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  • 151.
    Bartoszek, Krzysztof
    et al.
    Mathematical Sciences, Chalmers University of Technology and the University of Gothenburg, Gothenburg, Sweden.
    Pienaar, Jason
    Department of Genetics, University of Pretoria, Pretoria 0002, South Africa.
    Mostad, Petter
    Mathematical Sciences, Chalmers University of Technology and the University of Gothenburg, Gothenburg, Sweden.
    Andersson, Staffan
    Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden.
    Hansen, Thomas F.
    CEES, Department of Biology, University of Oslo, Oslo, Norway.
    A phylogenetic comparative method for studying multivariate adaptation2012In: Journal of Theoretical Biology, ISSN 0022-5193, E-ISSN 1095-8541, Vol. 314, p. 204-215Article in journal (Refereed)
    Abstract [en]

    Phylogenetic comparative methods have been limited in the way they model adaptation. Although some progress has been made, there are still no methods that can fully account for coadaptationbetween traits. Based on Ornstein-Uhlenbeck (OU) models of adaptive evolution, we present a method,with R implementation, in which multiple traits evolve both in response to each other and, as inprevious OU models, to fixed or randomly evolving predictor variables. We present the interpretation ofthe model parameters in terms of evolutionary and optimal regressions enabling the study of allometric and adaptive relationships between traits. To illustrate the method we reanalyze a data set of antlerand body-size evolution in deer (Cervidae).

  • 152.
    Bartoszek, Krzysztof
    et al.
    Department of Mathematics, Uppsala University, Uppsala, Sweden.
    Pietro, Lio'
    Computer Laboratory , University of Cambridge, Cambridge, Un ited Kingdom.
    A novel algorithm to reconstruct phylogenies using gene sequences and expression data2014In: International Proceedings of Chemical, Biological & Environmental Engineering; Environment, Energy and Biotechnology III, 2014, Vol. 70, p. 8-12Conference paper (Refereed)
    Abstract [en]

    Phylogenies based on single loci should be viewed with caution and the best approach for obtaining robust trees is to examine numerous loci across the genome. It often happens that for the same set of species trees derived from different genes are in conflict between each other. There are several methods that combine information from different genes in order to infer the species tree. One novel approach is to use informationfrom different -omics. Here we describe a phylogenetic method based on an Ornstein–Uhlenbeck process that combines sequence and gene expression data. We test our method on genes belonging to the histidine biosynthetic operon. We found that the method provides interesting insights into selection pressures and adaptive hypotheses concerning gene expression levels.

  • 153.
    Bartoszek, Krzysztof
    et al.
    Uppsala universitet, Tillämpad matematik och statistik.
    Sagitov, Serik
    A consistent estimator of the evolutionary rate2015In: Journal of Theoretical Biology, ISSN 0022-5193, E-ISSN 1095-8541, Vol. 371, p. 69-78Article in journal (Refereed)
    Abstract [en]

    We consider a branching particle system where particles reproduce according to the pure birth Yule process with the birth rate 2, conditioned on the observed number of particles to be equal to n. Particles are assumed to move independently on the real line according to the Brownian motion with the local variance sigma(2). In this paper we treat n particles as a sample of related species. The spatial Brownian motion of a particle describes the development of a trait value of interest (e.g. log-body-size). We propose an unbiased estimator 4 of the evolutionary rate rho(2) - sigma(2)/lambda. The estimator R-n(2) is proportional to the sample variance S-n(2) computed from n trait values. We find an approximate formula for the standard error of R-n(2), based on a neat asymptotic relation for the variance of S-n(2). (C) 2015 Elsevier Ltd. All rights reserved.

  • 154.
    Bartoszek, Krzysztof
    et al.
    Department of Mathematics, Uppsala University, Uppsala, Sweden.
    Sagitov, Serik
    Chalmers University of Technology and the Unversity of Gothenburg, Sweden.
    Phylogenetic confidence intervals for the optimal trait value2015In: Journal of Applied Probability, ISSN 0021-9002, E-ISSN 1475-6072, Vol. 52, no 4, p. 1115-1132Article in journal (Refereed)
    Abstract [en]

    We consider a stochastic evolutionary model for a phenotype developing amongst n related species with unknown phylogeny. The unknown tree ismodelled by a Yule process conditioned on n contemporary nodes. The trait value is assumed to evolve along lineages as an Ornstein–Uhlenbeck process. As a result, the trait values of the n species form a sample with dependent observations. We establish three limit theorems for the samplemean corresponding to three domains for the adaptation rate. In the case of fast adaptation, we show that for large n the normalized sample mean isapproximately normally distributed. Using these limit theorems, we develop novel confidence interval formulae for the optimal trait value.

  • 155.
    Baskar, Sushmitha
    et al.
    1Department of Environmental Science and Engineering, Guru Jambheshwar University of Science and Technology, Hisar, Haryana, India.
    Baskar, Ramanathan
    1Department of Environmental Science and Engineering, Guru Jambheshwar University of Science and Technology, Hisar, Haryana, India.
    Routh, Joyanto
    Department of Earth Sciences, IISER-Kolkata, Mohanpur, India / Department of Natural Sciences and Technology, MTM, Örebro University, Örebro, Sweden.
    Biogenic evidences of moonmilk deposition in the Mawmluh cave, Meghalaya, India2011In: Geomicrobiology Journal, ISSN 0149-0451, E-ISSN 1521-0529, Vol. 28, no 3, p. 252-265Article in journal (Refereed)
    Abstract [en]

    Moonmilk, a microcrystalline secondary cave deposit, actively forms on the floor of Krem Mawmluh - a limestone cave in Meghalaya, Northeastern India. Due to the abundance of micrite and calcified microbial filaments, we hypothesize that these deposits form as a result of ongoing microbial interactions. Consistent with this idea, we report electron microscopic and microbiological evidences for the biological origin of moonmilk in Krem Mawmluh. Scanning electron microscopy indicated abundant calcified microbial filaments, needle calcite, fibre calcites (micro-fibre and nano-fibre calcite crystals), biofilm and microbial filaments in the moonmilk. The total viable culturable microbes showed high population densities for microbes in the moonmilk and moonmilk pool waters. In vitro culture experiments, confirmed the capability of many of the isolated strains to precipitate calcite and some of the identified isolates belonged to the Bacillus sp. and Actinomycetes. These results clearly support the biogenic nature of the deposits.

  • 156.
    Baskar, Sushmitha
    et al.
    Indira Gandhi National Open University, India; University of Bergen, Norway.
    Routh, Joyanto
    Linköping University, Department of Thematic Studies, Tema Environmental Change. Linköping University, Faculty of Arts and Sciences.
    Baskar, Ramanathan
    Guru Jambheshwar University of Science and Technology, India.
    Kumar, Abhinav
    Indian Institute Science Educ and Research Kolkata, India.
    Miettinen, Hanna
    VTT Technical Research Centre Finland Ltd, Finland.
    Itaevaara, Merja
    VTT Technical Research Centre Finland Ltd, Finland.
    Evidences for Microbial Precipitation of Calcite in Speleothems from Krem Syndai in Jaintia Hills, Meghalaya, India2016In: Geomicrobiology Journal, ISSN 0149-0451, E-ISSN 1521-0529, Vol. 33, no 10, p. 906-933Article, review/survey (Refereed)
    Abstract [en]

    Speleothems from Krem Syndai, Meghalaya in Northeast India were studied for their microbial diversity using 16S rDNA-based phylogenetic approach and conventional microbiological techniques along with geochemistry, mineralogy and in vitro experiments to understand participation of microorganisms in CaCO3 precipitation. Speleothems imaged by scanning electron microscopy showed round coccoid-like, sporangia-like and spinose calcified structures, numerous broken cocci shells with spotted interiors inside a calcite crystal, honeycomb long reticulate, smooth, flat, twisted, ribbon-like, tubular, beaded, microbe-mineralized filaments and extracellular polymeric substances (EPS). Fourier spectroscopy indicated the presence of various organic compounds. C-13 and O-18 isotopic ratios of speleothems ranged from -4.65 to -7.34 parts per thousand and -3.06 to -6.80 parts per thousand, respectively. Total number of microbial cells using SYBR Gold was high. Fluorescence in situ hybridization (FISH) indicated approximately 3x 10(5) to 5x 10(5) cells g sed(-1) in the speleothems out of which the number of microbes belonging to Eubacteria ranged from 1.8x 10(5) to 3.6x 10(5) cells, g sed(-1). FISH showed approximate to 45% active microbial cells of the total cell number in samples. DNA-based high-throughput amplicon sequencing revealed 19 bacterial phyla in the speleothem. Approximately 42% of the sequences were similar to Proteobacteria (Alphaproteobacteria: 22.4%, Betaproteobacteria: 8.9%, Gammaproteobacteria: 8.6%). Sequences similar to Nitrospiraceae (22.8%) had the highest proportion of sequences belonging to a single family. Bacterial strains isolated from the speleothems raised alkalinity and precipitated calcite in the laboratory cultures which was confirmed by X-ray diffraction (XRD) analyses. These isolates belonged to Bacillus spp., Actinomycetes spp., Streptomyces spp., Pseudomonas spp., Micrococcus spp., Staphylococcus spp., Xanthobacter spp. and Arthrobacter spp. Overall, the results showed unequivocal evidence of bacterial fingerprints during CaCO3 precipitation in the cave.

  • 157.
    Bastviken, David
    et al.
    Linköping University, The Tema Institute, Department of Water and Environmental Studies. Linköping University, Faculty of Arts and Sciences.
    Svensson, Teresia
    Linköping University, The Tema Institute, Department of Water and Environmental Studies. Linköping University, Faculty of Arts and Sciences.
    Karlsson, Susanne
    Linköping University, The Tema Institute, Department of Water and Environmental Studies. Linköping University, Faculty of Arts and Sciences.
    Sandén, Per
    Linköping University, The Tema Institute, Department of Water and Environmental Studies. Linköping University, Faculty of Arts and Sciences.
    Öberg, Gunilla
    IRES, UBC, Canada.
    Temperature sensitivity indicates enzyme controlled chlorination of soil organic matter2009In: Environmental Science and Technology, ISSN 0013-936X, E-ISSN 1520-5851, Vol. 43, no 10, p. 3569-3573Article in journal (Refereed)
    Abstract [en]

    Old assumptions that chloride is inert and that most chlorinated organic matter in soils is anthropogenic have been challenged by findings of naturally formed organochlorines. Such natural chlorination has been recognized for several decades, but there are still very few measurements of chlorination rates or estimates of the quantitative importance of terrestrial chlorine transformations. While much is known about the formation of specific compounds, bulk chlorination remains poorly understood in terms of mechanisms and effects of environmental factors. We quantified bulk chlorination rates in coniferous forest soil using 36Cl-chloride in tracer experiments at different temperatures and with and without molecular oxygen (O2). Chlorination was enhanced by the presence of O2 and had a temperature optimum at 20 °C. Minimum rates were found at high temperatures (50 °C) or under anoxic conditions. The results indicate (1) that most of the chlorination between 4 and 40 °C was biotic and driven by O2 dependent enzymes, and (2) that there is also slower background chlorination occurring under anoxic conditions at 20 °C and under oxic conditions at 50 °C. Hence, while oxic and biotic chlorination clearly dominated, chlorination by other processes including possible abiotic reactions was also detected.

  • 158.
    Bauer, Eva
    et al.
    Technical University of Munich, Germany.
    Schmutzer, Thomas
    Leibniz Institute Plant Genet and Crop Plant Research IPK Gat, Germany.
    Barilar, Ivan
    University of Hohenheim, Germany.
    Mascher, Martin
    Leibniz Institute Plant Genet and Crop Plant Research IPK Gat, Germany.
    Gundlach, Heidrun
    Helmholtz Zentrum Munchen, Germany.
    Martis, Mihaela-Maria
    Linköping University, Department of Clinical and Experimental Medicine, Division of Cell Biology. Linköping University, Faculty of Medicine and Health Sciences. Helmholtz Zentrum Munchen, Germany.
    Twardziok, Sven O.
    Helmholtz Zentrum Munchen, Germany.
    Hackauf, Bernd
    Julius Kuhn Institute, Germany.
    Gordillo, Andres
    KWS LOCHOW GMBH, Germany.
    Wilde, Peer
    KWS LOCHOW GMBH, Germany.
    Schmidt, Malthe
    KWS LOCHOW GMBH, Germany.
    Korzun, Viktor
    KWS LOCHOW GMBH, Germany.
    Mayer, Klaus F. X.
    Helmholtz Zentrum Munchen, Germany.
    Schmid, Karl
    University of Hohenheim, Germany.
    Schoen, Chris-Carolin
    Technical University of Munich, Germany.
    Scholz, Uwe
    Leibniz Institute Plant Genet and Crop Plant Research IPK Gat, Germany.
    Towards a whole-genome sequence for rye (Secale cereale L.)2017In: The Plant Journal, ISSN 0960-7412, E-ISSN 1365-313X, Vol. 89, no 5, p. 853-869Article in journal (Refereed)
    Abstract [en]

    We report on a whole-genome draft sequence of rye (Secale cereale L.). Rye is a diploid Triticeae species closely related to wheat and barley, and an important crop for food and feed in Central and Eastern Europe. Through whole-genome shotgun sequencing of the 7.9-Gbp genome of the winter rye inbred line Lo7 we obtained a de novo assembly represented by 1.29 million scaffolds covering a total length of 2.8 Gbp. Our reference sequence represents nearly the entire low-copy portion of the rye genome. This genome assembly was used to predict 27 784 rye gene models based on homology to sequenced grass genomes. Through resequencing of 10 rye inbred lines and one accession of the wild relative S. vavilovii, we discovered more than 90 million single nucleotide variants and short insertions/deletions in the rye genome. From these variants, we developed the high-density Rye600k genotyping array with 600 843 markers, which enabled anchoring the sequence contigs along a high-density genetic map and establishing a synteny-based virtual gene order. Genotyping data were used to characterize the diversity of rye breeding pools and genetic resources, and to obtain a genome-wide map of selection signals differentiating the divergent gene pools. This rye whole-genome sequence closes a gap in Triticeae genome research, and will be highly valuable for comparative genomics, functional studies and genome-based breeding in rye.

  • 159.
    Bauer, M. K. A.
    et al.
    Department of Internal Medicine I, Medical Clinics, Eberhard-Karls-University, Tübingen.
    Vogt, M.
    Department of Internal Medicine I, Medical Clinics, Eberhard-Karls-University, Tübingen.
    Los, Marek Jan
    Department of Internal Medicine I, Medical Clinics, Eberhard-Karls-University, Tübingen, Germany.
    Siegel, J.
    Department of Virology, Albrecht-Ludwigs-University, Freiburg, Germany.
    Wesselborg, Sebastian
    Department of Internal Medicine I, Medical Clinics, Eberhard-Karls-University, Tübingen, Germany.
    Schulze-Osthoff, Klaus
    Department of Internal Medicine I, Medical Clinics, Eberhard-Karls-University, Tübingen.
    Role of reactive oxygen intermediates in activation-induced CD95 (APO-1/Fas) ligand expression1998In: Journal of Biological Chemistry, ISSN 0021-9258, E-ISSN 1083-351X, Vol. 273, no 14, p. 8048-8055Article in journal (Refereed)
    Abstract [en]

    Activation-induced cell death of T lymphocytes requires the inducible expression of CD95 (APO-1/Fas) ligand, which triggers apoptosis in CD95-bearing target cells by an autocrine or paracrine mechanism. Although execution of the CD95 death pathway is largely independent of reactive oxygen intermediates, activation-induced cell death is blocked by a variety of antioxidants. In the present study, we investigated the involvement of redox processes in the regulation of CD95 ligand (CD95L) expression in Jurkat T cells. We show that various antioxidants potently inhibited the transcriptional activation of CD95L following T cell receptor litigation or stimulation of cells with phorbol ester and ionomycin. Conversely, a prooxidant such as hydrogen peroxide alone was able to increase CD95L expression. As detected by Western blot and cytotoxicity assays, functional expression of CD95L protein was likewise diminished by antioxidants. Inhibition of CD95L expression was associated with a decreased DNA binding activity of nuclear factor (NF)-kappa B, an important redox-controlled transcription factor. Moreover, inhibition of NF-kappa B activity by a transdominant I kappa B mutant attenuated CD95L expression. Our data suggest that, although reactive oxygen intermediates do not act as mediators in the execution phase of CD95-mediated apoptosis, they are involved in the transcriptional regulation of CD95L expression.

  • 160.
    Baumgardt, Magnus
    Linköping University, Department of Clinical and Experimental Medicine, Developmental Biology, IKE. Linköping University, Faculty of Health Sciences.
    Genetic mechanisms behind cell specification in the Drosophila CNS2009Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The human central nervous system (CNS) contains a daunting number of cells and tremendous cellular diversity. A fundamental challenge of developmental neurobiology is to address the questions of how so many different types of neurons and glia can be generated at the precise time and place, making precisely the right connections. Resolving this issue involves dissecting the elaborate genetic networks that act within neurons and glia, as well as in the neural progenitor cells that generates them, to specify their identities.

    My PhD project has involved addressing a number of unresolved issues pertaining to how neural progenitor cells are specified to generate different types of neurons and glial cells in different temporal and spatial domains, and also how these early temporal and spatial cues are integrated to activate late cell fate determinants, which act in post-mitotic neural cells to activate distinct batteries of terminal differentiation genes.

    Analyzing the development of a specific Drosophila melanogaster (Drosophila) CNS stem cell – the neuroblast 5-6 (NB5-6) – we have identified several novel mechanisms of cell fate specification in the Drosophila CNS. We find that, within this lineage, the differential specification of a group of sequentially generated neurons – the Ap cluster neurons – is critically dependent upon the simultaneous triggering of two opposing feed-forward loops (FFLs) within the neuroblast. The first FFL involves cell fate determinants and progresses within the post-mitotic neurons to establish a highly specific combinatorial code of regulators, which activates a distinct battery of terminal differentiation genes. The second loop, which progresses in the neuroblast, involves temporal and sub-temporal genes that together oppose the progression of the first FFL. This leads to the establishment of an alternative code of regulators in late-born Ap cluster neurons, whereby alternative cell fates are specified. Furthermore, we find that the generation and specification of the Ap cluster neurons is modulated along the neuraxis by two different mechanisms. In abdominal segments, Hox genes of the Bithorax cluster integrates with Pbx/Meis factors to instruct NB5-6 to leave the cell cycle before the Ap cluster neurons are generated. In brain segments, Ap cluster neuron equivalents are generated, but improperly specified due to the absence of the proper Hox and temporal code. Additionally, in thoracic segments we find that the specification of the Ap cluster neurons is critically dependent upon the integration of the Hox, Pbx/Meis, and the temporal genes, in the activation of the critical cell fate determinant FFL.

    We speculate that the developmental principles of (i) feed-forward combinatorial coding; (ii) simultaneously triggered yet opposing feed-forward loops; and (iii) integration of different Hox, Pbx/Meis, and temporal factors, at different axial levels to control inter-segmental differences in lineage progression and specification; might be used widely throughout the animal kingdom to generate cell type diversity in the CNS.

    List of papers
    1. Specification of neuronal identities by feedforward combinatorial coding.
    Open this publication in new window or tab >>Specification of neuronal identities by feedforward combinatorial coding.
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    2007 (English)In: PLoS biology, ISSN 1544-9173, E-ISSN 1545-7885, Vol. 5, no 2, p. 0295-0308Article in journal (Refereed) Published
    Abstract [en]

    Neuronal specification is often seen as a multistep process: earlier regulators confer broad neuronal identity and are followed by combinatorial codes specifying neuronal properties unique to specific subtypes. However, it is still unclear whether early regulators are re-deployed in subtype-specific combinatorial codes, and whether early patterning events act to restrict the developmental potential of postmitotic cells. Here, we use the differential peptidergic fate of two lineage-related peptidergic neurons in the Drosophila ventral nerve cord to show how, in a feedforward mechanism, earlier determinants become critical players in later combinatorial codes. Amongst the progeny of neuroblast 5-6 are two peptidergic neurons: one expresses FMRFamide and the other one expresses Nplp1 and the dopamine receptor DopR. We show the HLH gene collier functions at three different levels to progressively restrict neuronal identity in the 5-6 lineage. At the final step, collier is the critical combinatorial factor that differentiates two partially overlapping combinatorial codes that define FMRFamide versus Nplp1/DopR identity. Misexpression experiments reveal that both codes can activate neuropeptide gene expression in vast numbers of neurons. Despite their partially overlapping composition, we find that the codes are remarkably specific, with each code activating only the proper neuropeptide gene. These results indicate that a limited number of regulators may constitute a potent combinatorial code that dictates unique neuronal cell fate, and that such codes show a surprising disregard for many global instructive cues.

    National Category
    Natural Sciences
    Identifiers
    urn:nbn:se:liu:diva-50010 (URN)10.1371/journal.pbio.0050037 (DOI)
    Note
    Original Publication: Magnus Baumgardt, Irene Miguel-Aliaga, Daniel Karlsson, Helen Ekman and Stefan Thor, Specification of neuronal identities by feedforward combinatorial coding., 2007, PLoS biology, (5), 2, e37. http://dx.doi.org/10.1371/journal.pbio.0050037 Licensee: PLoS Available from: 2009-10-11 Created: 2009-10-11 Last updated: 2017-12-12Bibliographically approved
    2. Neuronal Subtype Specification within a Lineage by Opposing Temporal Feed-Forward Loops
    Open this publication in new window or tab >>Neuronal Subtype Specification within a Lineage by Opposing Temporal Feed-Forward Loops
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    2009 (English)In: Cell, ISSN 0092-8674, E-ISSN 1097-4172, Vol. 139, no 5, p. 969-982Article in journal (Refereed) Published
    Abstract [en]

    Neural progenitors generate distinct cell types at different stages, but the mechanisms controlling these temporal transitions are poorly understood. In the Drosophila CNS, a cascade of transcription factors, the ‘temporal gene cascade’, has been identified, that acts to alter progenitor competence over time. However, many CNS lineages display broad temporal windows, and it is unclear how broad windows progress into sub-windows that generate unique cell types. We have addressed this issue in an identifiable Drosophila CNS lineage, and find that a broad castor temporal window is sub-divided by two different feed-forward loops, both of which are triggered by castor itself. The first loop acts to specify a unique cell fate, while the second loop suppresses the first loop, thereby allowing for the generation of alternate cell fates. This mechanism of temporal and ‘sub-temporal’ genes acting in opposing feed-forward loops may be used by many stem cell lineages to generate diversity.

    Place, publisher, year, edition, pages
    Cambridge,MA, USA: Cell Press, 2009
    Keywords
    neural progenitor, temporal transitions, feed-forward loops, combinatorial codes, cell fate specification
    National Category
    Developmental Biology
    Identifiers
    urn:nbn:se:liu:diva-51638 (URN)10.1016/j.cell.2009.10.032 (DOI)000272169400020 ()
    Note

    Original Publication: Magnus Baumgardt, Daniel Karlsson, Javier Terriente, Fernando J. Díaz-Benjumea and Stefan Thor, Neuronal Subtype Specification within a Lineage by Opposing Temporal Feed-Forward Loops, 2009, Cell, (139), 5, 969-982. http://dx.doi.org/10.1016/j.cell.2009.10.032 Copyright: Elsevier Science B.V., Amsterdam. http://www.cell.com/cellpress

    Available from: 2009-11-11 Created: 2009-11-11 Last updated: 2017-12-12Bibliographically approved
    3. Segment-specific Neuronal Sub-type Specification by the Integration of Anteroposterior and Temporal Cues
    Open this publication in new window or tab >>Segment-specific Neuronal Sub-type Specification by the Integration of Anteroposterior and Temporal Cues
    2010 (English)In: PLoS biology, ISSN 1544-9173, E-ISSN 1545-7885, Vol. 8, no 5Article in journal (Refereed) Published
    Abstract [en]

    The generation of distinct neuronal sub-types at different axial levels relies upon both anteroposterior and temporal cues. However, the integration between these cues is poorly understood. In the Drosophila CNS, the segmentally repeated neuroblast 5-6 generates a unique group of neurons, the Apterous cluster, only in thoracic segments. Recent studies have identified elaborate genetic pathways acting to control the generation of these neurons. These insights, combined with novel markers, provide a unique opportunity for addressing how anteroposterior and temporal cues are integrated to generate segment-specific neuronal sub-types. We find that Pbx/Meis, Hox and temporal genes act in three different ways. Posteriorly, Pbx/Meis and posterior Hox genes block lineage progression within an early temporal window, by triggering cell cycle exit. Because Ap neurons are generated late in the thoracic 5-6 lineage, this prevents generation of Ap cluster cells in the abdomen. Thoracically, Pbx/Meis and anterior Hox genes integrate with late temporal genes to specify Ap clusters, via activation of a specific feed-forward loop. In brain segments, ‘Ap cluster cells’ are present but lack both proper Hox and temporal coding. Only by simultaneously altering Hox and temporal gene activity in all segments can Ap clusters be generated throughout the neuroaxis. This study provides the first detailed analysis of an identified neuroblast lineage along the entire neuroaxis, and provides novel insight into how Hox/Pbx/Meis anteroposterior cues are integrated with temporal cues. It reveals a surprisingly restricted yet multifaceted function of the anteroposterior cues with respect to lineage control and cell fate specification.

    Keywords
    anteroposterior patterning, temporal transitions, Hox, Pbx/Meis, cell specification
    National Category
    Developmental Biology
    Identifiers
    urn:nbn:se:liu:diva-51641 (URN)10.1371/journal.pbio.1000368 (DOI)000278759600005 ()
    Note
    Original Publication: Daniel Karlsson, Magnus Baumgardt and Stefan Thor, Segment-specific Neuronal Sub-type Specification by the Integration of Anteroposterior and Temporal Cues, 2010, PLoS biology, (8), 5. http://dx.doi.org/10.1371/journal.pbio.1000368 Licensee: Public Library of Science http://www.plos.org/ Available from: 2009-11-11 Created: 2009-11-11 Last updated: 2017-12-12Bibliographically approved
    4. A genetic cascade involving the genes klumfuss, nab and castor specifies the abdominal leucokinergic neurons in the Drosophila CNS
    Open this publication in new window or tab >>A genetic cascade involving the genes klumfuss, nab and castor specifies the abdominal leucokinergic neurons in the Drosophila CNS
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    (English)Manuscript (preprint) (Other academic)
    Abstract [en]

    The genetic mechanisms underlying the specification of a large number of different cell fates starting from a limited group of progenitor cells are a major focus of investigations of central nervous system development. In Drosophila the identities of the different neuronal progenitor cells, the neuroblasts, are specified by a combination of spatial and temporal factors. But how each neuroblast gives rise to a specific repertoire of cell types via a precise programme is poorly understood. In this report we analyse the specification of a small set of peptidergic cells, the abdominal leucokinergic neurons. We identify the progenitors of these neurons, the temporal window in which they are specified, and the influence of the Notch signalling pathway on their specification. We also show that the products of the genes klumfuss, nab and castor play important roles in their specification via a genetic cascade.

    Keywords
    Drosophila, CNS development, neuronal fate specification, Leucokinin, ABLK
    National Category
    Developmental Biology
    Identifiers
    urn:nbn:se:liu:diva-51644 (URN)
    Available from: 2009-11-11 Created: 2009-11-11 Last updated: 2016-11-30Bibliographically approved
  • 161.
    Baumgardt, Magnus
    et al.
    Linköping University, Department of Clinical and Experimental Medicine, Developmental Biology. Linköping University, Faculty of Health Sciences.
    Karlsson, Daniel
    Linköping University, Department of Clinical and Experimental Medicine, Developmental Biology. Linköping University, Faculty of Health Sciences.
    Terriente, Javier
    Division of Developmental Neuroscience, MRC National Institute for Medical Research, Mill Hill, London NW7 1AA, United Kingdom.
    Díaz-Benjumea, Fernando J.
    Centro de Biología Molecular-Severo Ochoa/C.S.I.C., Universidad Autónoma-Cantoblanco, Madrid 28049, Spain.
    Thor, Stefan
    Linköping University, Department of Clinical and Experimental Medicine, Developmental Biology. Linköping University, Faculty of Health Sciences.
    Neuronal Subtype Specification within a Lineage by Opposing Temporal Feed-Forward Loops2009In: Cell, ISSN 0092-8674, E-ISSN 1097-4172, Vol. 139, no 5, p. 969-982Article in journal (Refereed)
    Abstract [en]

    Neural progenitors generate distinct cell types at different stages, but the mechanisms controlling these temporal transitions are poorly understood. In the Drosophila CNS, a cascade of transcription factors, the ‘temporal gene cascade’, has been identified, that acts to alter progenitor competence over time. However, many CNS lineages display broad temporal windows, and it is unclear how broad windows progress into sub-windows that generate unique cell types. We have addressed this issue in an identifiable Drosophila CNS lineage, and find that a broad castor temporal window is sub-divided by two different feed-forward loops, both of which are triggered by castor itself. The first loop acts to specify a unique cell fate, while the second loop suppresses the first loop, thereby allowing for the generation of alternate cell fates. This mechanism of temporal and ‘sub-temporal’ genes acting in opposing feed-forward loops may be used by many stem cell lineages to generate diversity.

  • 162.
    Baumgartner, Johanna
    et al.
    Linköping University, Department of Physics, Chemistry and Biology. Linköping University, Faculty of Science & Engineering.
    Jönsson, Jan-Ingvar
    Linköping University, Faculty of Medicine and Health Sciences. Linköping University, Department of Clinical and Experimental Medicine, Division of Hematopoiesis and Developmental Biology.
    Jager, Edwin W. H.
    Linköping University, Department of Physics, Chemistry and Biology, Sensor and Actuator Systems. Linköping University, Faculty of Science & Engineering.
    Switchable presentation of cytokines on electroactive polypyrrole surfaces for hematopoietic stem and progenitor cells2018In: Journal of Materials Chemistry B, ISSN 2050-750X, Vol. 6, p. 4665-4675Article in journal (Refereed)
    Abstract [en]

    Hematopoietic stem cells are used in transplantations for patients with hematologic malignancies. Scarce sources require efficient strategies of expansion, including polymeric biomaterials mimicking architectures of bone marrow tissue. Tissue microenvironment and mode of cytokine presentation strongly influence cell fate. Although several cytokines with different functions as soluble or membrane-bound mediators have already been identified, their precise roles have not yet been clarified. A need exists for in vitro systems that mimic the in vivo situation to enable such studies. One way is to establish surfaces mimicking physiological presentation using protein-immobilization onto polymer films. However these films merely provide a static presentation of the immobilized proteins. It would be advantageous to also dynamically change protein presentation and functionality to better reflect the in vivo conditions. The electroactive polymer polypyrrole shows excellent biocompatibility and electrochemically alters its surface properties, becoming an interesting choice for such setups. Here, we present an in vitro system for switchable presentation of membrane-bound cytokines. We use interleukin IL-3, known to affect hematopoiesis, and show that when immobilized on polypyrrole films, IL-3 is bioavailable for the bone marrow-derived FDC-P1 progenitor cell line. Moreover, IL-3 presentation can be successfully altered by changing the redox state of the film, in turn influencing FDC-P1 cell viability. This novel in vitro system provides a valuable tool for stimuli-responsive switchable protein presentation allowing the dissection of relevant mediators in stem and progenitor cell behavior.

  • 163. Baust, H.
    et al.
    Schiessl, I.
    Mueller, B.
    Roedel, F.
    Distel, L.
    Los, Marek Jan
    Manitoba Institute of Cell Biology, Cancer Care Manitoba; Manitoba Institute of Child Health; Department of Biochemistry and Medical Genetics; Department of Human Anatomy and Cell Science, University Manitoba, Winnipeg, Canada, .
    Thomas, S.
    Rolf, S.
    Implications for the role of PKD2 in the radiotherapy of tumours2006In: Strahlentherapie und Onkologie (Print), ISSN 0179-7158, E-ISSN 1439-099X, Vol. 182, p. 81-81Article in journal (Refereed)
  • 164.
    Baust, H.
    et al.
    Department of Radiation Oncology, University of Ulm, D-89081 Ulm, Germany.
    Schoke, A.
    Department of Internal Medicine, University of Ulm, D-89081 Ulm, Germany.
    Brey, A.
    Department of Internal Medicine, University of Ulm, D-89081 Ulm, Germany.
    Gern, U.
    Department of Internal Medicine, University of Ulm, D-89081 Ulm, Germany.
    Los, Marek Jan
    Institute of Experimental Dermatology, University of Muenster, D-48149 Muenster, Germany.
    Schmid, R. M.
    2nd Department of Internal Medicine, University of Munich, D-81675 Munich, Germany.
    Röttinger, E. M.
    Department of Radiation Oncology, University of Ulm, D-89081 Ulm, Germany.
    Seufferlein, T.
    Department of Internal Medicine, University of Ulm, D-89081 Ulm, Germany.
    Evidence for radiosensitizing by gliotoxin in HL-60 cells: implications for a role of NF-kappa B independent mechanisms2003In: Oncogene, ISSN 0950-9232, E-ISSN 1476-5594, Vol. 22, no 54, p. 8786-8796Article in journal (Refereed)
    Abstract [en]

    Radioresistance markedly impairs the efficacy of tumor radiotherapy and may involve antiapoptotic signal transduction pathways that prevent radiation-induced cell death. A common cellular response to genotoxic stress induced by radiation is the activation of the nuclear factor kappa B (NF-kappaB). NF-kappaB activation in turn can lead to an inhibition of radiation-induced apoptotic cell death. Thus, inhibition of NF-kappaB activation is commonly regarded as an important strategy to abolish radioresistance. Among other compounds, the fungal metabolite gliotoxin (GT) has been reported to be a highly selective inhibitor of NF-kappaB activation. Indeed, low doses of GT were sufficient to significantly enhance radiation-induced apoptosis in HL-60 cells. However, this effect turned out to be largely independent of NF-kappaB activation since radiation of HL-60 cells with clinically relevant doses of radiation induced only a marginal increase in NF-kappaB activity, and selective inhibition of NF-kappaB by SN50 did not result in a marked enhancement of GT-induced apoptosis. GT induced activation of JNKs, cytochrome c release from the mitochondria and potently stimulated the caspase cascade inducing cleavage of caspases -9, -8, -7 and -3. Furthermore, cleavage of the antiapoptotic protein X-linked IAP and downregulation of the G2/M-specific IAP-family member survivin were observed during GT-induced apoptosis. Finally, the radiation-induced G2/M arrest was markedly reduced in GT-treated cells most likely due to the rapid induction of apoptosis. Our data demonstrate that various other pathways apart from the NF-kappaB signaling complex can sensitize tumor cells to radiation and propose a novel mechanism for radio-sensitization by GT, the interference with the G2/M checkpoint that is important for repair of radiation-induced DNA damage in p53-deficient tumor cells.

  • 165.
    Baykov, Alexander A.
    et al.
    A. N. Belozersky Institute of Physico-Chemical Biology and School of Chemistry, Moscow State University, Russia.
    Hyytiä, Teppo
    Department of Chemistry, University of Pennsylvania, USA.
    Turkina, Maria V.
    A. N. Belozersky Institute of Physico-Chemical Biology and School of Chemistry, Moscow State University, Russia.
    Efimova, Irina S.
    A. N. Belozersky Institute of Physico-Chemical Biology and School of Chemistry, Moscow State University, Russia.
    Kasho, Vladimir N.
    Center for Ulcer Research and Education, Department of Medicine, University of California, Los Angeles, USA.
    Goldman, Adrian
    Department of Biochemistry University of Turku, Finland; Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland.
    Cooperman, Barry S.
    Department of Chemistry, University of Pennsylvania, USA.
    Lahti, Reijo
    Department of Biochemistry University of Turku, Finland.
    Functional characterization of Escherichia coli inorganic pyrophosphatase in zwitterionic buffers1999In: European Journal of Biochemistry, ISSN 0014-2956, E-ISSN 1432-1033, Vol. 260, no 2, p. 308-317Article in journal (Refereed)
    Abstract [en]

    Catalysis by Escherichia coli inorganic pyrophosphatase (E-PPase) was found to be strongly modulated by Tris and similar aminoalcoholic buffers used in previous studies of this enzyme. By measuring ligand-binding and catalytic properties of E-PPase in zwitterionic buffers, we found that the previous data markedly underestimate Mg2+-binding affinity for two of the three sites present in E-PPase (3.5- to 16-fold) and the rate constant for substrate (dimagnesium pyrophosphate) binding to monomagnesium enzyme (20- to 40-fold). By contrast, Mg2+-binding and substrate conversion in the enzyme-substrate complex are unaffected by buffer. These data indicate that E-PPase requires in total only three Mg2+ ions per active site for best performance, rather than four, as previously believed. As measured by equilibrium dialysis, Mg2+ binds to 2.5 sites per monomer, supporting the notion that one of the tightly binding sites is located at the trimer–trimer interface. Mg2+ binding to the subunit interface site results in increased hexamer stability with only minor consequences for catalytic activity measured in the zwitterionic buffers, whereas Mg2+ binding to this site accelerates substrate binding up to 16-fold in the presence of Tris. Structural considerations favor the notion that the aminoalcohols bind to the E-PPase active site.

  • 166.
    Belka, C.
    et al.
    Department of Radiation Oncology, University of Tuebingen (Germany), Hoppe Seyler Str. 3, 72076 Tuebingen, Germany.
    Marini, P.
    Department of Radiation Oncology, University of Tuebingen (Germany), Hoppe Seyler Str. 3, 72076 Tuebingen, Germany.
    Lepple-Wienhues, A.
    Department of Physiology, University of Tuebingen (Germany), Gmelinstrasse 5, 72076 Tuebingen, Germany.
    Budach, W.
    Department of Radiation Oncology, University of Tuebingen (Germany), Hoppe Seyler Str. 3, 72076 Tuebingen, Germany.
    Jekle, A.
    Department of Physiology, University of Tuebingen (Germany), Gmelinstrasse 5, 72076 Tuebingen, Germany.
    Los, Marek Jan
    Department of Internal Medicine I, University of Tuebingen (Germany), Otfried Müller Str. 10, 72076 Tuebingen, Germany.
    Lang, F.
    Department of Physiology, University of Tuebingen (Germany), Gmelinstrasse 5, 72076 Tuebingen, Germany.
    Schulze-Osthoff, K.
    Department of Internal Medicine I, University of Tuebingen (Germany), Otfried Müller Str. 10, 72076 Tuebingen, Germany.
    Gulbins, E.
    Department of Physiology, University of Tuebingen (Germany), Gmelinstrasse 5, 72076 Tuebingen, Germany.
    Bamberg, M.
    Department of Radiation Oncology, University of Tuebingen (Germany), Hoppe Seyler Str. 3, 72076 Tuebingen, Germany.
    The tyrosine kinase Lck is required for CD95-independent caspase-8 activation and apoptosis in response to ionizing radiation1999In: Oncogene, ISSN 0950-9232, E-ISSN 1476-5594, Vol. 18, no 35, p. 4983-4992Article in journal (Refereed)
    Abstract [en]

    Induction of apoptosis is a hallmark of cytostatic drug and radiation-induced cell death in human lymphocytes and lymphoma cells. However, the mechanisms leading to apoptosis are not well understood. We provide evidence that ionizing radiation induces a rapid activation of caspase-8 (FLICE) followed by apoptosis independently of CD95 ligand/receptor interaction. The radiation induced cleavage pattern of procaspase-8 into mature caspase-8 resembled that following CD95 crosslinking and resulted in cleavage of the proapoptotic substrate BID. Overexpression of dominant-negative caspase-8 interfered with radiation-induced apoptosis, Caspase-8 activation by ionizing radiation was not observed in cells genetically defective for the Src-like tyrosine kinase Lck, Cells lacking Lck also displayed a marked resistance towards apoptosis induction upon ionizing radiation. After retransfection of Lck, caspase-8 activation and the capability to undergo apoptosis in response to ionizing radiation was restored. We conclude that radiation activates caspase-8 via an Lck-controlled pathway independently of CD95 ligand expression, This is a novel signaling event required for radiation induced apoptosis in T lymphoma cells.

  • 167.
    Belogurov, G A
    et al.
    A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia.
    Fabrichniy, I P
    A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia.
    Pohjanjoki, P
    Department of Biochemistry, University of Turku, Turku, Finland.
    Kasho, V N
    Center for Ulcer Research and Education, Department of Medicine, University of California, Los Angeles, California, USA.
    Lehtihuhta, E
    Department of Biochemistry, University of Turku, Turku, Finland.
    Turkina, Maria V
    A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia.
    Cooperman, B S
    Department of Chemistry, University of Pennsylvania, Pennsylvania, USA.
    Goldman, A
    Institute of Biotechnology, University of Helsinki, Helsinki, Finland.
    Baykov, A A
    A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia.
    Lahti, R
    Department of Biochemistry, University of Turku, Turku, Finland.
    Catalytically important ionizations along the reaction pathway of yeast pyrophosphatase2000In: Biochemistry, ISSN 0006-2960, E-ISSN 1520-4995, Vol. 39, no 45, p. 13931-13938Article in journal (Refereed)
    Abstract [en]

    Five catalytic functions of yeast inorganic pyrophosphatase were measured over wide pH ranges: steady-state PP(i) hydrolysis (pH 4. 8-10) and synthesis (6.3-9.3), phosphate-water oxygen exchange (pH 4. 8-9.3), equilibrium formation of enzyme-bound PP(i) (pH 4.8-9.3), and Mg(2+) binding (pH 5.5-9.3). These data confirmed that enzyme-PP(i) intermediate undergoes isomerization in the reaction cycle and allowed estimation of the microscopic rate constant for chemical bond breakage and the macroscopic rate constant for PP(i) release. The isomerization was found to decrease the pK(a) of the essential group in the enzyme-PP(i) intermediate, presumably nucleophilic water, from >7 to 5.85. Protonation of the isomerized enzyme-PP(i) intermediate decelerates PP(i) hydrolysis but accelerates PP(i) release by affecting the back isomerization. The binding of two Mg(2+) ions to free enzyme requires about five basic groups with a mean pK(a) of 6.3. An acidic group with a pK(a) approximately 9 is modulatory in PP(i) hydrolysis and metal ion binding, suggesting that this group maintains overall enzyme structure rather than being directly involved in catalysis.

  • 168.
    Belogurov, Georgiy A
    et al.
    Department of Biochemistry and Food Chemistry, University of Turku, Turku, Finland; A. N. Belozersky Institute of Physico-Chemical Biology and School of Chemistry, Moscow State University, Moscow, Russia.
    Malinen, Anssi M
    Department of Biochemistry and Food Chemistry, University of Turku, Turku, Finland.
    Turkina, Maria V
    A. N. Belozersky Institute of Physico-Chemical Biology and School of Chemistry, Moscow State University, Moscow, Russia.
    Jalonen, Ulla
    Department of Biochemistry and Food Chemistry, University of Turku, Turku, Finland.
    Rytkönen, Kalle
    Department of Biochemistry and Food Chemistry, University of Turku, Turku, Finland.
    Baykov, Alexander A
    A. N. Belozersky Institute of Physico-Chemical Biology and School of Chemistry, Moscow State University, Moscow, Russia.
    Lahti, Reijo
    Department of Biochemistry and Food Chemistry, University of Turku, Turku, Finland.
    Membrane-bound pyrophosphatase of Thermotoga maritima requires sodium for activity2005In: Biochemistry, ISSN 0006-2960, E-ISSN 1520-4995, Vol. 44, no 6, p. 2088-2096Article in journal (Refereed)
    Abstract [en]

    Membrane-bound pyrophosphatase of the hyperthermophilic bacterium Thermotoga maritima(Tm-PPase), a homologue of H(+)-translocating pyrophosphatase, was expressed in Escherichia coli and isolated as inner membrane vesicles. In contrast to all previously studied H(+)-PPases, both native and recombinant Tm-PPases exhibited an absolute requirement for Na(+) but displayed the highest activity in the presence of millimolar levels of both Na(+) and K(+). Detergent-solubilized recombinant Tm-PPase was thermostable and retained the monovalent cation requirements of the membrane-embedded enzyme. Steady-state kinetic analysis of pyrophosphate hydrolysis by the wild-type enzyme suggested that two Na(+) binding sites and one K(+) binding site are involved in enzyme activation. The affinity of the site that binds Na(+) first is increased with increasing K(+) concentration. In contrast, only one Na(+) binding site (K(+)-dependent) and one K(+) binding site were involved in activation of the Asp(703) --> Asn variant. Thus, Asp(703) may form part of the K(+)-independent Na(+) binding site. Unlike all other membrane and soluble PPases, Tm-PPase did not catalyze oxygen exchange between phosphate and water. However, solubilized Tm-PPase exhibited low but measurable PP(i)-synthesizing activity, which also required Na(+) but was inhibited by K(+). These results demonstrate that T. maritima PPase belongs to a previously unknown subfamily of Na(+)-dependent H(+)-PPase homologues and may be an analogue of Na(+),K(+)-ATPase.

  • 169.
    Belogurov, Georgiy A
    et al.
    Department of Biochemistry and Food Chemistry, University of Turku, Turku, Finland; A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia.
    Turkina, Maria V
    A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia.
    Penttinen, Anni
    Department of Biochemistry and Food Chemistry, University of Turku, Turku, Finland.
    Huopalahti, Saila
    Department of Biochemistry and Food Chemistry, University of Turku, Turku, Finland.
    Baykov, Alexander A
    A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia.
    Lahti, Reijo
    Department of Biochemistry and Food Chemistry, University of Turku, Turku, Finland.
    H+-pyrophosphatase of Rhodospirillum rubrum. High yield expression in Escherichia coli and identification of the Cys residues responsible for inactivation my mersalyl2002In: Journal of Biological Chemistry, ISSN 0021-9258, E-ISSN 1083-351X, Vol. 277, no 25Article in journal (Refereed)
    Abstract [en]

    H(+)-translocating pyrophosphatase (H(+)-PPase) of the photosynthetic bacterium Rhodospirillum rubrum was expressed in Escherichia coli C43(DE3) cells. Recombinant H(+)-PPase was observed in inner membrane vesicles, where it catalyzed both PP(i) hydrolysis coupled with H(+) transport into the vesicles and PP(i) synthesis. The hydrolytic activity of H(+)-PPase in E. coli vesicles was eight times greater than that in R. rubrum chromatophores but exhibited similar sensitivity to the H(+)-PPase inhibitor, aminomethylenediphosphonate, and insensitivity to the soluble PPase inhibitor, fluoride. Using this expression system, we showed that substitution of Cys(185), Cys(222), or Cys(573) with aliphatic residues had no effect on the activity of H(+)-PPase but decreased its sensitivity to the sulfhydryl modifying reagent, mersalyl. H(+)-PPase lacking all three Cys residues was completely resistant to the effects of mersalyl. Mg(2+) and MgPP(i) protected Cys(185) and Cys(573) from modification by this agent but not Cys(222). Phylogenetic analyses of 23 nonredundant H(+)-PPase sequences led to classification into two subfamilies. One subfamily invariably contains Cys(222) and includes all known K(+)-independent H(+)-PPases, whereas the other incorporates a conserved Cys(573) but lacks Cys(222) and includes all known K(+)-dependent H(+)-PPases. These data suggest a specific link between the incidence of Cys at positions 222 and 573 and the K(+) dependence of H(+)-PPase.

  • 170.
    Beltéky, Johan
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Eklund, Beatrix
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Jensen, Per
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Gene expression of behaviorally relevant genes in the cerebral hemisphere changes after selection for tameness in Red Junglefowl.2017In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 12, no 5, article id e0177004Article in journal (Refereed)
    Abstract [en]

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

  • 171.
    Bengtsson, Therése
    Linköping University, Department of Physics, Chemistry and Biology. Linköping University.
    Eye preference in human subjects: Consistency across measures and correlation with handedness2010Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    The aim of the present study was to determine the distributions of and correlations between hand preference, visual acuity and eye preference through a series of tests in 50 males 50 females aged between 17 and 39 years. Handedness was determined through the Edinburgh handedness inventory questionnaire. The handedness distribution was: right-handed 90%, left-handed 1 %, and ambidextrous 9%. I found that 30 % had better visual acuity with their right eye, 39 % had better visual acuity with their left eye, and 31% had the same visual acuity with both eyes. 75.2% on average used their right eye in the battery of tests and 24.8% on average used their left eye. There were no statistically significant differences between the sexes or age groups with any of the measures. No correlation was found between eye preference and visual acuity or eye preference and hand preference among all subjects. No statistically significance between the sexes was found.

  • 172.
    Beni, Valerio
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Biosensors and Bioelectronics. Linköping University, Faculty of Science & Engineering.
    Nilsson, D.
    Acreo Swedish ICT AB, Sweden.
    Arven, P.
    Elect Engn J2 Holding AB, Sweden.
    Norberg, P.
    Acreo Swedish ICT AB, Sweden.
    Gustafsson, G.
    Acreo Swedish ICT AB, Sweden.
    Turner, Anthony
    Linköping University, Department of Physics, Chemistry and Biology, Biosensors and Bioelectronics. Linköping University, Faculty of Science & Engineering.
    Printed Electrochemical Instruments for Biosensors2015In: ECS Journal of Solid State Science and Technology, ISSN 2162-8769, E-ISSN 2162-8777, Vol. 4, no 10, p. S3001-S3005Article in journal (Refereed)
    Abstract [en]

    Mobile diagnostics for healthcare, food safety and environmental monitoring, demand a new generation of inexpensive sensing systems suitable for production in high volume. Herein we report on the development of a new disposable electrochemical instrument exploiting the latest advances in printed electronics and printed biosensors. The current system is manufactured under ambient conditions with all interconnections printed; electrochemical measurements and data elaboration are realized by the integration onto the platform of two chips: a MICROCHIP-PIC24F16KA101 and a Texas Instruments LMP91000. A PEDOT.PSS vertical electrochromic display (VECD) is also incorporated into the system to visualize the data. A printed Enfucell 3V manganese dioxide battery was used to deliver the required power. Finally, in order to demonstrate the utility of the system, screen-printed sensors for the detection of glucose were added and the performance of the overall system was evaluated.

  • 173.
    Benito-Sipos, Jonathan
    et al.
    Centro de Biología Molecular-Severo Ochoa, Universidad Autónoma de Madrid-C.S.I.C., Madrid, Spain.
    Estacio-Gómez, Alicia
    Centro de Biología Molecular-Severo Ochoa, Universidad Autónoma de Madrid-C.S.I.C., Madrid, Spain.
    Moris-Sanz, Marta
    Centro de Biología Molecular-Severo Ochoa, Universidad Autónoma de Madrid-C.S.I.C., Madrid, Spain.
    Baumgardt, Magnus
    Linköping University, Department of Clinical and Experimental Medicine, Developmental Biology, IKE. Linköping University, Faculty of Health Sciences.
    Thor, Stefan
    Linköping University, Department of Clinical and Experimental Medicine, Developmental Biology, IKE. Linköping University, Faculty of Health Sciences.
    Díaz-Benjumea, Fernando J.
    Centro de Biología Molecular-Severo Ochoa, Universidad Autónoma de Madrid-C.S.I.C., Madrid, Spain.
    A genetic cascade involving the genes klumfuss, nab and castor specifies the abdominal leucokinergic neurons in the Drosophila CNSManuscript (preprint) (Other academic)
    Abstract [en]

    The genetic mechanisms underlying the specification of a large number of different cell fates starting from a limited group of progenitor cells are a major focus of investigations of central nervous system development. In Drosophila the identities of the different neuronal progenitor cells, the neuroblasts, are specified by a combination of spatial and temporal factors. But how each neuroblast gives rise to a specific repertoire of cell types via a precise programme is poorly understood. In this report we analyse the specification of a small set of peptidergic cells, the abdominal leucokinergic neurons. We identify the progenitors of these neurons, the temporal window in which they are specified, and the influence of the Notch signalling pathway on their specification. We also show that the products of the genes klumfuss, nab and castor play important roles in their specification via a genetic cascade.

  • 174.
    Bennett, Alison E.
    et al.
    Department of Evolution, Ecology, and Organismal Biology, Ohio State University, Columbus, USA.
    Orrell, Peter
    Ecological Sciences, James Hutton Institute, Dundee, UK.
    Malacrinò, Antonino
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Pozo, Maria José
    Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín (CSIC), Granada, Spain.
    Fungal-Mediated Above–Belowground Interactions: The Community Approach, Stability, Evolution, Mechanisms, and Applications2018In: Aboveground–Belowground Community Ecology / [ed] Ohgushi, Takayuki; Wurst, Susanne; Johnson, Scott N., Springer, 2018, p. 85-116Chapter in book (Refereed)
    Abstract [en]

    Our goal within this chapter is to review fungal-mediated above–belowground interactions in which belowground organisms influence aboveground organisms (or vice versa) primarily via a shared host plant, but to also highlight what we feel are the biggest areas for future research within this field: the community approach, stability, evolution, mechanisms, and application of these interactions. First, the community approach examines multiple simultaneously interacting species as communities, an approach that will greatly benefit from the future use of -omics techniques. Examining a greater diversity of interactions (via competition, facilitation, or predation) will likely reveal more varied outcomes that better describe patterns in nature than when individual interactions are considered. Second, we explore the stability of fungal-mediated above–belowground interactions. Given that systems can have multiple stable states influenced by multiple factors, we ask how frequently these interactions occur across stable states. Third, we present three areas in which we expect selection to influence fungal above–belowground interactions: simple (one-way) selective influences of organisms; evolutionary feedbacks and co-evolutionary arms races; and indirect versus direct selective influences. Fourth, we identify mechanisms driving the indirect interactions observed via host plants in fungal-mediated above–belowground interactions and factors influencing their context dependency. Finally, we explore potential applications of these interactions as novel biotechnologies to promote agricultural production, restore natural and degraded habitats, promote ecosystem services, and mitigate against the impacts of climate change.

  • 175.
    Benselfelt, Tobias
    Linköping University, Department of Physics, Chemistry and Biology, Biotechnology. Linköping University, The Institute of Technology.
    Flow Cytometry Sensor System Targeting Escherichia Coli as an Indicator of Faecal Contamination of Water Sources2014Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Poor water quality is a global health concern affecting one billion people around the world. It is important to monitor water sources in order to maintain the quality of our drinking water and to avoid disease outbreaks. Targeting Escherichia coli as a faecal indicator is a widely used procedure, but the current methods are time consuming and not adequate to prevent spreading of faecal influence.

     

    This Master thesis demonstrates the development of a near infrared fluorescence flow cytometer sensor system targeting Escherichia coli, using fluorescently labeled chicken IgY antibodies. The near infrared light was chosen to avoid fluorescence from blue-green algae that are present in the water source.

     

    The hardware was developed with a 785  nm laser line to detect Alexa Fluor 790 labeled antibodies, using a photomultiplier tube or two different CMOS cameras. The antibodies were labeled using a commercial labeling kit, and evaluated using antibody binding assays and the developed hardware.

     

    The IgY antibodies were successfully labeled with Alexa Fluor 790 and the function was maintained after the labeling process. The result demonstrates the principles of the sensor system and how it solved to the problem with fluorescence from blue-green algae. An aperture was used to overcome the suboptimal laser and filter setup, and to increase the sensitivity of the system. However, only a small fraction of the cells could be detected, due to challenges with the focal depth and loss of sensitivity in the photomultiplier tube at near infrared wavelengths. Further development is required to create a working product.

  • 176.
    Bento, Luiz
    et al.
    University of Federal Rio de Janeiro, Brazil.
    Shizue Moriga Masuda, Laura
    University of Federal Rio de Janeiro, Brazil.
    Bittencourt Peixoto, Roberta
    University of Federal Rio de Janeiro, Brazil.
    Enrich Prast, Alex
    Linköping University, Department of Thematic Studies, Tema Environmental Change. Linköping University, Faculty of Arts and Sciences. University of Federal Rio de Janeiro, Brazil; University of Federal Rio de Janeiro, Brazil.
    Regulation in the Metabolism and Community Structure of a Tropical Salt Flat after Rainfall2017In: Journal of Coastal Research, ISSN 0749-0208, E-ISSN 1551-5036, Vol. 33, no 2, p. 304-308Article in journal (Refereed)
    Abstract [en]

    Tropical salt flats typically lack a water column for most of the year, which means that rainfall is probably one of the major factors that regulate benthic microalgae and metabolism in areas subjected to periodic drought. Therefore, the goal of this study was to evaluate the effects of rainfall on the ecological function and community structure of a tropical mangrove salt flat area. This study showed that the highest primary production and respiration fluxes were recorded on the last day of sampling when it rained (-7.6 and 4.7 mmol C-CO2 m(-2) h(-1), respectively). Net primary production increased significantly compared with the dry period that preceded the rain event. The results also suggested that community structure was regulated by rainfall. After the rain event, abundance increased by one order of magnitude, but the diversity and evenness indices decreased. These results demonstrate that rain does have strong regulatory effects on the ecological function and structure of tropical salt flats.

  • 177.
    Berg, Sofia
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology. Linköping University, The Institute of Technology. University of Skovde, Sweden.
    Pimenov, Alexander
    Weierstrass Institute, Germany; National University of Ireland University of Coll Cork, Ireland.
    Palmer, Catherine
    Weierstrass Institute, Germany.
    Emmerson, Mark
    Queens University of Belfast, North Ireland.
    Jonsson, Tomas
    University of Skovde, Sweden; Swedish University of Agriculture Science, Sweden.
    Ecological communities are vulnerable to realistic extinction sequences2015In: Oikos, ISSN 0030-1299, E-ISSN 1600-0706, Vol. 124, no 4, p. 486-496Article in journal (Refereed)
    Abstract [en]

    Loss of species will directly change the structure and potentially the dynamics of ecological communities, which in turn may lead to additional species loss (secondary extinctions) due to direct and/or indirect effects (e.g. loss of resources or altered population dynamics). Furthermore, the vulnerability of food webs to repeated species loss is expected to be affected by food web topology, species interactions, as well as the order in which species go extinct. Species traits such as body size, abundance and connectivity might determine a species vulnerability to extinction and, thus, the order in which species go primarily extinct. Yet, the sequence of primary extinctions, and their effects on the vulnerability of food webs to secondary extinctions, when species abundances are allowed to respond dynamically, has only recently become the focus of attention. Here, we analyse and compare topological and dynamical robustness to secondary extinctions of model food webs, in the face of 34 extinction sequences based on species traits. Although secondary extinctions are frequent in the dynamical approach and rare in the topological approach, topological and dynamical robustness tends to be correlated for many bottom-up directed, but not for top-down directed deletion sequences. Furthermore, removing species based on traits that are strongly positively correlated to the trophic position of species (such as large body size, low abundance, high net effect) is, under the dynamical approach, found to be as destructive as removing primary producers. Such top-down oriented removal of species are often considered to correspond to realistic extinction scenarios, but earlier studies, based on topological approaches, have found such extinction sequences to have only moderate effects on the remaining community. Thus, our result suggests that the structure of ecological communities, and therefore the integrity of important ecosystem processes could be more vulnerable to realistic extinction sequences than previously believed.

  • 178.
    Berg, Åke
    et al.
    Swedish University of Agriculture Science, Sweden.
    Bergman, Karl-Olof
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Wissman, Jorgen
    Swedish University of Agriculture Science, Sweden.
    Zmihorski, Michal
    Swedish University of Agriculture Science, Sweden; Polish Academic Science, Poland.
    Ockinger, Erik
    Swedish University of Agriculture Science, Sweden.
    Power-line corridors as source habitat for butterflies in forest landscapes2016In: Biological Conservation, ISSN 0006-3207, E-ISSN 1873-2917, Vol. 201, p. 320-326Article in journal (Refereed)
    Abstract [en]

    Modern intensified agriculture has decreased farmland heterogeneity, which has led to strong negative effects on farmland biodiversity. However, partly forested landscapes seem to offer many alternative habitats for open habitat species such as butterflies, since modern forestry and development of infrastructure has created several new environments such as forest road verges and power-line corridors. The aim of the present study was to investigate the importance of power-line corridors (PLCs) as butterfly habitats by testing i) if species richness and abundance of butterflies in PLCs are affected by adjacent habitat composition (i.e. comparisons of PLCs with different adjacent habitats), ii) if PLCs act as source habitat through spill-over of individuals into adjacent forest roads and semi-natural pastures and iii) if species composition differs among the investigated habitat types. To investigate this we censured the butterfly fauna in 23 study landscapes in south-central Sweden. We found support for the hypothesis that PLCs may act as source habitats for butterflies in forest roads and pastures, since species richness and abundance were decreasing with increasing distance to PLC from 0 to 500 m. In addition, the species composition in forest roads and pastures close to and far from PLCs was similar, suggesting that this increase was not due to an increase of PLC specialists in the other two habitats. Thus, we have shown that PLCs in themselves are important butterfly habitats independently of adjacent habitat composition (adjacent mature forest, clear cuts or arable land), and they contribute to increased species richness and abundance of butterflies in surrounding areas over 10 times larger than their own width. (C) 2016 Elsevier Ltd. All rights reserved.

  • 179.
    Bergamino, Maurizio
    et al.
    Laureate Institute for Brain Research, Tulsa, OK, USA.
    Farmer, Madison
    Roosevelt University, Department of Industrial and Organizational Psychology, Chicago, IL, USA.
    Yeh, Hung-Wen
    Laureate Institute for Brain Research, Tulsa, OK, USA.
    Paul, Elisabeth
    Linköping University, Department of Clinical and Experimental Medicine, Center for Social and Affective Neuroscience. Linköping University, Faculty of Medicine and Health Sciences.
    Hamilton, Paul J.
    Linköping University, Department of Clinical and Experimental Medicine, Center for Social and Affective Neuroscience. Linköping University, Faculty of Medicine and Health Sciences.
    Statistical differences in the white matter tracts in subjects with depression by using different skeletonized voxel-wise analysis approaches and DTI fitting procedures2017In: Brain Research, ISSN 0006-8993, E-ISSN 1872-6240, Vol. 1669, p. 131-140Article in journal (Refereed)
    Abstract [en]

    Major depressive disorder (MDD) is one of the most significant contributors to the global burden of illness. Diffusion tensor imaging (DTI) is a procedure that has been used in several studies to characterize abnormalities in white matter (WM) microstructural integrity in MDD. These studies, however, have provided divergent findings, potentially due to the large variety of methodological alternatives available in conducting DTI research. In order to determine the importance of different approaches to coregistration of DTI-derived metrics to a standard space, we compared results from two different skeletonized voxel-wise analysis approaches: the standard TBBS pipeline and the Advanced Normalization Tools (ANTs) approach incorporating a symmetric image normalization (SyN) algorithm and a group-wise template (ANTs TBSS). We also assessed effects of applying twelve different fitting procedures for the diffusion tensor. For our dataset, lower fractional anisotropy (FA) and axial diffusivity (AD) in depressed subjects compared with healthy controls were found for both methods and for all fitting procedures. No group differences were found for radial and mean diffusivity indices. Importantly, for the AD metric, the normalization methods and fitting procedures showed reliable differences, both in the volume and in the number of significant between-groups difference clusters detected. Additionally, a significant voxel-based correlation, in the left inferior fronto-occipital fasciculus, between AD and self-reported stress was found only for one of the normalization procedure (ANTs TBSS). In conclusion, the sensitivity to detect group-level effects on DTI metrics might depend on the DTI normalization and/or tensor fitting procedures used.

  • 180.
    Bergenholm, Linnéa
    Linköping University, Department of Biomedical Engineering. Linköping University, Faculty of Health Sciences.
    Modeling as a Tool to Support Self-Management of Type 1 Diabetes2013Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Type 1 diabetes (T1D) is an auto-immune disease characterized by insulin-deficiency. Insulin is a metabolic hormone that is involved in lowering blood glucose (BG) levels in order to control BG level to a tight range. In T1D this glycemic control is lost, causing chronic hyperglycemia (excess glucose in blood stream). Chronic hyperglycemia damages vital tissues. Therefore, glycemic control must be restored.

    A common therapy for restoring glycemic control is intensive insulin therapy, where the missing insulin is replaced with regular insulin injections. When dosing this compensatory insulin many factors that affect glucose metabolism must be considered. Linkura is a company that has developed tools for monitoring the most important factors, which are meals and exercise. In the Linkura meal and exercise tools, the nutrition content in meals and the calorie consumption during exercise are estimated. Another tool designed to aid control of BG is the bolus calculator. Bolus calculators use input of BG level, carbohydrate intake, and insulin history to estimate insulin need. The accuracy of these insulin bolus calculations suffer from two problems. First, errors occur when users inaccurately estimate the carbohydrate content in meals. Second, exercise is not included in bolus calculations. To reduce these problems, it was suggested that the Linkura web tools could be utilized in combination with a bolus calculator.

    For this purpose, a bolus calculator was developed. The bolus calculator was based on existing models that utilize clinical parameters to relate changes in BG levels to meals, insulin, and exercise stimulations. The bolus calculator was evaluated using data collected from Linkura's web tools. The collected data showed some inconsistencies which cannot be explained by any model.  The performance of the bolus calculator in predicting BG levels using general equations to derive the clinical parameters was inadequate. Performance was increased by adopting an update-algorithm where the clinical parameters were updated daily using previous data. Still, better model performance is prefered for use in a bolus calculator.  

    The results show potential in developing bolus calculator tools combined with the Linkura tools. For such bolus calculator, further evaluation on modeling long-term exercise and additional safety features minimizing risk of hypoglycemia are required.

  • 181.
    Bergfur, Jenny
    Linköping University, The Tema Institute, Department of Water and Environmental Studies. Linköping University, Faculty of Arts and Sciences.
    Temporal variation in carbon and nitrogen isotope ratios of aquatic biota in two contrasting boreal streams2013In: Fundamental and Applied Limnology, ISSN 1863-9135, Vol. 182, no 3, p. 205-218Article in journal (Refereed)
    Abstract [en]

    Natural abundant isotopes of carbon and nitrogen are frequently used to elucidate food webs and trace energy flows in aquatic ecosystems. Seasonal events such as leaf fall and algal blooms can influence temporal patterns and hence also affect interpretations of isotope data. This study examined such patterns in two contrasting streams in Sweden: Vadsbacken, which is heavily impacted by agriculture and has high nitrogen levels, and Pinnarpsbacken, which has a primarily forested catchment and lower nitrogen levels. Different organic compartments (e.g., detritus, biofilm, and invertebrates) were sampled in September, November, April, and June. Effects of sampling date on isotope signatures of leaf litter (delta N-15: p = 0.0001, delta C-13: p = 0.03), seston (delta N-15: p = 0.001, delta C-13: p = 0.001), FPOM (delta N-15: p = 0.03, delta C-13: p = 0.003), wood (delta C-13: p = 0.05) and invertebrates (delta N-15: p = 0.04) were found. However, there were site-specific temporal patterns in isotope signatures, probably reflecting disparate origins of allochthonous material related to the differences in catchment land use. Mixing models revealed no changes in resource partitioning that could be attributed to the above-mentioned seasonal events. The site-specific patterns recorded here indicate that generalisation regarding ecosystems with different perturbations should be done with caution.

  • 182.
    Bergfur, Jenny
    et al.
    Linköping University, The Tema Institute, Department of Water and Environmental Studies. Linköping University, Faculty of Arts and Sciences.
    Friberg, Nikolai
    Department of Bioscience, Aarhus University, Silkeborg, Denmark.
    Trade-offs between fungal and bacterial respiration along gradients in temperature, nutrients and substrata: Experiments with stream derived microbial communities2012In: Fungal ecology, ISSN 1754-5048, E-ISSN 1878-0083, Vol. 5, no 1, p. 46-52Article in journal (Refereed)
    Abstract [en]

    We examined the effects of temperature, nutrients and substrata on microbial respiration rates. Leaves of alder and oak were incubated in a natural stream. Leaf discs were incubated in antibiotics to manipulate the ratio of fungi to bacteria with three treatments: antifungal, antibacterial, and combined antifungal and antibacterial treatment in addition to controls. Discs were subsequently incubated in different nutrient set-ups and temperature regimes. Significant effects of temperature, nutrients, microbial treatment and leaf type on respiration rates were found. However, temperature did not significantly add to the effect of eutrophication on microbial respiration rates. A stronger effect of temperature on fungal mediated respiration than on bacterial mediated respiration was found. In streams where leaf litter constitutes the main energy source, fungi constitute the dominant microbial decomposer. Our results indicate that increased temperature due to global warming might have serious implications for ecosystem functioning when leaf litter constitutes the main energy source.

  • 183.
    Bergfur, Jenny
    et al.
    Department of Aquatic Sciences and Assessment, Swedish Agricultural University, Uppsala, Sweden; The Macaulay Land Use Research Institute, Craigiebuckler, Aberdeen, UK .
    Johnson, Richard K
    Department of Aquatic Sciences and Assessment, Swedish Agricultural University, Uppsala, Sweden.
    Sandin, Leonard
    Department of Aquatic Sciences and Assessment, Swedish Agricultural University, Uppsala, Sweden.
    Goedkoop, Willem
    Department of Aquatic Sciences and Assessment, Swedish Agricultural University, Uppsala, Sweden.
    Effects of nutrient enrichment on C and N stable isotope ratios of invertebrates, fish and their food resources in boreal streams2009In: Hydrobiologia, ISSN 0018-8158, E-ISSN 1573-5117, Vol. 628, p. 67-79Article in journal (Refereed)
    Abstract [en]

    Carbon and nitrogen stable isotopes are frequently used to study energy sources and food web structure in ecosystems, and more recently, to study the effects of anthropogenic stress on aquatic ecosystems. We investigated the effect of nutrient enrichment on  d13C and d15N in fine (FPOM), coarse (CPOM) particulate organic matter, periphyton, invertebrates and fish in nine boreal streams in south-central Sweden. In addition, we analysed the diet of benthic consumers using stable isotope data. Increases in d15N of periphyton (R2 = 0.88), CPOM (0.78), invertebrates (0.92) and fish (0.89) were related to nutrient enrichment. In contrast, d13C signatures did not change along the nutrient gradient. Our results show that d15N has potential as a sensitive indicator of nutrient enrichment in boreal streams. Carbon and nitrogen isotopes failed to elucidate putative diets of selected aquatic consumers. Indeed, comparison of low- and high-impact sites showed that d13C of many consumers were found outside the ranges of basal resource d13C. Moreover, ranges of basal resource d13C and d15N overlapped at both low and high sites, making discrimination between the importance of allochthonous and autochthonous production difficult. Our findings show that a fractionation rate of 3.4% is not always be appropriate to assess trophic interactions, suggesting that more studies are needed on fractionation rates along gradients of impairment.

  • 184.
    Berggren, Jenny
    Linköping University, Department of Physics, Chemistry and Biology.
    Histonmodifieringar och alternativ splicing2011Independent thesis Basic level (degree of Bachelor), 10,5 credits / 16 HE creditsStudent thesis
    Abstract [en]

    Alternative splicing of pre-mRNA generates protein diversity. Histone modifications are connected to the regulation of alternative splicing through adaptor systems that transfers the epigenetic information directly to the splicing factors. The cis- acting RNA elements on the exons and introns together with the trans- regulating splicing factors are therefore directly affected of specific histone modifications. An integrated model over several DNA process mechanisms is suggested. This complex model explains the interactions of the different parts and how they affect each other. Chromatin remodelers are required to obtain euchromatin. Nucleosome positioning at exon rich regions with a specific modification pattern point out where the exons are, and this enable the RNA polymerase II to find and bind to the DNA. It’s CTD domain recruits both splicing- and modifications factors. The transcription rate is also affected of the nucleosome positioning and that in turn affects the recruitment of the components of the spliceosomen, other trans- acting regulators and even the formation of the secondary structure of the pre-mRNA transcript. Chromatin- adaptor complex reads specific histone modifications and transfers this information to the splicing apparatus. All this creates the possibility to regulate important cell- and tissue specific alternative splicing patterns. The integrated model makes the complex processes more clearer when all these integrates with each other and the cis- acting regulating elements on the pre-mRNA transcript.

  • 185.
    Bergkvist, Liza
    Linköping University, Department of Physics, Chemistry and Biology, Chemistry. Linköping University, Faculty of Science & Engineering.
    Amyloid-β and lysozyme proteotoxicity in Drosophila: Beneficial effects of lysozyme and serum amyloid P component in models of Alzheimer’s disease and lysozyme amyloidosis2017Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    In the work presented this thesis, two different conditions that are classified as protein misfolding diseases: Alzheimer's disease and lysozyme amyloidosis and proteins that could have a beneficial effect in these diseases, have been studied using Drosophila melanogaster, commonly known as the fruit fly. The fruit fly has been used for over 100 years to study and better understand fundamental biological processes. Although the fruit fly, unlike humans, is an invertebrate, many of its central biological mechanisms are very similar to ours. The first transgenic flies were designed in the early 1980s, and since then, the fruit fly has been one of the most widely used model organisms in studies on the effects of over-expressed human proteins in a biological system; one can regard the fly as a living, biological test tube. For  most proteins, it is necessary that they fold into a three-dimensional structure to function properly. But sometimes the folding goes wrong; this may be due to mutations that make the protein unstable and subject to misfolding. A misfolded protein molecule can then aggregate with other misfolded proteins. In Alzheimer's disease, which is the most common form of dementia, protein aggregates are present in the brains of patients. These aggregates are composed of the amyloid-β (Aβ) peptide, a small peptide of around 42 amino acids which is cleaved from the larger, membrane-bound, protein AβPP by two different enzymes, BACE1 and γ-secretase. In the first part of this thesis, two different fly models for Alzheimer’s disease were used: the Aβ fly model, which directly expresses the Aβ peptide, and the AβPP-BACE1 fly model, in which all the components necessary to produce the Aβ peptide in the fly are expressed in the fly central nervous system (CNS). The two different fly models were compared and the results show that a significantly smaller amount of the Aβ peptide is needed to achieve the same, or an even greater, toxic effect in the AβPP-BACE1 model compared to the Aβ model. In the second part of the thesis, these two fly models for Alzheimer’s disease were again used, but now to investigate whether lysozyme, a protein involved in our innate immune system, can counteract the toxic effect of Aβ generated in the fly models. And indeed, lysozyme is able to save the flies from Aβ-induced toxicity. Aβ and lysozyme were found to interact with each other in vivo. The second misfolding disease studied in this thesis is lysozyme amyloidosis. It is a rare, dominantly inherited amyloid disease in which mutant variants of lysozyme give rise to aggregates, weighing up to several kilograms, that accumulate around the kidneys and liver, eventually leading to organ failure. In the third part of this thesis, a fly model for lysozyme amyloidosis was used to study the effect of co-expressing the serum amyloid P component (SAP), a protein that is part of all protein aggregates found within this disease class. SAP is able to rescue the toxicity induced by expressing the mutant variant of lysozyme, F57I, in the fly's CNS. To further investigate how SAP was able to do this, double-expressing lysozyme flies, which exhibit stronger disease phenotypes than those of the single-expressing lysozyme flies previously studied, were used in the fourth part of this thesis. SAP was observed to reduce F57I toxicity and promote F57I to form aggregates with more distinct amyloid characteristics. In conclusion, the work included in this thesis demonstrates that: i) Aβ generated from AβPP processing in the fly CNS results in higher proteotoxicity compared with direct expression of Aβ from the transgene, ii) lysozyme can prevent Aβ proteotoxicity in Drosophila and could thus be a potential therapeutic molecule to treat Alzheimer’s disease and iii) in a Drosophila model of lysozyme amyloidosis, SAP can prevent toxicity from the disease-associated lysozyme variant F57I and promote formation of aggregated lysozyme morphotypes with amyloid properties; this is important to take into account when a reduced level of SAP is considered as a treatment strategy for lysozyme amyloidosis.

    List of papers
    1. A beta PP processing results in greater toxicity per amount of A beta(1-42) than individually expressed and secreted A beta(1-42) in Drosophila melanogaster
    Open this publication in new window or tab >>A beta PP processing results in greater toxicity per amount of A beta(1-42) than individually expressed and secreted A beta(1-42) in Drosophila melanogaster
    2016 (English)In: BIOLOGY OPEN, ISSN 2046-6390, Vol. 5, no 8, p. 1030-1039Article in journal (Refereed) Published
    Abstract [en]

    The aggregation of the amyloid-beta (A beta) peptide into fibrillar deposits has long been considered the key neuropathological hallmark of Alzheimers disease (AD). A beta peptides are generated from proteolytic processing of the transmembrane A beta precursor protein (A beta PP) via sequential proteolysis through the beta-secretase activity of beta-site A beta PP-cleaving enzyme (BACE1) and by the intramembranous enzyme gamma-secretase. For over a decade, Drosophila melanogaster has been used as a model organism to study AD, and two different approaches have been developed to investigate the toxicity caused by AD-associated gene products in vivo. In one model, the A beta peptide is directly over-expressed fused to a signal peptide, allowing secretion of the peptide into the extracellular space. In the other model, human A beta PP is co-expressed with human BACE1, resulting in production of the A beta peptide through the processing of A beta PP by BACE1 and by endogenous fly gamma-secretase. Here, we performed a parallel study of flies that expressed the A beta(1-42) peptide alone or that co-expressed A beta PP and BACE1. Toxic effects (assessed by eye phenotype, longevity and locomotor assays) and levels of the A beta(1-42), A beta(1-40) and A beta(1-38) peptides were examined. Our data reveal that the toxic effect per amount of detected A beta(1-42) peptide was higher in the flies co-expressing A beta PP and BACE1 than in the A beta(1-42)-expressing flies, and that the co-existence of A beta(1-42) and A beta(1-40) in the flies co-expressing A beta PP and BACE1 could be of significant importance to the neurotoxic effect detected in these flies. Thus, the toxicity detected in these two fly models seems to have different modes of action and is highly dependent on how and where the peptide is generated rather than on the actual level of the A beta(1-42) peptide in the flies. This is important knowledge that needs to be taken into consideration when using Drosophila models to investigate disease mechanisms or therapeutic strategies in AD research.

    Place, publisher, year, edition, pages
    COMPANY OF BIOLOGISTS LTD, 2016
    Keywords
    Alzheimers disease; Amyloid-beta (A beta); A beta PP processing; Drosophila melanogaster; Proteotoxicity
    National Category
    Medical Biotechnology (with a focus on Cell Biology (including Stem Cell Biology), Molecular Biology, Microbiology, Biochemistry or Biopharmacy)
    Identifiers
    urn:nbn:se:liu:diva-131685 (URN)10.1242/bio.017194 (DOI)000382304400003 ()27387531 (PubMedID)
    Note

    Funding Agencies|Torsten Soderbergs Stiftelse [M26/11]; Alzheimer Foundation [03-069]; Dementia Foundation; Ahlen Foundation; Gamla Tjanarinnor [2015-00187]

    Available from: 2016-10-03 Created: 2016-09-30 Last updated: 2017-05-16
    2. Beneficial effects of increased lysozyme levels in Alzheimer’s disease modelled in Drosophila melanogaster
    Open this publication in new window or tab >>Beneficial effects of increased lysozyme levels in Alzheimer’s disease modelled in Drosophila melanogaster
    Show others...
    2016 (English)In: The FEBS Journal, ISSN 1742-464X, E-ISSN 1742-4658, Vol. 283, no 19, p. 3508-3522Article in journal (Refereed) Published
    Abstract [en]

    Genetic polymorphisms of immune genes that associate with higher risk to develop Alzheimer’s disease (AD) have led to an increased research interest on the involvement of the immune system in AD pathogenesis. A link between amyloid pathology and immune gene expression was suggested in a genome-wide gene expression study of transgenic amyloid mouse models. In this study, the gene expression of lysozyme, a major player in the innate immune system, was found to be increased in a comparable pattern as the amyloid pathology developed in transgenic mouse models of AD. A similar pattern was seen at protein levels of lysozyme in human AD brain and CSF, but this lysozyme pattern was not seen in a tau transgenic mouse model. Lysozyme was demonstrated to be beneficial for different Drosophila melanogaster models of AD. In flies that expressed Aβ1-42 or AβPP together with BACE1 in the eyes, the rough eye phenotype indicative of toxicity was completely rescued by coexpression of lysozyme. In Drosophila flies bearing the Aβ1-42 variant with the Arctic gene mutation, lysozyme increased the fly survival and decreased locomotor dysfunction dose dependently. An interaction between lysozyme and Aβ1-42 in the Drosophila eye was discovered. We propose that the increased levels of lysozyme, seen in mouse models of AD and in human AD cases, were triggered by Aβ1-42 and caused a beneficial effect by binding of lysozyme to toxic species of Aβ1-42, which prevented these from exerting their toxic effects. These results emphasize the possibility of lysozyme as biomarker and therapeutic target for AD.

    Place, publisher, year, edition, pages
    John Wiley & Sons, 2016
    Keywords
    Alzheimer’s disease, amyloid-β, Drosophila, lysozyme
    National Category
    Genetics Medical Genetics Developmental Biology Bioinformatics and Systems Biology Medical Biotechnology (with a focus on Cell Biology (including Stem Cell Biology), Molecular Biology, Microbiology, Biochemistry or Biopharmacy)
    Identifiers
    urn:nbn:se:liu:diva-131796 (URN)10.1111/febs.13830 (DOI)000386033700001 ()27562772 (PubMedID)
    Available from: 2016-10-07 Created: 2016-10-07 Last updated: 2018-03-20Bibliographically approved
    3. Serum Amyloid P Component Ameliorates Neurological Damage Caused by Expressing a Lysozyme Variant in the Central Nervous System of Drosophila melanogaster
    Open this publication in new window or tab >>Serum Amyloid P Component Ameliorates Neurological Damage Caused by Expressing a Lysozyme Variant in the Central Nervous System of Drosophila melanogaster
    2016 (English)In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 11, no 7, p. e0159294-Article in journal (Refereed) Published
    Abstract [en]

    Lysozyme amyloidosis is a hereditary disease in which mutations in the gene coding for lysozyme leads to misfolding and consequently accumulation of amyloid material. To improve understanding of the processes involved we expressed human wild type (WT) lysozyme and the disease-associated variant F57I in the central nervous system (CNS) of a Drosophila melanogaster model of lysozyme amyloidosis, with and without co-expression of serum amyloid p component (SAP). SAP is known to be a universal constituent of amyloid deposits and to associate with lysozyme fibrils. There are clear indications that SAP may play an important role in lysozyme amyloidosis, which requires further elucidation. We found that flies expressing the amyloidogenic variant F57I in the CNS have a shorter lifespan than flies expressing WT lysozyme. We also identified apoptotic cells in the brains of F57I flies demonstrating that the flies neurological functions are impaired when F57I is expressed in the nerve cells. However, co-expression of SAP in the CNS prevented cell death and restored the F57I flies lifespan. Thus, SAP has the apparent ability to protect nerve cells from damage caused by F57I. Furthermore, it was found that co-expression of SAP prevented accumulation of insoluble forms of lysozyme in both WT- and F57I-expressing flies. Our findings suggest that the F57I mutation affects the aggregation process of lysozyme resulting in the formation of cytotoxic species and that SAP is able to prevent cell death in the F57I flies by preventing accumulation of toxic F57I structures.

    Place, publisher, year, edition, pages
    PUBLIC LIBRARY SCIENCE, 2016
    National Category
    Developmental Biology
    Identifiers
    urn:nbn:se:liu:diva-131183 (URN)10.1371/journal.pone.0159294 (DOI)000380169300043 ()27428539 (PubMedID)
    Note

    Funding Agencies|Swedish Research Council; Soderberg foundation [M26/11]; Linkoping University Neurobiology Center

    Available from: 2016-09-19 Created: 2016-09-12 Last updated: 2017-11-21
  • 186.
    Berglund, Hilda-Linn
    Linköping University, Department of Physics, Chemistry and Biology.
    Effects of flower abundance and colour on pan-trap catches2016Independent thesis Advanced level (degree of Master (Two Years)), 40 credits / 60 HE creditsStudent thesis
    Abstract [sv]

    Pollinating insects are important for many plants and for the human population. To be able to monitor pollinators and assess improvements made for them, it is important to get information about pollinator population changes. Therefore, it is essential that the methods used to collect data are accurate (i.e. that they represent the pollinator fauna). One commonly used method is pan-traps, but this method is suggested to be affected by the abundance of surrounding flowers. The results in the present study showed that catches in pan-traps can be affected by flower cover and the colour of the flowers, depending on which colours are preferred by the insects. The effects differed when looking at a larger scale (2-6 ha) and a smaller scale (25 m2) around the pan-traps. When comparing cover of flowers with catches in pan-traps in the small scale there were some results that showed linear positive correlations (expected), but also, negative linear and quadratic correlations. In contrast, in the large scale there were no significant positive linear correlations. When comparing catches in hand-net and pan-traps, only in one out of six taxonomical groups there were a correlation. The results in this study show that catches in pan-traps can be misleading if catches are done to survey pollinator population fauna and the cover of flowers is not considered.

  • 187.
    Bergman, Karl-Olof
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Daniel Ferreira, Juliana Daniel
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering. Swedish Univ Agr Sci, Sweden.
    Milberg, Per
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Ockinger, Erik
    Swedish Univ Agr Sci, Sweden.
    Westerberg, Lars
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Butterflies in Swedish grasslands benefit from forest and respond to landscape composition at different spatial scales2018In: Landscape Ecology, ISSN 0921-2973, E-ISSN 1572-9761, Vol. 33, no 12, p. 2189-2204Article in journal (Refereed)
    Abstract [en]

    ContextLoss and fragmentation of semi-natural grasslands has critically affected many butterfly species in Europe. Habitat area and isolation can have strong effects on the local biodiversity but species may also be strongly affected by the surrounding matrix.ObjectivesWe explored how different land cover types in the landscape explained the occurrence of butterfly species in semi-natural grasslands.MethodsUsing data from 476 semi-natural grasslands in Sweden, we analysed the effect of matrix composition on species richness and occurrence. Additionally, we analysed at which spatial scales butterflies responded to matrix types (forests, semi-natural grasslands, arable land and water).ResultsForest cover showed the strongest positive effect on species richness, followed by semi-natural grasslands. Forest also had a positive effect on red-listed species at local scales. Responses to matrix composition were highly species-specific. The majority of the 30most common species showed strong positive responses to the amount of forest cover within 200-500m. There was a smaller group of species showing a positive response to arable land cover within 500-2000m. Thirteen species showed positive responses to the amount of semi-natural grasslands, generally at larger scales (10-30km).ConclusionsOur study showed that surrounding forest is beneficial for many grassland butterfly species and that forests might mitigate the negative effects of habitat loss caused by agricultural intensification. Also, semi-natural grasslands were an important factor for species richness at larger spatial scales, indicating that a landscape consisting mainly of supporting habitats (i.e. forests) are insufficient to sustain a rich butterfly fauna.

  • 188.
    Bergman Laurila, Jonas
    Linköping University. Linköping University, Department of Computer and Information Science.
    Ontology Slice Generation and Alignment for Enhanced Life Science Literature Search2009Independent thesis Advanced level (professional degree), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Query composition is an often complicated and cumbersome task for persons performing a literature search. This thesis is part of a project which aims to present possible queries to the user in form of natural language expressions. The thesis presents methods of ontology slice generation. Slices are parts of ontologies connecting two concepts along all possible paths between them. Those slices hence represent all relevant queries connecting the concepts and the paths can in a later step be translated into natural language expressions. Methods of slice alignment, connecting slices that originate from different ontologies, are also presented. The thesis concludes with some example scenarios and comparisons to related work.

  • 189.
    Bergner, Adam
    Linköping University, Department of Physics, Chemistry and Biology. Linköping University, The Institute of Technology.
    Studier av habitatval och revirstrukturer hos vassångare (Locustella luscinioides) i Tåkern2012Independent thesis Basic level (degree of Bachelor), 10,5 credits / 16 HE creditsStudent thesis
    Abstract [en]

    The Savi’s Warbler (Locustella luscinioides) is a recently established bird species in a few reedy shallow lakes of southern Sweden and has only been found nesting for the last twenty years. Little is known about the species' habitat preferences, breeding biology and demands for specific territory structures at breeding sites in Sweden. Knowledge of a newly established species’ habitat requirements is essential to maintain a viable population and design action plans. This study, the first of its kind in Sweden, examined the vegetation structures in occupied territories of Savi’s Warblers at Lake Tåkern, the country's stronghold for the species. The species was found to be associated with the outer edge zones and fragmented areas of reed (Phragmites australis). Occupied territories differed from randomly chosen unoccupied (control) territories by having a thicker layer of reed litter, and on average more bushes of Willow (Salix spp.) present. Reed density and reed height did not differ from areas that lacked Savi’s Warblers. Territorial and displaying males were concentrated in two edge areas with a mosaic of reed islets where the territories remained relatively close together.

  • 190.
    Bergner, Adam
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, The Institute of Technology.
    Avci, Mustafa
    Faculty of Forestry, Süleyman Demirel University, Isparta, Turkey.
    Eryigit, Hasan
    Isparta Province Forest District Directorate, Isparta, Turkey.
    Jansson, Nicklas
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, The Institute of Technology.
    Niklasson, Mats
    Southern Swedish Forest Research Centre, SLU, Alnarp, Sweden.
    Westerberg, Lars
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, The Institute of Technology.
    Milberg, Per
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, The Institute of Technology.
    Influences of forest type and habitat structure on bird assemblagesof oak (Quercus spp.) and pine (Pinus spp.) stands in southwesternTurkey2015In: Forest Ecology and Management, ISSN 0378-1127, E-ISSN 1872-7042, Vol. 336, p. 137-147Article in journal (Refereed)
    Abstract [en]

    The Mediterranean basin exhibits a multitude of forest habitats affected by former and current exploitation and management. Recent afforestation programs have resulted in an increase in the proportion of coniferous trees, while oak stands, formerly utilized for coppicing and grazing, are abandoned or converted into coniferous plantations. The loss of oak stands might negatively affect birds dependent upon broadleaved forests. Studies confirming or rejecting that statement are scarce, particularly in the eastern part of the region. Using a study area in southwestern Turkey we applied a guild-based approach to investigate how pine and oak stands across a chronosequence differ in their capacity to support forest bird assemblages. Variables describing the vegetation were sampled to characterize the stands and relate bird assemblages to stand structure. Bird abundance and species richness was positively associated with age for both stand types. Richness and diversity was highest in oak stands, while there were no differences in bird abundance between the two forest types. Pine stands supported a different bird species composition compared to oak stands of the same age. Stand age and structure, rather than forest type, held the highest explanatory powers for bird assembly structure. Primary cavity-nesters and ground-nesters were more abundant in oak stands, possibly reflecting differences in stand structure and resource distribution. To support these birds with suitable habitats, oaks stands need conservation. Management practices in pine stands should strive for increasing the amount of old trees and retain vegetation in the understory to benefit breeding birds.

  • 191.
    Bergqvist, Jonathan
    Linköping University, Department of Physics, Chemistry and Biology, Bioinformatics.
    Study of Protein Interfaces with Clustering2018Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Protein-protein interactions occur in nature and have different functions. The interacting surface between two interacting proteins contains the respective protein's interface residues.

    In this thesis, a series of Python scripts are presented which can perform interface-interface comparisons with the method InterComp, to obtain a distance matrix of different protein interfaces. The distance matrix can be studied with the use of clustering algorithms such as DBSCAN.

    The result from clustering using DBSCAN shows that for the 77,017 protein interfaces studied, a majority of the protein interfaces are part of a single cluster while most of the remaining interfaces are noise for the tested parameters Eps and MinPts.

    The conclusion of this thesis is the effect on the number of clusters for the tested parameters Eps and MinPts when performing DBSCAN.

  • 192.
    Bergqvist, Niclas
    et al.
    Linköping University, Department of Biomedical Engineering. Linköping University, Faculty of Science & Engineering.
    Nyman, Elin
    Linköping University, Department of Biomedical Engineering, Division of Biomedical Engineering. Linköping University, Faculty of Science & Engineering. AstraZeneca RandD, Sweden.
    Cedersund, Gunnar
    Linköping University, Department of Biomedical Engineering, Division of Biomedical Engineering. Linköping University, Faculty of Science & Engineering. Linköping University, Department of Clinical and Experimental Medicine. Linköping University, Faculty of Medicine and Health Sciences.
    Stenkula, Karin G.
    Lund University, Sweden.
    A systems biology analysis connects insulin receptor signaling with glucose transporter translocation in rat adipocytes2017In: Journal of Biological Chemistry, ISSN 0021-9258, E-ISSN 1083-351X, Vol. 292, no 27, p. 11206-11217Article in journal (Refereed)
    Abstract [en]

    Type 2 diabetes is characterized by insulin resistance, which arises from malfunctions in the intracellular insulin signaling network. Knowledge of the insulin signaling network is fragmented, and because of the complexity of this network, little consensus has emerged for the structure and importance of the different branches of the network. To help overcome this complexity, systems biology mathematical models have been generated for predicting both the activation of the insulin receptor (IR) and the redistribution of glucose transporter 4 (GLUT4) to the plasma membrane. Although the insulin signal transduction between IR and GLUT4 has been thoroughly studied with modeling and time-resolved data in human cells, comparable analyses in cells from commonly used model organisms such as rats and mice are lacking. Here, we combined existing data and models for rat adipocytes with new data collected for the signaling network between IR and GLUT4 to create a model also for their interconnections. To describe all data (amp;gt;140 data points), the model needed three distinct pathways from IR to GLUT4: (i) via protein kinase B (PKB) and Akt substrate of 160 kDa (AS160), (ii) via an AS160-independent pathway from PKB, and (iii) via an additional pathway from IR, e.g. affecting the membrane constitution. The developed combined model could describe data not used for training the model and was used to generate predictions of the relative contributions of the pathways from IR to translocation of GLUT4. The combined model provides a systems-level understanding of insulin signaling in rat adipocytes, which, when combined with corresponding models for human adipocytes, may contribute to model-based drug development for diabetes.

  • 193.
    Bergstedt, Johan
    Linköping University, Department of Physics, Measurement Technology, Biology and Chemistry. Linköping University, The Institute of Technology.
    Boreal vegetation responses to forestry as reflected in field trial and survey data2004Licentiate thesis, comprehensive summary (Other academic)
    Abstract [en]

    This thesis had two objectives: the first objective was to evaluate the response of forest ground vegetation to selected forestry operations, i.e. cutting of different intensities and scarification; the second objective was to compare the use of survey data in vegetation research with that of more traditional research using field trials - i.e. can survey data be used and produce results that comply with those emerging from field trials? Here, the results from an analysis of survey data has been compared with results emerging from a field trial.

    Survey data was analysed from the National Forest Inventory (NFI), using 789 sample plots in central and northern Sweden visited twice at an interval of 10-11 years, 294 of which had been subjected to logging between inventories. This was compared with a field trial in central Sweden: a complete block design with four replicates - three treatments and conventional harvesting as the control.

    The cutting intensity was found to have an impact on the ground-layer flora, the change being mostly differences in abundance rather than change in species richness. Those increasing were early successional species, i.e. crustose lichens, Deschampsia flexuosa. In contrast, Vaccinium myrtillus was decreasing substantially in response to increased cutting intensity. A number of species appeared to be indifferent to cutting, i.e. Vaccinium vitisidaea, Trientalis europaea.

    Scarification had a different impact on the flora than cutting: only Polytrichum spp. increased substantially, while many decreased.

    For those effects that were possible to compare in both studies, the results from survey data comply with those from the field trial, indicating that survey data is possible to use in forest vegetation research.

  • 194.
    Bergstedt, Johan
    Linköping University, Department of Physics, Chemistry and Biology, Ecology . Linköping University, The Institute of Technology.
    Boreal vegetation responses to forestry as reflected in field trial and survey data and the quality of cover estimates and presence/absence in vegetation inventory2008Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    This thesis has two main focuses; first, the response of forest ground layer flora on forestry, mainly harvesting and secondly, the quality of the vegetation assessment methods, cover estimates by eye and presence/absence data.

    The effect of harvesting intensity was evaluated with survey data from permanent plots as well as vegetation data from a field trial fourteen years after harvesting. Both data sets confirmed that response of ground layer flora increased with increasing logging intensity. Thereby, indicating that survey data is possible to use in research. From the survey data set, existence of a time lag was evident for several species and also a threshold level was evident in cutting intensity needed to affect a number of species. Logging had a modest, but significant positive effect on the change in species number per plot. Species turnover was influenced by the proportion of Picea abies in the tree canopy; site productivity; and logging intensity. In the field trial scarification had a strong effect that was different from the one created by cutting.

    In plant ecology cover estimate by eye and presence/absence recording are the two most frequent methods used. The methods were evaluated with survey data and a field trial.

    In the first data set vegetation was recorded independently by two observers in 342 permanent 100-m2 plots. Overall, one third of each occurrence was missed by one of the two observers, but with large differences among species. Species occurring at low abundance tended to be frequently overlooked. Observer-explained variance in cover estimates was <10% in 15 of 17 species.

    In the second data set, 10 observers independently estimated cover in sixteen 100-m2 plots in two different vegetation types. The bias connected to observer varied substantially between species. The estimates of missing field and bottom layer had the highest bias, indicating that missing layers are problematic to use in analysis of change. Experience had a surprisingly small impact on the bias connected to observer. Analyses revealed that for the statistical power, cover estimates by eye carries a higher information value than do presence/absence data when distinguishing between vegetation types, differences between observers is negligible, and using more than one observer had little effect.

    List of papers
    1. The impact of logging intensity on field-layer vegetation in Swedish boreal forests
    Open this publication in new window or tab >>The impact of logging intensity on field-layer vegetation in Swedish boreal forests
    2001 (English)In: Forest Ecology and Management, ISSN 0378-1127, Vol. 154, no 1-2, p. 105-115Article in journal (Refereed) Published
    Abstract [en]

    The relationship between logging intensity and changes in ground cover vegetation was studied in 16 species and groups of species recorded at 10- or 11-year intervals in mature conifer-dominated forests. The 789 plots located in northern and central Sweden had been surveyed by the National Forest Inventory and the National Survey of Forest Soil and Vegetation. Thirty-seven percent of the plots had been subjected to a thinning or clear-cutting between the inventories. A principal components analysis showed that, of the variables considered, logging intensity had the highest explanatory power regarding change in ground cover vegetation between the inventories (the other variables were sum of temperatures, age of stand, timber volume, percentage Pinus sylvestris and site productivity). A multivariate direct gradient analysis technique (Redundancy analysis) showed that the logging intensity significantly affected the change in cover. This analysis also ranked the species in their responsiveness to logging. Epilobium angustifolium, narrow-leaved grasses and broad-leaved grasses, increased most with logging intensity. The response was not linear and only detectable at high logging intensities (>80%). In contrast, Vaccinium myrtillus seemed to decrease linearly with increased logging intensity. There was several years time-lag in the response to logging of E. angustifolium, V. myrtillus and narrow-leaved grasses. Several species and groups of species seemed unaffected by the logging. In sample plots unaffected by logging the cover of most species decreased.

    Keywords
    Clear cut, Community, Cutting, Multivariate analysis, Sweden, Thinning
    Identifiers
    urn:nbn:se:liu:diva-13278 (URN)10.1016/S0378-1127(00)00642-3 (DOI)
    Available from: 2008-05-07 Created: 2008-05-07 Last updated: 2018-07-03
    2. Composition of vegetation after a modified harvesting and propagation method compared with conventional clear-cutting, scarification and planting: evaluation 14 years after logging
    Open this publication in new window or tab >>Composition of vegetation after a modified harvesting and propagation method compared with conventional clear-cutting, scarification and planting: evaluation 14 years after logging
    2008 (English)In: Applied Vegetation Science, ISSN 1402-2001, Vol. 11, no 2, p. 159-168Article in journal (Refereed) Published
    Abstract [en]

    Question: How does the vegetation of boreal forests respond to harvesting and scarification?

    Location: 650 m a.s.l., central Sweden (61°38' N).

    Methods: The response of boreal forest vegetation to cutting and scarification was studied in a field trial, which consisted of three treatments plus conventional harvesting as a control in a complete block design with four replicates. The cutting was done 14 years prior to vegetation inventory and scarification and planting were conducted the first or second years after cutting.

    Results: The species most abundant at higher cutting intensities were crustose lichens, Cladonia spp., Cladina arbuscula, Polytrichum spp. and pioneer mosses, the grass Deschampsia flexuosa, and the tree Betula pubescens, A few species had substantially lower abundance in treatments with higher cutting intensity, notably Hylocomium splendens and Vaccinium myrtillus. Scarification had a strong effect that was different from the one created by cutting. In scarification treatments, Polytrichum spp. were the only species with high abundance; most species had low abundance, i.e. Barbilophozia lycopodioides, Vaccinium vitis-idaea, Pleurozium schreberi, Carex globularis, Empetrum nigrum, Cladina arbuscula, Sphagnum spp.

    Conclusions: Our results elaborate on the details of the well-known effect of cutting on ground-layer flora, and also give support for the profound and long-lasting effect that soil scarification has on forest vegetation.

    Keywords
    Boreal forest, Cutting intensity, Field trial, Forest understorey, Logging, Propagation, Sweden
    National Category
    Natural Sciences
    Identifiers
    urn:nbn:se:liu:diva-13279 (URN)10.3170/2007-7-18343 (DOI)
    Available from: 2008-05-07 Created: 2008-05-07 Last updated: 2014-10-08
    3. Turnover of ground layer species in Swedish boreal forests and its response to logging
    Open this publication in new window or tab >>Turnover of ground layer species in Swedish boreal forests and its response to logging
    Manuscript (Other academic)
    Identifiers
    urn:nbn:se:liu:diva-13280 (URN)
    Available from: 2008-05-07 Created: 2008-05-07 Last updated: 2010-01-13
    4. Systematic and random variation in vegetation monitoring data
    Open this publication in new window or tab >>Systematic and random variation in vegetation monitoring data
    Show others...
    2008 (English)In: Journal of Vegetation Science, ISSN 1100-9233, E-ISSN 1654-1103, Vol. 19, p. 633-644Article in journal (Refereed) Published
    Abstract [en]

    Question: Detecting species presence in vegetation and making visual assessment of abundances involve a certain amount of skill, and therefore subjectivity. We evaluated the magnitude of the error in data, and its consequences for evaluating temporal trends.

    Location: Swedish forest vegetation.

    Methods: Vegetation data were collected independently by two observers in 342 permanent 100-m2 plots in mature boreal forests. Each plot was visited by one observer from a group of 36 and one of two quality assessment observers. The cover class of 29 taxa was recorded, and presence/absence for an additional 50.

    Results: Overall, one third of each occurrence was missed by one of the two observers, but with large differences among species. There were more missed occurrences at low abundances. Species occurring at low abundance when present tended to be frequently overlooked. Variance component analyses indicated that cover data on 5 of 17 species had a significant observer bias. Observer-explained variance was < 10% in 15 of 17 species.

    Conclusion: The substantial number of missed occurrences suggests poor power in detecting changes based on presence/absence data. The magnitude of observer bias in cover estimates was relatively small, compared with random error, and therefore potentially analytically tractable. Data in this monitoring system could be improved by a more structured working model during field work.

    Place, publisher, year, edition, pages
    Institutionen för fysik, kemi och biologi, 2008
    Keywords
    Forest, Observer error, Permanent plot, Statistical power, Sweden
    National Category
    Natural Sciences
    Identifiers
    urn:nbn:se:liu:diva-11872 (URN)10.3170/2008-8-18423 (DOI)
    Note
    Original publication: Milberg, P., Bergstedt, J., Fridman, J., Odell, G & Westerberg, L., Systematic and random variation in vegetation monitoring data, 2008, Journal of Vegetation Science, (19), 633-644. http://dx.doi.org/10.3170/2008-8-18423. Copyright: Opulus Press, http://www.opuluspress.se/index.phpAvailable from: 2008-05-22 Created: 2008-05-22 Last updated: 2017-12-13
    5. In the eye of the beholder: bias and stochastic variation in cover estimates
    Open this publication in new window or tab >>In the eye of the beholder: bias and stochastic variation in cover estimates
    Manuscript (Other academic)
    Identifiers
    urn:nbn:se:liu:diva-13282 (URN)
    Available from: 2008-05-07 Created: 2008-05-07 Last updated: 2010-01-13
  • 195.
    Bergstedt, Johan
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Biology.
    Axelsson, Anna-Lena
    SLU Umeå.
    Karlsson, Jesper
    Linköping University, Department of Physics, Chemistry and Biology, Biology.
    Lönander, Johanna
    Linköping University, Department of Physics, Chemistry and Biology, Biology.
    Törnqvist, Lina
    Linköping University, Department of Physics, Chemistry and Biology, Biology.
    Milberg, Per
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Förändringar i Eklandskapet 1927 till 2013: i den första riksskogstaxeringens fotspår2017In: Svensk Botanisk Tidskrift, ISSN 0039-646X, Vol. 111, no 6, p. 331-343Article in journal (Refereed)
    Abstract [en]

    Transects covering 90 km inan area south of Linköping in the province of Östergötland, SE Sweden, were relocated and reinventoried in 2013 using the same methodology as in the first national forest inventory of 1927. Data for land-use, forest type and species-specific tree sizes were obtained and compared with values from 1927. The results show that arable fields and pastures have decreased, while forests and areas covered by roads etc. have increased considerably. Picea abies has increased more than Pinus sylvestris. The reasons for the changes are discussed.

  • 196.
    Bergström, Gunnar
    Linköping University, Department of Physics, Chemistry and Biology, Biotechnology. Linköping University, Faculty of Science & Engineering.
    Microfluidic biosensor systems for cardiotoxicity assaying2015Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Toxicity screening is an important part of pharmaceutical development and early detection of toxic side effects provide the opportunity for early redesign or termination of unfeasible projects. Today toxicity testing is relying on experiments on animals. Ethical concerns, high costs and problems with interspecies variability in animal experiments have introduced incentives for cell-based toxicity assays. The recent development of stem cell technology have raised the hope for toxicity testing with higher predictivity that can reduce the amount of animals sacrificed, increase the patient safety and reduce the costs in pharmaceutical development.

    Cell development and behavior is to a large extent dependent on the microenvironment. Microfluidic techniques can be used to build small-sized structures that provide the opportunity to introduce a high degree of control of the cell culture environment with features in cell sizes. In this thesis is demonstrated two different methods for infusing cells into microfluidic cell culture devices using either cells clustered in cardiac bodies during differentiation or cells pre-seeded in microporous carriers prior to infusion.

    Microfluidic cell culture devices are well suited for optical  evaluation. Demonstrated in this thesis is fluorescent staining in combination with confocal microscopy as well as automated imaging with evaluation of beating frequency of cardiomyocyte cell clusters can be used to assess toxicity of cells cultured in microfluidic devices.

    Biosensors use biological recognition elements to measure the presence of a chemical substance, for example low concentrations of biomarkers secreted by cells in a toxicity assay. Especially capacitive biosensors have shown very low limit of detection. In addition, protein G is demonstrated as an affinity ligand to capture IgG antibodies used as recognition element in a biosensor application or used for antibody screening.

    List of papers
    1. Orientation and capturing of antibody affinity ligands: Applications to surface plasmon resonance biochips
    Open this publication in new window or tab >>Orientation and capturing of antibody affinity ligands: Applications to surface plasmon resonance biochips
    2011 (English)In: Sensors and actuators. B, Chemical, ISSN 0925-4005, E-ISSN 1873-3077, Vol. 158, no 1, p. 265-270Article in journal (Refereed) Published
    Abstract [en]

    A surface plasmon resonance (SPR) sensor chip with immobilized protein G was used for simultaneously capturing, purifying and orienting antibody ligands. The ligands were further stabilized by chemical cross-linking. This procedure of designing the sensor chip improved efficient use of the ligands and could prolong the analytical use. less thanbrgreater than less thanbrgreater thanThe procedure was evaluated on standard dextran-coated sensor chips onto which commercial semi-purified antibodies towards human serum albumin and human troponin where captured and used for analysing their antigens. less thanbrgreater than less thanbrgreater thanThe procedure demonstrates a general design approach for presenting the biorecognition element on a biosensor surface which enhances sensitivity, stability and selectivity at the same time as an impure ligand is purified.

    Place, publisher, year, edition, pages
    Elsevier, 2011
    Keywords
    Biosensor, Affinity interaction, SPR, Biacore, Protein G, Sensor chip
    National Category
    Engineering and Technology
    Identifiers
    urn:nbn:se:liu:diva-71770 (URN)10.1016/j.snb.2011.06.017 (DOI)000295500200037 ()
    Note

    Funding Agencies|European Commission|LSHB-CT-2007-037636|

    Available from: 2011-11-04 Created: 2011-11-04 Last updated: 2019-01-22
    2. Macroporous microcarriers for introducing cells into a microfluidic chip
    Open this publication in new window or tab >>Macroporous microcarriers for introducing cells into a microfluidic chip
    2014 (English)In: Lab on a Chip, ISSN 1473-0197, E-ISSN 1473-0189, Vol. 14, no 18, p. 3502-3504Article in journal (Refereed) Published
    Abstract [en]

    Macroporous gelatin beads (CultiSpher™ microcarriers) provide a convenient method for rapidly and reliably introducing cells cultured ex situ into a microfluidic device, where the spheres create a 3D environment for continued cell proliferation. We demonstrate the usefulness of this technique with a proof-of-concept viability analysis of cardiac cells after treatment with doxorubicin. © 2014 the Partner Organisations.

    Place, publisher, year, edition, pages
    Royal Society of Chemistry, 2014
    National Category
    Biological Sciences Physical Sciences
    Identifiers
    urn:nbn:se:liu:diva-109971 (URN)10.1039/c4lc00693c (DOI)000340474300008 ()25068539 (PubMedID)2-s2.0-84905837163 (Scopus ID)
    Funder
    Swedish Research Council, 2008-7537 2011-6404
    Note

    Acknowledgements

    The primary embryonic cardiomyocytes were provided byJordi Altimiras, Department of Physics, Chemistry andBiology, Linköping University. The authors thank the SwedishResearch Council (Vetenskapsrådet) for fundingviagrants 2008-7537 and 2011-6404

    Available from: 2014-08-29 Created: 2014-08-29 Last updated: 2019-01-22Bibliographically approved
    3. Capacitive biosensor for detection of toxicity biomarkers
    Open this publication in new window or tab >>Capacitive biosensor for detection of toxicity biomarkers
    2015 (English)Manuscript (preprint) (Other academic)
    Abstract [en]

    Microfluidic devices are rapidly gaining importance for in vitro toxicity testing. Biomarker detection in microfluidic assays are however challenging due to small sample sizes and low analyte concentration. Capacitive electrochemical biosensors have been reported to have high sensitivity and properties that are amenable for implementation into microfluidic devices.

    In this work a biosensor application for troponin T (TnT) is presented. The sensor showed linear response to analyte over five orders of magnitude with the lowest detectable signal at 10-13 M. The sensor proved to be able to detect TnT spiked in cell culture media at concentrations relevant for cell cultures.

    National Category
    Biological Sciences Physical Sciences
    Identifiers
    urn:nbn:se:liu:diva-118293 (URN)
    Available from: 2015-05-26 Created: 2015-05-26 Last updated: 2019-01-22
    4. Stem cell derived in vivo-like human cardiac bodies in a microfluidic device for toxicity testing by beating frequency imaging
    Open this publication in new window or tab >>Stem cell derived in vivo-like human cardiac bodies in a microfluidic device for toxicity testing by beating frequency imaging
    Show others...
    2015 (English)In: Lab on a Chip, ISSN 1473-0197, E-ISSN 1473-0189, Vol. 15, no 15, p. 3242-3249Article in journal (Refereed) Published
    Abstract [en]

    Beating in vivo-like human cardiac bodies (CBs) were used in a microfluidic device for testing cardiotoxicity. The CBs, cardiomyocyte cell clusters derived from induced pluripotent stem cells, exhibited typical structural and functional properties of the native human myocardium. The CBs were captured in niches along a perfusion channel in the device. Video imaging was utilized for automatic monitoring of the beating frequency of each individual CB. The device allowed assessment of cardiotoxic effects on the 3D clustered cardiomyocytes from the drug substances doxorubicin, verapamil and quinidine. Beating frequency data recorded over a period of 6 hours are presented and compared to literature data. The results indicate that this microfluidic setup with imaging of CB characteristics provides a new opportunity for label-free, non-invasive investigation of toxic effects in a 3D microenvironment.

    Place, publisher, year, edition, pages
    Royal Society of Chemistry, 2015
    National Category
    Biological Sciences Physical Sciences
    Identifiers
    urn:nbn:se:liu:diva-118294 (URN)10.1039/c5lc00449g (DOI)000358022900017 ()
    Available from: 2015-05-26 Created: 2015-05-26 Last updated: 2019-01-22Bibliographically approved
  • 197.
    Bergström, Gunnar
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Biotechnology. Linköping University, The Institute of Technology.
    Christoffersson, Jonas
    Linköping University, Department of Physics, Chemistry and Biology, Biotechnology. Linköping University, Faculty of Science & Engineering.
    Schwanke, Kristin
    Hannover Medical School, Leibniz Research Laboratories for Biotechnology and Artificial Organs -LEBAO-, Hannover, Germany.
    Zweigerdt, Robert
    Hannover Medical School, Leibniz Research Laboratories for Biotechnology and Artificial Organs -LEBAO-, Hannover, Germany.
    Mandenius, Carl-Fredrik
    Linköping University, Department of Physics, Chemistry and Biology, Biotechnology. Linköping University, The Institute of Technology.
    Stem cell derived in vivo-like human cardiac bodies in a microfluidic device for toxicity testing by beating frequency imaging2015In: Lab on a Chip, ISSN 1473-0197, E-ISSN 1473-0189, Vol. 15, no 15, p. 3242-3249Article in journal (Refereed)
    Abstract [en]

    Beating in vivo-like human cardiac bodies (CBs) were used in a microfluidic device for testing cardiotoxicity. The CBs, cardiomyocyte cell clusters derived from induced pluripotent stem cells, exhibited typical structural and functional properties of the native human myocardium. The CBs were captured in niches along a perfusion channel in the device. Video imaging was utilized for automatic monitoring of the beating frequency of each individual CB. The device allowed assessment of cardiotoxic effects on the 3D clustered cardiomyocytes from the drug substances doxorubicin, verapamil and quinidine. Beating frequency data recorded over a period of 6 hours are presented and compared to literature data. The results indicate that this microfluidic setup with imaging of CB characteristics provides a new opportunity for label-free, non-invasive investigation of toxic effects in a 3D microenvironment.

  • 198.
    Bergström, Gunnar
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Biotechnology. Linköping University, The Institute of Technology.
    Kuusk, Ave
    Linköping University, Department of Physics, Chemistry and Biology. Linköping University, Faculty of Science & Engineering.
    Mandenius, Carl-Fredrik
    Linköping University, Department of Physics, Chemistry and Biology, Biotechnology. Linköping University, The Institute of Technology.
    Capacitive biosensor for detection of toxicity biomarkers2015Manuscript (preprint) (Other academic)
    Abstract [en]

    Microfluidic devices are rapidly gaining importance for in vitro toxicity testing. Biomarker detection in microfluidic assays are however challenging due to small sample sizes and low analyte concentration. Capacitive electrochemical biosensors have been reported to have high sensitivity and properties that are amenable for implementation into microfluidic devices.

    In this work a biosensor application for troponin T (TnT) is presented. The sensor showed linear response to analyte over five orders of magnitude with the lowest detectable signal at 10-13 M. The sensor proved to be able to detect TnT spiked in cell culture media at concentrations relevant for cell cultures.

  • 199.
    Bergström, Gunnar
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Biotechnology. Linköping University, The Institute of Technology.
    Nilsson, K.
    Percell Biolytica AB, Åstorp, Sweden.
    Mandenius, Carl-Fredrik
    Linköping University, Department of Physics, Chemistry and Biology, Biotechnology. Linköping University, The Institute of Technology.
    Robinson, Nathaniel D
    Linköping University, Department of Physics, Chemistry and Biology, Surface Physics and Chemistry. Linköping University, The Institute of Technology.
    Macroporous microcarriers for introducing cells into a microfluidic chip2014In: Lab on a Chip, ISSN 1473-0197, E-ISSN 1473-0189, Vol. 14, no 18, p. 3502-3504Article in journal (Refereed)
    Abstract [en]

    Macroporous gelatin beads (CultiSpher™ microcarriers) provide a convenient method for rapidly and reliably introducing cells cultured ex situ into a microfluidic device, where the spheres create a 3D environment for continued cell proliferation. We demonstrate the usefulness of this technique with a proof-of-concept viability analysis of cardiac cells after treatment with doxorubicin. © 2014 the Partner Organisations.

  • 200.
    Bergvall, Caroline
    Linköping University, Department of Physics, Chemistry and Biology. Linköping University, The Institute of Technology.
    The domestication effects on social support in chickens (Gallus gallus)2012Independent thesis Basic level (degree of Bachelor), 10,5 credits / 16 HE creditsStudent thesis
    Abstract [en]

    When animals are stressed they use a trait called social support to alleviate their stress responses. With domestication many traits from the ancestor red junglefowl have changed in the domesticated breed white leghorn. White leghorns are bred to be able to live in large groups where it becomes hard to recognize every chicken. They are therefore not as dependent of familiar stimuli birds for social support as red junglefowl. Our hypotheses were that red jungle males would be more interested in unfamiliar stimuli birds than white leghorn male before stress due to their territoriality. We tested total 56 chickens in an open field test. The test arena was divided in three zones and the time the focal birds spent in each zone was recorded. The focal bird was recorded in 300 seconds before being stressed by being suspended in a net and then recorded again in 300 seconds. The results showed that social support and social behaviour differs between females and males for both breeds. No significant differences were found between the breeds. There was a tendency for significant of breed (P=0.08) effects in the central zone unstressed. The two interactions before stressed between breed and sex, central zone (P<0.01) and unfamiliar zone (P<0.01) had significant effects. We observed fights between white leghorn males and familiar stimuli. Waltzing did also occur in red jungle males in front of unfamiliar. In conclusion, numeric differences can be seen but not large enough to be significant and our hypotheses are not confirmed.

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