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  • 1.
    Asghar, Naveed
    et al.
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Biology. Örebro universitet.
    Lee, Yi-Ping
    Umeå universitet.
    Nilsson, Emma
    Umeå universitet.
    Lindqvist, Rickard
    Umeå universitet.
    Melik, Wessam
    Örebro universitet.
    Kröger, Andrea
    6Helmholtz Centre for Infection Research, Braunschweig, Germany / University of Magdeburg, Magdenbrug, Germany.
    Överby, Anna K.
    Umeå universitet.
    Johansson, Magnus
    Örebro universitet.
    The role of the poly(A) tract in the replication and virulence of tick-borne encephalitis virus2016In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, no 6, 39265Article in journal (Refereed)
    Abstract [en]

    The tick-borne encephalitis virus (TBEV) is a flavivirus transmitted to humans, usually via tick bites. The virus causes tick-borne encephalitis (TBE) in humans, and symptoms range from mild flu-like symptoms to severe and long-lasting sequelae, including permanent brain damage. It has been suggested that within the population of viruses transmitted to the mammalian host, quasispecies with neurotropic properties might become dominant in the host resulting in neurological symptoms. We previously demonstrated the existence of TBEV variants with variable poly(A) tracts within a single blood-fed tick. To characterize the role of the poly(A) tract in TBEV replication and virulence, we generated infectious clones of Torö-2003 with the wild-type (A)3C(A)6 sequence (Torö-6A) or with a modified (A)3C(A)38 sequence (Torö-38A). Torö-38A replicated poorly compared to Torö-6A in cell culture, but Torö-38A was more virulent than Torö-6A in a mouse model of TBE. Next-generation sequencing of TBEV genomes after passaging in cell culture and/or mouse brain revealed mutations in specific genomic regions and the presence of quasispecies that might contribute to the observed differences in virulence. These data suggest a role for quasispecies development within the poly(A) tract as a virulence determinant for TBEV in mice.

  • 2.
    Asghar, Naveed
    et al.
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Biology.
    Lindblom, Pontus
    Melik, Wessam
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Biology.
    Lindqvist, Richard
    Haglund, Mats
    Forsberg, Pia
    Overby, Anna K
    Andreassen, Ashild
    Lindgren, Per-Eric
    Johansson, Magnus
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Biology. Örebro University.
    Tick-borne encephalitis virus sequenced directly from questing and blood-feeding ticks reveals quasispecies variance.2014In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 9, no 7, e103264- p.Article in journal (Refereed)
    Abstract [en]

    The increased distribution of the tick-borne encephalitis virus (TBEV) in Scandinavia highlights the importance of characterizing novel sequences within the natural foci. In this study, two TBEV strains: the Norwegian Mandal 2009 (questing nymphs pool) and the Swedish Saringe 2009 (blood-fed nymph) were sequenced and phylogenetically characterized. Interestingly, the sequence of Mandal 2009 revealed the shorter form of the TBEV genome, similar to the highly virulent Hypr strain, within the 3' non-coding region (3'NCR). A different genomic structure was found in the 3'NCR of Saringe 2009, as in-depth analysis demonstrated TBEV variants with different lengths within the poly(A) tract. This shows that TBEV quasispecies exists in nature and indicates a putative shift in the quasispecies pool when the virus switches between invertebrate and vertebrate environments. This prompted us to further sequence and analyze the 3'NCRs of additional Scandinavian TBEV strains and control strains, Hypr and Neudoerfl. Toro 2003 and Habo 2011 contained mainly a short (A)3C(A)6 poly(A) tract. A similar pattern was observed for the human TBEV isolates 1993/783 and 1991/4944; however, one clone of 1991/4944 contained an (A)3C(A)11 poly(A) sequence, demonstrating that quasispecies with longer poly(A) could be present in human isolates. Neudoerfl has previously been reported to contain a poly(A) region, but to our surprise the re-sequenced genome contained two major quasispecies variants, both lacking the poly(A) tract. We speculate that the observed differences are important factors for the understanding of virulence, spread, and control of the TBEV.

  • 3.
    Asghar, Naveed
    et al.
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Biology. Örebro universitet.
    Petersson, Mona
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Geography.
    Johansson, Magnus
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Biology. Örebro univarsitet.
    Dinnétz, Patrik
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Environmental Science.
    Local land-scape effects on population dynamics of Ixodes ricinus2016In: Geospatial Health, ISSN 1827-1987, Vol. 11, 283-289 p., 487Article in journal (Refereed)
  • 4.
    Asghar, Naveed
    et al.
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Biology. Örebro universitet.
    Pettersson, John H-O
    Norwegian Institute of Public Health, Oslo, Norway / Statens veterinärmedicinska anstalt.
    Dinnétz, Patrik
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Environmental Science.
    Andreassen, Åshild
    Norwegian Institute of Public Health, Oslo, Norway.
    Johansson, Magnus
    Örebro universitet.
    Deep sequencing analysis of tick-borne encephalitis virusfrom questing ticks at natural foci reveals similaritiesbetween quasispecies pools of the virusManuscript (preprint) (Other academic)
  • 5.
    Bertrand, Yann J.
    et al.
    Science and Historical Investigations of Evolution Laboratory of Dubá, Dubá, Czech Republic.
    Johansson, Magnus
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Biology. Örebro University.
    Norberg, Peter
    Sahlgrenska University.
    Revisiting Recombination Signal in the Tick-Borne Encephalitis Virus: A Simulation Approach2016In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 11, no 10, e0164435Article in journal (Refereed)
    Abstract [en]

    The hypothesis of wide spread reticulate evolution in Tick-Borne Encephalitis virus (TBEV) has recently gained momentum with several publications describing past recombination events involving various TBEV clades. Despite a large body of work, no consensus has yet emerged on TBEV evolutionary dynamics. Understanding the occurrence and frequency of recombination in TBEV bears significant impact on epidemiology, evolution, and vaccination with live vaccines. In this study, we investigated the possibility of detecting recombination events in TBEV by simulating recombinations at several locations on the virus' phylogenetic tree and for different lengths of recombining fragments. We derived estimations of rates of true and false positive for the detection of past recombination events for seven recombination detection algorithms. Our analytical framework can be applied to any investigation dealing with the difficult task of distinguishing genuine recombination signal from background noise. Our results suggest that the problem of false positives associated with low detection P-values in TBEV, is more insidious than generally acknowledged. We reappraised the recombination signals present in the empirical data, and showed that reliable signals could only be obtained in a few cases when highly genetically divergent strains were involved, whereas false positives were common among genetically similar strains. We thus conclude that recombination among wild-type TBEV strains may occur, which has potential implications for vaccination with live vaccines, but that these events are surprisingly rare.

  • 6.
    Bonow, Madeleine
    et al.
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Environmental Science.
    Olsén, HåkanSödertörn University, School of Natural Sciences, Technology and Environmental Studies, Biology.Svanberg, IngvarUppsala universitet.
    Historical Aquaculture in Northern Europe2016Collection (editor) (Refereed)
    Abstract [en]

    How were fishponds introduced, farmed and spread in Scandinavia and the Baltic Region in early modern times? What was their economic, social and religious importance? Which fish species were significant and why?

    This book uncovers a long, now broken, tradition that barely left traces in the written record or physical environment. Its broad and multidisciplinary scope highlights the situation from medieval times until the late nineteenth century. Besides Scandinavia and the Baltic States, insights from England are also introduced.

    Several socio-cultural domains have been identified: late medieval monastic fishponds; late medieval aristocratic fishponds associated with castles and manors; seventeenth and eighteenth century ponds rectory ponds as well as urban ponds from the seventeenth century to the nineteenth century.

  • 7.
    Bonow, Madeleine
    et al.
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Meal Sciences. Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Geography.
    Svanberg, Ingvar
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Biology.
    Karpfiskarnas tillbakagång i svenskt kosthåll2013In: Från matproduktion till gastronomi / [ed] Paulina Rytkönen, Madeleine Bonow, Per Wramner, Huddinge: Södertörns högskola , 2013, 91-114 p.Chapter in book (Other academic)
  • 8.
    Boss, John
    et al.
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies. Karolinska Institute.
    Liedvogel, Miriam
    Lund University / Max Planck Institute for Evolutionary Biology, Plön, Germany.
    Lundberg, Max
    Lund University.
    Olsson, Peter
    Lund University.
    Reischke, Nils
    Lund University.
    Naurin, Sara
    Lund University.
    Åkesson, Susanne
    Lund University.
    Hasselquist, Dennis
    Lund University.
    Wright, Anthony
    Karolinska Institute.
    Grahn, Mats
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Biology.
    Bensch, Staffan
    Lund University.
    Gene expression in the brain of a migratory songbird during breeding and migration2016In: Movement Ecology, E-ISSN 2051-3933, Vol. 4Article in journal (Refereed)
    Abstract [en]

    BACKGROUND: We still have limited knowledge about the underlying genetic mechanisms that enable migrating species of birds to navigate the globe. Here we make an attempt to get insight into the genetic architecture controlling this complex innate behaviour. We contrast the gene expression profiles of two closely related songbird subspecies with divergent migratory phenotypes. In addition to comparing differences in migratory strategy we include a temporal component and contrast patterns between breeding adults and autumn migrating juvenile birds of both subspecies. The two willow warbler subspecies, Phylloscopus trochilus trochilus and P. t. acredula, are remarkably similar both in phenotype and genotype and have a narrow contact zone in central Scandinavia. Here we used a microarray gene chip representing 23,136 expressed sequence tags (ESTs) from the zebra finch Taeniopygia guttata to identify mRNA level differences in willow warbler brain tissue in relation to subspecies and season.

    RESULTS: Out of the 22,109 EST probe sets that remained after filtering poorly binding probes, we found 11,898 (51.8 %) probe sets that could be reliably and uniquely matched to a total of 6,758 orthologous zebra finch genes. The two subspecies showed very similar levels of gene expression with less than 0.1 % of the probe sets being significantly differentially expressed. In contrast, 3,045 (13.8 %) probe sets were found to be differently regulated between samples collected from breeding adults and autumn migrating juvenile birds. The genes found to be differentially expressed between seasons appeared to be enriched for functional roles in neuronal firing and neuronal synapse formation.

    CONCLUSIONS: Our results show that only few genes are differentially expressed between the subspecies. This suggests that the different migration strategies of the subspecies might be governed by few genes, or that the expression patterns of those genes are time-structured or tissue-specific in ways, which our approach fails to uncover. Our findings will be useful in the planning of new experiments designed to unravel the genes involved in the migratory program of birds.

  • 9.
    Caspillo, Nasim Reyhanian
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Biology. Örebro universitet.
    Hitting the mark: Studies of alterations in behaviour and fertility in ethinyl estradiol-exposed zebrafish and search related biomarkers2016Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    In this thesis, we have analysed the effects of EE2 on non-reproductive behaviours and fertility. We have showed that two doses of EE2 in male adult short-term exposures evokes opposite behaviours in the novel tank test. A lower dose induced increased bottom-dwelling, a sign of increased anxiety and a higher dose increased surface-dwelling, which would likely expose themselves to predation in a natural environment. Increased shoaling was observed in both exposures, possibly affecting feeding and reproduction opportunities. Fertility analysis of these fish demonstrated a complete inhibition of spawning in the highest dose group. To investigate mechanisms behind the spawning failure, we examined expression levels of genes involved in zebrafish sex differentiation and maintenance of gonadal function. We found downregulated transcription levels of male-predominant genes, suggesting a demasculinization of the testes contributing to functional sterility in these fish. We have demonstrated that non-reproductive behaviour in zebrafish is highly sensitive to EE2 exposure during development. After exposing male and female zebrafish to low doses of EE2 followed by remediation in clean water until adulthood, the fish displayed increased anxiety and shoaling behaviour, demonstrating persistent effects of EE2. Furthermore, behavioural effects were transferred to their progeny. Decreased fertilisation success of the developmentally exposed fish was observed in both sexes when mated to untreated animals of the opposite sex. These fertility effects persisted although the fish had a long remediation period, implying likely reduced fitness of fish populations in aquatic environments. Based on our findings on non-reproductive behaviours and fertility, we performed RNAsequencing analysis of the brain and testes in order to investigate possible biological mechanisms behind the persistent effects. There is a need for biomarkers allowing detection of both reversible and irreversible effects in animals exposed to estrogenic substances, hopefully contributing to better risk assessments for EDCs. Results from RNA-sequencing would serve as a basis for continued studies in pursuit of potential biomarkers.

  • 10.
    Ceken, Fatma
    et al.
    Södertörn University, Teacher Education.
    Mutvei, Ann
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Biology.
    Mattsson, Jan-Eric
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Biology.
    The use of the theory of conceptual profiles to assess learning outcome2016In: Electronic Proceedings of the ESERA 2015 Conference: Science education research: Engaging learners for a sustainable future, Part 16 / [ed] J. Lavonen, K. Juuti, J. Lampiselkä, A. Uitto & K. Hahl (Eds.); co-eds. P. Kariotoglou & T. Russell, Helsinki: University of Helsinki, 2016, 2716-2721 p.Conference paper (Refereed)
    Abstract [en]

    The Swedish Schools Inspectorate (2012) made an evaluation of the quality in science teaching in year 1–3 in the Swedish compulsory school. Large differences were found among the 30 schools studied. Often teaching only consisted of mediating facts or experiments made by the teacher. The students rarely got an opportunity to learn through systematic investigations. Less than 60% of the lessons observed involved activities were the students to large extent met scientific methods. Also, good examples were found in schools were the teachers consciously let the students make hypotheses about what will happen in an experiment. In many schools the teacher use readymade teaching packages. Generally, they consist of instructions for how series of lessons with different themes may be planned and performed by using the material included. Some of the packages also include education of the teachers. According to the School Inspectorate teachers without education in science claim that with help of the packages they have been able to teach in all areas of school science. Teachers sometime use the packages as inspiration, but chose other methods for their teaching. The purpose of this study was to examine how students in primary school use concepts and to study their conceptual development during two sequences of lessons, primarily based on the student’s own documentations. Written diaries and reports of the students were analysed in order to construct their conceptual profiles and to follow their development. The assessment of the performances in relation to the knowledge requirement evaluated students ability to discuss simple questions concerning chemical processes, plan simple experiments and formulate simple question. The study shows that observations, discussions, and written documentation of simple experiments promotes conceptual development.

  • 11.
    Dalusi, Lucy
    et al.
    Amana Regional Referral Hospital, Dar es Salaam, Tanzania / University of Dar es Salaam, Dar es Salaam, Tanzania.
    Lyimo, Thomas J
    University of Dar es Salaam, Dar es Salaam, Tanzania.
    Lugomela, Charles
    University of Dar es Salaam, Dar es Salaam, Tanzania.
    Hosea, Ken M M
    University of Dar es Salaam, Dar es Salaam, Tanzania.
    Sjöling, Sara
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Biology.
    Toxigenic Vibrio cholerae identified in estuaries of Tanzania using PCR techniques2015In: FEMS Microbiology Letters, ISSN 0378-1097, E-ISSN 1574-6968, Vol. 362, no 5Article in journal (Refereed)
    Abstract [en]

    The current study assessed the occurrence of the Vibrio cholerae serogroups O1 and O139 in environmental samples along salinity gradients in three selected estuaries of Tanzania both through culture independent methods and by cultured bacteria. Occurrence of V. cholerae was determined by PCR targeting the V. cholerae outer membrane protein gene ompW. Furthermore, the presence of toxigenic strains and serogroups O1 and O139 was determined using multiplex PCR with specific primers targeting the cholera toxin gene subunit A, ctxA, and serotype specific primers, O1-rfb and O139-rfb, respectively. Results showed that V. cholerae occurred in approximately 10% (n = 185) of both the environmental samples and isolated bacteria. Eight of the bacteria isolates (n = 43) were confirmed as serogroup O1 while one belonged to serogroup O139, the first reported identification of this epidemic strain in East African coastal waters. All samples identified as serogroup O1 or O139 and a number of non-O1/O139 strains were ctxA positive. This study provides in situ evidence of the presence of pathogenic V. cholerae O1 and O139 and a number of V. cholerae non-O1/O139 that carry the cholera toxin gene in estuaries along the coast of Tanzania.

  • 12. Dealtry, Simone
    et al.
    Ding, Guo-Chun
    Weichelt, Viola
    Dunon, Vincent
    Schlüter, Andreas
    Martini, María Carla
    Papa, María Florencia Del
    Lagares, Antonio
    Amos, Gregory Charles Auton
    Wellington, Elizabeth Margaret Helen
    Gaze, William Hugo
    Sipkema, Detmer
    Sjöling, Sara
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Biology.
    Springael, Dirk
    Heuer, Holger
    van Elsas, Jan Dirk
    Thomas, Christopher
    Smalla, Kornelia
    Cultivation-Independent Screening Revealed Hot Spots of IncP-1, IncP-7 and IncP-9 Plasmid Occurrence in Different Environmental Habitats.2014In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 9, no 2, e89922Article in journal (Refereed)
    Abstract [en]

    IncP-1, IncP-7 and IncP-9 plasmids often carry genes encoding enzymes involved in the degradation of man-made and natural contaminants, thus contributing to bacterial survival in polluted environments. However, the lack of suitable molecular tools often limits the detection of these plasmids in the environment. In this study, PCR followed by Southern blot hybridization detected the presence of plasmid-specific sequences in total community (TC-) DNA or fosmid DNA from samples originating from different environments and geographic regions. A novel primer system targeting IncP-9 plasmids was developed and applied along with established primers for IncP-1 and IncP-7. Screening TC-DNA from biopurification systems (BPS) which are used on farms for the purification of pesticide-contaminated water revealed high abundances of IncP-1 plasmids belonging to different subgroups as well as IncP-7 and IncP-9. The novel IncP-9 primer-system targeting the rep gene of nine IncP-9 subgroups allowed the detection of a high diversity of IncP-9 plasmid specific sequences in environments with different sources of pollution. Thus polluted sites are "hot spots" of plasmids potentially carrying catabolic genes.

  • 13.
    Dionisi, Hebe
    et al.
    Patagonian Natl Res Ctr CENPAT CONICET, Buenos Aires, DF, Argentina.
    Matos, Marina
    Patagonian Natl Res Ctr CENPAT CONICET, Buenos Aires, DF, Argentina.
    Anselmino, Luciano
    Patagonian Natl Res Ctr CENPAT CONICET, Buenos Aires, DF, Argentina.
    Lozada, Mariana
    Patagonian Natl Res Ctr CENPAT CONICET, Buenos Aires, DF, Argentina.
    Mac Cormack, Walter
    Argentinean Antarctic Inst, Buenos Aires, DF, Argentina / Natl Univ Buenos Aires, Buenos Aires, DF, Argentina.
    Carroll, Jolynn
    Univ Tromsö, N-9001 Tromsö, Norway / Akvaplan Niva AS, FRAM High North Res Ctr Climate & Environm, Tromsö, Norway.
    Lundgren, Leif
    Stockholm University.
    Sjöling, Sara
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Biology.
    Chavarria, Krystle
    Lawrence Berkeley Natl Labs, Berkeley, CA USA.
    Henrissat, Bernard
    Ctr Natl Rech Sci, Marseille, France.
    Jansson, Janet
    Lawrence Berkeley Natl Labs, Berkeley, CA USA.
    Mining alginate lyases in sediment metagenomes from four geographically distant cold coastal environments2014In: New Biotechnology, ISSN 1871-6784, E-ISSN 1876-4347, Vol. 31, S69-S70 p.Article in journal (Refereed)
  • 14.
    Divakar, Pradeep K.
    et al.
    Univ Complutense Madrid, Madrid, Spain.
    Crespo, Ana
    Univ Complutense Madrid, Madrid, Spain.
    Wedin, Mats
    Swedish Museum Nat Hist..
    Leavitt, Steven D.
    Field Museum, Chicago, USA..
    Hawksworth, David L.
    Univ Complutense Madrid, Madrid, Spain..
    Myllys, Leena
    Univ Helsinki, Bot Museum, Finnish Museum Nat Hist, Helsinki, Finland..
    McCune, Bruce
    Oregon State Univ, Corvallis, USA..
    Randlane, Tiina
    Univ Tartu, Tartu, Estonia..
    Bjerke, Jarle W.
    High North Res Ctr Climate & Environm, Norwegian Inst Nat Res NINA, FRAM, Tromso, Norway..
    Ohmura, Yoshihito
    Natl Museum Nat & Sci, Tsukuba, Japan..
    Schmitt, Imke
    Biodivers & Climate Res Ctr BiK F, Frankfurt, Germany.;Goethe Univ Frankfurt, Dept Biol Sci, Inst Ecol Evolut & Div, D-60438 Frankfurt, Germany..
    Boluda, Carlos G.
    Univ Complutense Madrid, Madrid, Spain..
    Alors, David
    Univ Complutense Madrid, Madrid, Spain..
    Roca-Valiente, Beatriz
    Univ Complutense Madrid, Madrid, Spain..
    Del-Prado, Ruth
    Univ Complutense Madrid, Madrid, Spain..
    Ruibal, Constantino
    Univ Complutense Madrid, Madrid, Spain..
    Buaruang, Kawinnat
    Univ Complutense Madrid, Madrid, Spain.;Ramkhamhang Univ, Bangkok, Thailand..
    Nunez-Zapata, Jano
    Univ Complutense Madrid, Madrid, Spain..
    Amo de Paz, Guillermo
    Univ Complutense Madrid, Madrid, Spain..
    Rico, Victor J.
    Univ Complutense Madrid, Madrid, Spain..
    Carmen Molina, M.
    Univ Rey Juan Carlos, Madrid, Spain..
    Elix, John A.
    Australian Natl Univ, Canberra, Australia..
    Esslinger, Theodore L.
    N Dakota State Univ, Fargo, USA..
    Tronstad, Inger Kristin K.
    Univ Tromso, Arctic Univ Norway, Tromso Univ Museum, Tromso, Norway..
    Lindgren, Hanna
    Univ Helsinki, Bot Museum, Finnish Museum Nat Hist, Helsinki, Finland..
    Ertz, Damien
    Natl Bot Garden Belgium, Meise, Belgium..
    Gueidan, Cecile
    Nat Hist Museum, London, England..
    Saag, Lauri
    Univ Tartu, Tartu, Estonia..
    Mark, Kristiina
    Univ Tartu, Tartu, Estonia..
    Singh, Garima
    Biodivers & Climate Res Ctr BiK F, Frankfurt, Germany..
    Dal Grande, Francesco
    Biodivers & Climate Res Ctr BiK F, Frankfurt, Germany..
    Parnmen, Sittiporn
    Field Museum, Chicago, IL 60605 USA.;Minist Publ Hlth, Nonthaburi, Thailand..
    Beck, Andreas
    Botan Staatssammlung, Munich, Germany..
    Benatti, Michel Navarro
    Inst Bot, Nucleo Pesquisa Micol, Sao Paulo, SP, Brazil..
    Blanchon, Dan
    Unitec Inst Technol, Auckland, New Zealand..
    Candan, Mehmet
    Anadolu Univ, Eskisehir, Turkey..
    Clerc, Philippe
    Conservatoire & Jardin Bot Ville Geneve, Chambesy, Switzerland..
    Goward, Trevor
    Univ British Columbia, UBC Herbarium, Beaty Museum, Vancouver, Canada..
    Grube, Martin
    Karl Franzens Univ Graz, Graz, Austria..
    Hodkinson, Brendan P.
    Univ Penn, , Philadelphia, USA..
    Hur, Jae-Seoun
    Sunchon Natl Univ, Korean Lichen Res Inst, Sunchon, South Korea..
    Kantvilas, Gintaras
    Tasmanian Herbarium, Hobart, Australia..
    Kirika, Paul M.
    Natl Museums Kenya, Nairobi, Kenya..
    Lendemer, James
    New York Bot Garden, Bronx, USA..
    Mattsson, Jan-Eric
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Biology.
    Ines Messuti, Maria
    Univ Comahue, CONICET, San Carlos De Bariloche, Rio Negro, Argentina..
    Miadlikowska, Jolanta
    Duke Univ, Dept Biol, Durham, USA..
    Nelsen, Matthew
    Field Museum, Chicago, USA..
    Ohlson, Jan I.
    Swedish Museum Nat Hist..
    Perez-Ortega, Sergio
    CSIC, Museo Nacl Ciencias Nat, Madrid, Spain..
    Saag, Andres
    Univ Tartu, Tartu, Estonia..
    Sipman, Harrie J. M.
    Free Univ Berlin, Berlin, Germany..
    Sohrabi, Mohammad
    Iranian Res Org Sci & Technol, Tehran, Iran..
    Thell, Arne
    Lund Univ..
    Thor, Goran
    Swedish Univ Agr Sci, Dept Ecol, SE-75007 Uppsala, Sweden..
    Truong, Camille
    Conservatoire & Jardin Bot Ville Geneve, CH-1292 Chambesy, Switzerland..
    Yahr, Rebecca
    Royal Bot Gardens, Edinburgh EH3 5LR, Midlothian, Scotland..
    Upreti, Dalip K.
    CSIR, Natl Bot Res Inst, Lucknow 226001, Uttar Pradesh, India..
    Cubas, Paloma
    Univ Complutense Madrid, Madrid, Spain..
    Lumbsch, H. Thorsten
    Field Museum, Chicago, USA..
    Evolution of complex symbiotic relationships in a morphologically derived family of lichen-forming fungi2015In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 208, no 4, 1217-1226 p.Article in journal (Refereed)
    Abstract [en]

    We studied the evolutionary history of the Parmeliaceae (Lecanoromycetes, Ascomycota), one of the largest families of lichen-forming fungi with complex and variable morphologies, also including several lichenicolous fungi. We assembled a six-locus data set including nuclear, mitochondrial and low-copy protein-coding genes from 293 operational taxonomic units (OTUs). The lichenicolous lifestyle originated independently three times in lichenized ancestors within Parmeliaceae, and a new generic name is introduced for one of these fungi. In all cases, the independent origins occurred c. 24 million yr ago. Further, we show that the Paleocene, Eocene and Oligocene were key periods when diversification of major lineages within Parmeliaceae occurred, with subsequent radiations occurring primarily during the Oligocene and Miocene. Our phylogenetic hypothesis supports the independent origin of lichenicolous fungi associated with climatic shifts at the Oligocene-Miocene boundary. Moreover, diversification bursts at different times may be crucial factors driving the diversification of Parmeliaceae. Additionally, our study provides novel insight into evolutionary relationships in this large and diverse family of lichen-forming ascomycetes.

  • 15.
    Dublinowska, M.
    et al.
    University of Gdańsk, Gdynia, Poland.
    Smolarz, K.
    University of Gdańsk, Gdynia, Poland.
    Zabrzańska, S.
    University of Gdańsk, Gdynia, Poland.
    Larsson, Josefine
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Biology.
    Czerniawska, N.
    University of Gdańsk, Gdynia, Poland.
    Intersexuality in the Blue Mussel Mytilus edulis Complex (Mytilidae) from the Baltic Sea and the Danish Strait2016In: American Malacological Bulletin, ISSN 0740-2783, E-ISSN 2162-2698, Vol. 34, no 1, 28-39 p.Article in journal (Refereed)
    Abstract [en]

    Populations of Mytilus edulis complex were studied from 13 stations located at three areas of the Baltic Sea (the Gulf of Gdańsk, Poland; Tvärminne area, Finland; Trosa Archipelago, Sweden) and the Skagerrak sound (Kristineberg, Sweden). The main purpose of the study was to document the occurrence of intersexuality along longitudinal salinity change using squash and histology for comparative reasons. Intersex was identified in all four geographical areas at an average frequency of 1.8%. Squash technique revealed the highest intersex frequency in the Gulf of Gdańsk (up to 6.25%) whereas histology examination did so in the Kristineberg area (up to 10%). In the Tvärminne area and in the Trosa Archipelago the average frequency of intersex did not exceed 2% regardless of the technique used; this suggests a natural induction of the phenomenon. Statistically significant spatial differences in intersex frequency were confirmed for mussels inhabiting polluted hotspots in the Gulf of Gdańsk and at the west coast of Sweden (Kristineberg). Therefore, for these localities artificial induction of intersexuality as a consequence of adverse environmental threats (pollution, parasite outbreaks) is further suggested. Furthermore, squash technique - being less sensitive in identifying intersex when compared to histology - is not recommended for mussels with severe reproductive impairments making a proper analysis of gonads impossible. Intersexual individuals were also characterized by less developed gonads and lower gonado-somatic index (GSI) than males and females. Significantly lower GSI revealed less energy allocation towards reproduction in populations from the Trosa Archipelago and Tvärminne area in comparison to those from the Gulf of Gdańsk and from Kristineberg.

  • 16.
    Dumanski, Jan P.
    et al.
    Uppsala University.
    Rasi, Chiara
    Uppsala University.
    Lönn, Mikael
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Biology.
    Davies, Hanna
    Uppsala University.
    Ingelsson, Martin
    Uppsala University.
    Giedraitis, Vilmantas
    Uppsala University.
    Lannfelt, Lars
    Uppsala University.
    Magnusson, Patrik K. E.
    Karolinska Institutet.
    Lindgren, Cecilia M.
    University of Oxford, Oxford, United Kingdom.
    Morris, Andrew P.
    University of Oxford, Oxford, United Kingdom.
    Cesarini, David
    New York University, New York, USA.
    Johannesson, Magnus
    Stockholm School of Economics.
    Janson, Eva Tiensuu
    Uppsala University.
    Lind, Lars
    Uppsala University.
    Pedersen, Nancy L.
    Karolinska Institutet.
    Ingelsson, Erik
    Uppsala Univiversity.
    Forsberg, Lars A.
    Uppsala Univiversity.
    Smoking is associated with mosaic loss of chromosome Y2015In: Cancer Research, ISSN 0008-5472, E-ISSN 1538-7445, Vol. 75, 4683Article in journal (Other academic)
  • 17.
    Dumanski, Jan P
    et al.
    Uppsala University.
    Rasi, Chiara
    Uppsala University.
    Lönn, Mikael
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Biology.
    Davies, Hanna
    Uppsala University.
    Ingelsson, Martin
    Uppsala University.
    Giedraitis, Vilmantas
    Uppsala University.
    Lannfelt, Lars
    Uppsala University.
    Magnusson, Patrik K E
    Karolinska Institutet.
    Lindgren, Cecilia M
    Morris, Andrew P
    University of Liverpool, Liverpool, UK..
    Cesarini, David
    New York University, New York, USA..
    Johannesson, Magnus
    Stockholm School of Economics.
    Tiensuu Janson, Eva
    Uppsala University.
    Lind, Lars
    Uppsala University.
    Pedersen, Nancy L
    Karolinska Institutet.
    Ingelsson, Erik
    Uppsala University.
    Forsberg, Lars A
    Uppsala University.
    Smoking is associated with mosaic loss of chromosome Y2015In: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 347, no 6217, 81-83 p.Article in journal (Refereed)
    Abstract [en]

    Tobacco smoking is a risk factor for numerous disorders, including cancers affecting organs outside the respiratory tract. Epidemiological data suggest that smoking is a greater risk factor for these cancers in males compared to females. This observation, together with the fact that males have a higher incidence of and mortality from most non-sex-specific cancers, remains unexplained. Loss of chromosome Y (LOY) in blood cells is associated with increased risk of nonhematological tumors. We demonstrate here that smoking is associated with LOY in blood cells in three independent cohorts [TwinGene: odds ratio (OR) = 4.3, 95% CI = 2.8-6.7; ULSAM: OR = 2.4, 95% CI = 1.6-3.6; and PIVUS: OR = 3.5, 95% CI = 1.4-8.4] encompassing a total of 6014 men. The data also suggest that smoking has a transient and dose-dependent mutagenic effect on LOY status. The finding that smoking induces LOY thus links a preventable risk factor with the most common acquired human mutation.

  • 18. Engel, Katja
    et al.
    Ashby, Deborah
    Brady, Sean F.
    Cowan, Don A.
    Doemer, John
    Edwards, Elizabeth A.
    Fiebig, Klaus
    Martens, Eric C.
    McCormac, Dennis
    Mead, David A.
    Miyazaki, Kentaro
    Moreno-Hagelsieb, Gabriel
    O'Gara, Fergal
    Reid, Alexandra
    Rose, David R.
    Simonet, Pascal
    Sjöling, Sara
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Biology.
    Smalla, Kornelia
    Streit, Wolfgang R.
    Tedman-Jones, Jennifer
    Valla, Svein
    Wellington, Elizabeth M. H.
    Wu, Cheng-Cang
    Liles, Mark R.
    Neufeld, Josh D.
    Sessitsch, Angela
    Charles, Trevor C.
    Meeting Report: 1st International Functional Metagenomics Workshop May 7-8, 2012, St. Jacobs, Ontario, Canada2013In: Standards in Genomic Sciences, ISSN 1944-3277, E-ISSN 1944-3277, Vol. 8, no 1, 106-111 p.Article in journal (Other academic)
    Abstract [en]

    This report summarizes the events of the 1st International Functional Metagenomics Workshop. The workshop was held on May 7 and 8, 2012, in St. Jacobs, Ontario, Canada and was focused on building an international functional metagenomics community, exploring strategic research areas, and identifying opportunities for future collaboration and funding. The workshop was initiated by researchers at the University of Waterloo with support from the Ontario Genomics Institute (OGI), Natural Sciences and Engineering Research Council of Canada (NSERC) and the University of Waterloo.

  • 19.
    Gilek, Michael
    et al.
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Environmental Science.
    Hassler, Björn
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Environmental Science.
    Engkvist, Fanny
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Biology.
    Kern, Kristine
    The HELCOM Baltic Sea Action Plan: challenges of implementing an innovative ecosystem approach2013In: Political State of the Region Report 2013: Trends and Directions in the Baltic Sea Region / [ed] Bernd Henningsen, Tobias Etzold and Anna-Lena Pohl, Copenhagen: Baltic Development Forum , 2013, 58-61 p.Chapter in book (Other academic)
  • 20.
    Hamilton, P. B.
    et al.
    University of Exeter, Exeter, UK.
    Cowx, I. G.
    University of Hull, Hull, UK.
    Oleksiak, M. F.
    University of Miami, Miami, FL, USA.
    Griffiths, A. M.
    University of Bristol, Bristol, UK.
    Grahn, Mats
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Biology.
    Stevens, J. R.
    University of Exeter, Exeter, UK.
    Carvalho, G. R.
    Bangor University, Bangor, Gwynedd, UK.
    Nicol, E.
    Bangor University, Bangor, Gwynedd, UK.
    Tyler, C. R.
    University of Exeter, Exeter, UK.
    Population-level consequences for wild fish exposed to sublethal concentrations of chemicals: a critical review2016In: Fish and Fisheries, ISSN 1467-2960, E-ISSN 1467-2979, Vol. 17, no 3, 545-566 p.Article, review/survey (Refereed)
    Abstract [en]

    Concentrated chemical spills have been shown to impact adversely on fish populations and even cause localized population extinctions. Evaluating population-level impacts of sublethal exposure concentrations is, however, complex and confounded by other environmental pressures. Applying effect measures derived from laboratory-based chemical exposures to impacts in wild fish populations is constrained by uncertainty on how biochemical response measures (biomarkers) translate into health outcomes, lack of available data for chronic exposures and the many uncertainties in available fish population models. Furthermore, wild fish show phenotypic plasticity and local adaptations can occur that adds geographic and temporal variance on responses. Such population-level factors are rarely considered in the chemical risk assessment process and can probably be derived only from studies on wild fish. Molecular technologies, including microsatellite and SNP genotyping, and RNASeq for gene expression studies, are advancing our understanding of mechanisms of eco-toxicological response, tolerance, adaptation and selection in wild populations. We examine critically the application of such approaches with examples including using microsatellites that has identified roach (Rutilus rutilus) populations living in rivers contaminated with sewage effluents that are self-sustaining, and studies of stickleback (Gasterosteus aculeatus) and killifish (Fundulus heteroclitus) that have identified genomic regions under selection putatively related to pollution tolerance. Integrating data on biological effects between laboratory-based studies and wild populations, and building understanding on adaptive responses to sublethal exposure are some of the priority research areas for more effective evaluation of population risks and resilience to contaminant exposure.

  • 21. Hamsten, C.
    et al.
    Starkhammar, M.
    Tran, T. A. T.
    Johansson, Magnus
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Biology. Örebro University.
    Bengtsson, U.
    Ahlen, G.
    Sallberg, M.
    Gronlund, H.
    van Hage, M.
    Identification of galactose-alpha-1,3-galactose in the gastrointestinal tract of the tick Ixode sricinus; possible relationship with red meat allergy2013In: Allergy. European Journal of Allergy and Clinical Immunology, ISSN 0105-4538, E-ISSN 1398-9995, Vol. 68, no 4, 549-552 p.Article in journal (Refereed)
    Abstract [en]

    Patients with IgE antibodies against the carbohydrate epitope galactose--1,3-galactose (-Gal) have reported severe allergic reactions after consumption of red meat. Investigations have revealed associations between IgE to -Gal and tick bites. We provide the first direct evidence that -Gal is present within ticks thus potentially explaining the relationship between tick exposure and sensitization to -Gal, with development of red meat allergy as a secondary phenomena. Serum from Swedish patients with delayed severe reactions to red meat was included in the study. A dose-dependent inhibition of IgE responses to -Gal by the tick Ixodesricinus is demonstrated. Furthermore, using cryostat-cut sections of I.ricinus, we show that both a monoclonal and a polyclonal antibody against -Gal stains the gastrointestinal tract of the tick. The same pattern is seen when staining with patient sera IgE positive to -Gal. These results confirm that the -Gal epitope is present in I.ricinus and imply host exposure to -Gal during a tick bite. This provides further evidence that tick bites are associated with IgE responses to -Gal and red meat allergy.

  • 22.
    Hellström, Gustav
    et al.
    SLU, Umeå.
    Prestegaard, Tore
    SLU, Uppsala .
    Dannewitz, Johan
    SLU, Uppsala.
    Olsén, Håkan
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Environmental Science. Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Biology.
    Sperm from pheromone primed brown trout (Salmo trutta L.) produce more larvae2013In: Fish Physiology & Biochemistry, ISSN 0920-1742, E-ISSN 1573-5168, Vol. 39, no 3, 471-478 p.Article in journal (Refereed)
  • 23.
    Henriksson, Oskar
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Biology. Stockholms universitet.
    Genetic connectivity of fish in the Western Indian Ocean2013Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    An almost unbroken fringing reef runs along the east coast of Africa, the lagoon inside the reef is the foundation of almost all artisanal fisheries. It is a low-tech fishery conducted by many people. Some areas can have up to 19 fishermen per square kilometer. High fishing pressures, coupled with declining fish stocks has led to changes in mean size and reproductive age of many exploited species. There is a vital and urgent need for scientifically based management systems, including the utilization of genetic information to guide management practices.

    This thesis aims to investigate the presence of genetic structures in the western Indian Ocean. In order to do that we first investigated the historical patterns of connectivity throughout the region (paper I). In papers II and III we focused on local scale connectivity in Kenya and Tanzania and finally in paper IV we investigate the large-scale contemporary gene flow throughout the Western Indian Ocean. In paper III we also investigate the temporal genetic variation at one site and compare it to the small-scale genetic variation along a stretch of the Kenyan coastline. Some overall conclusions that can be drawn from my body of work are: there are genetic structures present in the western Indian Ocean even though the apparent lack of physical barriers. Major oceanic currents aid evolutionary dispersal patterns. A single geographic site need not be genetically homogenous or temporally stable. Island sites are genetically more homogenous than mainland sites.

    In conclusion, there are clear and distinct genetic structures present especially in Siganus sutor, the most targeted fish for the artisanal fishery in East Africa.

  • 24.
    Henriksson, Oskar
    et al.
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Biology. Stockholms universitet.
    Grahn, Mats
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Biology.
    Contrasting population genetic structure of Siganus sutor between mainland coastal and oceanic island populationsManuscript (preprint) (Other academic)
    Abstract [en]

    Studies on genetic connectivity are important for the management of fisheries. In this study we used AFLP to investigate population structure of the endemic Spinefoot shoemaker, Siganus sutor, from 6 countries, Kenya, Tanzania, Comoros, Seychelles and Mauritius in the Western Indian Ocean. We collected 506 samples from 20 fish landing sites, 171 variable loci were used in the statistical analysis. Global FST was significant and showed a pattern of isolation by distance, mostly influenced by remote oceanic islands. In a previous study we have described the temporal variation of Siganus sutor to be about 1/5 of the global variation, and by applying a 1/5 of the global variation cut of value for the pair-wise comparisons we were able to account some of the pair- wise genetic variation as temporal fluctuations. A STRUCTURE analysis was also preformed that corroborates the pair-wise FST comparisons. Overall these results show that S. sutor is genetically diverse and subdivided throughout the region, but also that the current management regime might not be optimal. 

  • 25.
    Henriksson, Oskar
    et al.
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Biology. Stockholms universitet.
    Larsson, Josefine
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Environmental Science.
    Grahn, Mats
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Biology.
    Temporal genetic variability of landed Siganus sutor reveals a mixed stock fishery in coastal KenyaManuscript (preprint) (Other academic)
    Abstract [en]

    Artisanal fisheries in Kenya have been in decline since the 1980’s and are currently managed by gear restriction and no take zones. The fishery is a mixed species fishery but the Shoemaker spinefoot (Siganus sutor) comprise a large portion of the total catches. The sustainable use of these resources is dependent on informed assessment and management of the harvested species. In Kenya there is a lack of critical information about landings, fish stock productivity and genetic stock structure, and there is no knowledge of populations size or genetic variation of S. sutor. In this study we used the molecular marker, AFLP to investigate the genetic variation within and between sites of S. sutor landed along the 200 km coast of Kenya. We compared the spatial genetic variation among sites with the within site temporal genetic variation from a single site, adjacent to a number of spawning aggregations. Our results show that the there is genetic variation among the sites (spatial variation) and that the temporal genetic variation with in a six week period was about 1/5 of the spatial genetic variation. We believe these findings to be an important aspect to considered for both future scientific research as well as management.

  • 26.
    Hjort, Karin
    et al.
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Biology. Uppsala University.
    Presti, Ilaria
    University of Insubria.
    Elväng, Annelie
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Biology.
    Marinelli, Flavia
    University of Insubria.
    Sjöling, Sara
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Biology.
    Bacterial chitinase with phytopathogen control capacity from suppressive soil revealed by functional metagenomics2014In: Applied Microbiology and Biotechnology, ISSN 0175-7598, E-ISSN 1432-0614, Vol. 98, no 6, 2819-2828 p.Article in journal (Refereed)
    Abstract [en]

    Plant disease caused by fungal pathogens results in vast crop damage globally. Microbial communities of soil that is suppressive to fungal crop disease provide a source for the identification of novel enzymes functioning as bioshields against plant pathogens. In this study, we targeted chitin-degrading enzymes of the uncultured bacterial community through a functional metagenomics approach, using a fosmid library of a suppressive soil metagenome. We identified a novel bacterial chitinase, Chi18H8, with antifungal activity against several important crop pathogens. Sequence analyses show that the chi18H8 gene encodes a 425-amino acid protein of 46 kDa with an N-terminal signal peptide, a catalytic domain with the conserved active site F175DGIDIDWE183, and a chitinase insertion domain. Chi18H8 was expressed (pGEX-6P-3 vector) in Escherichia coli and purified. Enzyme characterization shows that Chi18H8 has a prevalent chitobiosidase activity with a maximum activity at 35 °C at pH lower than 6, suggesting a role as exochitinase on native chitin. To our knowledge, Chi18H8 is the first chitinase isolated from a metagenome library obtained in pure form and which has the potential to be used as a candidate agent for controlling fungal crop diseases. Furthermore, Chi18H8 may also answer to the demand for novel chitin-degrading enzymes for a broad range of other industrial processes and medical purposes.

  • 27.
    Janson, Sven
    et al.
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies.
    Wouters, Johanna
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Biology.
    Bonow, Madeleine
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Geography.
    Svanberg, Ingvar
    Uppsala University.
    Olsén, K. Håkan
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Biology.
    Population genetic structure of crucian carp (Carassius carassius) in man-made ponds and wild populations in Sweden2015In: Aquaculture International, ISSN 0967-6120, E-ISSN 1573-143X, Vol. 23, no 1, 359-368 p.Article in journal (Other academic)
    Abstract [en]

    Although once popular prior to the last century, the aquaculture of crucian carp Carassius carassius (L. 1758) in Sweden gradually fell from favour. This is the first genetic comparison of crucian carp from historic man-made ponds in the Scandinavian Peninsula. The aim was to identify old populations without admixture and to compare the relationship of pond populations from different provinces in Sweden. In total, nine microsatellite loci from 234 individuals from 20 locations in varied parts of Sweden were analysed. The genetic distances of crucian carp populations indicated that the populations in the southernmost province of Sweden, Scania, shared a common history. A pond population in the province Småland also showed a common inheritance with this group. In the province Uppland, further north in Sweden, the population genetic distances suggested a much more complex history of crucian carp distributions in the ponds. The data showed that there are some ponds with potentially old populations without admixture, but also that several ponds might have been stocked with fish from many sources. © 2014 The Author(s).

  • 28.
    Jeffries, Daniel L
    et al.
    University of Hull, Hull, UK.
    Copp, Gordon H
    Bournemouth University, Poole, UK.
    Lawson Handley, Lori
    University of Hull, Hull, UK.
    Olsén, K. Håkan
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Biology.
    Sayer, Carl D
    University College London, London, UK.
    Hänfling, Bernd
    University of Hull, Hull, UK.
    Comparing RADseq and microsatellites to infer complex phylogeographic patterns, an empirical perspective in the Crucian carp, Carassius carassius, L2016In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 25, no 13, 2997-3018 p.Article in journal (Refereed)
    Abstract [en]

    The conservation of threatened species must be underpinned by phylogeographic knowledge. This need is epitomised by the freshwater fish Carassius carassius, which is in decline across much of its European range. Restriction site associated DNA sequencing (RADseq) is increasingly used for such applications, however RADseq is expensive, and limitations on sample number must be weighed against the benefit of large numbers of markers. This trade-off has previously been examined using simulation studies, however, empirical comparisons between these markers, especially in a phylogeographic context, are lacking. Here, we compare the results from microsatellites and RADseq for the phylogeography of C. carassius to test whether it is more advantageous to genotype fewer markers (microsatellites) in many samples, or many markers (SNPs) in fewer samples. These datasets, along with data from the mitochondrial cytochrome b gene, agree on broad phylogeographic patterns; showing the existence of two previously unidentified C. carassius lineages in Europe; one found throughout northern and central-eastern European drainages, and a second almost exclusively confined to the Danubian catchment. These lineages have been isolated for approximately 2.15 M years, and should be considered separate conservation units. RADseq recovered finer population structure and stronger patterns of IBD than microsatellites, despite including only 17.6% of samples (38% of populations and 52% of samples per population). RADseq was also used along with Approximate Bayesian Computation to show that the postglacial colonisation routes of C. carassius differ from the general patterns of freshwater fish in Europe, likely as a result of their distinctive ecology.

  • 29.
    Kagoshima, Hiroshi
    et al.
    Universität Basel, Basel, Switzerland /National Institute of Genetics, Shizuoka, Japan / Research Organization of Information and Systems (ROIS), Tokyo, Japan.
    Cassata, Giuseppe
    Universität Basel, Basel, Switzerland.
    Tong, Yong Guang
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Biology. Karolinska Institute.
    Pujol, Nathalie
    Aix-Marseille Université, Marseille, France.
    Niklaus, Gisela
    Universität Basel, Basel, Switzerland.
    Bürglin, Thomas R.
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Biology. Karolinska Institute / Universität Basel, Basel, Switzerland.
    The LIM homeobox gene ceh-14 is required for phasmid function and neurite outgrowth2013In: Developmental Biology, ISSN 0012-1606, E-ISSN 1095-564X, Vol. 380, no 2, 314-323 p.Article in journal (Refereed)
    Abstract [en]

    Transcription factors play key roles in cell fate specification and cell differentiation. Previously, we showed that the LIM homeodomain factor CEH-14 is expressed in the AFD neurons where it is required for thermotaxis behavior in Caenorhabditis elegans. Here, we show that ceh-14 is expressed in the phasmid sensory neurons, PHA and PHB, a number of neurons in the tail, i.e., PHC, DVC, PVC, PVN, PVQ PVT, PVW and PVR, as well as the touch neurons. Analysis of the promoter region shows that important regulatory elements for the expression in most neurons reside from -4 kb to -1.65 kb upstream of the start codon. Further, within the first introns are elements for expression in the hypodermis. Phylogenetic footprinting revealed numerous conserved motifs in these regions. In addition to the existing deletion mutation ceh-14(ch3), we isolated a new allele, ceh-14(ch2), in which only one LIM domain is disrupted. The latter mutant allele is partially defective for thermosensation. Analysis of both mutant alleles showed that they are defective in phasmid dye-filling. However, the cell body, dendritic outgrowth and ciliated endings of PHA and PHB appear normal, indicating that ceh-14 is not required for growth. The loss of a LIM domain in the ceh-14(ch2) allele causes a partial loss-of-function phenotype. Examination of the neurites of ALA and tail neurons using a ceh-14::GFP reporter shows abnormal axonal outgrowth and pathfinding.

  • 30.
    Kellner, Martin
    et al.
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Environmental Science.
    Porseryd, Tove
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Environmental Science.
    Hallgren, S
    Uppsala University.
    Porsch-Hällström, Inger
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Biology.
    Hansen, S H
    University of Copenhagen, Denmark.
    Olsén, K Håkan
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Biology.
    Waterborne citalopram has anxiolytic effects and increases locomotor activity in the three-spine stickleback (Gasterosteus aculeatus)2016In: Aquatic Toxicology, ISSN 0166-445X, E-ISSN 1879-1514, Vol. 173, 19-28 p.Article in journal (Refereed)
    Abstract [en]

    Citalopram is an antidepressant drug, which acts by inhibiting the re-uptake of serotonin from the synaptic cleft into the pre-synaptic nerve ending. It is one of the most common drugs used in treatment of depression, it is highly lipophilic and frequently found in sewage treatment plant effluents and surface waters around the world. Citalopram and other selective serotonin re-uptake inhibitors have, at concentrations that occur in nature, been shown to have behavioural as well as physiological effects on fish and other animals. This study is the result of several different experiments, intended to analyse different aspects of behavioural effects of chronic citalopram exposure in fish. Our model species the three-spine stickleback is common in the entire northern hemisphere and is considered to be a good environmental sentinel species. Female three-spine sticklebacks were exposed to 0, 1.5 and 15μg/l nominal concentrations of citalopram for 21 days and subjected to the novel tank (NT) diving test. In the NT test, the fish exposed to 1.5μg/l, but not the 15μg/l fish made a significantly higher number of transitions to the upper half and stayed there for significantly longer time than the fish exposed to 0μg/l. The 15μg/l group, however, displayed a significantly lower number of freeze bouts and a shorter total freezing time. The test for locomotor activity included in the NT test showed that fish treated with 1.5 and 15μg/l displayed a significantly higher swimming activity than control fish both 5-7 and 15-17min after the start of the experiment. In the next experiment we compared fish exposed to 1.5μg/l and 0.15μg/l to pure water controls with regard to shoaling intensity and found no effect of treatment. In the final experiment the propensity of fish treated with 1.5μg/l to approach an unknown object and aggressive behaviour was investigated using the Novel Object test and a mirror test, respectively. The exposed fish ventured close to the unknown object significantly more often and stayed there for significantly longer time than unexposed fish. The aggression test yielded no statistically significant effects. It is concluded that citalopram changes the behaviour of the three-spine stickleback in a way that is likely to have ecological consequences and that it must not be considered an environmentally safe pharmaceutical.

  • 31.
    Kellner, Martin
    et al.
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Environmental Science.
    Porseryd, Tove
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Environmental Science.
    Porsch-Hällström, Inger
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Biology.
    Hansen, Steen
    Univ. of Copenhagen.
    Olsén, K. Håkan
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Biology.
    Environmentally relevant concentrations of citalopram partially inhibit feeding in the three-spine stickleback (Gasterosteus aculeatus)2015In: Aquatic Toxicology, ISSN 0166-445X, E-ISSN 1879-1514, Vol. 158, 165-170 p.Article in journal (Refereed)
    Abstract [en]

    Selective Serotonin Re-uptake Inhibitors (SSRI) are mood-altering, psychotropic drugs commonly used in the treatment of depression and other psychological illnesses. Many of them are poorly degraded in sewage treatment plants and enter the environment unaltered. In laboratory studies, they have been demonstrated to affect a wide range of behaviours in aquatic organisms. In this study we investigated the effect of a three-week exposure to 0.15 and 1.5 μg/l of the SSRI citalopram dissolved in the ambient water on the feeding behaviour in three-spine stickleback (Gasterosteus aculeatus). Feeding, measured as the number of attacks performed on a piece of frozen bloodworms during a 10-min period, was reduced by 30–40% in fish exposed to both 0.15 and 1.5 μg/l citalopram. The effects of the environmentally relevant concentration 0.15 μg/l on feeding, an important fitness characteristic, suggests that the ecological significance of environmental SSRI exposure may be pronounced.

  • 32.
    Larsson, Josefine
    et al.
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Environmental Science.
    Lind, E. E.
    SLU.
    Corell, H.
    Göteborgs universitet.
    Grahn, Mats
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Biology.
    Smolarz, K.
    University of Gdańsk, Gdynia, Poland.
    Lönn, Mikael
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Biology.
    Regional genetic differentiation in the blue mussel from the Baltic Sea area2016In: Estuarine, Coastal and Shelf Science, ISSN 0272-7714, E-ISSN 1096-0015Article in journal (Refereed)
    Abstract [en]

    Connectivity plays an important role in shaping the genetic structure and in evolution of local adaptation. In the marine environment barriers to gene flow are in most cases caused by gradients in environmental factors, ocean circulation and/or larval behavior. Despite the long pelagic larval stages, with high potential for dispersal many marine organisms have been shown to have a fine scale genetic structuring. In this study, by using a combination of high-resolution genetic markers, species hybridization data and biophysical modeling we can present a comprehensive picture of the evolutionary landscape for a keystone species in the Baltic Sea, the blue mussel. We identified distinct genetic differentiation between the West Coast, Baltic Proper and Bothnian Sea regions, with lower gene diversity in the Bothnian Sea. Oceanographic connectivity together with salinity and to some extent species identity provides explanations for the genetic differentiation between the West Coast and the Baltic Sea (Baltic Proper and Bothnian Sea). The genetic differentiation between the Baltic Proper and Bothnian Sea cannot be directly explained by oceanographic connectivity, species identity or salinity, while the lower connectivity to the Bothnian Sea may explain the lower gene diversity. © 2016.

  • 33.
    Larsson, Josefine
    et al.
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Biology.
    Lind, Emma
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Biology. Stockholms universitet.
    Hallgren, Stefan
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Biology.
    From AFLP to sequence specific markers: Identifying genomic regions under selection in the three-spined stickleback caused by pulp mill effluentsManuscript (preprint) (Other academic)
    Abstract [en]

    The processes underlying divergent selection and genetic adaptation have been on the evolutionary biologists agenda for a long time. In this study we used the three-spined stickleback (Gasterosteus aculeatus) study system, a perfect system to study the evolution of similar traits in different lineages exposed to similar environmental conditions. Lind and Grahn (2011) have found directional selection caused by pulp mill effluent on populations of three-spined stickleback along the Swedish coast. In their study, they identified 21 AFLP- outlier loci indicated to be under selection. Here we converted some of these anonymous AFLP loci into sequenced markers and aligned them to the stickleback genome. Four out of five loci, aligned within or close to coding regions, on chromosome I, chromosome VIII, chromosome XIX and chromosome XX. One of the locus, located on chromosome VIII, have been identified to be under selection for fresh water adaption in other studies, including Baltic Sea stickleback populations (Mäkinen et al. 2008a,b). We believe that this is feasibly method that can be used as a starting point for identification of genes and genomic regions possible involved in adaptation, both for model and non-model organisms. 

  • 34.
    Larsson, Josefine
    et al.
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Environmental Science.
    Lönn, Mikael
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Biology.
    Lind, Emma E
    SLU.
    Świeżak, Justyna
    University of Gdansk, Gdynia , Poland.
    Smolarz, Katarzyna
    University of Gdansk, Gdynia , Poland.
    Grahn, Mats
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Biology.
    Sewage treatment plant associated genetic differentiation in the blue mussel from the Baltic Sea and Swedish west coast2016In: PeerJ, ISSN 2167-8359, E-ISSN 2167-8359, Vol. 4, e2628Article in journal (Refereed)
    Abstract [en]

    Human-derived environmental pollutants and nutrients that reach the aquatic environment through sewage effluents, agricultural and industrial processes are constantly contributing to environmental changes that serve as drivers for adaptive responses and evolutionary changes in many taxa. In this study, we examined how two types of point sources of aquatic environmental pollution, harbors and sewage treatment plants, affect gene diversity and genetic differentiation in the blue mussel in the Baltic Sea area and off the Swedish west coast (Skagerrak). Reference sites (REF) were geographically paired with sites from sewage treatments plant (STP) and harbors (HAR) with a nested sampling scheme, and genetic differentiation was evaluated using a high-resolution marker amplified fragment length polymorphism (AFLP). This study showed that genetic composition in the Baltic Sea blue mussel was associated with exposure to sewage treatment plant effluents. In addition, mussel populations from harbors were genetically divergent, in contrast to the sewage treatment plant populations, suggesting that there is an effect of pollution from harbors but that the direction is divergent and site specific, while the pollution effect from sewage treatment plants on the genetic composition of blue mussel populations acts in the same direction in the investigated sites.

  • 35.
    Lind, Emma
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Biology. Stockholms universitet.
    Genetic response to pollution in sticklebacks; natural selection in the wild2013Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The last century, humans have been altering almost all natural environments at an accelerating rate, including the Baltic Sea that has highly eutrophicated areas and many coastal industries such as Pulp-mills. For animals living in a habitat that changes there are basically two alternatives, either to cope with the change or become locally extinct. This thesis aims to investigate if recent anthropogenic disturbance in the Baltic Sea can affect natural populations on a genetic level through natural selection.

    First, we found a fine-scale genetic structure in three-spine sticklebacks (Gasterosteus aculeatus) populations along the Swedish coast (paper I), indicating limited gene-flow between populations in geographic proximity. Different genetic markers, specifically Amplified Fragment Lenght Polymorpism (AFLP, and microsatellites,  gave different results, highlighting the heterogeneous character of genomes which demonstrates that it is important to choose a genetic marker that is relevant for the question at hand. With a population genomic approach, and a multilocus genetic marker (AFLP), we detected convergent evolution in genotype composition in stickleback populations living in environments affected by pulp-mill effluent (paper II) and in highly eutrophicated environments (paper III), compared to adjacent reference populations. We found loci, in both studies (paper II, III), that were different from a neutral distribution and thus probably under divergent selection for the habitat differences investigated. The selective effect from pulp-mill effluents were more pronounced, but the two different habitats had mutual characters (AFLP loci). In paper IV, we converted five anonymous AFLP loci to sequenced markers and aligned them to the stickleback genome. Four out of five loci aligned within, or close to, coding regions on chromosome I, chromosome VIII, chromosome XIX and chromosome XX. One of the loci, located on chromosome VIII and identified as under divergent selection in both paper II and III, has been identified in other studies as to be under selection for fresh water adaptation, including Baltic Sea stickleback populations.

    In conclusion, anthropogenic alterations of natural environments can have evolutionary consequences, probably adaptive, for the animals living there and the evolutionary response exhibited by natural populations can be very fast.

  • 36.
    Lind, Emma
    et al.
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Biology. Stockholms universitet.
    Larsson, Josefine
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Biology.
    Tuomainen, Ulla
    University of Helsinki.
    Borg, Malin
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies.
    Candolin, Ulrika
    University of Helsinki.
    Grahn, Mats
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Biology.
    Genetic response to eutrophication in three-spined sticklebacks (Gasterosteus aculeatus): A study of multiple Baltic Sea populationsManuscript (preprint) (Other academic)
    Abstract [en]

    Anthropogenic activities are causing change in natural habitats at an accelerating rate and affecting populations by altered selection pressures. One example is human-induced eutrophication in the Baltic Sea, were behaviour alterations are well documented in three-spined sticklebacks (Gasterosteus aculeatus). Here we have used 204 variable Amplified Fragment Length Polymorphism (AFLP) markers to investigate genetic differences between a set of ten hierarchal sampled populations of sticklebacks, five populations inhabiting eutrophicated habitats and five from control populations, in total 292 individuals. We found significant genetic variation that could be attributed to habitat (4.3% AMOVA). A combination of FST outlier analysis and classification analysis revealed seven AFLP-loci likely to be affected by divergent selection by eutrophication. Four of these seven loci have earlier been identified as under selection in stickleback populations living in pulp-mill effluents suggesting some similar selective factors between eutrophication and pulp-mill effluent effected habitats. 

  • 37.
    Lind, Emma
    et al.
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Biology. Stockholms universitet.
    Ohlin, Helena
    Mälardalens högskola.
    Grahn, Mats
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Biology.
    Fine scale genetic structure in Thresspine sticklback (Gasterosteus aculeatus) along Sweden's coastManuscript (preprint) (Other academic)
    Abstract [en]

    There are three basic types of population structures in marine environments; populations that are distinct, with a continuous change and without any differentiation. In each type the population units are characterized by groups of individuals with panmixia within groups and site fidelity to a limited geographic area. Earlier studies of the population genetic structure on sticklebacks in the Baltic Sea have shown none or only little structure. We have sampled 8 sites (253 individuals) along Sweden’s coast to estimate the genetic structure, using five microsatellites and 173 Amplified Fragment Length Polymorphism (AFLP) markers and detected a fine scale genetic structure (AFLP FST= 25%, microsatellites FST = 2.7%). With AFLPs the observed variation followed isolation by distance model (but not with microsatellites). Even sites separated by only 2 km of water are significantly separated. Both Bayesian clustering analysis and Capscale separated populations and identified populations from Gulf of Bothnia (4 psu) and from the west coast (20 psu) as genetically distinctly different from Baltic populations (about 7-8 psu).  In conclusion, gene flow is limited between sampled sites, and since no geographic barriers can be distinguished the population structure is likely caused by the sticklebacks’ behavior. Hence, we have probably sampled either stationary populations of marine sticklebacks, or homing sticklebacks. In this study AFLP and microsatellites did not give congruent results; with AFLPs we got high separation, and genetic variation followed isolation by distance model and supported the continuous change type of population structure.

  • 38.
    Lugomela, Charles
    et al.
    Department of Aquatic Sciences and Fisheries, University of Dar es Salaam, PO Box 35064 Dar es Salaam, Tanzania.
    Lyimo, Thomas J.
    Department of Molecular Biology and Biotechnology, University of Dar es Salaam, PO Box 35179, Dar es Salaam, Tanzania.
    Namkinga, Lucy A
    Department of Molecular Biology and Biotechnology, University of Dar es Salaam, PO Box 35179, Dar es Salaam, Tanzania.
    Moyo, Sabina
    Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, PO Box 65001 Dar es Salaam, Tanzania.
    Goericke, Ralph
    Scripps Institution of Oceanography, University of California, San Diego, 9500 Gilman Dr., La Jolla, 92093, USA.
    Sjöling, Sara
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Biology.
    Co-variation of Cholera with Climatic and Environmental Parameters in Coastal Regions of Tanzania2014In: Western Indian Ocean journal of marine science, ISSN 0856-860X, Vol. 13, no 1, 93-105 p.Article in journal (Refereed)
    Abstract [en]

    The bacterium causing cholera, Vibrio cholerae, is essentially a marine organism and its ecological dynamics have been linked to oceanographic conditions and climate. We used autoregressive models with external inputs to identify potential relationships between the number of cholera cases in the coastal regions of mainland Tanzania with climatic and environmental indices (maximum air temperature, sea surface temperature, wind speed and chlorophyll a). Results revealed that, between 2004 and 2010, coastal regions of mainland Tanzania inhabited by approximately 21% of the total population accounted for approximately 50% of the cholera cases and 40% of the total mortality. Significant co-variations were found between seasonally adjusted cholera cases and coastal ocean chlorophyll a and, to some degree, sea surface temperature, the outbreaks lagging behind by one to four months. Cholera cases in Dar es Salaam were also weakly related to the Indian Ocean Dipole Mode Index, lagging by five months, suggesting that it may be possible to predict cholera outbreaks for Dar es Salaam this period ahead. The results also suggest that the severity of cholera in coastal regions can be predicted by ocean conditions and that longer-term environmental and climate parameters may be used to predict cholera outbreaks along the coastal regions.

  • 39. Lundberg, Max
    et al.
    Boss, John
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Biology.
    Canbäck, Björn
    Liedvogel, Miriam
    Larson, Keith W
    Grahn, Mats
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Biology.
    Akesson, Susanne
    Bensch, Staffan
    Wright, Anthony
    Characterisation of a transcriptome to find sequence differences between two differentially migrating subspecies of the willow warbler Phylloscopus trochilus.2013In: BMC Genomics, ISSN 1471-2164, Vol. 14, 330- p.Article in journal (Refereed)
    Abstract [en]

    BACKGROUND: Animal migration requires adaptations in morphological, physiological and behavioural traits. Several of these traits have been shown to possess a strong heritable component in birds, but little is known about their genetic architecture. Here we used 454 sequencing of brain-derived transcriptomes from two differentially migrating subspecies of the willow warbler Phylloscopus trochilus to detect genes potentially underlying traits associated with migration.

    RESULTS: The transcriptome sequencing resulted in 1.8 million reads following filtering steps. Most of the reads (84%) were successfully mapped to the genome of the zebra finch Taeniopygia gutatta. The mapped reads were situated within at least 12,101 predicted zebra finch genes, with the greatest sequencing depth in exons. Reads that were mapped to intergenic regions were generally located close to predicted genes and possibly located in uncharacterized untranslated regions (UTRs). Out of 85,000 single nucleotide polymorphisms (SNPs) with a minimum sequencing depth of eight reads from each of two subspecies-specific pools, only 55 showed high differentiation, confirming previous studies showing that most of the genetic variation is shared between the subspecies. Validation of a subset of the most highly differentiated SNPs using Sanger sequencing demonstrated that several of them also were differentiated between an independent set of individuals of each subspecies. These SNPs were clustered in two chromosome regions that are likely to be influenced by divergent selection between the subspecies and that could potentially be associated with adaptations to their different migratory strategies.

    CONCLUSIONS: Our study represents the first large-scale sequencing analysis aiming at detecting genes underlying migratory phenotypes in birds and provides new candidates for genes potentially involved in migration.

  • 40.
    Lättman, Håkan
    et al.
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Environmental Science. Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Biology. Linköping University.
    Bergman, K. -O
    Linköping University.
    Rapp, M.
    Linköping University.
    Tälle, M.
    Linköping University.
    Westerberg, L.
    Linköping University.
    Milberg, P.
    Linköping University.
    Decline in lichen biodiversity on oak trunks due to urbanization2014In: Nordic Journal of Botany, ISSN 0107-055X, Vol. 32, no 4, 518-528 p.Article in journal (Other academic)
    Abstract [en]

    Biodiversity often suffers from urbanization. In the present study, we focused on how the duration of urbanization affects the richness of 17 epiphytic lichen species and their cover on large oaks in urban environments in a city of 100 000 inhabitants in southeast Sweden. We also surveyed trees in adjacent rural areas, selected to have similar distributions of tree trunk circumference and surrounding oak density (within 300 m). Lichen richness and cover were lower on urban trees compared to rural trees. Furthermore, richness and cover decreased with the length of time that urban trees had been surrounded by houses. Most of the species that were analysed demonstrated a decline in occurrence with respect to the duration of housing development. The reduction in the probability of occurrence varied from 60% (Calicium viride, Evernia prunastri), 80% (Chrysothrix candelaris) to 90% (Ramalina spp.) during the considered 160-year period of urbanization. Therefore, even if valuable trees survive over the course of development, their lichen biota is likely to become depleted over time. © 2014 The Authors.

  • 41.
    López, J L
    et al.
    Universidad de Buenos Aires, Argentina.
    Golemba, M
    Hospital de Pediatría "Juan P. Garrahan", Argentina.
    Hernández, E
    UNSAM Campus Miguelete, Argentina / Universidad de Buenos Aires, Argentina.
    Lozada, M
    Centro Nacional Patagónico-CONICET, Argentina.
    Dionisi, H M
    Centro Nacional Patagónico-CONICET, Argentina.
    Jansson, J
    Pacific Northwest National Laboratory, Richland, WA, USA.
    Carroll, J
    UiT The Arctic University of Norway, Tromsø, Norway / Fram - High North Research Centre for Climate and the Environment, Tromsø, Norway.
    Lundgren, L
    Stockholm University.
    Sjöling, Sara
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Biology.
    Cormack, W P Mac
    UNSAM Campus Miguelete, Argentina / Universidad de Buenos Aires, Argentina.
    Microbial and viral-like rhodopsins present in coastal marine sediments from four polar and subpolar regions.2016In: FEMS Microbiology Ecology, ISSN 0168-6496, E-ISSN 1574-6941, Vol. 93, no 1, fiw216Article in journal (Refereed)
    Abstract [en]

    Rhodopsins are broadly distributed. In this work we analyzed 23 metagenomes corresponding to marine sediment samples from four regions which share cold climate conditions (Norway; Sweden; Argentina and Antarctica). In order to investigate the genes evolution of viral-rodopsins, an initial set of 6224 bacterial rhodopsins sequences according COG5524 were retrieved from the 23 metagenomes. After selection by the presence of transmembrane domains and alignment 123 viral (51) and non-viral (72) sequences (>50 aminoacids) were finally included in further analysis. Viral rhodopsin genes were homologues of Phaeocystis globosa virus and Organic lake Phycodnavirus Non-viral microbial rhodopsin genes were ascribed to Bacteroidetes, Planctomycetes, Firmicutes, Actinobacteria, Cyanobacteria, Proteobacteria, Deinococcus-Thermus as well as Cryptophyta and Fungi. A re-screening using Blastp, using as queries the viral sequences previously described, retrieved 30 sequences (>100 aminoacids). Phylogeographic analysis revealed a geographycal clustering of the sequences affiliated to the viral group. This clustering was not observed for the microbial non-viral sequences. The phylogenetic reconstruction allowed us to propose the existence of a putative ancestor of viral rhodopsins (PAVR) genes related to Actinobacteria and Chloroflexi This is the first report about the existence of a phylogeographic association of the viral rhodopsins sequences from marine sediments.

  • 42.
    Lönn, Mikael
    et al.
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Biology.
    Mutvei, Ann
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Biology.
    Mattsson, Jan-Eric
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Biology.
    Results and Comparison of Different Complementary Assessment Methods of Science Learning Outcome2015In: Conference proceedings. New perspectives in science education, 4th ed., Libreriauniversitaria.it , 2015, -5 p.Conference paper (Refereed)
    Abstract [en]

    To assess the quality of different aspects of the learning outcomes in relation to knowledge requirements as results of teaching several assessment methods have to be used. For most teachers it is also obvious that students differ in their ability to demonstrate the learning outcome depending on the assessment method used. In order to compare different assessment methods of the learning outcome of pre-school teacher students’ different types of tasks were evaluated and compared in order to identify the potential of each method to give the students fair chances of showing their skills. Thus, assessments based on multiple choice questionnaires of different types, long answer questions, practical laboratory experiments, experiment construction and the students ability to evaluate experiment plans were compared. Having Swedish as mother tongue also was included as an explanatory variable since we suspected that some of the assessment methods in reality rather evaluates the linguistic skills in interpreting texts rather than evaluating the content knowledge of the subject. The results for each student when different methods were used were compared in order to evaluate if some of the methods for assessment gave similar results or if the methods induced differences in the results for the same student. We use ordination techniques to assess and visualize main trends in the data and linear models and classification trees to evaluate specific associations. There is correlation between results from several assessment methods, there are positive correlation between combinations of results from long answers, experiment and experiment construction, meaning students who showed good results with one method did so also with the others - but in some comparisons like long answer questions and multiple choice questions good results were independent of each other. There was a negative effect of having a non-Swedish mother tongue on the results in multiple choice questionnaires, but a positive effect of a non-Swedish mother tongue on the combined scores on experimental construction and experiment. Linear models show that good achievements in experimental construction are explained by high summed scores of Doll´s criteria, the four R’s richness, recursion, relations, and rigor.

  • 43.
    Matos, Marina N
    et al.
    Centro para el Estudio de Sistemas Marinos, Puerto Madryn, Argentina.
    Lozada, Mariana
    Centro para el Estudio de Sistemas Marinos, Puerto Madryn, Argentina.
    Anselmino, Luciano E
    Centro para el Estudio de Sistemas Marinos, Puerto Madryn, Argentina.
    Musumeci, Matías A
    Centro para el Estudio de Sistemas Marinos, Puerto Madryn, Argentina.
    Henrissat, Bernard
    Aix-Marseille Université, Marseille, France / INRA, Marseille, France / King Abdulaziz University, Jeddah, Saudi Arabia.
    Jansson, Janet K.
    Pacific Northwest National Laboratory, Richland, USA.
    Mac Cormack, Walter P
    Instituto Antártico Argentino, Ciudad Autónoma de Buenos Aires, Argentina / Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina.
    Carroll, JoLynn
    High North Research Centre for Climate and the Environment, Tromsø, Norway / UiT The Arctic University of Norway, Tromsø, Norway.
    Sjöling, Sara
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Biology.
    Lundgren, Leif
    Stockholm University.
    Dionisi, Hebe M
    Centro para el Estudio de Sistemas Marinos, Puerto Madryn, Argentina.
    Metagenomics unveils the attributes of the alginolytic guilds of sediments from four distant cold coastal environments2016In: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 18, no 12, 4471-4484 p.Article in journal (Refereed)
    Abstract [en]

    Alginates are abundant polysaccharides in brown algae that constitute an important energy source for marine heterotrophic bacteria. Despite the key role of alginate degradation processes in the marine carbon cycle, little information is available on the bacterial populations involved in these processes. The aim of this work was to gain a better understanding of alginate utilization capabilities in cold coastal environments. Sediment metagenomes from four high-latitude regions of both Hemispheres were interrogated for alginate lyase gene homologue sequences and their genomic context. Sediments contained highly abundant and diverse bacterial assemblages with alginolytic potential, including members of Bacteroidetes and Proteobacteria, as well as several poorly characterized taxa. The microbial communities in Arctic and Antarctic sediments exhibited the most similar alginolytic profiles, whereas brackish sediments showed distinct structures with a higher proportion of novel genes. Examination of the gene neighbourhood of the alginate lyase homologues revealed distinct patterns depending on the potential lineage of the scaffolds, with evidence of evolutionary relationships among alginolytic gene clusters from Bacteroidetes and Proteobacteria. This information is relevant for understanding carbon fluxes in cold coastal environments and provides valuable information for the development of biotechnological applications from brown algae biomass.

  • 44.
    Mattsson, Jan-Eric
    et al.
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Biology.
    Mutvei, Ann
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Biology.
    How to teach evolution2015In: Procedia - Social and Behavioral Sciences, ISSN 1877-0428, Vol. 167, 170-177 p.Article in journal (Refereed)
    Abstract [en]

    Out of identified general didactic problems when teaching evolutionary theory, structured learning situations for pre-service teacher students were created together with performance assessment. The students’ discussions showed almost no use of evolutionary concepts and well-structured learning situations failed as many students worked in an arbitrarily manner. The performance assessment showed anyhow good results as questions with open answers gave opportunity for constructive thinking. One conclusion is the strength in open questions, promoting the students’ creation of reasonable explanations within a theoretical framework.

  • 45.
    Mattsson, Jan-Eric
    et al.
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Biology.
    Mutvei, Ann
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Biology.
    Aim: To practise scientific methods. Result: Personal development2014In: Ebook proceedings of the ESERA 2013 Conference: Science Education Research For Evidence-based Teaching andCoherence in Learning / [ed] Constantinou, C. P., Papadouris, N. & Hadjigeorgiou, A. : (co-ed. Avraamidou, L. and Michelini, M.), Nicosia, Cypern: European Science Education Research Association , 2014, 2410-2417 p.Conference paper (Refereed)
    Abstract [en]

    Field work in a teacher training program was focussed on the collection and presentation of data showing changes in the environment depending on variable factors. The observations should be possible to use as models for studies performed by children at school. The instructions were sparse and many of the observations from the first visit to the sites were impossible to repeat. The first four observations were made during autumn every month while the last was made in late spring sixteen months later. After this the students wrote short reflections on their impressions and experiences during the last visit compared to the earlier ones. These were analysed in order to reveal the impact on the students. Most of the students were very uncertain about what to do the first time. Almost none of them complained about this afterwards. Many were astonished over their own incapability of understanding or declared their lack of understanding general ideas. Many students wrote about strong emotions when returning to a familiar site that appeared to have changed and described how this created a strong attachment to the site. What was more surprising was that some students experienced their own development, in some cases towards becoming a teacher but also on a more private or personal level. They not only recognized themselves as the inexperienced student from the first visit and what was achieved later. They also realized how the relation between themselves and the site had a chronological development in accordance with their own development. The simple activity of field observations in combination with personal reflection created complicated processes beneficial for the student.

    Thus, we achieved and observed unexpected results together with what was expected.

  • 46.
    Mattsson, Jan-Eric
    et al.
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Biology.
    Mutvei, Ann
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Biology.
    Forces, to visualise the invisible2016In: Conference proceedings: 5th Conference edition, Florence, Italy, 17-18 March 2016, Fitenze: Libreria Universitaria, 2016, 537-541 p.Conference paper (Refereed)
    Abstract [en]

    “This is hard to understand as you can’t see the forces” exclaimed a student during a science course. Basic concepts in physics like force, energy, power are difficult to observe. Usually we often only make conclusions about their existence out of the resulting effects of their appearances. In addition, the use of similar words in other contexts, sometimes metaphorically, sometimes with other meaning, make the situation even worse. In science courses for pre-service primary school teacher students we have tried to design learning situations where students get personal experiences of the world behind the concepts described in words.

    Thus, we designed situations when the students themselves were subjected to different forces or had the opportunity to observe the effects of forces. They wrote reflections on their experiences and we discussed these together in order to get used to how to describe and explain these type of experiences.

    The learning outcome was assessed by analyses of written reflections of experiences from different attractions of an amusement park. One of the main outcomes of these reflections were the differences in the observations of the students. Often they had to do several rides to observe the forces they were subjected to. They also found differences in their personal ability to identify the forces. Some students were better in observing some of the forces than the others.

    Thus, the participation in one activity with the aim of observing something does not necessarily lead to similar observations of other participants. Previous experiences seem to affect the observations so forces in some directions may be regarded as more powerful or easier to identify by some persons than others. This may be a general characteristic of observations in common situations. In that case this may be one explanation why, e.g., students have different focus in the classroom and learn other things than those intended by the teacher.

  • 47.
    Mattsson, Jan-Eric
    et al.
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Biology.
    Mutvei, Ann
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Biology.
    Conceptual profiles for Doll’s four R's.2016In: Electronic Proceedings of the ESERA 2015 Conference: Science education research: Engaging learners for a sustainable future, Part 1 / [ed] J. Lavonen, K. Juuti, J. Lampiselkä, A. Uitto & K. Hahl (Eds.);(co-eds. O. Finlayson & R. Pinto, Helsinki: University of Helsinki, 2016, 72-77 p.Conference paper (Refereed)
    Abstract [en]

    As academic organisers and teachers with different positions teacher training programs at Södertörn University we have had the opportunity to develop and assess different types of pedagogic activities and use, e.g., the 4 R´s proposed by Doll, recursion, relations, richness, and rigor in assessments. Here pre-service teacher student reflections assessed by use of the 4R’s are compared with other texts by the same students in order to assess the quality of their understanding of evolutionary theory. Written performances of biology students are also compared with those of pre-service teacher students in order to reveal differences in the use of scientific concepts between the groups. Analysis of student performances show a relation between the use of the 4R’s, and the use of scientific concepts. Analyses of texts by students in evolution theory show a relatively low use of scientific concepts often regarded as important in scientific text. This may be explained by students’ good skills in giving scientific explanations in every-day language. Teacher students used more biological and evolutionary concepts compared to biology students. The emphasis on the use of concepts, especially in school, may be exaggerated. Professional biologists have to communicate with people outside the scientific community but teachers often cares about a strict scientific language. This is also found here where teacher students use the concepts to a larger extent than biology students. School biology should focus on the basic processes of organic evolution as the foundation of all teaching in order to enhance the students’ deeper understanding.

  • 48.
    Mattsson, Jan-Eric
    et al.
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Biology.
    Mutvei, Ann
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Biology.
    Lönn, Mikael
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Biology.
    Students´ Different Strategies in their Development of Knowledge, Understanding, and Skills in Science Education2015In: Conference proceedings. New perspectives in science education, 4th ed., Libreriauniversitaria.it , 2015, -4 p.Conference paper (Refereed)
    Abstract [en]

    Students differ in their ways of accomplishing varied forms of knowledge, develop personal understanding and improve their skills. Likewise, teachers differ in their way of teaching depending on earlier experiences and training, thus, for teachers it is important understand the different strategies of the students and their own pedagogic profile in order to design learning situations advantageous for all students.

    In this study we try to describe the development and the persistence of the learning outcome of five pre-service primary school teacher students and their teachers during one semester of science and technology teaching. The assessment of the students’ fulfilment of the knowledge requirements was made during and shortly after the course, all of them passed. The focus here is to analyse the students and teachers different routes to achieve professional skills and was made eight months after the finished course. The students and the teachers met and discussed their experiences of their development during the course. The discussions in the whole group and in smaller subgroups were recorded and analysed. One area of interest was to describe the personal and professional development during that semester and how this was regarded retrospectively. This may be regarded as an assessment of the pedagogic activities and their relevance for the different students.

    Another important objective was to describe the conceptual development of both the students and their teachers and to investigate if there were differences in their development. The development of the conceptual profiles of each person was constructed out of the discussions analysed to reveal developmental changes. The conceptual profiles were regarded to contain three basic zones, externalism, internalism and relational.

    A third objective was to investigate the quality of the development out of the criteria of Doll, the four R’s richness, recursion, relations, and rigor and to what extent these criteria were visible in the conceptual development?

    On the professional and personal level all participants recognized a development, for the students supported by experiences during practical training at schools. The result also show that type of conceptual development varied between participants but large similarities in the degree of conceptual development of different concepts in one person. Finally, many of the generative phases of conceptual development were correlated to Doll’s criteria of quality in teaching and learning.

  • 49.
    Mutvei, Ann
    et al.
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Biology.
    Bollner, Tomas
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Biology.
    Mattsson, Jan-Eric
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Biology.
    Evolution, Teaching and Assessment of Students in Pre-Service Primary School Teacher Education2015In: Conference proceedings. New perspectives in science education, 4th ed., Libreriauniversitaria.it , 2015, -3 p.Conference paper (Refereed)
    Abstract [en]

    This project aims at assessment of learning outcome of teaching evolutionary theory to pre-service primary school teacher students. The quality of the students understanding and use of evolutionary theory after their participation in seminars and lectures was made by analysing written reflections of the students. The texts were primarily written by students to show that the knowledge requirements of the course were accomplished but they were here used to analyse their ability to communicate the content but also to evaluate the depth of their understanding of evolutionary theory. For this assessment two different methods were used aiming at the two different targets. One was focused on the students’ use of evolutionary terminology and to what extent they used the language of an evolutionist. Here, we also analysed whether the students gave accurate explanations or descriptions without using the traditional evolutionary terminology. Thus, mainly the students´ ability in their own writing to present evolutionary reflections in an everyday language was here investigated. This ability may be useful when teaching young students without using a theoretical framework. For the assessment of quality of the students’ own understanding of the theory Doll’s criteria, the four R´s, richness, recursion, relations, and rigor, were used. Richness refers to the depth, the layers of meaning in their texts. Recursion is here referring to the students’ use of making thoughts loop back on themselves and earlier experiences. The use of relations are important when developing thinking in different areas. Here, both the students’ references to relations to other persons as well as to objects, theories, places etc. were recorded. Rigor means in this context to purposely look for different alternatives, relations, connections, new combinations, interpretations and patterns.

    The results may briefly be summarized as follows: 1) most of the students use evolutionary terminology and 2) are fairly good at presenting their thoughts within the theoretical framework in everyday language, although 3) they often show problems in distinguishing processes on molecular, individual, and population levels.

  • 50.
    Mutvei, Ann
    et al.
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Biology.
    Lönn, Mikael
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Biology.
    Mattsson, Jan-Eric
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Biology.
    Observation not only perception but also cognition2016In: Conference proceedings: New perspectives in science education : 5th conference edition : Florence, Italy, 17-18 March 2016, Padova: Libreria Universitaria, 2016, 365-369 p.Conference paper (Refereed)
    Abstract [en]

    According to the Swedish curriculum for primary school it is important in science subjects to develop skills to observe, to describe the observations and to put them into a theoretical framework already starting year 1–3.

    Thus, it may be important for the teacher not only to be accustomed to the methods of observing but also to be an expert on using these observations in order to design teaching situations where these skills may be developed.

    Here we present a study where 25 pre-service primary school teacher students at the beginning of a 20 weeks course established a relation to a study site focused on ecological questions. The task during the first week of that course was to observe and describe two habitats in the field and suggest what abiotic and biotic factors that had shaped the variation focussing at competition as an important ecological factor. In order to connect those ecological aspects with evolutionary aspects, specimen of the common species in the two habitats were collected and brought to the lab where the students constructed phenetic trees based on morphology but also on ecologically relevant properties like roots/no roots, expecting the set-up to awake evolutionary reflection. A main goal with this week was to give the students tools to investigate nature – to observe and describe patterns and to explain them by observing abiotic and biotic variation and evolutionary features and limitations.

    Later during the course we created other, often not obviously similar, situations where the students had the opportunity to use the experiences of this first training week. We used open questions for reflections and examinations in order to get written material to assess the development of the skills.

    We found notable personal development in most students and a greater awareness about the importance of personal cognitive activities in order to create better understanding and ability to use achieved knowledge in different situations.

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