronny
    Polismyndigheten - Nationellt Forensiskt Centrum.
    Interpretation of DNA Evidence: Implications of Thresholds Used in the Forensic Laboratory2014Conference paper (Other academic)
    Abstract [en]

    Evaluation of forensic evidence is a process lined with decisions and balancing, not infrequently with a substantial deal of subjectivity. Already at the crime scene a lot of decisions have to be made about search strategies, the amount of evidence and traces recovered, later prioritised and sent further to the forensic laboratory etc. Within the laboratory there must be several criteria (often in terms of numbers) on how much and what parts of the material should be analysed. In addition there is often a restricted timeframe for delivery of a statement to the commissioner, which in reality might influence on the work done. The path of DNA evidence from the recovery of a trace at the crime scene to the interpretation and evaluation made in court involves several decisions based on cut-offs of different kinds. These include quality assurance thresholds like limits of detection and quantitation, but also less strictly defined thresholds like upper limits on prevalence of alleles not observed in DNA databases. In a verbal scale of conclusions there are lower limits on likelihood ratios for DNA evidence above which the evidence can be said to strongly support, very strongly support, etc. a proposition about the source of the evidence. Such thresholds may be arbitrarily chosen or based on logical reasoning with probabilities. However, likelihood ratios for DNA evidence depend strongly on the population of potential donors, and this may not be understood among the end-users of such a verbal scale. Even apparently strong DNA evidence against a suspect may be reported on each side of a threshold in the scale depending on whether a close relative is part of the donor population or not. In this presentation we review the use of thresholds and cut-offs in DNA analysis and interpretation and investigate the sensitivity of the final evaluation to how such rules are defined. In particular we show what are the effects of cut-offs when multiple propositions about alternative sources of a trace cannot be avoided, e.g. when there are close relatives to the suspect with high propensities to have left the trace. Moreover, we discuss the possibility of including costs (in terms of time or money) for a decision-theoretic approach in which expected values of information could be analysed.

  • 36.
    Ansell, Ricky
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, The Institute of Technology. Statens kriminaltekniska laboratorium, SKL, Linköping.
    Stegeryd, Yvonne
    Statens kriminaltekniska laboratorium, SKL, Linköping.
    Hallingström, Marie-Louise
    Rättsmedicinalverket, RMV, Linköping.
    Spårsäkringssats efter sexuella övergrepp anpassas till PUST2013In: Kriminalteknik, ISSN 1653-6169, p. 20-21Article in journal (Other (popular science, discussion, etc.))
  • 37.
    Ansell, Ricky
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, The Institute of Technology.
    Widén, Christina
    Statens kriminaltekniska laboratorium.
    Ny lagstiftning för DNA elimineringsbas i Sverige2014In: Kriminalteknik, Vol. 4, p. 28-30Article in journal (Other (popular science, discussion, etc.))
  • 38.
    Ansell, Ricky
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering. Swedish National Forensic Centre, Linköping, Sweden.
    Widén, Christina
    Biology Unit, Swedish National Forensic Centre (NFC), Link€oping, Sweden.
    Swedish Legislation Regarding Forensic DNA Elimination Databases2016In: Forensic Science Policy & Management: An International Journal , ISSN 1940-9044, Vol. 7, no 1-2, p. 20-36Article in journal (Refereed)
    Abstract [en]

    Evidence contaminated with DNA from staff, police, and other individuals can have a dramaticimpact on an investigation and can mislead police inquiries. Forensic DNA elimination databases(EDB) are used to minimize the risks associated with DNA contamination. Central issues withmaintaining such databases include the basis for sample collection, sample, and profile integrity, aswell as retention times, database access, and procedures when a database match occurs. Followingyears of discussion, debate, and the use of an “in house” EDB at the Swedish National ForensicCentre (NFC), these issues have now been resolved by passing legislation on DNA EDB. According tothe legislation, sampling for EDB purposes is mandatory for certain forensic professionals, as well asfor other individuals who need access to the premises handling DNA evidence. In the event of adatabase match, the match can only be reviewed and evaluated for quality purposes and the nameof the donor cannot be disclosed to the crime inquiry. Thus, as a consequence, if a contaminationevent is not the probable cause the legal limitation opens for impunity for individuals included inthe database.KEYWORDSContamination; DNA;elimination database;forensic science; legislationIntroduction

  • 39.
    Arshamian, Artin
    et al.
    Karolinska Institute, Sweden; Radboud University of Nijmegen, Netherlands; Radboud University of Nijmegen, Netherlands; Stockholm University, Sweden.
    Laska, Matthias
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Gordon, Amy R.
    Karolinska Institute, Sweden; Monell Chemistry Senses Centre, PA 19104 USA.
    Norberg, Matilda
    Linköping University, Department of Physics, Chemistry and Biology. Linköping University, Faculty of Science & Engineering.
    Lahger, Christian
    Linköping University, Department of Physics, Chemistry and Biology. Linköping University, Faculty of Science & Engineering.
    Porada, Danja K.
    Karolinska Institute, Sweden.
    Jelvez Serra, Nadia
    Lund University, Sweden.
    Johansson, Emilia
    Karolinska Institute, Sweden.
    Schaefer, Martin
    Karolinska Institute, Sweden.
    Amundin, Mats
    Kolmarden Wildlife Pk, Sweden.
    Melin, Harald
    Karolinska Institute, Sweden.
    Olsson, Andreas
    Karolinska Institute, Sweden.
    Olsson, Mats J.
    Karolinska Institute, Sweden.
    Stensmyr, Marcus
    Lund University, Sweden.
    Lundstrom, Johan N.
    Karolinska Institute, Sweden; Monell Chemistry Senses Centre, PA 19104 USA; University of Penn, PA 19104 USA.
    A mammalian blood odor component serves as an approach-avoidance cue across phylum border - from flies to humans2017In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 7, article id 13635Article in journal (Refereed)
    Abstract [en]

    Chemosignals are used by predators to localize prey and by prey to avoid predators. These cues vary between species, but the odor of blood seems to be an exception and suggests the presence of an evolutionarily conserved chemosensory cue within the blood odor mixture. A blood odor component, E2D, has been shown to trigger approach responses identical to those triggered by the full blood odor in mammalian carnivores and as such, is a key candidate as a food/alarm cue in blood. Using a multidisciplinary approach, we demonstrate that E2D holds the dual function of affecting both approach and avoidance behavior in a predator-prey predicted manner. E2D evokes approach responses in two taxonomically distant blood-seeking predators, Stable fly and Wolf, while evoking avoidance responses in the prey species Mouse. We extend this by demonstrating that this chemical cue is preserved in humans as well; E2D induces postural avoidance, increases physiological arousal, and enhances visual perception of affective stimuli. This is the first demonstration of a single chemical cue with the dual function of guiding both approach and avoidance in a predator-prey predicted manner across taxonomically distant species, as well as the first known chemosignal that affects both human and non-human animals alike.

  • 40.
    Arwin, Hans
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Applied Optics . Linköping University, The Institute of Technology.
    Berlind, Torun
    Linköping University, Department of Physics, Chemistry and Biology, Applied Optics . Linköping University, The Institute of Technology.
    Birch, Jens
    Linköping University, Department of Physics, Chemistry and Biology, Thin Film Physics. Linköping University, The Institute of Technology.
    Fernández del Río, Lia
    Linköping University, Department of Physics, Chemistry and Biology, Applied Optics . Linköping University, The Institute of Technology.
    Gustafson, Johan
    Linköping University, Department of Physics, Chemistry and Biology, Applied Optics . Linköping University, The Institute of Technology.
    Landin, Jan
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, The Institute of Technology.
    Magnusson, Roger
    Linköping University, Department of Physics, Chemistry and Biology, Applied Optics . Linköping University, The Institute of Technology.
    Åkerlind, Christina
    Linköping University, Department of Physics, Chemistry and Biology, Applied Optics . Linköping University, The Institute of Technology.
    Järrendahl, Kenneth
    Linköping University, Department of Physics, Chemistry and Biology, Applied Optics . Linköping University, The Institute of Technology.
    Polarization effects in reflection from the cuticle of scarab beetles studied by spectroscopic Mueller-matrix ellipsometry2012In: AES 2012, Advanced Electromagnetics Symposium, 2012Conference paper (Other academic)
    Abstract [en]

    Polarization effects in reflection from the cuticle of scarab beetles studied by spectroscopic Mueller-matrix ellipsometry

     

    H. Arwin*, T. Berlind, J. Birch, L. Fernandez Del Rio, J. Gustafson, J. Landin,

    R. Magnusson, C. Åkerlind, and K. Järrendahl

    Department of Physics, Chemistry and Biology, Linköping University, Sweden

    *corresponding author: han@ifm.liu.se

     

    Abstract- Many scarab beetles exhibit structural colors and complex polarization phenomena in reflection. These effects are characterized with spectroscopic Mueller-matrix ellipsometry in our work. The polarization ellipse of reflected light as well as the degree of polarization is presented including variations with angle of incidence and wavelength. Emphasis is on beetles showing chiral effects and structural modeling of cuticle nanostructure is discussed.

     

    Background Since one hundred years it is known that some scarab beetles reflect elliptically polarized light as demonstrated by Michelson for the beetle Chrysina resplendens [1]. The handedness of the polarization is in a majority of the cases left-handed but also right-handed polarization has been found [2,3]. The ellipticity varies with wavelength and viewing angle but can be close to +1 or -1 (right or left circular polarization, respectively) and in addition these beetles may exhibit beautiful structural colors. The polarization and color effects are generated in the outer part of the exoskeleton, the cuticle. These natural photonic structures are often multifunctional and play important roles for survival of beetles, e.g. for hiding from or scaring predators, for intraspecies communication, etc. [4]. However, such structures may find use in many commercial applications and a major motivation for detailed studies of natural photonic structures is that they inspire to biomimetic applications [5,6].

    Approach Our objective is to use spectral Mueller-matrix data on scarab beetles to parameterize reflection properties in terms of polarization parameters and degree of polarization. The studied beetles all are phytophagous and include species from the Cetoniinae subfamily (e.g. Cetonia aurata and Coptomia laevis,), the Rutelinae subfamily (e.g. Chrysina argenteola and Chrysina resplendens) and the Melolonthinae subfamily (Cyphochilus insulanus). Furthermore, structural modeling is presented on Cetonia aurata and a few more beetles to demonstrate that structural parameters can be extracted by advanced modeling of Mueller-matrix data.

    Experimental A dual rotating compensator ellipsometer (RC2, J. A. Woollam Co., Inc.) is used to record all 16 Mueller-matrix elements mij (i,j=1..4) in the spectral range 300 – 900 nm at angles of incidence in the range 20-70º. The elements are normalized to m11 and thus have values between -1 and +1. All measurements are performed on the scutellum (a small triangular part on the dorsal side of the beetles) with focusing optics resulting in a spot size of the order of 50-100 mm. The software CompleteEASE (J. A. Woollam Co., Inc.) is used for analysis.

    Results and discussion As an example, Fig. 1 shows contour plots of Mueller-matrix data measured on Cetonia aurata. This beetle has a metallic shine and if illuminated with unpolarized white light it reflects left-handed polarized green light as revealed by the non-zero Mueller-matrix elements m14 and m41 in the green spectral region for angles of incidence below about 45º. This is clearly seen in the graph to the right in Fig. 1 which shows a spectrum for Mueller-matrix element m41at 20º as well as fitted model data. A model based on a twisted lamella structure, also called Bouligand structure, is used to model the chiral nanostructure [4]. Given the complexity of the nanostructure, an excellent model fit is achieved. The obtained model parameters are the spectral variation of the refractive index of the birefringent lamellas and the pitch. The model also includes a dielectric surface layer.

     

     

     

    Fig.1. Left: Mueller-matrix data on Cetonia aurata. Each contour plot shows mij, where i and j correspond to the row and column, respectively. m11 =1 and is not shown but is replaced with a photo of the beetle. Right: Experimental and model-generated Mueller-matrix element m41at an angle of incidence of 20º.

     

    From the Mueller-matrix data one can also determine so called derived parameters including azimuth and ellipticity of the polarization ellipse and the degree of polarization. The variations of these parameters with angle of incidence are presented for a selection of scarab beetles. Examples of both left-handed and right-handed polarization effects are shown and the importance of degree of polarization will be discussed.

    Concluding remarks Mueller-matrix spectra at oblique incidence are very rich in information about reflection properties and allows parameterization of polarization parameters of the reflected light. Both left-handed and right-handed reflected light is found in scarab beetles. Mueller-matrix data can also be used for a detailed modeling of the nanostructure of the cuticle of beetles.

    AcknowledgementsFinancial support was obtained from the Knut and Alice Wallenberg foundation and the Swedish Research Council. The Museum of Natural History in Stockholm, the National Museum of Natural Science in Madrid, the Berlin Museum of Natural History and the Natural History Museum in London are acknowledged for loan of beetles.

     

    REFERENCES

    1. Michelson, A. A. “On Metallic Colouring in Birds and Insects,” Phil. Mag., 21, 554-567, 1911.
    2. Goldstein, D. H. “Polarization properties of Scarabaeidae,” Appl. Opt., 45, 7944-7950, 2006.
    3. Hodgkinson, I., Lowrey, S., Bourke, L., Parker, A. and McCall, M. W. “Mueller-matrix characterization of beetle cuticle polarized and unpolarized reflections from representative architectures,” Appl. Opt., 49, 4558-4567, 2010.
    4. Vukusic, P. and Sambles, J. R. “Photonic structures in biology,” Nature, 424, 852-855, 2003.
    5. Lenau, T. and Barfoed, M. “Colours and Metallic Sheen in Beetle Shells - A Biomimetic Search for Material Structuring Principles Causing Light Interference,” Adv. Eng. Mat., 10, 299-314. 2008.
    6. Parker, A. R. and Townley, H. E “Biomimetics of photonic nanostructures,” Nature Nanotech., 2, 347-351, 2007.
  • 41.
    Arwin, Hans
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Applied Optics . Linköping University, The Institute of Technology.
    Magnusson, Roger
    Linköping University, Department of Physics, Chemistry and Biology, Applied Optics . Linköping University, The Institute of Technology.
    Fernández del Río, Lia
    Linköping University, Department of Physics, Chemistry and Biology, Applied Optics . Linköping University, The Institute of Technology.
    Åkerlind, Christina
    Linköping University, Department of Physics, Chemistry and Biology, Applied Optics . Linköping University, The Institute of Technology. Swedish Defence Research Agency, Linköping, Sweden.
    Muñoz-Pineda, Eloy
    Linköping University, Department of Physics, Chemistry and Biology, Applied Optics . Linköping University, The Institute of Technology. Cinvestav-IPN, Unidad Querétaro, Libramiento Norponiente 2000, 76230 Querétaro, Mexico.
    Landin, Jan
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Mendoza-Galván, Arturo
    Linköping University, Department of Physics, Chemistry and Biology, Applied Optics . Cinvestav-IPN, Unidad Querétaro, Libramiento Norponiente 2000, 76230 Querétaro, Mexico.
    Järrendahl, Kenneth
    Linköping University, Department of Physics, Chemistry and Biology, Applied Optics . Linköping University, Faculty of Science & Engineering.
    Exploring optics of beetle cuticles with Mueller-matrix ellipsometry2014In: Materials Today, ISSN 1369-7021, E-ISSN 1873-4103, Vol. 1S, p. 155-160Article in journal (Refereed)
    Abstract [en]

    Spectroscopic Mueller-matrix ellipsometry at variable angles of incidence is applied to beetle cuticles using a small (50 -100 μm) spot size. It is demonstrated how ellipticity and degree of polarization of the reflected light can be derived from a Mueller matrix providing a detailed insight into reflection properties. Results from Cetonia aurata, Chrysina argenteola and Cotinis mutabilis are presented. The use of Mueller matrices in regression analysis to extract structural and optical parameters of cuticles is briefly described and applied to cuticle data from Cetonia aurata whereby the pitch of the twisted layered structure in the cuticle is determined as well as the refractive indices of the epicuticle and the exocuticle.

  • 42.
    Atikuzzaman, Mohammad
    et al.
    Linköping University, Department of Clinical and Experimental Medicine, Division of Clinical Sciences. Linköping University, Faculty of Medicine and Health Sciences.
    Alvarez-Rodriguez, Manuel
    Linköping University, Department of Clinical and Experimental Medicine, Division of Children's and Women's health. Linköping University, Faculty of Medicine and Health Sciences.
    Carrillo, Alejandro Vicente
    Linköping University, Department of Clinical and Experimental Medicine, Division of Clinical Sciences. Linköping University, Faculty of Medicine and Health Sciences.
    Johnsson, Martin
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Wright, Dominic
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Rodriguez-Martinez, Heriberto
    Linköping University, Department of Clinical and Experimental Medicine, Division of Children's and Women's health. Linköping University, Faculty of Medicine and Health Sciences.
    Conserved gene expression in sperm reservoirs between birds and mammals in response to mating.2017In: BMC Genomics, ISSN 1471-2164, E-ISSN 1471-2164, Vol. 18, no 1Article in journal (Refereed)
    Abstract [en]

    BACKGROUND: Spermatozoa are stored in the oviductal functional sperm reservoir in animals with internal fertilization, including zoologically distant classes such as pigs or poultry. They are held fertile in the reservoir for times ranging from a couple of days (in pigs), to several weeks (in chickens), before they are gradually released to fertilize the newly ovulated eggs. It is currently unknown whether females from these species share conserved mechanisms to tolerate such a lengthy presence of immunologically-foreign spermatozoa. Therefore, global gene expression was assessed using cDNA microarrays on tissue collected from the avian utero-vaginal junction (UVJ), and the porcine utero-tubal junction (UTJ) to determine expression changes after mating (entire semen deposition) or in vivo cloacal/cervical infusion of sperm-free seminal fluid (SF)/seminal plasma (SP).

    RESULTS: In chickens, mating changed the expression of 303 genes and SF-infusion changed the expression of 931 genes, as compared to controls, with 68 genes being common to both treatments. In pigs, mating or SP-infusion changed the expressions of 1,722 and 1,148 genes, respectively, as compared to controls, while 592 genes were common to both treatments. The differentially expressed genes were significantly enriched for GO categories related to immune system functions (35.72-fold enrichment). The top 200 differentially expressed genes of each treatment in each animal class were analysed for gene ontology. In both pig and chicken, an excess of genes affecting local immune defence were activated, though frequently these were down-regulated. Similar genes were found in both the chicken and pig, either involved in pH-regulation (SLC16A2, SLC4A9, SLC13A1, SLC35F1, ATP8B3, ATP13A3) or immune-modulation (IFIT5, IFI16, MMP27, ADAMTS3, MMP3, MMP12).

    CONCLUSION: Despite being phylogenetically distant, chicken and pig appear to share some gene functions for the preservation of viable spermatozoa in the female reservoirs.

  • 43.
    Atikuzzaman, Mohammad
    et al.
    Linköping University, Department of Clinical and Experimental Medicine, Division of Clinical Sciences. Linköping University, Faculty of Medicine and Health Sciences.
    Alvarez-Rodriguez, Manuel
    Linköping University, Department of Clinical and Experimental Medicine, Division of Children's and Women's health. Linköping University, Faculty of Medicine and Health Sciences.
    Vicente Carrillo, Alejandro
    Linköping University, Department of Clinical and Experimental Medicine, Division of Clinical Sciences. Linköping University, Faculty of Medicine and Health Sciences.
    Johnsson, Martin
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Wright, Dominic
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Rodriguez-Martinez, Heriberto
    Linköping University, Department of Clinical and Experimental Medicine, Division of Children's and Women's health. Linköping University, Faculty of Medicine and Health Sciences.
    Correction: Conserved gene expression in sperm reservoirs between birds and mammals in response to mating (vol 18, 98, 2017)2017In: BMC Genomics, ISSN 1471-2164, E-ISSN 1471-2164, Vol. 18, article id 563Article in journal (Other academic)
    Abstract [en]

    n/a

  • 44.
    Atikuzzaman, Mohammad
    et al.
    Linköping University, Department of Clinical and Experimental Medicine, Division of Clinical Sciences. Linköping University, Faculty of Medicine and Health Sciences.
    Bhai Mehta, Ratnesh
    Linköping University, Faculty of Medicine and Health Sciences. Linköping University, Department of Clinical and Experimental Medicine, Division of Neuro and Inflammation Science.
    Fogelholm, Jesper
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Wright, Dominic
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Rodriguez-Martinez, Heriberto
    Linköping University, Department of Clinical and Experimental Medicine, Division of Clinical Sciences. Linköping University, Faculty of Medicine and Health Sciences.
    Mating induces the expression of immune- and pH-regulatory genes in the utero-vaginal junction containing mucosal sperm-storage tubuli of hens2015In: Reproduction, Vol. 150, no 6, p. 473-483Article in journal (Refereed)
    Abstract [en]

    The female chicken, as with other species with internal fertilization, can tolerate the presence of spermatozoa within specialized sperm-storage tubuli (SST) located in the mucosa of the utero-vaginal junction (UVJ) for days or weeks, without eliciting an immune response. To determine if the oviduct alters its gene expression in response to sperm entry, segments from the oviduct (UVJ, uterus, isthmus, magnum and infundibulum) of mated and unmated (control) hens, derived from an advanced inter-cross line between Red Junglefowl and White Leghorn, were explored 24 h after mating using cDNA microarray analysis. Mating shifted the expression of fifteen genes in the UVJ (53.33% immune-modulatory and 20.00% pH-regulatory) and seven genes in the uterus, none of the genes in the latter segment overlapping the former (with the differentially expressed genes themselves being less related to immune-modulatory function). The other oviductal segments did not show any significant changes. These findings suggest sperm deposition causes a shift in expression in the UVJ (containing mucosal SST) and the uterus for genes involved in immune-modulatory and pH-regulatory functions, both relevant for sperm survival in the hen's oviduct.

  • 45.
    Atikuzzaman, Mohammad
    et al.
    Linköping University, Department of Clinical and Experimental Medicine, Division of Clinical Sciences. Linköping University, Faculty of Medicine and Health Sciences.
    Sanz, Libia
    Instituto de Biomedicina de Valencia, CSIC, Valencia, Spain.
    Pla, Davinia
    Instituto de Biomedicina de Valencia, CSIC, Valencia, Spain.
    Alvarez-Rodriguez, Manuel
    Linköping University, Department of Clinical and Experimental Medicine, Division of Children's and Women's health. Linköping University, Faculty of Medicine and Health Sciences.
    Rubér, Marie
    Linköping University, Department of Clinical and Experimental Medicine, Division of Children's and Women's health. Linköping University, Faculty of Medicine and Health Sciences.
    Wright, Dominic
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Calvete, Juan J.
    Instituto de Biomedicina de Valencia, CSIC, Valencia, Spain.
    Rodriguez-Martinez, Heriberto
    Linköping University, Department of Clinical and Experimental Medicine, Division of Children's and Women's health. Linköping University, Faculty of Medicine and Health Sciences.
    Selection for higher fertility reflects in the seminal fluid proteome of modern domestic chicken2017In: Comparative Biochemistry and Physiology - Part D: Genomics and Proteomics, ISSN 1744-117X, E-ISSN 1878-0407, Vol. 21, p. 27-40Article in journal (Refereed)
    Abstract [en]

    The high egg-laying capacity of the modern domestic chicken (i.e. White Leghorn, WL) has arisen from the low egg-laying ancestor Red Junglefowl (RJF) via continuous trait selection and breeding. To investigate whether this long-term selection impacted the seminal fluid (SF)-proteome, 2DE electrophoresis-based proteomic analyses and immunoassays were conducted to map SF-proteins/cytokines in RJF, WL and a 9th generation Advanced Intercross Line (AIL) of RJF/WL-L13, including individual SF (n = 4, from each RJF, WL and AIL groups) and pools of the SF from 15 males of each group, analyzed by 2DE to determine their degree of intra-group (AIL, WL, and RJF) variability using Principal Component Analysis (PCA); respectively an inter-breed comparative analysis of intergroup fold change of specific SF protein spots intensity between breeds. The PCA clearly highlighted a clear intra-group similarity among individual roosters as well as a clear inter-group variability (e.g. between RJF, WL and AIL) validating the use of pools to minimize confounding individual variation. Protein expression varied considerably for processes related to sperm motility, nutrition, transport and survival in the female, including signaling towards immunomodulation. The major conserved SF-proteins were serum albumin and ovotransferrin. Aspartate aminotransferase, annexin A5, arginosuccinate synthase, glutathione S-transferase 2 and l-lactate dehydrogenase-A were RJF-specific. Glyceraldehyde-3-phosphate dehydrogenase appeared specific to the WL-SF while angiotensin-converting enzyme, γ-enolase, coagulation factor IX, fibrinogen α-chain, hemoglobin subunit α-D, lysozyme C, phosphoglycerate kinase, Src-substrate protein p85, tubulins and thioredoxin were AIL-specific. The RJF-SF contained fewer immune system process proteins and lower amounts of the anti-inflammatory/immunomodulatory TGF-β2 compared to WL and AIL, which had low levels- or lacked pro-inflammatory CXCL10 compared to RJF. The seminal fluid proteome differs between ancestor and modern chicken, with a clear enrichment of proteins and peptides related to immune-modulation for sperm survival in the female and fertility.

  • 46.
    Backlund, Emma
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, The Institute of Technology.
    Assessment of ventricular morphology using echocardiography in Ornate tinamous (Nothoprocta ornata) and domestic chickens (Gallus domesticus)2014Independent thesis Basic level (degree of Bachelor), 10,5 credits / 16 HE creditsStudent thesis
    Abstract [en]

    The Ornate Tinamou (Nothoprocta ornata), an ancient bird, has adapted to life at high altitude (>2.400 m.a.s.l) for a longer period than the domestic chicken (Gallus domesticus), which came to South America with the Spanish conquerors. Ornate tinamous have a smaller heart in relation to body size than domestic chickens. This study was made to evaluate heart morphometric measurements comparing Ornate Tinamou and domestic chicken using echocardiography measurements to determine wall thickness and chamber size and to evaluate whether it can retrieve measurements consistent with previous results on dissected hearts. I was also interested in evaluating potential adaptations of the Ornate Tinamou to life in hypoxic environments by exposing the heart to positive inotropic stimulation. The results were compared with those previously obtained on dissected hearts. The results showed that the chamber size of the domestic chicken was significantly larger than in Ornate Tinamou, both in conscious and anesthetized birds. Injection of 1µg/kg isoproterenol caused domestic chickens’ systolic chamber size to decrease significantly and fractional shortening to increase significantly. The same changes were seen in the Ornate Tinamou but they were not significant. In conclusion, this study confirms that echocardiography is a valid method for retrieving cardiac measurements without euthanizing animals, opening for the possibility of taking several measurements at different ages.

  • 47.
    Backman, J.S.K.
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, The Institute of Technology.
    Hermansson, A.
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, The Institute of Technology.
    Tebbe, C.C.
    Institut für Agrarökologie, Bfa. für Landwirtschaft, D-38116 Braunschweig, Germany.
    Lindgren, P.-E.
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, The Institute of Technology.
    Liming induces growth of a diverse flora of ammonia-oxidising bacteria in acid spruce forest soil as determined by SSCP and DGGE2003In: Soil Biology and Biochemistry, ISSN 0038-0717, E-ISSN 1879-3428, Vol. 35, no 10, p. 1337-1347Article in journal (Refereed)
    Abstract [en]

    The autotrophic ammonia-oxidising bacterial (AOB) community composition was studied in acid coniferous forest soil profiles at a site in southwestern Sweden 6 years after liming. Liming caused a significant increase in pH in the organic horizons, while the mineral soil was unaffected. The AOB communities were studied by single-strand conformation polymorphism (SSCP) in parallel with denaturing gradient gel electrophoresis (DGGE) analysis of partial 16S rRNA genes amplified by PCR using primers reported to be specific for ß-Proteobacteria AOB, followed by nucleotide sequencing. High genetic diversity of Nitrosospira-like sequences was found in the limed soil profiles, whereas no AOB-like sequences were detected in the control soil at any depth, according to both the SSCP and DGGE analyses. This clearly showed that liming induced growth of a diverse flora of AOB at this forest site. Both Nitrosospira cluster 2 and cluster 4 sequences were present in the limed soil profiles, regardless of soil pH, but we found a higher number of sequences affiliated with cluster 4. The high lime dose seemed to affect the AOB community more than the low dose, and its effects reached deeper into the soil profile. Seven different Nitrosospira-like sequences were found 10 cm under the litter layer in the soil limed with the high dose, but only two in the soil amended with the low lime dose. © 2003 Elsevier Ltd. All rights reserved.

  • 48.
    Backman, J.S.K.
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, The Institute of Technology.
    Klemedtsson, A.K.
    Klemedtsson, Å.K., Dept. of Informatics and Mathematics, Univ. of Trollhättan/Uddevalla, SE-46129 Trollhättan, Sweden.
    Increased Nitrification in Acid Coniferous Forest Soil Due to High Nitrogen Deposition and Liming2003In: Scandinavian Journal of Forest Research, ISSN 0282-7581, E-ISSN 1651-1891, Vol. 18, no 6, p. 514-524Article in journal (Refereed)
    Abstract [en]

    This study investigated whether liming stimulates the potential nitrification of acid forest soils in southern Sweden, and whether such stimulation (if present) is more pronounced in areas receiving high nitrogen (N) deposition. A short-term (30 h) soil-slurry incubation technique was used, which reduces the risk of bacterial growth, nitrate immobilization and denitrification during the incubation. The nitrate and nitrite produced were measured after biological conversion to nitrous oxide. The investigation was performed 6-7 yrs after the liming at four coniferous forest sites in the central and western parts of southern Sweden, which receive low and high deposition of N, respectively. Overall, liming had increased pH significantly down to 10 cm soil depth, but at 20 cm depth there was no difference between the limed and non-limed soil. In cases when liming had affected the total N pool and the potential nitrification, this was also limited to the uppermost 10 cm. It seems likely that the effects of liming on the potential nitrification were dependent on N availability, which is in turn influenced by N mineralization, trees' demands for N, and atmospheric N inputs. The strongest stimulatory effect of liming on the potential nitrification was seen on the west coast, indicating that these sites had the highest availability of ammonia for nitrifiers. However, liming also increased nitrification at one of the sites in south-central Sweden, which could have been mediated by increased rates of N mineralization.

  • 49.
    Bastviken, David
    et al.
    Linköping University, The Tema Institute, Department of Water and Environmental Studies. Linköping University, Faculty of Arts and Sciences.
    Olsson, M
    Linköping University, Department of Physics, Chemistry and Biology, Biology.
    Tranvik, L
    Department of Limnology, Uppsala University.
    Simultaneous measurements of organic carbon mineralization and bacterial production in oxic and anoxic lake sediments2003In: Microbial Ecology, ISSN 0095-3628, E-ISSN 1432-184X, Vol. 46, no 1, p. 73-82Article in journal (Refereed)
    Abstract [en]

    Based on work in marine sediments it can be hypothesized that (i) overall OM mineralization depends on the enzymatic capacity and is largely independent from the energy yield, (ii) similar oxic and anoxic rates are expected for fresh OM, while oxic rates should be faster for old OM that is partially degraded or adsorbed to particles, and (iii) that the thermodynamic energy yield does not regulate mineralization, but primarily determines the energy fraction allocated to bacterial production (BP). We addressed these hypotheses by simultaneous measurements of mineralization rates (MR) and BP in sediments from a eutrophic lake, along with MR measurements in sediments of a dystrophic lake. Anoxic MR were 44 and 78% of oxic MR in the eutrophic and dystrophic lake, respectively, which was always higher than expected given the theoretical energy yields. The BP:MR ratio was 0.94 and 0.24 in the oxic and anoxic treatments, respectively, in accordance with the expected energy yields. Thus, the results support all three hypotheses above. We also critically discuss BP measurements in sediments and suggest that bacterial growth efficiency values from simultaneous MR and BP measurements can be used to evaluate the reliability of BP estimates.

  • 50.
    Beltéky, Johan
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Eklund, Beatrix
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Jensen, Per
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Gene expression of behaviorally relevant genes in the cerebral hemisphere changes after selection for tameness in Red Junglefowl.2017In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 12, no 5, article id e0177004Article in journal (Refereed)
    Abstract [en]

    The process of domestication in animals has led to alterations in behavior, physiology and phenotypic traits, changes that may be driven by correlations with reduced fear of humans. We used Red Junglefowl, ancestors of all domesticated chickens selected for either high or low fear of humans for five generations to study the effects of selection on gene transcription in the cerebral hemisphere, which is heavily involved in behaviour control. A total of 24 individuals from the parental generation as well as from the fifth selected generation were used. Twenty-two genes were significantly differentially expressed at p < 0.05 after false discovery rate (FDR) correction. Those genes that were upregulated in the low fearful animals were found to be involved in neural functions. Gene ontology and pathway analysis revealed enrichment for terms associated with behavioural processes. We conclude that five generations of divergent selection for high or low tameness has significantly changed gene expression patterns in the cerebral hemisphere in the Red Junglefowl population used here, which could underlie a range of changes in the domestic phenotype.

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