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  • 51. Bauer, S H J
    et al.
    Månsson, Martin
    Södertörns högskola, Avdelning Naturvetenskap.
    Hood, D W
    Richards, J C
    Moxon, E R
    Schweda, Elke K H
    Södertörns högskola, Avdelning Naturvetenskap.
    A rapid and sensitive procedure for determination of 5-N-acetyl neuraminic acid in lipopolysaccharides of Haemophilus influenzae: a survey of 24 non-typeable H-influenzae strains2001Inngår i: Carbohydrate Research, ISSN 0008-6215, E-ISSN 1873-426X, Vol. 335, nr 4, s. 251-260Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    In view of the importance of 5-N-acetyl neuraminic acid in bacterial pathogenesis, a sensitive, reproducible and reliable method for the determination of 5-N-acetyl neuraminic acid levels in lipopolysaccharide (LPS) is described and applied to 24 different non-typeable Haemophilus influenzae (NTHi) strains. The method involves analysis by high-performance anion-exchange chromatography with pulsed amperometric detection (HPAEC-PAD) of terminal 5-N-acetyl neuraminic acid residues released by neuraminidase treatment of O-deacylated LPS. The procedure is relatively fast and the instrumental effort is moderate. The results of the procedure were compared with data obtained by H-1 NMR and electrospray ionisation-mass spectrometry (ESI-MS). The analysis of LPS from 24 NTHi strains showed that 5-N-acetyl neuraminic acid was found to be a common constituent of LPS in NTHi. Only one strain (NTHi 432) did not show any sialylation. Molar ratios (LPS /5-N-acetyl neuraminic acid) ranged between 5/1 and 500/1. Several strains in which no 5-N-acetyl neuraminic acid could be determined by other methods including 1H NMR and ESI-MS were shown to contain 5-N-acetyl neuraminic acid by this HPAEC-PAD procedure. The method was applied to determine levels of terminal 5-N-acetyl neuraminic acid in LPS from NTHi strains grown under different conditions and mutant strains containing inactive LPS biosynthetic genes.

  • 52. Beckman, M
    et al.
    Kihlmark, Madeleine
    Södertörns högskola, Institutionen för kemi, biologi, geografi och miljövetenskap.
    Iverfeldt, K
    Hallberg, Einar
    Södertörns högskola, Institutionen för kemi, biologi, geografi och miljövetenskap.
    Degradation of GFP-labelled POM121, a non-invasive sensor of nuclear apoptosis, precedes clustering of nuclear pores and externalisation of phosphatidylserine2004Inngår i: Apoptosis (London), ISSN 1360-8185, E-ISSN 1573-675X, Vol. 9, nr 3, s. 363-368Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The nuclear pore membrane protein POM121 is specifically degraded during apoptosis by a caspase-3-dependent process enabling early detection of apoptosis in living cells expressing POM121-GFP. Here we further investigated temporal aspects of apoptotic degradation of POM121-GFP. We demonstrate that decreased POM121-GFP fluorescence precedes annexin V-labelling of apoptotic cells. This indicates that degradation of the nuclear pore complex starts prior to redistribution of plasma membrane phosphatidylserine, which serves as a signal for phagocytotic elimination of apoptotic cells. Furthermore, a caspase-resistant GFP-labelled mutant of POM121 resisted degradation even in late apoptosis and was detected in clustered nuclear pores. Thus, it can be concluded that loss of POM121-GFP is a specific sensor of the activation of caspase-3-dependent proteolysis at the nuclear pores.

  • 53.
    Beckman, Marie
    et al.
    Södertörns högskola, Institutionen för livsvetenskaper, Molekylärbiologi.
    Freeman, Craig
    Parish, Christopher R.
    Small, David H.
    Activation of cathepsin D by glycosaminoglycans2009Inngår i: The FEBS Journal, ISSN 1742-464X, E-ISSN 1742-4658, Vol. 276, nr 24, s. 7343-7352Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We have previously shown that heparin can increase the activity of the proenzyme form of Alzheimer's beta-site amyloid precursor protein cleaving enzyme 1 (BACE1). Cathepsin D (CD) is a member of the aspartic protease family and has sequence similarity to BACE1. Therefore, we examined whether heparin and other glycosaminoglycans (GAGs) can influence the activity of CD. Heparin and other GAGs were found to stimulate the activity of recombinant proCD. Desulfation of heparin almost abolished the stimulation, indicating that sulfate groups were important for the stimulatory effect. In addition, the stimulation was dependent on the length of the GAG chain, as larger GAGs were more potent in their ability to stimulate proCD than shorter fragments. In the presence of heparin, limited autocatalytic proteolysis of the proenzyme was increased, suggesting that heparin increases the activity of proCD by accelerating the conversion of proCD, which has little activity, to pseudoCD, an active form lacking residues 1-26 of the prodomain. Furthermore, the activity of spleen-derived mature CD, which lacks the entire 44 amino acid residue prodomain, was also increased by heparin, indicating that the catalytic domain of CD contains at least one region to which GAGs bind and stimulate enzyme activity. Because heparin also stimulated the activity of pseudoCD, proenzyme activation was probably accelerated by the interaction of heparin with the catalytic domain of pseudoCD. However, it is possible that heparin may also activate the proenzyme directly. On the basis of this study, we propose that GAGs may regulate CD activity in vivo.

  • 54. Belyaev, I Y
    et al.
    Eriksson, S
    Nygren, Jonas
    Södertörns högskola, Avdelning Naturvetenskap. Karolinska Institute / Stockholm University.
    Torudd, J
    Harms-Ringdahl, M
    Effects of ethidium bromide on DNA loop organisation in human lymphocytes measured by anomalous viscosity time dependence and single cell gel electrophoresis1999Inngår i: Biochimica et Biophysica Acta - General Subjects, ISSN 0304-4165, E-ISSN 1872-8006, Vol. 1428, nr 2-3, s. 348-356Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The effects of ethidium bromide (EtBr) on human lymphocytes were studied by the method of anomalous viscosity time dependence (AVTD) and by the comet assay. EtBr at low concentrations increased the maximum viscosity and time of radial migration as measured with AVTD at neutral conditions of lysis. A pronounced relaxation of DNA loops was observed with the neutral comet assay. The maximal comet length corresponded to 2 Mb DNA loops. At high concentrations of EtBr, 2. mg/ml, significant reduction in AVTD below control level was seen that suggested hypercondensation of chromatin. The hypercondensation was directly observed with the neutral comet assay. EtBr did not induce DNA strand breaks as measured by the alkaline comet assay. The hypercondensed nuclei could be decondensed by irradiation with gamma-rays or exposure to light. The data provide evidence that EtBr at high concentrations resulted in hypercondensation of chromatin below control level. The comet assay confirmed that the increase in AVTD peaks deals with relaxation of loops and AVTD decrease is caused by chromatin condensation. The prediction of the AVTD theory for a correlation between time of radial migration and condensation of chromatin was verified. Further, the data show that the comet assay at neutral conditions of lysis is rather sensitive to DNA loop relaxation in the absence of DNA damage. Finally, donor specificity was found for the hypercondensation.

  • 55. Benach, J
    et al.
    Filling, C
    Oppermann, U C T
    Roversi, P
    Bricogne, G
    Berndt, Kurt D
    Södertörns högskola, Avdelning Naturvetenskap. Karolinska Institutet.
    Jörnvall, H
    Ladenstein, R
    Structure of bacterial 3 beta/17 beta-hydroxysteroid dehydrogenase at 1.2 angstrom resolution: A model for multiple steroid recognition2002Inngår i: Biochemistry, ISSN 0006-2960, E-ISSN 1520-4995, Vol. 41, nr 50, s. 14659-14668Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The enzyme 3beta/17beta-hydroxysteroid dehydrogenase (3beta/17beta-HSD) is a steroid-inducible component of the Gram-negative bacterium Conramonas testosteroni. It catalyzes the reversible reduction/ dehydrogenation of the oxo/beta-hydroxy groups at positions 3 and 17 of steroid compounds, including hormones and isobile acids. Crystallographic analysis at 1.2 Angstrom resolution reveals the enzyme to have nearly identical subunits that form a tetramer with 222 symmetry. This is one of the largest oligomeric structures refined at this resolution. The subunit consists of a monomer with a single-domain structure built around a seven-stranded beta-sheet flanked by six alpha-helices. The active site contains a Ser-Tyr-Lys triad, typical for short-chain dehydrogenases/reductases (SDR). Despite their highly diverse substrate specificities, SDR members show a close to identical folding pattern architectures and a common catalytic mechanism. In contrast to other SDR apostructures determined, the substrate binding loop is well-defined. Analysis of structure-activity relationships of catalytic cleft residues, docking analysis of substrates and inhibitors, and accessible surface analysis explains how 3beta/17beta-HSD accommodates steroid substrates of different conformations.

  • 56. Bensch, Staffan
    et al.
    Grahn, Mats
    Södertörns högskola, Institutionen för livsvetenskaper, Biologi. Södertörns högskola, Institutionen för livsvetenskaper, Miljövetenskap.
    Müller, Nils
    Gay, Laurene
    Åkesson, Susanne
    Genetic, morphological, and feather isotope variation of migratory willow warblers show gradual divergence in a ring.2009Inngår i: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 18, nr 14, s. 3087-96Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The circular distribution of the willow warbler Phylloscopus trochilus around the Baltic Sea shares many features with the classic examples of ring species; however, the system is much younger. It has previously been shown that a secondary contact zone is located in central Scandinavia, where there are narrow clines for several morphological traits coincident with a migratory divide. Here we analyse multiple traits and genes from > 1700 males captured on breeding territories at 77 sites spread around the Baltic Sea to test the following hypothesis. If the secondary contact zone in Scandinavia is a result of divergence in two allopatric refuge populations during the last glaciation, we expect to find a similar secondary contact zone somewhere else around the circular distribution. Our results show that the trait clines were wider and displaced from each other along the eastern side of the Baltic Sea. Analyses of 12 microsatellite loci confirmed that the genome is very similar between the terminal forms (F(ST) = 0). Two AFLP-derived markers filtered out from a genomic scan instead appear to be maintained by selection. These markers exhibited steep clines at the secondary contact zone in Scandinavia, but as for the phenotypic traits, had vastly different cline centres east of the Baltic Sea. The trait clines along the ring distribution outside the Scandinavian secondary contact zone thus seem to have been shaped by independent action of selection or drift during the process of postglacial colonization.

  • 57. Berger, Juerg
    et al.
    Senti, Kirsten-Andre
    Senti, Gabriele
    Södertörns högskola, Institutionen för livsvetenskaper. Karolinska Institute.
    Newsome, Timothy P.
    Åsling, Bengt
    Dickson, Barry J.
    Suzuki, Takashi
    Systematic identification of genes that regulate neuronal wiring in the Drosophila visual system2008Inngår i: PLOS Genetics, ISSN 1553-7390, E-ISSN 1553-7404, Vol. 4, nr 5, s. Online-Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Forward genetic screens in model organisms are an attractive means to identify those genes involved in any complex biological process, including neural circuit assembly. Although mutagenesis screens are readily performed to saturation, gene identification rarely is, being limited by the considerable effort generally required for positional cloning. Here, we apply a systematic positional cloning strategy to identify many of the genes required for neuronal wiring in the Drosophila visual system. From a large-scale forward genetic screen selecting for visual system wiring defects with a normal retinal pattern, we recovered 122 mutations in 42 genetic loci. For 6 of these loci, the underlying genetic lesions were previously identified using traditional methods. Using SNP-based mapping approaches, we have now identified 30 additional genes. Neuronal phenotypes have not previously been reported for 20 of these genes, and no mutant phenotype has been previously described for 5 genes. The genes encode a variety of proteins implicated in cellular processes such as gene regulation, cytoskeletal dynamics, axonal transport, and cell signalling. We conducted a comprehensive phenotypic analysis of 35 genes, scoring wiring defects according to 33 criteria. This work demonstrates the feasibility of combining large-scale gene identification with large-scale mutagenesis in Drosophila, and provides a comprehensive overview of the molecular mechanisms that regulate visual system wiring.

  • 58. Bergh, F T
    et al.
    Flinn, Elisabeth M
    Södertörns högskola, Avdelning Naturvetenskap. Karolinska Institute.
    Svaren, J
    Wright, Anthony P
    Södertörns högskola, Avdelning Naturvetenskap. Karolinska Institute.
    Horz, W
    Comparison of nucleosome remodeling by the yeast transcription factor Pho4 and the glucocorticoid receptor2000Inngår i: Journal of Biological Chemistry, ISSN 0021-9258, E-ISSN 1083-351X, Vol. 275, nr 12, s. 9035-9042Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Chromatin reorganization of the PHO5 and murine mammary tumor virus (MMTV) promoters is triggered by binding of either Pho4 or the glucocorticoid receptor (GR), respectively. In order to compare the ability of Pho4 and GR to remodel chromatin and activate transcription, hybrid promoter constructs were created by insertion of the MMTV B nucleosome sequence into the PHO5 promoter and then transformed into a yeast strain expressing GR, Activation of either Pho4 (by phosphate depletion) or GR (by hormone addition) resulted in only slight induction of hybrid promoter activity. However, simultaneous activation of both Pho4 and GR resulted in synergistic activation to levels exceeding that of the wild type PHO5 promoter. Under these conditions, Pho4 completely disrupted the nucleosome containing its binding site. In contrast, GR had little effect on the stability of the MMTV B nucleosome. A minimal transactivation domain of the GR fused to the Pho4 DNA-binding domain is capable of efficiently disrupting the nucleosome with a Pho4-binding site, whereas the complementary hybrid protein (Pho4 activation domain, GR DNA-binding domain) does not labilize the B nucleosome. Therefore, we conclude that significant activation by Pho4 requires nucleosome disruption, whereas equivalent transcriptional activation by GR is not accompanied by overt perturbation of nucleosome structure. Our results show that the DNA-binding domains of the two factors play critical roles in determining how chromatin structure is modified during promoter activation.

  • 59. Bernard, Pascal
    et al.
    Schmidt, Christine Katrin
    Vaur, Sabine
    Dheur, Sonia
    Drogat, Julie
    Genier, Sylvie
    Ekwall, Karl
    Södertörns högskola, Institutionen för livsvetenskaper.
    Uhlmann, Frank
    Javerzat, Jean-Paul
    Cell-cycle regulation of cohesin stability along fission yeast chromosomes2008Inngår i: EMBO Journal, ISSN 0261-4189, E-ISSN 1460-2075, Vol. 27, nr 1, s. 111-121Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Sister chromatid cohesion is mediated by cohesin, but the process of cohesion establishment during S-phase is still enigmatic. In mammalian cells, cohesin binding to chromatin is dynamic in G1, but becomes stabilized during S-phase. Whether the regulation of cohesin stability is integral to the process of cohesion establishment is unknown. Here, we provide evidence that fission yeast cohesin also displays dynamic behavior. Cohesin association with G1 chromosomes requires continued activity of the cohesin loader Mis4/Ssl3, suggesting that repeated loading cycles maintain cohesin binding. Cohesin instability in G1 depends on wpl1, the fission yeast ortholog of mammalian Wapl, suggestive of a conserved mechanism that controls cohesin stability on chromosomes. wpl1 is nonessential, indicating that a change in wpl1-dependent cohesin dynamics is dispensable for cohesion establishment. Instead, we find that cohesin stability increases at the time of S-phase in a reaction that can be uncoupled from DNA replication. Hence, cohesin stabilization might be a pre-requisite for cohesion establishment rather than its consequence.

  • 60.
    Berndt, Kurt D
    University of Chicago, USA.
    Design, synthesis, and characterization of amphiphilic helical peptides as models of protein structure1989Doktoravhandling, monografi (Annet vitenskapelig)
  • 61.
    Berndt, Kurt D
    et al.
    Eidgenössische Technische Hochschule-Hönggerberg, Zürich, Switzerland.
    Beunink, J
    Schröder, W
    Wüthrich, K
    Designed replacement of an internal hydration water molecule in BPTI: structural and functional implications of a glycine-to-serine mutation.1993Inngår i: Biochemistry, ISSN 0006-2960, E-ISSN 1520-4995, Vol. 32, s. 4564-4570Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The three-dimensional structure of the basic pancreatic trypsin inhibitor (BPTI) contains four internal water molecules, which form a total of nine intermolecular hydrogen bonds with the BPTI polypeptide chain. To investigate the effect of such internal hydration on protein structure and stability, we displaced one of the internal water molecules in a recombinant BPTI analogue, BPTI(G36S), in which Gly 36 is replaced by serine. The replacement of a water molecule by the seryl side chain was established by the absence of the protein-water nuclear Overhauser effects (NOE) that had been attributed to the water molecule near Gly 36 in wild-type BPTI and by the presence of new, intramolecular NOEs to the hydroxyl proton of Ser 36. BPTI(G36S) has slightly reduced thermal stability compared to BPTI, corresponding to a destabilization by delta (delta G) approximately 0.7 kcal/M in 6 M guanidinium hydrochloride solution. Additionally, the stabilities of the complexes formed between BPTI(G36S) and trypsin, plasmin, or kallikrein are significantly reduced when compared to the corresponding complexes with wild-type BPTI.

  • 62.
    Berndt, Kurt D
    et al.
    Eidgenossische TH-Honggerberg, Zürich, Switzerland.
    Güntert, P
    Wüthrich, K
    Nuclear-Magnetic-Resonance Solution Structure of Dendrotoxin-K from the Venom of Dendroaspis-Polylepis-Polylepis1993Inngår i: Journal of Molecular Biology, ISSN 0022-2836, E-ISSN 1089-8638, Vol. 234, nr 3, s. 735-750Artikkel i tidsskrift (Fagfellevurdert)
  • 63.
    Berndt, Kurt D
    et al.
    Eidgenösische Technische Hochschule-Hönggerberg, Zürich, Switzerland.
    Güntert, Peter
    Orbons, Leonard P.M.
    Wüthrich, Kurt
    Determination of a high-quality nuclear magnetic resonance solution structure of the bovine pancreatic trypsin inhibitor and comparison with three crystal structures1992Inngår i: Journal of Molecular Biology, Vol. 227, s. 757-775Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    A high-quality three-dimensional structure of the bovine pancreatic trypsin inhibitor (BPTI) in aqueous solution was determined by 1H nuclear magnetic resonance (n.m.r.) spectroscopy and compared to the three available high-resolution X-ray crystal structures. A newly collected input of 642 distance constraints derived from nuclear Overhauser effects and 115 dihedral angle constraints was used for the structure calculations with the program DIANA, followed by restrained energy minimization with the program AMBER. The BPTI solution structure is represented by a group of 20 conformers with an average root-mean-square deviation (RMSD) relative to the mean solution structure of 0.43 A for backbone atoms and 0.92 A for all heavy atoms of residues 2 to 56. The pairwise RMSD values of the three crystal structures relative to the mean solution structure are 0.76 to 0.85 A for the backbone atoms and 1.24 to 1.33 A for all heavy atoms of residues 2 to 56. Small local differences in backbone atom positions between the solution structure and the X-ray structures near residues 9, 25 to 27, 46 to 48 and 52 to 58, and conformational differences for individual amino acid side-chains were analyzed for possible correlations with intermolecular protein-protein contacts in the crystal lattices, using the pairwise RMSD values among the three crystal structures as a reference.

  • 64.
    Berndt, Kurt D
    et al.
    Eidgenössische TH-Hönggerberg, Zürich, Switzerland.
    Güntert, Peter
    Wüthrich, Kurt
    Conformational sampling by NMR solution structures calculated with the program DIANA evaluated by comparison with long-time molecular dynamics calculations in explicit water1996Inngår i: Proteins: Structure, Function, and Bioinformatics, ISSN 0887-3585, E-ISSN 1097-0134, Vol. 24, s. 304-313Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The NMR solution structure of bovine pancreatic trypsin inhibitor (BPTI) obtained by distance geometry calculations with the program DIANA is compared with groups of conformers generated by molecular dynamics (MD) simulations in explicit water at ambient temperature and pressure. The MD simulations started from a single conformer and were free or restrained either by the experimental NOE distance restraints or by time-averaged restraints; the groups of conformers were collected either in 10 ps intervals during 200 ps periods of simulation, or in 50 ps intervals during a 1 ns period of simulation. Overall, these comparisons show that the standard protein structure determination protocol with the program DIANA provides a picture of the protein structure that is in agreement with MD simulations using "realistic" potential functions over a nanosecond timescale. For well-constrained molecular regions there is a trend in the free MD simulation of duration 1 ns that the sampling of the conformation space is slightly increased relative to the DIANA calculations. In contrast, for surface-exposed side-chains that are less extensively constrained by the NMR data, the DIANA conformers tend to sample larger regions of conformational space than conformers selected from any of the MD trajectories. Additional insights into the behavior of surface side-chains come from comparison of the MD runs of 200 ps or 1 ns duration. In this time range the sampling of conformation space by the protein surface depends strongly on the length of the simulation, which indicates that significant side-chain transitions occur on the nanosecond timescale and that much longer simulations will be needed to obtain statistically significant data on side-chain dynamics.

  • 65.
    Bertrand, Yann
    Södertörns högskola, Institutionen för livsvetenskaper. Muséum National d'Histoire Naturelle, Paris, France / Göteborgs universitet.
    Contrasting the general with the particular in phylogenetics - a proposal to keep the meanings of mono/paraphyletic and clade/grade separated2008Inngår i: Taxon, ISSN 0040-0262, E-ISSN 1996-8175, Vol. 57, nr 3, s. 705-708Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Clade and monophyletic group on one hand and grade and paraphyletic group on the other hand are commonly used as pairs of interchangeable terms. I question this apparent synonymy and propose that "monophyly" and "paraphyly" should refer to a property of a set, whereas "clade" and "grade" should apply to individuals resulting from evolutionary process.

  • 66.
    Bertrand, Yann
    Södertörns högskola, Institutionen för livsvetenskaper. Göteborgs universitet.
    Relationships between nomenclature, phylogenetics and systematics2008Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    Systematists have become increasingly aware of the limits imposed by the current system of nomenclature for accurately representing evolutionary relationships and managing efficiently names associated with clades. In reaction, a new system of nomenclature, the PhyloCode is being developed that fully recognizes the historical nature of taxonomy and the importance of the cladistics revolution. As a consequence, questions emerge about the new historical entities of systematics, questions that can be apprehended through the lens of epistemology, philosophy of language and metaphysics. What is the ontological nature of entities that lack any other essential features besides spatiotemporal properties? How to depart from the fixed realm of immutable and transcendental essence into a worldview wherein all biological entities are characterized by their temporality and materiality? What are the consequences of nomenclatural decisions on other sectors of biology? With the ever growing sequencing capacity and tree reconstructing abilities, our conceptualization of phylogenetic relationships is changing at an unprecedented pace. Then it begs the question, what prevents communication break down when the references of clades’ names are changing almost on a daily basis. These are some of the fundamental issues I am tackling in the present work. Addressing the ontological issue, I argue that species and clades are best perceived as mereological sums of individuals, which means that each biological individual is the unique individual composed of all its less inclusive individuals and nothing more. I propose to separate the meanings of “clade” and “monophyletic group”. I suggest to use “monophyletic” for an epithet referring to a defining property of a set (a natural kind) and “clade” for a noun which corresponds to a historical entity (an individual) resulting from evolutionary process. I present the idea that a phyloname is not attached to a single clade but to a natural kind containing as members the clades that would be selected in counterfactual phylogenies. The defining properties of this natural kind are provided by the phylogenetic definition. Finally I stress that taxonomists are also driven by the will to narrate the same sort of history, when they adjust the reference of names in light of new phylogenetic data, which leads me to submit that taxa can also be perceived as narratives.

  • 67.
    Bertrand, Yann
    Södertörns högskola, Institutionen för livsvetenskaper. Muséum National d'Histoire Naturelle, Paris, France / Göteborgs universitet.
    Species individuality and integrationManuskript (preprint) (Annet vitenskapelig)
  • 68.
    Bertrand, Yann J.
    et al.
    Science and Historical Investigations of Evolution Laboratory of Dubá, Dubá, Czech Republic.
    Johansson, Magnus
    Södertörns högskola, Institutionen för naturvetenskap, miljö och teknik, Biologi. Örebro University.
    Norberg, Peter
    Sahlgrenska University.
    Revisiting Recombination Signal in the Tick-Borne Encephalitis Virus: A Simulation Approach2016Inngår i: PLOS ONE, E-ISSN 1932-6203, Vol. 11, nr 10, artikkel-id e0164435Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

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

  • 69.
    Bertrand, Yann
    et al.
    Södertörns högskola, Institutionen för livsvetenskaper. Muséum National d'Histoire Naturelle, Paris, France.
    Pteijel, F.
    Göteborgs universitet.
    Rouse, G. W.
    Adelaide University, Australia.
    Taxonomic surrogacy in biodiversity assessments, and the meaning of Linnaean ranks2006Inngår i: Systematics and Biodiversity, ISSN 1477-2000, E-ISSN 1478-0933, Vol. 4, nr 2, s. 149-159Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The majority of biodiversity assessments use species as the base unit. Recently, a series of studies have suggested replacing numbers of species with higher ranked taxa (genera, families, etc.); a method known as taxonomic surrogacy that has an important potential to save time and resources in assesments of biological diversity. We examine the relationships between taxa and ranks, and suggest that species/higher taxon exchanges are founded on misconceptions about the properties of Linnaean classification. Rank allocations in current classifications constitute a heterogeneous mixture of various historical and contemporary views. Even if all taxa were monophyletic, those referred to the same rank would simply denote separate clades without further equivalence. We conclude that they are no more comparable than any other, non-nested taxa, such as, for example, the genus Rattus and the phylum Arthropoda, and that taxonomic surrogacy tacks justification. These problems are also illustrated with data of polychaetous annelid worms from a broad-scale study of benthic biodiversity and species distributions in the Irish Sea. A recent consensus phylogeny for polychaetes is used to provide three different family-level classifications of polychaetes. We use families as a surrogate for species, and present Shannon-Wiener diversity indices for the different sites and the three different classifications, showing how the diversity measures rely on subjective rank allocations.

  • 70.
    Bertrand, Yann
    et al.
    Göteborg University.
    Töpel, Mats
    Göteborg University.
    Elväng, Annelie
    Södertörns högskola, Institutionen för livsvetenskaper, Molekylärbiologi.
    Melik, Wessam
    Södertörns högskola, Institutionen för livsvetenskaper, Kemi. Södertörns högskola, Institutionen för livsvetenskaper, Molekylärbiologi.
    Johansson, Magnus
    Södertörns högskola, Institutionen för livsvetenskaper, Kemi. Södertörns högskola, Institutionen för livsvetenskaper, Internationell hälsa.
    First Dating of a Recombination Event in Mammalian Tick-Borne Flaviviruses2012Inngår i: PLOS ONE, E-ISSN 1932-6203, Vol. 7, nr 2, s. e31981-Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The mammalian tick-borne flavivirus group (MTBFG) contains viruses associated with important human and animal diseases such as encephalitis and hemorrhagic fever. In contrast to mosquito-borne flaviviruses where recombination events are frequent, the evolutionary dynamic within the MTBFG was believed to be essentially clonal. This assumption was challenged with the recent report of several homologous recombinations within the Tick-borne encephalitis virus (TBEV). We performed a thorough analysis of publicly available genomes in this group and found no compelling evidence for the previously identified recombinations. However, our results show for the first time that demonstrable recombination (i.e., with large statistical support and strong phylogenetic evidences) has occurred in the MTBFG, more specifically within the Louping ill virus lineage. Putative parents, recombinant strains and breakpoints were further tested for statistical significance using phylogenetic methods. We investigated the time of divergence between the recombinant and parental strains in a Bayesian framework. The recombination was estimated to have occurred during a window of 282 to 76 years before the present. By unravelling the temporal setting of the event, we adduce hypotheses about the ecological conditions that could account for the observed recombination.

  • 71. Beskow, Anne
    et al.
    Wright, Anthony P. H.
    Södertörns högskola, Institutionen för livsvetenskaper.
    Comparative analysis of regulatory transcription factors in Schizosaccharomyces pombe and budding yeasts2006Inngår i: Yeast, ISSN 0749-503X, E-ISSN 1097-0061, Vol. 23, nr 13, s. 929-935Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Regulatory transcription factors (rTFs), which bind specific DNA sequences in the regulatory regions of genes and subsequently activate or repress transcription, play a central role in programming genomic expression. The number of rTFs in a species might therefore reflect its functional complexity. For simple organisms like yeast, a relatively small number of rTFs might be expected that is fairly constant between yeast species. We show that the budding yeast, Saccharomyces cerevisiae, contains 201 rTfs, which is one of the largest rTF numbers found in yeast species for which genome sequences are available. This is a much higher number than the 129 rTFs found in the fission yeast, Schizosaccharomyces pombe, which is currently the yeast with the lowest number of rTFs. Comparative analysis of several different budding yeast species shows that most of the 'extra' rTFs found in S. cerevisiae were probably acquired as a result of a whole genome duplication (WGD) event that occurred in an ancestor of a subset of budding yeast species. However, we also show that budding yeast species that have not been affected by the WGD contain a greater number of rTFs than S. pombe (mean = 145). Thus, two or more mechanisms have led to the 60% increase in rTFs in S. cerevisiae compared to S. pombe. This difference may correlate with a more extensive functional divergence in budding yeasts compared to fission yeasts. The relatively small number of rTFs in S. pombe make this organism an attractive model for global studies of mechanisms that programme gene expression.

  • 72.
    Bidla, Gawa
    et al.
    Stockolms universitet.
    Lindgren, Malin
    Södertörns högskola, Institutionen för livsvetenskaper.
    Theopold, Ulrich
    Stockholms universitet.
    Dushay, Mitchell S.
    Södertörns högskola, Institutionen för livsvetenskaper.
    Hemolymph coagulation and phenoloxidase in Drosophila larvae2005Inngår i: Developmental and Comparative Immunology, ISSN 0145-305X, E-ISSN 1879-0089, Vol. 29, nr 8, s. 669-679Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Hemolymph coagulation is a first response to wounding in insects. Although studies have been performed in large-bodied insects such as the moth Galleria mellonella, less is known about clotting in Drosophila melanogaster, the insect most useful for genetic and molecular analyses of innate immunity. Here we show the similarities between clots in Drosophila and Galleria by light- and electron microscopy. Phenoloxidase changes the Drosophila clot's physical properties through cross-linking and melanization, but it is not necessary for preliminary soft clot formation. Bacteria associate with the clot, but this alone does not necessarily kill them. The stage is now set for rapid advances in our understanding of insect hemolymph coagulation, its roles in immune defense and wound healing, and for a more comprehensive grasp of the insect immune system in general.

  • 73.
    Bjerling, Pernilla
    et al.
    Södertörns högskola, Avdelning Naturvetenskap. Karolinska Institute.
    Ekwall, Karl
    Södertörns högskola, Avdelning Naturvetenskap. Karolinska Institute.
    Centromere domain organization and histone modifications2002Inngår i: Brazilian journal of medical and biological research, ISSN 0100-879X, E-ISSN 1414-431X, Vol. 35, nr 5, s. 499-507Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Centromere function requires the proper coordination of several subfunctions, such as kinetochore assembly, sister chromatid cohesion, binding of kinetochore microtubules, orientation of sister kinetochores to opposite spindle poles, and their movement towards the spindle poles. Centromere structure appears to be organized in different, separable domains in order to accomplish these functions. Despite the conserved nature of centromere functions, the molecular genetic definition of the DNA sequences that form a centromere in the yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe, in the fruit fly Drosophila melanogaster, and in humans has revealed little conservation at the level of centromere DNA sequences. Also at the protein level few centromere proteins are conserved in all of these four organisms and many are unique to the different organisms. The recent analysis of the centromere structure in the yeast S. pombe by electron microscopy and detailed immunofluorescence microscopy of Drosophila centromeres have brought to light striking similarities at the overall structural level between these centromeres and the human centromere. The structural organization of the centromere is generally multilayered with a heterochromaun domain and a central core/inner plate region, which harbors the outer plate structures of the kinetochore. It is becoming increasingly clear that the key factors for assembly and function of the centromere structure are the specialized histories and modified histones which are present in the centromeric heterochromatin and in the chromatin of the central core. Thus, despite the differences in the DNA sequences and the proteins that define a centromere, there is an overall structural similarity between centromeres in evolutionarily diverse eukaryotes.

  • 74.
    Bjerling, Pernilla
    et al.
    Södertörns högskola, Institutionen för kemi, biologi, geografi och miljövetenskap. Uppsala University / University of Copenhagen, Denmark .
    Ekwall, Karl
    Södertörns högskola, Institutionen för kemi, biologi, geografi och miljövetenskap.
    Egel, R
    Thon, G
    A novel type of silencing factor, Clr2, is necessary for transcriptional silencing at various chromosomal locations in the fission yeast Schizosaccharomyces pombe2004Inngår i: Nucleic Acids Research, ISSN 0305-1048, E-ISSN 1362-4962, Vol. 32, nr 15, s. 4421-4428Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The mating-type region of the fission yeast Schizosaccharomyces pombe comprises three loci: mat1, mat2-P and mat3-M. mat1 is expressed and determines the mating type of the cell. mat2-P and mat3-M are two storage cassettes located in a 17 kb heterochromatic region with features identical to those of mammalian heterochromatin. Mutations in the swi6(+), clr1(+), clr2(+), clr3(+), clr4(+) and clr6(+) genes were obtained in screens for factors necessary for silencing the mat2-P-mat3-M region. swi6(+) encodes a chromodomain protein, clr3(+) and clr6(+) histone deacetylases, and clr4(+) a histone methyltransferase. Here, we describe the cloning and characterization of clr2(+). The clr2(+) gene encodes a 62 kDa protein with no obvious sequence homologs. Deletion of clr2(+) not only affects transcriptional repression in the mating-type region, but also centromeric silencing and silencing of a PolII-transcribed gene inserted in the rDNA repeats. Using chromatin immunoprecipitation, we show that Clr2 is necessary for histone hypoacetylation in the mating-type region, suggesting that Clr2 acts upstream of histone deacetylases to promote transcriptional silencing.

  • 75.
    Bjerling, Pernilla
    et al.
    Södertörns högskola, Avdelning Naturvetenskap. Karolinska Institutet.
    Silverstein, Rebecca A
    Södertörns högskola, Avdelning Naturvetenskap. Karolinska Institutet.
    Thon, G
    Caudy, A
    Grewal, S
    Ekwall, Karl
    Södertörns högskola, Avdelning Naturvetenskap. Karolinska Institutet.
    Functional divergence between histone deacetylases in fission yeast by distinct cellular localization and in vivo specificity2002Inngår i: Molecular and Cellular Biology, ISSN 0270-7306, E-ISSN 1098-5549, Vol. 22, nr 7, s. 2170-2181Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Histone deacetylases (HDACs) are important for gene regulation and the maintenance of heterochromatin in eukaryotes. Schizosaccharomyces pombe was used as a model system to investigate the functional divergence within this conserved enzyme family. S. pombe has three HDACs encoded by the hda1(+), clr(3+), and clr6(+) genes. Strains mutated in these genes have previously been shown to display strikingly different phenotypes when assayed for viability, chromosome loss, and silencing. Here, conserved differences in the substrate binding pocket identify Clr6 and Hda1 as class I HDACs, while Clr3 belongs in the class II family. Furthermore, these HDACs were shown to have strikingly different subcellular localization patterns. Hda1 was localized to the cytoplasm, while most of Clr3 resided throughout the nucleus. Finally, Clr6 was localized exclusively on the chromosomes in a spotted pattern. Interestingly, Clr3, the only HDAC present in the nucleolus, was required for ribosomal DNA (rDNA) silencing. Clr3 presumably acts directly on heterochromatin, since it colocalized with the centromere, mating-type region, and rDNA as visualized by in situ hybridization. In addition, Clr3 could be cross-linked to mat3 in chromatin immunoprecipitation experiments. Western analysis of bulk histone preparations indicated that Hda1 (class I) had a generally low level of activity in vivo and Clr6 (class 1) had a high level of activity and broad in vivo substrate specificity, whereas Clr3 (class II) displayed its main activity on acetylated lysine 14 of histone H3. Thus, the distinct functions of the S. pombe HDACs are likely explained by their distinct cellular localization and their different in vivo specificities.

  • 76.
    Björk, Mats
    et al.
    Stockholm University, Sweden.
    Asplund, Maria E
    University of Gothenburg, Sweden.
    Deyanova, Diana
    University of Gothenburg, Sweden.
    Gullström, Martin
    Södertörns högskola, Institutionen för naturvetenskap, miljö och teknik, Miljövetenskap.
    The amount of light reaching the leaves in seagrass (Zostera marina) meadows2021Inngår i: PLOS ONE, E-ISSN 1932-6203, Vol. 16, nr 9, artikkel-id e0257586Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Seagrass meadows, and other submerged vegetated habitats, support a wide range of essential ecological services, but the true extents of these services are in many ways still not quantified. One important tool needed to assess and model many of these services is accurate estimations of the systems´ primary productivity. Such productivity estimations require an understanding of the underwater light field, especially regarding the amount of light that actually reaches the plants' photosynthetic tissue. In this study, we tested a simple practical approach to estimate leaf light exposure, relative to incoming light at the canopy, by attaching light sensitive film at different positions on leaves of Zostera marina, eelgrass, in four seagrass meadows composed of different shoot density and at two different depths. We found that the light reaching the leaves decreased linearly down through the canopy. While the upper parts of the leaves received approximately the same level of light (photosynthetic photon flux density, PPFD) as recorded with a PAR meter at the canopy top, the average light that the seagrass leaves were exposed to varied between 40 and 60% of the light on top of the canopy, with an overall average of 48%. We recommend that actual light interception is measured when assessing or modelling light depending processes in submerged vegetation, but if this is not achievable a rough estimation for vegetation similar to Z. marina would be to use a correction factor of 0.5 to compensate for the reduced light due to leaf orientation and internal shading.

  • 77.
    Björk, Petra
    et al.
    Stockholm University.
    Baurén, Göran
    Stockholm University.
    Jin, ShaoBo
    Stockholm University.
    Tong, Yong-Guang
    Karolinska Institutet.
    Bürglin, Thomas R.
    Karolinska Institutet.
    Hellman, Ulf
    Ludwig Institute for Cancer Research.
    Wieslander, Lars
    Stockholm University.
    A novel conserved RNA-binding domain protein, RBD-1, is essential for ribosome biogenesis2002Inngår i: Molecular Biology of the Cell, ISSN 1059-1524, E-ISSN 1939-4586, Vol. 13, nr 10, s. 3683-3695Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Synthesis of the ribosomal subunits from pre-rRNA requires a large number of trans-acting proteins and small nucleolar ribonucleoprotein particles to execute base modifications, RNA cleavages, and structural rearrangements. We have characterized a novel protein, RNA-binding domain-1 (RBD-1), that is involved in ribosome biogenesis. This protein contains six consensus RNA-binding domains and is conserved as to sequence, domain organization, and cellular location from yeast to human. RBD-1 is essential in Caenorhabditis elegans. In the dipteran Chironomus tentans, RBD-1 (Ct-RBD-1) binds pre-rRNA in vitro and anti-Ct-RBD-1 antibodies repress pre-rRNA processing in vivo. Ct-RBD-1 is mainly located in the nucleolus in an RNA polymerase I transcription-dependent manner, but it is also present in discrete foci in the interchromatin and in the cytoplasm. In cytoplasmic extracts, 20-30% of Ct-RBD-1 is associated with ribosomes and, preferentially, with the 40S ribosomal subunit. Our data suggest that RBD-1 plays a role in structurally coordinating pre-rRNA during ribosome biogenesis and that this function is conserved in all eukaryotes.

  • 78. Blacque, O E
    et al.
    Perens, E A
    Boroevich, K A
    Inglis, P N
    Li, C M
    Warner, A
    Khattra, J
    Holt, R A
    Ou, G S
    Mah, A K
    McKay, S J
    Huang, P
    Swoboda, Peter
    Södertörns högskola, Institutionen för livsvetenskaper. Karolinska Institute.
    Jones, S J M
    Marra, M A
    Baillie, D L
    Moerman, D G
    Shaham, S
    Leroux, M R
    Functional genomics of the cilium, a sensory organelle2005Inngår i: Current Biology, ISSN 0960-9822, E-ISSN 1879-0445, Vol. 15, nr 10, s. 935-941Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Cilia and flagella play important roles in many physiological processes, including cell and fluid movement, sensory perception, and development [1]. The biogenesis and maintenance of cilia depend on intraflagellar transport (IFT), a motility process that operates bidirectionally along the ciliary axoneme [1, 2]. Disruption in IFT and cilia function causes several human disorders, including polycystic kidneys, retinal dystrophy, neurosensory impairment, and Bardet-Bledl syndrome (BBS) [3-5]. To uncover new ciliary components, including IFT proteins, we compared C. elegans ciliated neuronal and nonciliated cells through serial analysis of gene expression (SAGE) and screened for genes potentially regulated by the cillogenic transcription factor, DAF-19 [6]. Using these complementary approaches, we identified numerous candidate ciliary genes and confirmed the ciliated-cell-specific expression of 14 novel genes. One of these, C27H5.7a, encodes a ciliary protein that undergoes IFT. As with other IFT proteins, its ciliary localization and transport is disrupted by mutations in IFT and bbs genes. Furthermore, we demonstrate that the ciliary structural defect of C. elegans dyf-13(mn396) mutants is caused by a mutation in C27H5.7a. Together, our findings help define a ciliary transcriptome and suggest that DYF-13, an evolutionarily conserved protein, is a novel core IFT component required for cilia function.

  • 79.
    Blom, Eva-Lotta
    et al.
    University of Gothenburg.
    Kvarnemo, Charlotta
    University of Gothenburg.
    Dekhla, Isabelle
    University of Gothenburg.
    Schöld, Sofie
    University of Gothenburg.
    Andersson, Mathias H.
    Swedish Defence Research Agency.
    Svensson, Ola
    Södertörns högskola, Institutionen för naturvetenskap, miljö och teknik, Matematikens didaktik. University of Gothenburg.
    Amorim, M Clara P
    ISPA-Instituto Universitário, Lisboa, Portugal; Universidade de Lisboa, Lisboa, Portugal.
    Continuous but not intermittent noise has a negative impact on mating success in a marine fish with paternal care2019Inngår i: Scientific Reports, E-ISSN 2045-2322, Vol. 9, nr 1, artikkel-id 5494Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Anthropogenic underwater noise is a global pollutant of increasing concern but its impact on reproduction in fish is largely unknown. Hence, a better understanding of its consequences for this important link to fitness is crucial. Working in aquaria, we experimentally tested the impact of broadband noise exposure (added either continuously or intermittently), compared to a control, on the behaviour and reproductive success of the common goby (Pomatoschistus microps), a vocal fish with exclusive paternal care. Compared to the intermittent noise and control treatments, the continuous noise treatment increased latency to female nest inspection and spawning and decreased spawning probability. In contrast, many other female and male pre-spawning behaviours, and female ventilation rate (proxies for stress levels) did not differ among treatments. Therefore, it is likely that female spawning decisions were delayed by a reduced ability to assess male acoustic signals, rather than due to stress per se and that the silent periods in the intermittent noise treatment provided a respite where the females could assess the males. Taken together, we show that noise (of similar frequency range as anthropogenic boat noise) negatively affects reproductive success, particularly under a continuous noise exposure.

    Fulltekst (pdf)
    Continuous but not intermittent noise has a negative impact on mating success in a marine fish with paternal care
  • 80.
    Boalt, Elin
    Södertörns högskola, Institutionen för livsvetenskaper.
    Ecology and evolution of tolerance in two cruciferous species2008Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    Tolerance to herbivory is the ability of plants to maintain fitness in spite of damage. The goal of this thesis is to investigate the genetic variation and expression of tolerance within species, determine whether and in what conditions tolerance has negative side-effects, and how tolerance is affected by different ecological factors. Tolerance is investigated with special focus on the effects of different damage types, competitive regimes, history of herbivory, and polyploidization in plants. Studies are conducted as a literature review and three experiments on two cruciferous species Raphanus raphanistrum and Cardamine pratensis.

    In the tolerance experiments, plants are subjected to artificial damage solely, or in a combination with natural damage. A literature review was conducted in order to investigate the effects of damage method. We found that traits related to tolerance, such as growth and fitness were not as sensitive in regard to damage method as measures of induced chemical traits, or measures of secondary herbivory.

    Genetic variation of tolerance was demonstrated within populations of R. raphanistrum and between subspecies of C. pratensis. In R. raphanistrum, traits involved in floral display and male fitness were positively associated with plant tolerance to herbivore damage. A potential cost of tolerance was demonstrated as a negative correlation between levels of tolerance in high and low competitive regimes. I found no evidence of other proposed costs of tolerance in terms of highly tolerant plants suffering of reduced fitness in the absence of herbivores or trade-offs in terms of a negative association between tolerance to apical and leaf damage, or between tolerance and competitive ability. In C. pratensis, higher ploidy level in plants involved higher levels of tolerance measured as clonal reproduction. Furthermore, populations exposed to higher levels of herbivory had better tolerance than populations exposed to lower levels of herbivory. In this thesis, I demonstrate evidence of different components for the evolution of tolerance in plants: genotypic variation, selective factors in terms of costs and ploidization, and selective agents in terms of changing environment or herbivore pressure.

    Download (jpg)
    presentationsbild
  • 81.
    Boalt, Elin
    et al.
    Södertörns högskola, Institutionen för livsvetenskaper, Miljövetenskap. Södertörns högskola, Institutionen för livsvetenskaper, Biologi.
    Arvanitis, Leena
    Lehtilä, Kari
    Södertörns högskola, Institutionen för livsvetenskaper, Miljövetenskap. Södertörns högskola, Institutionen för livsvetenskaper, Biologi.
    Ehrlén, Johan
    The association among herbivory tolerance, ploidy level, and herbivory pressure in Cardamine pratensis2010Inngår i: Evolutionary Ecology, ISSN 0269-7653, E-ISSN 1573-8477, Vol. 24, nr 5, s. 1101-1113Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We tested whether differences in ploidy level and previous exposure to herbivory can affect plant tolerance to herbivory. We conducted a common garden experiment with 12 populations of two ploidy levels of the perennial herb Cardamine pratensis (five populations of tetraploid ssp. pratensis and seven populations of octoploid ssp. paludosa). Earlier studies have shown that attack rates by the main herbivore, the orange tip butterfly Anthocharis cardamines, are lower in populations of octoploids than in populations of tetraploids, and vary among populations. In the common garden experiment, a combination of natural and artificial damage significantly reduced seed and flower production. We measured tolerance based on four plant-performance metrics: survival, growth, seed production and clonal reproduction. For three of these measurements, tolerance of damage did not differ between ploidy levels. For clonal reproduction, the octoploids had a higher tolerance than the tetraploids, although they experience lower herbivore attack rates in natural populations. Populations from sites with high levels of herbivory had higher tolerance, measured by seed production, than populations with low levels of herbivory. We did not detect any significant costs of tolerance. We conclude that high intensity of herbivory has selected for high tolerance measured by seed production in C. pratensis.

  • 82. Bommarco, Riccardo
    et al.
    Lönn, Mikael
    Södertörns högskola, Institutionen för livsvetenskaper, Miljövetenskap. Södertörns högskola, Institutionen för livsvetenskaper, Biologi.
    Danzer, Ulrika
    Pålsson, Karl-Johan
    Torstensson, Peter
    Genetic and phenotypic differences between thistle populations in response to habitat and weed management practices2010Inngår i: Biological Journal of the Linnean Society, ISSN 0024-4066, E-ISSN 1095-8312, Vol. 99, nr 4, s. 797-807Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Rapid evolutionary change is increasingly being recognized as commonplace, but the evolutionary consequences for species and ecosystems under human-induced selection regimes have not been explored in detail, although many species occur in such environments. In a common garden experiment and with amplified fragment length polymorphism markers, we examined whether genetic differentiation has taken place between spatially intermixed populations of creeping thistles Cirsium arvense (Asteraceae) collected from a natural habitat (maritime shores), a semi-natural habitat (road verges) and arable fields under two management regimes: conventional and organic farming. Populations of C. arvense have altered genetically and locally adapted their growth patterns with changed land use. Although plants from different habitats showed similar total biomass production, shoot and root production was higher for maritime populations, suggesting selection for increased competitive ability. Competitive ability then declined in the order semi-natural, conventional farms and organic farms. Thistles in arable fields may be more selected for tolerance against disturbances from herbicides and mechanical weed control. In addition, early shoot sprouting and genetic analysis showed differentiation between plants originating from conventional farms and farms that were converted to organic 9–30 years ago, suggesting some adaptation to altered crop cultivation practices

  • 83.
    Borg, Malin
    Södertörns högskola, Institutionen för livsvetenskaper.
    Does eutrophication cause directional genetic selection in three-spined stickleback (Gasterosteus aculeatus)?: A study of multiple Baltic Sea populations.2011Independent thesis Basic level (degree of Bachelor), 10 poäng / 15 hpOppgave
    Abstract [en]

    Human-induced eutrophication is indirectly affecting aquatic organisms by altering their environment. This brings on altered selective pressures and could thereby cause changes in the genetic composition of exposed populations. Since anthropogenic environmental changes are usually occurring at a much higher rate than naturally occurring changes, they force populations to adapt to the new conditions faster than normal. Here, I have studied populations of three-spined sticklebacks (Gasterosteus aculeatus) from four eutrophicated and four adjacent reference sites, along the coast of Finland, to investigate if this species has responded genetically to the human-induced eutrophication of the Baltic Sea. For this purpose I used amplified fragment length polymorphism (AFLP) and found distinctions in genetic composition between the two habitats, as well as similarities between populations from eutrophicated sites. This suggests a similar genetic response to eutrophicated conditions by stickleback populations from different geographical areas. Moreover I found a distinct geographic structure among three-spined sticklebacks in the Baltic Sea.

    Fulltekst (pdf)
    Does_eutrophication_cause_directional_genetic_selection_in_three-spined_stickleback
  • 84.
    Borg, Malin
    Södertörns högskola, Institutionen för livsvetenskaper.
    Does eutrophication cause directional genetic selection in three-spined sticklebacks (Gasterosteus aculeatus)?: A study of multiple Baltic Sea populations2011Independent thesis Basic level (degree of Bachelor), 10 poäng / 15 hpOppgave
    Abstract [en]

    Human-induced eutrophication is indirectly affecting aquatic organisms by altering their environment. This brings on altered selective pressures and could thereby cause changes in the genetic composition of exposed populations. Since anthropogenic environmental changes are usually occurring at a much higher rate than naturally occurring changes, they force populations to adapt to the new conditions faster than normal. Here, I have studied populations of three-spined sticklebacks (Gasterosteus aculeatus) from four eutrophicated and four adjacent reference sites, along the coast of Finland, to investigate if this species has responded genetically to the human-induced eutrophication of the Baltic Sea. For this purpose I used amplified fragment length polymorphism (AFLP) and found distinctions in genetic composition between the two habitats, as well as similarities between populations from eutrophicated sites. This suggests a similar genetic response to eutrophicated conditions by stickleback populations from different geographical areas. Moreover I found a distinct geographic structure among three-spined sticklebacks in the Baltic Sea.

    Fulltekst (pdf)
    Does eutrophication cause directional genetic selection in three-spined sticklebacks
  • 85.
    Boss, John
    Södertörns högskola, Institutionen för livsvetenskaper.
    Adaptive evolution of Transcription Factors in European and wine yeast2009Independent thesis Advanced level (degree of Master (One Year)), 20 poäng / 30 hpOppgave
    Abstract [en]

    The mutability of transcription factors (TF) is thought to be of high importance for the evolutionary change of living organisms. Transcription factors, coactivators, coregulators, kinases, chromatin remodelers conditional factors and other proteins together govern the timing and level of gene expression. About 10% of the genes in the human genome are predicted to be TFs and mutational changes in these genes or in the target regulatory sequences they bind will potentially give rise to evolutionary advantages or malfunctions for the organism. Recent research has suggested that the parts of the transcription factors that are not structurally defined in solution, so called intrinsically disordered regions (IDRs), have a higher potential for evolutionary diversification than more structurally rigid regions. This suggests that these domains that earlier have been considered mostly unimportant may have an important potential for evolutionary diversification. This project aimed to further evaluate evidence supporting the hypothesis that variable-structured domains in transcription factors are of significant importance for functional diversification. This was be done by comparing the rate of synonymous and non-synonymous genetic variation in the coding regions of 12 selected TFs within a highly conserved clade of European wine yeasts and by comparing this variation to divergent phenotypic patterns within the strains. The frequency of non-synonymous mutations was much greater than for synonymous mutations indicating an important role of positive selection acting on these TFs during diversification of the different strains. No significant connections were discovered between the distribution of DNA variation and phenotypic patterns.

    Fulltekst (pdf)
    FULLTEXT01
  • 86.
    Boss, John
    et al.
    Södertörns högskola, Institutionen för naturvetenskap, miljö och teknik. Karolinska Institute.
    Liedvogel, Miriam
    Lund University / Max Planck Institute for Evolutionary Biology, Plön, Germany.
    Lundberg, Max
    Lund University.
    Olsson, Peter
    Lund University.
    Reischke, Nils
    Lund University.
    Naurin, Sara
    Lund University.
    Åkesson, Susanne
    Lund University.
    Hasselquist, Dennis
    Lund University.
    Wright, Anthony
    Karolinska Institute.
    Grahn, Mats
    Södertörns högskola, Institutionen för naturvetenskap, miljö och teknik, Biologi.
    Bensch, Staffan
    Lund University.
    Gene expression in the brain of a migratory songbird during breeding and migration2016Inngår i: Movement Ecology, E-ISSN 2051-3933, Vol. 4, artikkel-id 4Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

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

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

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

  • 87.
    Bradshaw, Clare
    et al.
    Södertörns högskola, Institutionen för naturvetenskap, miljö och teknik. Stockholm University.
    Golz, A. -L
    Stockholm University.
    Gustafsson, Kerstin
    Södertörns högskola, Institutionen för naturvetenskap, miljö och teknik.
    Coastal ecosystem effects of increased summer temperature and contamination by the flame retardant HBCDD2017Inngår i: Journal of Marine Science and Engineering, E-ISSN 2077-1312, Vol. 5, nr 2, s. -20, artikkel-id 18Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The combined effects of ocean warming and contaminants on marine ecosystems are poorly understood. In this study, we exposed model ecosystems comprising typical shallow coastal Baltic Sea communities to elevated temperature (+5 °C) and the flame retardant hexabromocyclododecane (HBCDD), both singly and in combination, for 13 days. Higher temperatures caused the release of PO4 from the sediment, which in turn stimulated the growth of the cyanobacteria Dolichospermum sp. This in turn led to an increase in the copepod Acartia bifilosa and other indirect effects in the plankton, interpreted as being caused by changes in predation, grazing, and competition. Elevated temperatures also stimulated benthic primary production and increased production of benthic mollusk larvae. Although increased temperature was the dominant driver of effects in these systems, HBCDD also appeared to have some effects, mainly in the zooplankton (both direct and indirect effects) and benthic meiofauna (an interactive effect with temperature). Although the study used model ecosystems, which are an approximation of field conditions, it highlights that interactive ecosystem effects between two stressors are possible and demonstrates the ecological and temporal complexity of such responses. Such unpredictable responses to warming and contaminants are a major challenge for ecosystem management to deal with multistressor situations in the Baltic Sea. 

  • 88.
    Bradshaw, Clare
    et al.
    Södertörns högskola, Institutionen för naturvetenskap, miljö och teknik. Stockholm University.
    Strid, Anna
    Stockholm University.
    von Stedingk, Hans
    Stockholm University.
    Gustafsson, Kerstin
    Södertörns högskola, Institutionen för naturvetenskap, miljö och teknik.
    Effects of benthos, temperature and dose on the fate of HBCDD in experimental coastal ecosystems2015Inngår i: Environmental Toxicology and Chemistry, ISSN 0730-7268, E-ISSN 1552-8618, Vol. 34, nr 6, s. 1246-1257Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We studied the fate of the brominated flame retardant hexabromocyclododecane (HBCDD) added in a particulate suspension to experimental ecosystems assembled from brackish (Baltic Sea) coastal bays. Two experiments examined how A) benthic macrofauna (over 21 d), and B) increased temperature (14 d), affected HBCDD concentrations and fractionation of α, β and γ diastereomers in the water, sediment and biota. A third experiment (C) run over three seasons (231 d), studied the effect of HBCDD dose on the same endpoints. In all treatments of the three experiments, HBCDD partitioned mainly to the sediment, and this proportion increased with time. Presence of macrofauna tended to increase the HBCDD concentration in the sediment and decreased its concentration in the water. Increased temperature (+5 °C) decreased the amount of HBCDD in sediment and water but not in the filter- and deposit-feeding infaunal bivalves (Macoma balthica). The partitioning between water, sediment and biota was not concentration dependent. In all treatments, sediment became enriched in γ-HBCDD, M. balthica in α-HBCDD and water in α- and β-HBCDD. Bioaccumulation of HBCDD in M. balthica was high in all experiments (logBSAF > 1.25), the α diastereomer contributing the most (logBSAF 2.1 to 5.2). There is a risk of trophic transfer of HBCDD from benthic to pelagic food webs, and secondary poisoning of marine consumers. This article is protected by copyright. All rights reserved.

  • 89. Bratic, Ivana
    et al.
    Hench, Jürgen
    Södertörns högskola, Institutionen för livsvetenskaper.
    Henriksson, Johan
    Södertörns högskola, Institutionen för livsvetenskaper, Molekylärbiologi.
    Antebi, Adam
    Bürglin, Thomas R.
    Trifunovic, Aleksandra
    Mitochondrial DNA level, but not active replicase, is essential for Caenorhabditis elegans development2009Inngår i: Nucleic Acids Research, ISSN 0305-1048, E-ISSN 1362-4962, Vol. 37, nr 6, s. 1817-1828Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    A number of studies showed that the development and the lifespan of Caenorhabditis elegans is dependent on mitochondrial function. In this study, we addressed the role of mitochondrial DNA levels and mtDNA maintenance in development of C. elegans by analyzing deletion mutants for mitochondrial polymerase gamma (polg-1(ok1548)). Surprisingly, even though previous studies in other model organisms showed necessity of polymerase gamma for embryonic development, homozygous polg-1(ok1548) mutants had normal development and reached adulthood without any morphological defects. However, polg-1 deficient animals have a seriously compromised gonadal function as a result of severe mitochondrial depletion, leading to sterility and shortened lifespan. Our results indicate that the gonad is the primary site of mtDNA replication, whilst the mtDNA of adult somatic tissues mainly stems from the developing embryo. Furthermore, we show that the mtDNA copy number shows great plasticity as it can be almost tripled as a response to the environmental stimuli. Finally, we show that the mtDNA copy number is an essential limiting factor for the worm development and therefore, a number of mechanisms set to maintain mtDNA levels exist, ensuring a normal development of C. elegans even in the absence of the mitochondrial replicase.

  • 90.
    Bredenberg, Johan
    et al.
    Södertörns högskola, Avdelning Naturvetenskap. Karolinska Institutet.
    Nilsson, L
    Karolinska Institutet.
    Conformational states of the glucocorticoid receptor DNA-binding domain from molecular dynamics simulations2002Inngår i: Proteins: Structure, Function, and Bioinformatics, ISSN 0887-3585, E-ISSN 1097-0134, Vol. 49, nr 1, s. 24-36Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Molecular dynamics simulations (MD) have been performed on variant crystal and NMR-derived structures of the glucocorticoid receptor DNA-binding domain (GR DBD). A loop region five residues long, the so-called D-box, exhibits significant flexibility, and transient perturbations of the tetrahedral geometry of two structurally important Cys4 zinc finger are seen, coupled to conformational changes in the D-box. In some cases, one of the Cys ligands to zinc exchanges with water, although no global distortion of the protein structure is observed. Thus, from MD simulation, dynamics of the D-box could partly be explained by solvent effects in conjunction with structural reformation of the zinc finger.

  • 91. Brenden, N.
    et al.
    Böhme, Jan
    Södertörns högskola, Avdelning Naturvetenskap. Karolinska Institute.
    Differential MHC expression requirements for positive selection of separate TCR Vb families1999Inngår i: Immunogenetics, ISSN 0093-7711, E-ISSN 1432-1211, Vol. 49, nr 1, s. 1-6Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Positive selection has been proposed to be involved in protection from diabetes. We examined positive selection by fluorescence-activated cell sorter analyses in thymocytes of protected and susceptible E-transgenic and non-transgenic NOD mice. Three Vb families showed positive selection in E-transgenic mice. Vb6+CD4+ and Vb10+CD4+ thymocytes were found at higher frequencies in both protected NOD-Ea and susceptible NOD-DY mice. The increased frequencies of Vb13+CD8+ thymocytes were found in protected NOD-Ea mice only, and not in susceptible NOD-DY transgenic mice. These three Vb families were further examined in bone-marrow chimeras between NOD-Ea and non-transgenic NOD mice, where we could examine the contribution of E-expressing bone-marrow-derived cells in positive selection. We find that NOD-Ea→NOD-Ea chimeras have an increased positive selection of Vb13+CD8+ cells and that positive selection is more efficient when both thymic epithelium and bone-marrow-derived cells express the E molecule. This was also seen for Vb6+CD4+ cells. However, for Vb6, bone-marrow-derived cells alone were also capable of positive selection. Positive selection of Vb10+CD4+ cells was restricted to E-expressing thymic epithelium only. For Vb13+CD8+ cells, we found that positive selection is most efficient with E-expression on both thymic epithelium and bone-marrow-derived cells, although positive selection also occurs with E-positive epithelium only. For Vb6+CD4+ cells, the dominating selecting cells are bone-marrow-derived cells, and Vb10+CD4+ cells seem to be selected exclusively by the thymic epithelium. Thus, the conditions for positive selection seem to vary considerably between different Vb families.

  • 92. Brenden, N.
    et al.
    Böhme, Jan
    Södertörns högskola, Avdelning Naturvetenskap. Karolinska Institute.
    Disease-protected major histocompatibility complex Ea-transgenic non- obese diabetic (NOD) mice show interleukin-4 production not seen in susceptible Ea-transgenic and non-transgenic NOD mice1998Inngår i: Immunology, ISSN 0019-2805, E-ISSN 1365-2567, Vol. 95, nr 1, s. 1-7Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The non-obese diabetic (NOD) mouse is an animal model for insulin- dependent diabetes that has many similarities to the human disease. NOD mice transgenic for the Ea gene, allowing expression of the E molecule, are protected from diabetes and rarely develop insulitis. An Ea transgene mutated in the promoter region, (ΔY) lacks E expression on most B cells, thymic medullary epithelium and primary antigen-presenting cells, and confers no protection whatsoever. We have used these transgenic NOD mice, together with non-transgenic NOD mice, to study the correlation of E expression and production of interleukin-4 (IL-4) and interferon-γ (IFN-γ). We show that protected E-transgenic NOD mice have elevated levels of IL-4 compared with non-transgenic mice, both in the thymus and in the periphery. However, susceptible ΔY-transgenic mice have elevated thymic IL-4 levels, but express almost as little IL-4 as non-transgenic NOD mice in the periphery. This drop in peripheral IL-4 production seen in ΔY-transgenic mice thus correlates with the decreased E expression in the periphery of ΔY-transgenic NOD mice. In contrast, there were no differences in IFN-γ production between the three NOD lines. We suggest that Ea-transgenic NOD mice have E-selected regulatory T cells producing IL-4, which are subsequently activated by E-expressing primary antigen-presenting cells in the periphery. This activation would then be instrumental for the E-mediated protection from disease in NOD mice. Such a process would explain the total absence of protection in ΔY-transgenic NOD mice, despite their widespread E expression.

  • 93. Brenden, N.
    et al.
    Rietz, C.
    Böhme, Jan
    Södertörns högskola, Avdelning Naturvetenskap. Karolinska Institute.
    E expression is needed on both bone marrow derived cells and thymic epithelium to increase IL-4 production and achieve protection in NOD bone marrow chimeras1999Inngår i: Cytokine, ISSN 1043-4666, E-ISSN 1096-0023, Vol. 11, nr 10, s. 766-772Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The NOD mouse is an animal model for insulin-dependent diabetes with many similarities to the human disease. NOD mice which are transgenic for the Ea gene, allowing expression of the E molecule, are protected from diabetes and rarely develop insulitis. We have constructed bone marrow chimeras between transgenic and non-transgenic NOD mice to study the correlation of E expression on bone marrow derived cells and thymic epithelium vs the production of IL-4 and IFN-γ. We show that NOD-E→NOD-E and NOD-E→NOD chimeras have elevated levels of IL-4 compared to NOD→NOD and NOD→NOD-E chimeras in the thymus. However, in the periphery the protected NOD-E→NOD-E show much higher IL-4 levels than any of the other chimeras. This drop in peripheral IL-4 production seen in NOD-E→NOD, NOD→NOD-E and NOD→NOD chimeras correlates with the increased insulitis seen in these mice compared to NOD-E→NOD-E. In contrast, there were no differences in IFN-γ production between the chimeras. We suggest that the precommitted, regulatory T cells, selected in an E-expressing thymic environment, need continuous interaction with E-expressing primary antigen presenting cells in the periphery for optimal IL-4 production. Decrease in IL-4 production correlates with increased insulitis.

  • 94.
    Broman, Elias
    et al.
    Södertörns högskola, Institutionen för naturvetenskap, miljö och teknik, Miljövetenskap. Stockholm University, Sweden.
    Abdelgadir, Mohanad
    Södertörns högskola, Institutionen för naturvetenskap, miljö och teknik, Miljövetenskap.
    Bonaglia, Stefano
    University of Gothenburg, Sweden.
    Forsberg, Sara C.
    Södertörns högskola, Institutionen för naturvetenskap, miljö och teknik, Miljövetenskap. Stockholm University, Sweden.
    Wikström, Johan
    Stockholm University, Sweden.
    Gunnarsson, Jonas S.
    Stockholm University, Sweden.
    Nascimento, Francisco J. A.
    Stockholm University, Sweden.
    Sjöling, Sara
    Södertörns högskola, Institutionen för naturvetenskap, miljö och teknik, Miljövetenskap.
    Long-Term Pollution Does Not Inhibit Denitrification and DNRA by Adapted Benthic Microbial Communities2023Inngår i: Microbial Ecology, ISSN 0095-3628, E-ISSN 1432-184X, Vol. 86, s. 2357-2372Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Denitrification in sediments is a key microbial process that removes excess fixed nitrogen, while dissimilatory nitrate reduction to ammonium (DNRA) converts nitrate to ammonium. Although microorganisms are responsible for essential nitrogen (N) cycling, it is not yet fully understood how these microbially mediated processes respond to toxic hydrophobic organic compounds (HOCs) and metals. In this study, we sampled long-term polluted sediment from the outer harbor of Oskarshamn (Baltic Sea), measured denitrification and DNRA rates, and analyzed taxonomic structure and N-cycling genes of microbial communities using metagenomics. Results showed that denitrification and DNRA rates were within the range of a national reference site and other unpolluted sites in the Baltic Sea, indicating that long-term pollution did not significantly affect these processes. Furthermore, our results indicate an adaptation to metal pollution by the N-cycling microbial community. These findings suggest that denitrification and DNRA rates are affected more by eutrophication and organic enrichment than by historic pollution of metals and organic contaminants.

  • 95.
    Broniarczyk, Justyna
    et al.
    Department of Molecular Virology, Adam Mickiewicz University.
    Wigerius, Michael
    Södertörns högskola, Institutionen för livsvetenskaper, Molekylärbiologi. Södertörns högskola, Institutionen för livsvetenskaper, Kemi.
    Johansson, Magnus
    Södertörns högskola, Institutionen för livsvetenskaper, Internationell hälsa. Södertörns högskola, Institutionen för livsvetenskaper, Kemi.
    The NS1 protein of Influenza A virus targets human Scribble in asubtype specific mannerManuskript (preprint) (Annet vitenskapelig)
  • 96.
    Browall, Sarah
    Södertörns högskola, Institutionen för livsvetenskaper.
    Comparative genomic analyse by microarray technology of pneumococci with different potential to cause disease.2007Independent thesis Basic level (professional degree), 20 poäng / 30 hpOppgave
    Abstract [en]

    Streptococcus pneumoniae is a gram-positive bacterium that can be found in both healthy carriers as well as in people that have developed disease. One of the major virulence factors of pneumococci is their polysaccharide capsule. Based on the capsule that surrounds the bacteria, pneumococci are divided into at least 90 different serotypes. Some serotypes seem to be more related to virulence than others.

    I have with comparative genome hybridization microarray technique, studied gene differences between 18 epidemiological well-characterised pneumococcal strains with different potential to cause disease. A microarray chip based on two sequenced pneumococcal genomes, R6 and TIGR4, has already been designed. According to Hierarchical clustering, both the serotype and the genetic type as assessed by MLST (sequence type or ST) seem to have impact on the relationship of clinical isolates. Most clinical isolates of the same serotype are clustered together except for serotype 14 isolates that seem to be more divergent. Further more the number of genes that are divergent between clinical isolates compared to R6 and TIGR4 differ from 65 to 289. Preliminary results indicate that although there is diversity among clinical isolates some are more closely related to each other then others. Absent genes seem to be evenly distributed among all 18 clinical isolates tested but hypothetical genes and genes for cell envelope are two groups of role categories that are absent to the largest extent in all isolates.

    According to results from microarray analysis, a gene region, spr0112-spr1015- is present in all type 9V isolates and absent in many isolates of serotype 14, 19F and 7F. These results have been confirmed by polymerase chain reaction (PCR).

    Conserved genes in a region around the capsule genes have been sequenced to identify marker genes for a capsulular switch between serotype 9V and 14. Preliminary results of the sequencing showed that as much as 750kb might have been transferred in the event of capsular switch.

    Fulltekst (pdf)
    FULLTEXT01
  • 97. Brunne, R M
    et al.
    Berndt, Kurt D
    ETH Hönggerberg, Zürich, Switzerland.
    Güntert, P
    Wüthrich, K
    van Gunsteren, W F
    Güntert, P
    Wüthrich, K
    Van Gunsteren, W F
    Structure and internal dynamics of the bovine pancreatic trypsin inhibitor in aqueous solution from long-time molecular dynamics simulations1995Inngår i: Proteins: Structure, Function, and Bioinformatics, ISSN 0887-3585, E-ISSN 1097-0134, Vol. 23, nr 1, s. 49-62Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Structural and dynamic properties of bovine pancreatic trypsin inhibitor (BPTI) in aqueous solution are investigated using two molecular dynamics (MD) simulations: one of 1.4 ns length and one of 0.8 ns length in which atom-atom distance bounds derived from NMR spectroscopy are included in the potential energy function to make the trajectory satisfy these experimental data more closely. The simulated properties of BPTI are compared with crystal and solution structures of BPTI, and found to be in agreement with the available experimental data. The best agreement with experiment was obtained when atom-atom distance restraints were applied in a time-averaged manner in the simulation. The polypeptide segments found to be most flexible in the MD simulations coincide closely with those showing differences between the crystal and solution structures of BPTI.

  • 98.
    Bräutigam, Lars
    et al.
    Södertörns högskola, Institutionen för livsvetenskaper, Molekylärbiologi.
    Hillmer, Janine M.
    Södertörns högskola, Institutionen för livsvetenskaper, Molekylärbiologi.
    Söll, Iris
    Södertörns högskola, Institutionen för livsvetenskaper, Molekylärbiologi.
    Hauptmann, Giselbert
    Södertörns högskola, Institutionen för livsvetenskaper, Molekylärbiologi.
    Localized Expression of Urocortin Genes in the Developing Zebrafish rain2010Inngår i: Journal of Comparative Neurology, ISSN 0021-9967, E-ISSN 1096-9861, Vol. 518, nr 15, s. 2978-2995Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The corticotropin-releasing hormone (CRH) family consists of four aralogous genes, CRH and urocortins (UCNs) 1, 2, and 3. In a previous tudy, we analyzed CRH in the teleost model organism zebrafish and its ranscript distribution in the embryonic brain. Here, we describe ull-length cDNAs encoding urotensin 1 (UTS1), the teleost UCN1 rtholog, and UCN3 of zebrafish. Major expression sites of uts1 in adult ebrafish are the caudal neurosecretory system and brain. By using T-PCR analysis, we show that uts1 mRNA is also present in ovary, aternally contributed to the embryo, and expressed throughout embryonic evelopment. Expression of ucn3 mRNA was detected in a range of adult issues and during developmental stages from 24 hours post fertilization nward. Analysis of spatial transcript distributions by whole-mount in itu hybridization revealed limited forebrain expression of uts1 and cn3 during early development. Small numbers of uts1-synthesizing eurons were found in subpallium, hypothalamus, and posterior iencephalon, whereas ucn3-positive cells were restricted to elencephalon and retina. The brainstem was the main site of uts1 and cn3 synthesis in the embryonic brain. uts1 Expression was confined to he midbrain tegmentum; distinct hindbrain cell groups, including locus oeruleus and Mauthner neurons; and the spinal cord. ucn3 Expression was ocalized to the optic tectum, serotonergic raphe, and distinct hombomeric cell clusters. The prominent expression of uts1 and ucn3 in rainstem is consistent with proposed roles of CRH-related peptides in tress-induced modulation of locomotor activity through monoaminergic rainstem neuromodulatory systems. J. Comp. Neurol. 518:2978-2995, 2010.

  • 99.
    Buch, Charlotta
    Södertörns högskola, Institutionen för livsvetenskaper. Karolinska Institutet.
    Dynamic protein trafficking of the nuclear membrane and in peroxisomes2009Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    The cell nucleus is enclosed by the nuclear envelope (NE), a double lipid membrane separating the nucleoplasm from the cytoplasm. Transport of macromolecules between the nucleus and the cytoplasm takes places through nuclear pore complexes (NPCs) in a selective and energy dependent manner. The inner nuclear membrane (INM) contains transmembrane proteins that interact with the nuclear lamina and chromatin. In addition to being a barrier between the nucleoplasm and cytoplasm, an emerging view is that the NE has an active role in chromatin organization and gene regulation.

    In order to study structural and functional organization of the NE in live cells, we have used green fluorescent protein (GFP)-labeled proteins and laser scanning confocal microscopy (LSCM). In order to investigate dynamic properties of specific proteins or protein complexes we have used photobleaching techniques. In order to understand the organization of the NPC it is essential to study components necessary for NPC biogenesis and maintenance. We have investigated the possible alterations in the NPC in cells naturally lacking one of the integral membrane proteins of the NPC, gp210. Despite the lack of gp210, we observed no difference in distribution or density of pores. Neither did cell cycle progression nor generation time differ between cells having or lacking gp210. In addition, targeting or dynamic properties of the NPC proteins POM121, Nup107 or Nup153 were unaltered in the absence of gp210. We conclude that gp210 can not be essential for NPC biogenesis or maintaining stability of the NPC.

    The steps involved in onset of nuclear apoptosis are unclear. We studied nuclear alterations during apoptosis. We show that the nucleocytoplasmic barrier is disrupted early in apoptosis at the same time as chromatin collapses against the nuclear periphery but prior to nucleosomal DNA fragmentation. In addition, the disruption of nucleocytoplasmic transport correlates with caspase-3 dependent cleavage of POM121 at aspartate-531.

    The INM is estimated to contain ~70 uncharacterized transmembrane proteins. We characterized a novel putative mammalian NE protein that we termed Samp1. We show that Samp1 is an integral membrane protein specifically localized to the inner nuclear membrane during interphase. Interestingly, during mitosis a sub fraction of Samp1 distributed in the polar region of the mitotic spindle, colocalizing with tubulin and a lipid marker. However, another inner nuclear membrane protein, emerin, was excluded from this area. Thus Samp1 appears to define a specific membrane domain associated with the mitotic machinery.

    The distribution of peroxisomal fatty acid metabolizing enzymes have been reported to vary in different tissues. We investigated whether photobleaching techniques could be used to study the distribution of peroxisomal matrix proteins. We used GFP-labeled peroxisomal proteins and fluorescence recovery after photobleaching to show that peroxisomal matrix proteins become “trapped” inside peroxisomes after import. Thus we conclude that fluorescence loss in photobleaching can be used to distinguish between a strictly cytoplasmic localization and a dual localization when a protein is present both in the cytoplasm and in peroxisomes. Using this technique we determined that GFP-BAAT (bile acid-CoA:amino acid N-acyltransferase) is exclusively localized to the cytoplasm in HeLa cells.

  • 100.
    Buch, Charlotta
    et al.
    Södertörns högskola, Institutionen för livsvetenskaper.
    Hunt, Mary C.
    Alexson, Stefan E. H.
    Hallberg, Einar
    Södertörns högskola, Institutionen för livsvetenskaper.
    Localization of peroxisomal matrix proteins by photobleaching2009Inngår i: Biochemical and Biophysical Research Communications - BBRC, ISSN 0006-291X, E-ISSN 1090-2104, Vol. 388, nr 2, s. 355-359Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The distribution of some enzymes between peroxisomes and cytosol, or a dual localization in both these compartments, can be difficult to reconcile. We have used photobleaching in live cells expressing green fluorescent protein (GFP)-fusion proteins to show that imported bona fide peroxisomal matrix proteins are retained in the peroxisome. The high mobility of the GFP-fusion proteins in the cytosol and absence of peroxisomal escape makes it possible to eliminate the cytosolic fluorescence by photobleaching, to distinguish between exclusively cytosolic proteins and proteins that are also present at low levels in peroxisomes. Using this technique we found that GFP tagged bile acid-CoA:amino acid N-acyltransferase (BAAT) was exclusively localized in the cytosol in HeLa cells. We conclude that the cytosolic localization was due to its carboxyterminal non-consensus peroxisomal targeting signal (-SQL) since mutation of the -SQL to -SKL resulted in BAAT being efficiently imported into peroxisomes.

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