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  • 301.
    Jakobsson, Hedvig
    et al.
    Swedish Institute for Infectious Disease Control.
    Jernberg, Cecilia
    Karolinska Institute.
    Sjölund, Maria
    Central Hospital, Växjö.
    Jansson, Janet
    Swedish University of Agricultural Sciences.
    Engstrand, Lars
    Swedish Institute for Infectious Disease Control.
    Molecular analysis of ecological changes in the human normal microflora after treatment with clarithromycin and metronidazoleManuscript (preprint) (Other academic)
  • 302.
    Janson, Sven
    et al.
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies.
    Wouters, Johanna
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Biology.
    Bonow, Madeleine
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Geography.
    Svanberg, Ingvar
    Uppsala University.
    Olsén, K. Håkan
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Biology.
    Population genetic structure of crucian carp (Carassius carassius) in man-made ponds and wild populations in Sweden2015In: Aquaculture International, ISSN 0967-6120, E-ISSN 1573-143X, Vol. 23, no 1, p. 359-368Article in journal (Other academic)
    Abstract [en]

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

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  • 303.
    Jeffries, Daniel L
    et al.
    University of Hull, Hull, UK.
    Copp, Gordon H
    Bournemouth University, Poole, UK.
    Lawson Handley, Lori
    University of Hull, Hull, UK.
    Olsén, K. Håkan
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Biology.
    Sayer, Carl D
    University College London, London, UK.
    Hänfling, Bernd
    University of Hull, Hull, UK.
    Comparing RADseq and microsatellites to infer complex phylogeographic patterns, an empirical perspective in the Crucian carp, Carassius carassius, L2016In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 25, no 13, p. 2997-3018Article in journal (Refereed)
    Abstract [en]

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

  • 304. Jensen, Lasse Dahl Ejby
    et al.
    Cao, Renhai
    Hedlund, Eva-Maria
    Söll, Iris
    Södertörn University, School of Life Sciences, Molecular biology.
    Lundberg, Jon O.
    Hauptmann, Giselbert
    Södertörn University, School of Life Sciences, Molecular biology.
    Steffensen, John Fleng
    Cao, Yihai
    Nitric oxide permits hypoxia-induced lymphatic perfusion by controlling arterial-lymphatic conduits in zebrafish and glass catfish2009In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 106, no 43, p. 18408-18413Article in journal (Refereed)
    Abstract [en]

    The blood and lymphatic vasculatures are structurally and functionally coupled in controlling tissue perfusion, extracellular interstitial fluids, and immune surveillance. Little is known, however, about the molecular mechanisms that underlie the regulation of bloodlymphatic vessel connections and lymphatic perfusion. Here we show in the adult zebrafish and glass catfish (Kryptopterus bicirrhis) that blood-lymphatic conduits directly connect arterial vessels to the lymphatic system. Under hypoxic conditions, arterial-lymphatic conduits (ALCs) became highly dilated and linearized by NO-induced vascular relaxation, which led to blood perfusion into the lymphatic system. NO blockage almost completely abrogated hypoxia-induced ALC relaxation and lymphatic perfusion. These findings uncover mechanisms underlying hypoxia-induced oxygen compensation by perfusion of existing lymphatics in fish. Our results might also imply that the hypoxia-induced NO pathway contributes to development of progression of pathologies, including promotion of lymphatic metastasis by modulating arterial-lymphatic conduits, in the mammalian system.

  • 305.
    Jenvert, Rose-Marie
    Södertörn University, School of Life Sciences. Stockholms universitet.
    The ribosome, stringent factor and the bacterial stringent response2007Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The stringent response plays a significant role in the survival of bacteria during different environmental conditions. It is activated by the binding of stringent factor (SF) to stalled ribosomes that have an unacylated tRNA in the ribosomal A-site which leads to the synthesis of (p)ppGpp. ppGpp binds to the RNA polymerase, resulting in a rapid down-regulation of rRNA and tRNA transcription and up-regulation of mRNAs coding for enzymes involved in amino acid biosynthesis. The importance of the A-site and unacylated tRNA in the activation of SF was confirmed by chemical modification and subsequent primer extension experiments (footprinting experiments) which showed that binding of SF to ribosomes resulted in the protection of regions in 23S rRNA, the A-loop and helix 89 that are involved in the binding of the A-site tRNA. An in vitro assay showed that the ribosomal protein L11 and its flexible N-terminal part was important in the activation of SF. Interestingly the N-terminal part of L11 was shown to activate SF on its own and this activation was dependent on both ribosomes and an unacylated tRNA in the A-site. The N-terminal part of L11 was suggested to mediate an interaction between ribosome-bound SF and the unacylated tRNA in the A-site or interact with SF and the unacylated tRNA independently of each other. Footprinting experiments showed that SF bound to the ribosome protected bases in the L11 binding domain of the ribosome that were not involved in an interaction with ribosomal protein L11. The sarcin/ricin loop, in close contact with the L11 binding domain on the ribosome and essential for the binding and activation of translation elongation factors was also found to be protected by the binding of SF. Altogether the presented results suggest that SF binds to the factor-binding stalk of the ribosome and that activation of SF is dependent on the flexible N-terminal domain of L11 and an interaction of SF with the unacylated tRNA in the A-site of the 50S subunit.

  • 306.
    Jenvert, Rose-Marie
    et al.
    Södertörn University, School of Life Sciences. Stockholms universitet.
    Holmberg Schiavone, Lovisa
    Södertörn University, School of Life Sciences. Karolinska institutet.
    Mapping the interaction between stringent factor and the ribosome by footprinting of ribosomal RNAManuscript (preprint) (Other academic)
  • 307.
    Jenvert, Rose-Marie
    et al.
    Södertörn University, School of Life Sciences. Stockholm University.
    Holmberg Schiavone, Lovisa
    Södertörn University, School of Life Sciences.
    The flexible n-terminal domain of ribosomal protein L11 from Escherichia coli is necessary for the activation of stringent factor2007In: Journal of Molecular Biology, ISSN 0022-2836, E-ISSN 1089-8638, Vol. 365, no 3, p. 764-772Article in journal (Refereed)
    Abstract [en]

    The stringent response is activated by the binding of stringent factor to stalled ribosomes that have an unacylated tRNA in the ribosomal aminoacyl-site. Ribosomes lacking ribosomal protein L11 are deficient in 2 stimulating stringent factor. L11 consists of a dynamic N-terminal domain (amino acid residues 1-72) connected to an RNA-binding C-terminal domain (amino acid residues 76-142) by a flexible linker (amino acid residues 73-75). In vivo data show that mutation of proline 22 in the N-terminal domain is important for initiation of the stringent response. Here, six different L11 point and deletion-mutants have been constructed to determine which regions of L11 are necessary for the activation of stringent factor. The different mutants were reconstituted with programmed 70 S (Delta L11) ribosomes and tested for their ability to stimulate stringent factor in a sensitive in vitro pppGpp synthesis assay. It was found that a single-site mutation at proline 74 in the linker region between the two domains did not affect the stimulatory activity of the reconstituted ribosomes, whereas the single-site mutation at proline 22 reduced the activity of SF to 33% compared to ribosomes reconstituted with wild-type L11. Removal of the entire linker between the N and C-terminal domains or removal of the entire proline-rich helix beginning at proline 22 in L11 resulted in an L11 protein, which was unable to stimulate stringent factor in the ribosome-dependent assay. Surprisingly, the N-terminal domain of L11 on its own activated stringent factor in a ribosome-dependent manner without restoring the L11 footprint in 23 S rRNA in the 50 S subunit. This suggests that the N-terminal domain can activate stringent factor in trans. It is also shown that this activation is dependent on unacylated tRNA.

  • 308.
    Jernberg, Cecilia
    Södertörn University, School of Life Sciences. Karolinska Institutet.
    Use of microbiomics to study human impacts on complex microbial communities2006Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The study of bacterial communities in nature is currently a challenge. The majority of bacteria in clinical and environmental samples have not yet been cultured and therefore we cannot fully understand their roles in nature and how the ecological balance in a specific microbial ecosystem can be disrupted. For example, exposure to pollutants in soil and antibiotics in the human gut can have large consequences on microbial populations but the magnitude of these impacts is difficult to assess. In this thesis, a combination of molecular techniques, microbiomics, were used to assess complex microbial communities in soil and the human gut. One goal of this thesis was to study the impact of the toxic compound, 4-chlorophenol, on the soil microbiota. In addition, a specific 4-chlorophenol degrading bacterium, Arthrobacter chlorophenolicus, was monitored in soil. In order to monitor the cells they were chromosomally tagged with marker genes encoding either the green fluorescent protein (the gfp gene) or firefly luciferase (the luc gene). During degradation of high levels of 4-chlorophenol in soil, total cells counts of A. chlorophenolicus cells could be measured by flow cytometry (GFP protein) and the metabolic activity could be measured by lurninometry (luciferase activity). In addition, the relative abundance of A. chlorophenolicus in soil could be measured by terminal restriction fragment length polymorphism (T-RFLP) and a higher relative abundance was detected in soil contaminated with 4chlorophenol compared with non-treated soil. The impacts of 4-chlorophenol and A. chlorophenolicus on the dominant members of the soil microbiota were also assessed by T-RFLP. Another goal of this thesis was to study the impact of a short term antibiotic administration in a long term perspective, using either clindamycin, in a two year study or a triple therapy for eradication of Helicobacter pylori containing clarithromycin and metronidazole, in a four year study, on the human fecal microbiota. Both the total bacterial community and specific populations, i.e. Bacteroides spp. and Enterococcus spp., were monitored by T-RFLP. The Bacteroides populations never returned to their pre-treatment composition after clindamycin exposure during the two year study period. Selection and persistence of resistant Bacteroides clones up to two years after treatment was furthermore detected. In the four year study, Enterococcus populations increased as a response to the clarithromycin and metronidazole treatment. An increase in the levels of antibiotic resistance genes, specific erm genes, conferring resistance to macrolides and lincosamides were detected for up to 2 and 4 years after both types of antibiotic treatments in the respective studies. It was also possible to specifically monitor two probiotic Lactobacillus strains and their transient colonization by T-RFLP. In conclusion, the use of a polyphasic approach with complementary analytical tools made it possible to obtain a comprehensive picture of complex microbial communities. In addition, specific bacteria of interest in complex soil and fecal samples could be monitored using microbiomics approaches.

  • 309.
    Jernberg, Cecilia
    et al.
    Södertörn University, Avdelning Naturvetenskap. Karolinska Institutet.
    Jansson, Janet K
    Södertörn University, Avdelning Naturvetenskap.
    Impact of 4-chlorophenol contamination and/or inoculation with the 4-chlorophenol-degrading strain, Arthrobacter chlorophenolicus A6L, on soil bacterial community structure2002In: FEMS Microbiology Ecology, ISSN 0168-6496, E-ISSN 1574-6941, Vol. 42, no 3, p. 387-97Article in journal (Refereed)
    Abstract [en]

    The 4-chlorophenol-degrading strain, Arthrobacter chlorophenolicus A6L (chromosomally tagged with the firefly luciferase gene, luc) was inoculated into 4-chlorophenol-contaminated soil to assess the impact of bioaugmentation with a biodegrading strain on the indigenous microbiota. Simultaneously, the impact of 4-chlorophenol alone, or inoculation with A. chlorophenolicus into non-contaminated soil, was addressed. Using terminal restriction fragment length polymorphism (T-RFLP) several significant changes were detected in community fingerprint patterns obtained from soil microcosms treated under the different conditions. The relative abundances of some populations, as judged by the relative intensity of terminal restriction fragments, were significantly impacted by either 4-chlorophenol, A. chlorophenolicus inoculation, or by a combination of both inoculation and 4-chlorophenol contamination. Some populations were significantly stimulated and others were significantly repressed when compared to control soil with no additions. For several peaks, the positive or negative impact imposed by the treatments increased over the 13-day incubation period. Some members of the bacterial community were specifically sensitive to A. chlorophenolicus inoculation or to 4-chlorophenol contamination, whereas other populations remained relatively unaffected by any of the treatments. The A. chlorophenolicus inoculum was also monitored by T-RFLP and was found to have a significantly higher relative abundance in soil contaminated with 4-chlorophenol. These results were substantiated by a high correlation to luciferase activity measurements and the number of colony forming units of the inoculum. Therefore, the A. chlorophenolicus A6L population was positively stimulated by the presence of the 4-chlorophenol substrate (180 microg g(-1) soil) that it catabolized during the first 8 days of the incubation period as a carbon and energy source. Together, these results demonstrate that specific populations in the soil bacterial community rapidly fluctuated in response to specific disturbances and the resulting shifts in the community may therefore represent an adjustment in community structure favoring those populations best capable of responding to novel stress scenarios.

  • 310.
    Jernberg, Cecilia
    et al.
    Karolinska Institutet.
    Löfmark, Sonja
    Karolinska Institutet.
    Edlund, Charlotta
    Karolinska Institutet / Medical Products Agency.
    Jansson, Janet K.
    Swedish University of Agricultural Sciences.
    Long-term ecological impacts of antibiotic administration on the human intestinal microbiota2007In: The ISME Journal, ISSN 1751-7362, E-ISSN 1751-7370, Vol. 1, no 1, p. 56-66Article in journal (Refereed)
    Abstract [en]

    Antibiotic administration is known to cause short-term disturbances in the microbiota of the human gastrointestinal tract, but the potential long-term consequences have not been well studied. The aims of this study were to analyse the long-term impact of a 7-day clindamycin treatment on the faecal microbiota and to simultaneously monitor the ecological stability of the microbiota in a control group as a baseline for reference. Faecal samples from four clindamycin-exposed and four control subjects were collected at nine different time points over 2 years. Using a polyphasic approach, we observed highly significant disturbances in the bacterial community that persisted throughout the sampling period. In particular, a sharp decline in the clonal diversity of Bacteroides isolates, as assessed by repetitive sequence-based PCR (rep-PCR) and long-term persistence of highly resistant clones were found as a direct response to the antibiotic exposure. The Bacteroides community never returned to its original composition during the study period as assessed using the molecular fingerprinting technique, terminal restriction fragment length polymorphism (T-RFLP). Furthermore, using real-time PCR we found a dramatic and persistent increase in levels of specific resistance genes in DNA extracted from the faeces after clindamycin administration. The temporal variations in the microbiota of the control group were minor compared to the large and persistent shift seen in the exposed group. These results demonstrate that long after the selection pressure from a short antibiotic exposure has been removed, there are still persistent long term impacts on the human intestinal microbiota that remain for up to 2 years post-treatment.

  • 311.
    Jernberg, Cecilia
    et al.
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. Karolinska Institute.
    Sullivan, A
    Karolinska Institute.
    Edlund, Charlotta
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. Karolinska Institute.
    Jansson, J K
    Swedish University of Agricultural Sciences.
    Monitoring of antibiotic-induced alterations in the human intestinal microflora and detection of probiotic strains by use of terminal restriction fragment length polymorphism2005In: Applied and Environmental Microbiology, ISSN 0099-2240, E-ISSN 1098-5336, Vol. 71, no 1, p. 501-506Article in journal (Refereed)
    Abstract [en]

    Terminal restriction fragment length polymorphism (T-RFLP) was investigated as a tool for monitoring the human intestinal microflora during antibiotic treatment and during ingestion of a probiotic product. Fecal samples from eight healthy volunteers were taken before, during, and after administration of clindamycin. During treatment, four subjects were given a probiotic, and four subjects were given a placebo. Changes in the microbial intestinal community composition and relative abundance of specific microbial populations in each subject were monitored by using viable counts and T-RFLP fingerprints. T-RFLP was also used to monitor specific bacterial populations that were either positively or negatively affected by clindamycin. Some dominant bacterial groups, such as Eubacterium spp., were easily monitored by T-RFLP, while they were hard to recover by cultivation. Furthermore, the two probiotic Lactobacillus strains were easily tracked by T-RFLP and were shown to be the dominant Lactobacillus community members in the intestinal microflora of subjects who received the probiotic.

  • 312. Jimenez, A
    et al.
    Johansson, C
    Ljung, J
    Sagemark, Johan
    Södertörn University, Avdelning Naturvetenskap. Karolinska Institutet.
    Berndt, Kurt D
    Södertörn University, Avdelning Naturvetenskap. Karolinska Institutet.
    Ren, B
    Tibbelin, G
    Ladenstein, R
    Kieselbach, T
    Holmgren, A
    Gustafsson, J A
    Miranda-Vizuete, A
    Human spermatid-specific thioredoxin-1 (Sptrx-1) is a two-domain protein with oxidizing activity2002In: FEBS Letters, ISSN 0014-5793, E-ISSN 1873-3468, Vol. 530, no 1-3, p. 79-84Article in journal (Refereed)
    Abstract [en]

    Spermatid-specific thioredoxin-1 (Sptrx-1) is the first member of the thioredoxin family of proteins with a tissue-specific expression pattern, found exclusively in the tail of elongating spermatids and spermatozoa. We describe here further biochemical characterization of human Sptrx-1 protein structure and enzymatic activity. In gel filtration chromatography human Sptrx-1 eluates as a 400 kDa protein consistent with either an oligomeric form, not maintained by intermolecular disulfide bonding, and/or a highly asymmetrical structure. Analysis of circular dichroism spectra of fragments 1-360 and 361-469 and comparison to spectra of full-length Sptrx-1 supports a two-domain organization with a largely unstructured N-terminal domain and a folded thioredoxin-like C-terminal domain. Functionally, Sptrx-1 behaves as an oxidant in vitro when using selenite, but not oxidized glutathione, as electron acceptor. This oxidizing enzymatic activity suggests that Sptrx-1 might govern the stabilization (by disulfide cross-linking) of the different structures in the developing tail of spermatids and spermatozoa.

  • 313. Johannesson, Kerstin
    et al.
    Smolarz, Katarzyna
    Södertörn University, Centre for Baltic and East European Studies (CBEES).
    Grahn, Mats
    Södertörn University, School of Life Sciences, Environmental science. Södertörn University, School of Life Sciences, Biology.
    André, Carl
    The future of Baltic Sea populations: local extinction or evolutionary rescue?2011In: Ambio, ISSN 0044-7447, E-ISSN 1654-7209, Vol. 40, no 2, p. 179-190Article in journal (Refereed)
    Abstract [en]

    Environmental change challenges local and global survival of populations and species. In a species-poor environment like the Baltic Sea this is particularly critical as major ecosystem functions may be upheld by single species. A complex interplay between demographic and genetic characteristics of species and populations determines risks of local extinction, chances of re-establishment of lost populations, and tolerance to environmental changes by evolution of new adaptations. Recent studies show that Baltic populations of dominant marine species are locally adapted, have lost genetic variation and are relatively isolated. In addition, some have evolved unusually high degrees of clonality and others are representatives of endemic (unique) evolutionary lineages. We here suggest that a consequence of local adaptation, isolation and genetic endemism is an increased risk of failure in restoring extinct Baltic populations. Additionally, restricted availability of genetic variation owing to lost variation and isolation may negatively impact the potential for evolutionary rescue following environmental change.

  • 314.
    Johansson, Ambjörn
    Södertörn University College, School of Life Sciences.
    Evolution toward pollution-resistant ecotypes of Baltic threespine stickleback, Gasterosteus aculeatus, suggested by AFLP markers2008Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    This study used amplified fragment length polymorphism (AFLP) to detect changes of genetic variation in threespine stickleback exposed to industrial pollution from pulp- and paper mills along the southern east coast of Sweden. A general loss of allelic diversity was associated with exposure (table 3, linear model, F1,4=7.2 [P=0.055]) and exposed populations also displayed a similar pattern of response (fig 5) despite geographic distance, indicating that evolution toward pollution resistant ecotypes of threespine stickleback is occurring in the Baltic Sea. The result suggests that pollution can be regarded as an agent of directional selection, causing a decrease of evolutionary potential of exposed species in the Baltic Sea.

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  • 315. Johansson, J
    et al.
    Gudmundsson, G H
    Rottenberg, M E
    Berndt, Kurt D
    Karolinska Institutet.
    Agerberth, B
    Conformation-dependent antibacterial activity of the naturally occurring human peptide LL-371998In: Journal of Biological Chemistry, ISSN 0021-9258, E-ISSN 1083-351X, Vol. 273, no 6, p. 3718-3724Article in journal (Refereed)
    Abstract [en]

    The influence of ion composition, pH, and peptide concentration on the conformation and activity of the 37-residue human antibacterial peptide LL-37 has been studied. At micromolar concentration in water, LL-37 exhibits a circular dichroism spectrum consistent with a disordered structure. The addition of 15 mM HCO3-, SO42-, or CF3CO2- causes the peptide to adopt a helical structure, with approximately equal efficiency, while 160 mM Cl- is less efficient, A cooperative transition from disordered to helical structure is observed as the peptide concentration is increased, consistent with formation of an oligomer, The extent of alpha-helicity correlates with the antibacterial activity of LL-37 against both Gram-positive and Gram-negative bacteria. Two homologous peptides, FF-33 and SK-29, containing 4 and 8 residue deletions at the N terminus, respectively, require higher concentrations of anions for helix formation and are less active than LL 37 against Escherichia coli D21. Below pH 5, the helical content of LL-37 gradually decreases, and at pH 2 it is entirely disordered, In contrast, the helical structure is retained at pH over 13. The minimal inhibitory concentration of LL-37 against E. coli is 5 mu M, and at 13-25 mu M the peptide is cytotoxic against several eukaryotic cells, In solutions containing the ion compositions of plasma, intracellular fluid, or interstitial fluid, LL-37 is helical, and hence it could pose a danger to human cells upon release. However, in the presence of human serum, the antibacterial and the cytotoxic activities of LL-37 are inhibited.

  • 316. Johansson, Victor
    et al.
    Bergman, Karl-Olof
    Lättman, Håkan
    Södertörn University, School of Life Sciences, Biology. Södertörn University, School of Life Sciences, Environmental science.
    Milberg, Per
    Tree and site quality preferences of six epiphytic lichens growing on oaks in southeastern Sweden2009In: Annales Botanici Fennici, ISSN 0003-3847, E-ISSN 1797-2442, Vol. 46, no 6, p. 496-506Article in journal (Refereed)
    Abstract [en]

    Oaks (Quercus robur) can reach a considerable age, which makes them an important substrate for many epiphytic lichens, including several red-listed species. We studied the importance of tree size and other environmental factors for the occurrence of six epiphytic lichens at two sites, in southeastern Sweden, differing in quality as judged by tree size distribution and number of old trees. The effects of tree circumference, light availability, trunk inclination and site were analysed. Results showed that different lichen species responded differently to these factors, but, overall, tree size was most important for lichen occurrence. Five species showed a positive relation to tree size, but the 50% probability of occurrence was reached at different tree sizes among these species and there were also site differences. This study shows that the maintenance of old trees is crucial for several lichen species, which highlights the importance of long-term management plans.

  • 317.
    Johnsson, Anna
    Södertörn University, School of Life Sciences, Molecular biology. Karolinska Institutet.
    Characterization of Gcn5 histone acetyltransferase in Schizosaccharomyces pombe2009Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The organisation of eukaryotic DNA into chromatin provides a natural barrier that prevents full access to the DNA thereby inhibiting events such as transcription, replication and repair. In order for these DNA-related events to occur, the chromatin needs to be modified by chromatin remodelling or, by reversible post-translational modifications. Histone acetylation is such a modification and is essential of numerous DNA related events. The enzymes involved in this event are conserved throughout evolution, underscoring their importance. This thesis describes the role of the conserved histone acetyltransferase (HAT) Gcn5 in transcriptional regulation in Schizosaccharomyces pombe. Here we show that Gcn5 plays an important role in stress response. We map genome-wide Gcn5 occupancy and show that Gcn5 is predominantly localized to coding regions of highly transcribed genes. We also map H3K14 acetylation during salt stress and show that Gcn5 collaborates antagonistically with the class-II histone deacetylase, Clr3, to modulate H3K14ac levels and transcriptional elongation. The interplay between Gcn5 and Clr3 is crucial for the regulation of many stress-response genes. Our findings suggest a new role for Gcn5 during transcriptional elongation, in addition to its known role in transcriptional initiation. We also investigate the interactions between Gcn5 and other histone deacetylases and acetyltransferases and show overlapping functionality between Gcn5 and another histone acetyltransferase, Mst2, in stress response, regulation of subtelomeric genes and DNA damage repair. Finally, we show that the role of Gcn5 in stress response is mediated by its catalytic activity and that its function in stress response is conserved among yeast species.

  • 318.
    Johnsson, Anna
    et al.
    Södertörn University, School of Life Sciences, Molecular biology. Karolinska Institutet.
    Durand-Dubief, Mickael
    Karolinska Intitutet.
    Xue-Franzen, Yongtao
    Södertörn University, School of Life Sciences, Molecular biology. Karolinska Institutet.
    Rönnerblad, Michelle
    Karolinska Institutet.
    Ekwall, Karl
    Södertörn University, School of Life Sciences, Molecular biology. Karolinska Institutet.
    Wright, Anthony P. H.
    Södertörn University, School of Life Sciences, Molecular biology. Karolinska Institutet.
    HAT-HDAC interplay modulates global histone H3K14 acetylation in gene-coding regions during stress2009In: EMBO Reports, ISSN 1469-221X, E-ISSN 1469-3178, Vol. 10, no 9, p. 1009-1014Article in journal (Refereed)
    Abstract [en]

    Histone acetylation and deacetylation are important for gene regulation. The histone acetyltransferase, Gcn5, is an activator of transcriptional initiation that is recruited to gene promoters. Here, we map genome-wide Gcn5 occupancy and histone H3K14ac at high resolution. Gcn5 is predominantly localized to coding regions of highly transcribed genes, where it collaborates antagonistically with the class-II histone deacetylase, Clr3, to modulate H3K14ac levels and transcriptional elongation. An interplay between Gcn5 and Clr3 is crucial for the regulation of many stress-response genes. Our findings suggest a new role for Gcn5 during transcriptional elongation, in addition to its known role in transcriptional initiation.

  • 319.
    Johnsson, Anna E.
    et al.
    Södertörn University, School of Life Sciences, Molecular biology.
    Wright, Anthony P. H.
    Södertörn University, School of Life Sciences, Molecular biology.
    The role of specific HAT-HDAC interactions in transcriptional elongation2010In: Cell Cycle, ISSN 1538-4101, E-ISSN 1551-4005, Vol. 9, no 3, p. 467-471Article in journal (Refereed)
    Abstract [en]

    We previously reported genome-wide evidence that the Gcn5 histone cetyltransferase (HAT) is located in the transcribed region of highly xpressed genes and that it plays an important role in transcriptional longation in the fission yeast, Schizosaccharomyces pombe (EMBO Reports 009; 10: 1009-14). Furthermore, the specific interplay between Gcn5 and he Clr3 histone deacetylase (HDAC) controls the acetylation levels of ysine-14 in histone H3 in the same class of highly expressed genes. utants of histone H3 that cannot be acetylated at residue 14 show imilar stress phenotypes to those observed for mutants lacking Gcn5. In his Extra View article we review these findings in relation to related iterature and extend important aspects of the original study. Notably, cn5 and Gcn5-dependent acetylation of histone H3K14 tend to be more nriched in the upstream regions of genes that require Gcn5 for correct xpression compared to genes that are independent of Gcn5. This suggests critical role of Gcn5 in the transcriptional initiation of these enes. Gcn5 is however most highly enriched in the transcribed regions f these gene sets but there is no difference between Gcn5-dependent and cn5-independent gene sets. Thus we suggest that Gcn5 plays an important ut redundant role in the transcriptional elongation of these genes. The ir2 HDAC has a similar genomic localization and enzymatic activity to lr3. We studied gcn5 Delta sir2 Delta double mutants that do not show a uppressed phenotype in relation to gcn5 Delta single mutants, compared o gcn5 Delta clr3 Delta mutants that do, in order to better understand he specificity of the interplay between Gcn5 and Clr3. In some classes f non-highly expressed genes the clr3 Delta mutant tends to restore evels of histone H3K14 acetylation in the double mutant strain more ffectively than sir2 Delta.

  • 320.
    Johnsson, Anna
    et al.
    Södertörn University, School of Life Sciences, Molecular biology. Karolinska Institutet.
    Xue-Franzen, Yongtao
    Södertörn University, School of Life Sciences, Molecular biology. Karolinska Intitutet.
    Lundin, Maria
    Södertörn University, School of Life Sciences, Molecular biology. Karolinska Institutet.
    Wright, Anthony P. H.
    Södertörn University, School of Life Sciences, Molecular biology. Karolinska Institutet.
    Stress-specific role of fission yeast Gcn5 histone acetyltransferase in programming a subset of stress response genes2006In: Eukaryotic Cell, ISSN 1535-9778, E-ISSN 1535-9786, Vol. 5, no 8, p. 1337-1346Article in journal (Refereed)
    Abstract [en]

    Gcn5 is a coactivator protein that contributes to gene activation by acetylating specific lysine residues within the N termini of histone proteins. Gcn5 has been intensively studied in the budding yeast, Saccharomyces cerevisiae, but the features of genes that determine whether they require Gcn5 during activation have not been conclusively clarified. To allow comparison with S. cerevisiae, we have studied the genome-wide role of Gcn5 in the distantly related fission yeast, Schizosaccharomyces pombe. We show that Gcn5 is specifically required for adaptation to KCl- and CaCl2-mediated stress in S. pombe. We have characterized the genome-wide gene expression responses to KCl stress and show that Gcn5 is involved in the regulation of a subset of stress response genes. Gcn5 is most clearly associated with KCl-induced genes, but there is no correlation between Gcn5 dependence and the extent of their induction. Instead, Gen5-dependent KCl-induced genes are specifically enriched in four different DNA motifs. The Gcn5-dependent KCl-induced genes are also associated with biological process gene ontology terms such as carbohydrate metabolism, glycolysis, and nicotinamide metabolism that together constitute a subset of the ontology parameters associated with KCl-induced genes.

  • 321.
    Jonsson, Magnus
    et al.
    Södertörn University, School of Life Sciences.
    Bertilsson, Maria
    Ehrlén, Johan
    Lönn, Mikael
    Södertörn University, School of Life Sciences.
    Genetic divergence of climatically marginal populations of Vicia pisiformis on the Scandinavian Peninsula2008In: Hereditas, ISSN 0018-0661, E-ISSN 1601-5223, Vol. 145, no 1, p. 1-8Article in journal (Refereed)
    Abstract [en]

    Vicia pisiformis L. is a perennial leguminous plant with a main distribution in broadleaved forest-steppes of eastern Europe. The species is classified as endangered (EN) according to the IUCN red-lists in both Norway and Sweden, due to severe fragmentation, small population sizes and continuing population decline. The populations on the Scandinavian Peninsula constitute the northern limit of the species distribution and are mostly restricted to warm stony slopes with predominantly southern aspects. In this study we used the AFLP method, which is a high-resolution genetic fingerprint method. Samples were collected from 22 Scandinavian populations. The overall genetic structure was analysed in an AMOVA, in a Mantel test and through constrained correspondence analysis (CCA). The ordination scores representing non-geographic genetic divergence were extracted from the CCA and analysed in a linear model using habitat variables and population size as explanatory variables. We found (i) a strong geographic structure, (ii) significant genetic divergence between populations, (iii) that this genetic divergence remained significant even after removing the effect of geography in a partial CCA and (iv) that the remaining non-geographic part of genetic divergence (distance from the ordination centre) was associated with aspect, populations with a northern aspect were more genetically divergent. Aspect explains more variation than population size and is the only variable retained in the minimal adequate model. We suggest that local adaptation has caused this divergence from an expected geographical pattern of genetic variation. This explanation is further supported by the association between aspect and specific AFLP fragments. Many plant populations are relics of a different climate (Aguirre-Planter et al. 2000; Despres et al. 2002; Pico and Riba 2002). In response to long-term climate change, populations can either migrate towards a more favourable climate or adapt to the new conditions (delaVega 1996; Jump et al. 2006). Species with limited dispersal ability are at risk of reaching isolated dead-ends of decreasingly suitable habitat, without any suitable habitat within dispersal distance (Colas et al. 1997). Isolated populations have to use their inherent evolutionary potential and adapt to changes in environmental conditions, or they will go extinct. As population fragments go extinct, those that remain will become increasingly isolated from each other both spatially and also genetically as the level of gene flow declines with increasing distance. Such correlation between genetic dissimilarities and geographic distances, known as isolation by distance (Slatkin 1993; Wright 1943), when found, suggests a history of geographically limited gene flow (Kimura and Weiss 1964). On top of an isolation by distance pattern there might be other genetic structures to be found. Occasional long-distance dispersal events for example may disturb geographic patterns with puzzling allele distributions as a result (Nichols and Hewitt 1994). Genetic drift is a process that will affect any pattern of genetic variation in a random fashion. Local adaptation through natural selection is a process that, if sufficiently strong in comparison with gene flow and genetic drift, will create patterns where genetic differentiation is associated with certain environmental conditions (Wright 1951). Several studies have shown the importance of local adaptation of populations (reviewed by Kawecki and Ebert 2004) (see also Bonin et al. 2006; Knight and Miller 2004; Kolseth and Lönn 2005; Lönn et al. 1998). Local adaptation can be strong also at small spatial scales (Snaydon and Davies 1976; Lönn 1993) even though it is sometimes very limited in terms of the number of genes involved (Kärkkainen et al. 2004) Environmental variability provides a base for biological variation by imposing differentiated selection pressures resulting in local adaptation. Topography provides large environmental variation within a relatively small area and thereby provides a basis for small-scale local adaptations. Depending on the local topographic possibilities populations can either migrate up and down slopes or along the same altitude to a different aspect to find a suitable microclimate. The dispersal distance will be much shorter per degree of temperature change during altitudinal migration (Hewitt 1996), than during simple latitudinal migration across a flat landscape. Slope and aspect are two important topographic parameters that determine the influx level of solar radiation, especially towards the poles where the total global radiation decreases (Larcher 2003). Vicia pisiformis is an endangered poorly-dispersed long-lived forest herb with its main distribution across the semi-open broadleaved forest steppes of eastern Europe. The Scandinavian populations are believed to be climate relict populations from warmer times. Earlier genetic studies of V. pisiformis using allozymes, RAPD:s and morhology, have found low to very low levels of genetic variation (Gustafsson and Gustafsson 1994; Black-Samuelsson et al. 1997; Black-Samuelsson and Lascoux 1999). Therefore we used AFLP (amplified fragment length polymorphism) markers, which detect even very small genetic differences between individuals. AFLP mainly analyse neutral variation, as the major fraction of most genomes is assumed to be neutral. However, since the AFLP-fragments are distributed randomly throughout the whole genome some fragments may be situated so close to regions under selection that they become more or less linked to them. This linkage disequilibrium between molecular markers and regions under selection, often referred to as quantitative trait loci (QTL), forms the basis for both QTL-mapping and marker assisted selection (MAS), reviewed by Dekkers and Hospital (2002). Gardner and Latta (2006) for example, found QTL under selection in both natural environments and in the greenhouse. Markers have been found to be connected to biomass production (Cavagnaro et al. 2006) and environmental variation (Bonin et al. 2006; Jump et al. 2006; Porcher et al. 2006). In this study we examine 22 Swedish and Norwegian populations of Vicia pisiformis and ask (i) if there is genetic differentiation between these populations, (ii) if there is can it be explained in its entirety by geographic location or (iii) can it partly be explained by habitat characteristics, suggesting local adaptation, or population size, suggesting genetic drift. We show that populations are differentiated geographically and that genetic variation in addition to the geographical pattern is associated with habitat.

  • 322. Juntti-Berggren, L
    et al.
    Webb, D L
    Arkhammar, P O G
    Schultz, V
    Schweda, Elke K H
    Södertörn University, Avdelning Naturvetenskap.
    Tornheim, K
    Berggren, P O
    Dihydroxyacetone-induced oscillations in cytoplasmic free Ca2+ and the ATP/ADP ratio in pancreatic beta-cells at substimulatory glucose2003In: Journal of Biological Chemistry, ISSN 0021-9258, E-ISSN 1083-351X, Vol. 278, no 42, p. 40710-40716Article in journal (Refereed)
    Abstract [en]

    Glucose stimulation of pancreatic beta-cells causes oscillatory influx of Ca2+, leading to pulsatile insulin secretion. We have proposed that this is due to oscillations of glycolysis and the ATP/ADP ratio, which modulate the activity of ATP-sensitive K+ channels. We show here that dihydroxyacetone, a secretagogue that feeds into glycolysis below the putative oscillator phosphofructokinase, could cause a single initial peak in cytoplasmic free Ca2+ ([Ca2+](i)) but did not by itself cause repeated oscillations in [Ca2+](i) in mouse pancreatic beta-cells. However, in the presence of a substimulatory concentration of glucose (4 mM), dihydroxyacetone induced [Ca2+](i) oscillations. Furthermore, these oscillations correlated with oscillations in the ATP/ADP ratio, as seen previously with glucose stimulation. Insulin secretion in response to dihydroxyacetone was transient in the absence of glucose but was considerably enhanced and somewhat prolonged in the presence of a substimulatory concentration of glucose, in accordance with the enhanced [Ca2+](i) response. These results are consistent with the hypothesized role of phosphofructokinase as the generator of the oscillations. Dihydroxyacetone may affect phosphofructokinase by raising the free concentration of fructose 1,6-bisphosphate to a critical level at which it activates the enzyme autocatalytically, thereby inducing the pulses of phosphofructokinase activity that cause the metabolic oscillations.

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

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

  • 324. Kaiser, L
    et al.
    Velickovic, T C
    Badia-Martinez, D
    Adedoyin, J
    Thunberg, S
    Hallen, D
    Berndt, Kurt D
    Karolinska Institutet.
    Gronlund, H
    Gafvelin, G
    van Hage, M
    Achour, A
    Structural characterization of the tetrameric form of the major cat allergen Fel d 12007In: Journal of Molecular Biology, ISSN 0022-2836, E-ISSN 1089-8638, Vol. 370, no 4, p. 714-727Article in journal (Refereed)
    Abstract [en]

    Felis domesticus allergen 1(Fel d 1) is a 35 kDa tetrameric glycoprotein formed by two heterodimers which elicits IgE responses in 95% of patients with allergy to cat. We have previously established in vitro conditions for the appropriate folding of recombinant Fel d 1 using a direct linkage of chain 1 to chain 2 (construct Fel d 1 (1+2)) and chain 2 to chain 1 (construct Fel d 1 (2+1)). Although the crystal structure of Fel d 1 (2+1) revealed a striking structural similarity to that of uteroglobin, a steroid-inducible cytokine-like molecule with anti-inflammatory and immunomodulatory properties, no functional tetrameric form of Fel d 1 could be identified. Here we present the crystal structure of the Fel d 1 (1+2) tetramer at 1.6 A resolution. Interestingly, the crystal structure of tetrameric Fel d 1 reveals two different calcium-binding sites. Symmetrically positioned on each side of the Fel d 1 tetramer, the external Ca(2+)-binding sites correspond to a putative Ca(2+)-binding site previously suggested for uteroglobin. The second Ca(2+)-binding site lies within the dimerization interface, stabilizing the formation of the Fel d 1 tetramer, and inducing important local conformational changes that directly govern the shape of two water-filled cavities. The crystal structure suggests a potential portal for an unknown ligand. Alternatively, the two cavities could be used by the allergen as a conditional inner space allowing for the spatial rearrangement of centrally localized side-chains, such as Asp130, without altering the overall fold of the molecule. The striking structural similarity of the major cat allergen to uteroglobin, coupled to the identification in the present study of a common Ca(2+)-binding site, let us speculate that Fel d 1 could provoke an allergic response through the modulation of phospholipase A2, by sequestering Ca ions in a similar manner as previously suggested for uteroglobin.

  • 325. Karlsson, C.
    et al.
    Korayem, A. M.
    Scherfer, C.
    Loseva, O.
    Dushay, Mitchell S.
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science.
    Theopold, U.
    Proteomic analysis of the Drosophila larval hemolymph clot2004In: Journal of Biological Chemistry, ISSN 0021-9258, E-ISSN 1083-351X, Vol. 279, no 50, p. 52033-52041Article in journal (Refereed)
    Abstract [en]

    Components of the insect clot, an extremely rapid forming and critical part of insect immunity, are just beginning to be identified (1). Here we present a proteomic comparison of larval hemolymph before and after clotting to learn more about this process. This approach was supplemented by the identification of substrates for the enzyme transglutaminase, which plays a role in both vertebrate blood clotting (as factor XIIIa) and hemolymph coagulation in arthropods. Hemolymph proteins present in lower amounts after clotting include CG8502 (a protein with a mucin-type domain and a domain with similarity to cuticular components), CG11313 (a protein with similarity to prophenoloxidase-activating proteases), and two phenoloxidases, lipophorin, a secreted gelsolin, and CG15825, which had previously been isolated from clots (2). Proteins whose levels increase after clotting include a ferritin-subunit and two members of the immunoglobulin family with a high similarity to the small immunoglobulin-like molecules involved in mammalian innate immunity. Our results correlate with findings from another study of coagulation (2) that involved a different experimental approach. Proteomics allows the isolation of novel candidate clotting factors, leading to a more complete picture of clotting. In addition, our two-dimensional protein map of cell-free Drosophila hemolymph includes many additional proteins that were not found in studies performed on whole hemolymph.

  • 326. Karlsson, Mikael
    Biosafety principles for GMOs in the context of sustainable development2003In: International Journal of Sustainable Development and World Ecology, ISSN 1350-4509, E-ISSN 1745-2627, Vol. 10, no 1, p. 15-26Article in journal (Refereed)
    Abstract [en]

    If genetically modified organisms are to contribute to welfare they must be considered in the context of sustainable development. Biosafety implies considering the environmental, economic and social dimensions of sustainable development. These dimensions can be interpreted through the principles of precaution, polluter pays and public participation. In this article, these key biosafety principles are operationalised and ways of implementing them in society are discussed. A comparison is made between the principles and the present EU law for deliberate release of GMOs. It is concluded that several improvements in EU policy are necessary to ensure sustainable development really is promoted.

  • 327. Karlsson, Mikael
    Ethics of sustainable development - a study of Swedish regulations for genetically modified organisms2003In: Journal of Agricultural and Environmental Ethics, ISSN 1187-7863, E-ISSN 1573-322X, Vol. 16, no 1, p. 51-62Article in journal (Refereed)
    Abstract [en]

    In spite of stricter provisions in the new EU directive on deliberate release of genetically modified organisms (GMOs), critics still advocate a moratorium on permits for cultivation of GMOs. However, in an attempt to meet concerns raised by the public, the directive explicitly gives Member States the possibility to take into consideration ethical aspects of GMOs in the decision-making. This article investigates the potential effects of such formulation by means of an empirical analysis of experiences gained the last years from similar Swedish regulations for GMOs, aiming at promoting sustainable development. The faulty implementation shown in the Swedish case indicates that legal stipulations for ethics as such have limited importance. It is suggested that public participation is an important factor for successful implementation of the ethics of sustainable development.

  • 328.
    Karlsson, Mikael
    Karlstads universitet.
    Managing complex environmental risks for sustainable development: policies for hazardous chemicals and genetically modified organisms2005Doctoral thesis, comprehensive summary (Other academic)
  • 329. Karlsson, Mikael
    Regulatory frameworks for sustainable control of genetically modified organisms2000In: Third International Conference of the European Society for Ecological Economics on transitions towards a sustainable Europe: ecology, economy, policy : Vienna, May 3 to 6, 2000, Vienna, 2000Conference paper (Other academic)
  • 330. Karlsson, Mikael
    Science and norms in policies for sustainable development: Assessing and managing risks of chemical substances and genetically modified organisms in the European Union2006In: Regulatory toxicology and pharmacology, ISSN 0273-2300, E-ISSN 1096-0295, Vol. 44, no 1, p. 49-56Article in journal (Refereed)
    Abstract [en]

    Use of chemical substances and genetically modified organisms cause complex problems characterised by scientific uncertainty and controversies. Aiming at sustainable development, policies for assessment, and management of risks in the two areas are under development in the European Union. The article points out that both science and norms play a central role in risk assessment as well as risk management and Suggests that the precautionary principle, the principle of public participation, and the polluter pays principle, all adopted in the European Union, offer a way to operationalise the concept of sustainable development. It is shown, however, that a number of steps ought to be taken to better implement the principles through different policy measures. In doing so, and by recognising the role of both science and norms, the decision-making on risks related to the use of chemicals or genetically modified organisms can be improved to better promote Sustainable development.

  • 331. Karlsson, Mikael
    Theories on Risk, and the Management of Genetically Modified Organisms: a Stakeholders AnalysisManuscript (preprint) (Other academic)
  • 332. Kaumaya, P T P
    et al.
    Berndt, Kurt D
    University of Chicago, USA.
    Heidorn, D B
    Trewhella, J
    Kezdy, F J
    Goldberg, E
    Synthesis and Biophysical Characterization of Engineered Topographic Immunogenic Determinants with Alpha-Alpha-Topology1990In: Biochemistry, ISSN 0006-2960, E-ISSN 1520-4995, Vol. 29, no 1, p. 13-23Article in journal (Refereed)
  • 333.
    Kellner, Martin
    et al.
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Environmental Science.
    Porseryd, Tove
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Environmental Science.
    Hallgren, S
    Uppsala University.
    Porsch-Hällström, Inger
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Biology.
    Hansen, S H
    University of Copenhagen, Denmark.
    Olsén, K Håkan
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Biology.
    Waterborne citalopram has anxiolytic effects and increases locomotor activity in the three-spine stickleback (Gasterosteus aculeatus)2016In: Aquatic Toxicology, ISSN 0166-445X, E-ISSN 1879-1514, Vol. 173, p. 19-28Article in journal (Refereed)
    Abstract [en]

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

  • 334. Khorosjutina, Olga
    et al.
    Wanrooij, Paulina H.
    Walfridsson, Julian
    Södertörn University, School of Life Sciences, Molecular biology.
    Szilagyi, Zsolt
    Zhu, Xuefeng
    Baraznenok, Vera
    Ekwall, Karl
    Södertörn University, School of Life Sciences, Molecular biology.
    Gustafsson, Claes M.
    A Chromatin-remodeling Protein Is a Component of Fission Yeast Mediator2010In: Journal of Biological Chemistry, ISSN 0021-9258, E-ISSN 1083-351X, Vol. 285, no 39, p. 29729-29737Article in journal (Refereed)
    Abstract [en]

    The multiprotein Mediator complex is an important regulator of RNA polymerase II-dependent genes in eukaryotic cells. In contrast to the situation in many other eukaryotes, the conserved Med15 protein is not a stable component of Mediator isolated from fission yeast. We here demonstrate that Med15 exists in a protein complex together with Hrp1, a CHD1 ATP-dependent chromatin-remodeling protein. The Med15-Hrp1 subcomplex is not a component of the core Mediator complex but can interact with the L-Mediator conformation. Deletion of med15(+) and hrp1(+) causes very similar effects on global steady-state levels of mRNA, and genome-wide analyses demonstrate that Med15 associates with a distinct subset of Hrp1-bound gene promoters. Our findings therefore indicate that Mediator may directly influence histone density at regulated promoters.

  • 335.
    Kieselbach, T
    et al.
    Karolinska Institutet.
    Bystedt, Maria
    Södertörn University, Avdelning Naturvetenskap. Karolinska Institutet.
    Hynds, P
    University of Warwick, UK.
    Robinson, C
    University of Warwick, UK.
    Schröder, Wolfgang P
    Södertörn University, Avdelning Naturvetenskap.
    A peroxidase homologue and novel plastocyanin located by proteomics to the Arabidopsis chloroplast thylakoid lumen2000In: FEBS Letters, ISSN 0014-5793, E-ISSN 1873-3468, Vol. 480, no 2-3, p. 271-276Article in journal (Refereed)
    Abstract [en]

    A study by two-dimensional electrophoresis showed that the soluble, lumenal fraction of Arabidopsis thaliana thylakoids can be resolved into 300 protein spots. After subtraction of low-intensity spots and accounting for low-level stromal contamination, the number of more abundant, lumenal proteins was estimated to be between 30 and 60. Two of these proteins have been identified: a novel plastocyanin that also was the predominant component of the total plastocyanin pool, and a putative ascorbate peroxidase. Import studies shamed that these proteins are routed to the thylakoid lumen by the Sec- and delta pH-dependent translocation pathways, respectively, In addition, novel isoforms of PsbO and PsbQ were identified.

  • 336.
    Kiessling, Anders
    et al.
    SLU.
    Futter, Martyn
    SLU.
    Elofsson, Katarina
    Södertörn University, School of Social Sciences, Economics. SLU.
    Vidakovic, Aleksandar
    SLU.
    Musselodling i Östersjön som miljöåtgärd: nya positiva data från tre pågående EU-projekt2019Report (Other (popular science, discussion, etc.))
    Abstract [sv]

    Nya resultat visar att musselodlingar i Östersjön har en betydande potential att bidra till att minska övergödningen samtidigt som förutsättningar skapas för en cirkulär ekonomi/produktion. För att ta musselodling till nästa nivå krävs dels ytterligare förfining av den nya tekniken, men framförallt fler och i förlängningen också större odlingar samtidigt som vi måste vidareutveckla alla de initiativ som nu pågår hur näringen kan återanvändas i livsmedelssystemet på ett effektivt och ekonomiskt lönsamt sätt.

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  • 337.
    Kihlmark, Madeleine
    Södertörn University, Avdelning Naturvetenskap. Stockholms universitet.
    Targeting of a nascent integral membrane protein to the nuclear pores and its degradation during apoptosis2002Doctoral thesis, comprehensive summary (Other academic)
  • 338.
    Kihlmark, Madeleine
    et al.
    Södertörn University, Avdelning Naturvetenskap.
    Imreh, Gabriela
    Södertörn University, Avdelning Naturvetenskap.
    Hallberg, Einar
    Södertörn University, Avdelning Naturvetenskap.
    Sequential degradation of proteins from the nuclear envelope during apoptosis2001In: Journal of Cell Science, ISSN 0021-9533, E-ISSN 1477-9137, Vol. 114, no 20, p. 3643-3653Article in journal (Refereed)
    Abstract [en]

    We have produced new antibodies specific for the integral pore membrane protein POM121. Using these antibodies we show that during apoptosis POM121 becomes proteolytically degraded in a caspase-dependent manner. The POM121 antibodies and antibodies specific for other proteins of the nuclear envelope were used in a comparative study of nuclear apoptosis in staurosporine-treated buffalo rat liver cells. Nuclei from these cells were classified in three different stages of apoptotic progression: stage I, moderately condensed chromatin surrounded by a smooth nuclear periphery; stage II, compact patches of condensed chromatin collapsing against a smooth nuclear periphery; stage III, round compact chromatin bodies surrounded by grape-shaped nuclear periphery. We have performed double labeling immunofluorescence microscopy of individual apoptotic cells and quantitative immunoblotting analysis of total proteins from apoptotic cell cultures. The results showed that degradation of nuclear envelope marker proteins occurred in a specific order. POM121 degradation occurred surprisingly early and was initiated before nucleosomal DNA degradation could be detected using TUNEL assay and completed before clustering of the nuclear pores. POM121 was eliminated significantly more rapid compared with NUP153 (a peripheral protein located in the nucleoplasmic basket of the nuclear pore complex) and lamin B (a component of the nuclear lamina). Disappearance of NUP153 and lamin B was coincident with onset of DNA fragmentation and clustering of nuclear pores. By contrast, the peripheral NPC protein p62 was degraded much later. The results suggest that degradation of POM121 may be an important early step in propagation of nuclear apoptosis.

  • 339.
    Kihlmark, Madeleine
    et al.
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. Stockholm University.
    Rustum, Cecilia
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. Stockholm University.
    Eriksson, Charlotta
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. Karolinska Institutet.
    Beckman, M
    Stockholm University.
    Iverfeldt, K
    Stockholm University.
    Hallberg, Einar
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science.
    Correlation between nucleocytoplasmic transport and caspase-3-dependent dismantling of nuclear pores during apoptosis2004In: Experimental Cell Research, ISSN 0014-4827, E-ISSN 1090-2422, Vol. 293, no 2, p. 346-356Article in journal (Refereed)
    Abstract [en]

    During apoptosis (also called programmed cell death), the chromatin condenses and the DNA is cleaved into oligonucleosomal fragments. Caspases are believed to play a major role in nuclear apoptosis. However, the relation between dismantling of nuclear pores, disruption of the nucleocytoplasmic barrier, and nuclear entry of caspases is unclear. We have analyzed nuclear import of the green fluorescent protein fused to a nuclear localization signal (GFP-NLS) in tissue culture cells undergoing apoptosis. Decreased nuclear accumulation of GFP-NLS could be detected at the onset of nuclear apoptosis manifested as dramatic condensation and redistribution of chromatin toward the nuclear periphery. At this step, dismantling of nuclear pores was already evident as indicated by proteolysis of the nuclear pore membrane protein POM121. Thus, disruption of nuclear compartmentalization correlated with early signs of nuclear pore damage. Both these events clearly preceded massive DNA fragmentation, detected by TUNEL assay. Furthermore, we show that in apoptotic cells, POM121 is specifically cleaved at aspartate-531 in its large C-terminal portion by a caspase-3-dependent mechanism. Cleavage of the C-terminal portion of POM121, which is adjoining the nuclear pore complex, is likely to disrupt interactions with other nuclear pore proteins affecting the stability of the pore complex. A temporal correlation of apoptotic events supports a model where caspase-dependent disassembly of nuclear pores and disruption of the nucleocytoplasmic barrier paves the way for nuclear entry of caspases and subsequent activation of CAD-mediated DNA fragmentation.

  • 340.
    Kihlmark, Madeleine
    et al.
    Södertörn University, Avdelning Naturvetenskap. Stockholms unviersitet.
    Rustum, Cecilia
    Södertörn University, Avdelning Naturvetenskap. Stockholms universitet.
    Eriksson, Charlotta
    Södertörn University, Avdelning Naturvetenskap. Karolinska institutet.
    Beckman, M
    Stockholms universitet.
    Iverfeldt, Kerstin
    Stockholms universitet.
    Hallberg, Einar
    Södertörn University, Avdelning Naturvetenskap.
    Caspase-3 dependent cleavage of POM121 in relation to nuclear apoptosisManuscript (preprint) (Other academic)
  • 341.
    Kitambi, Satish S.
    et al.
    Södertörn University, School of Life Sciences. Karolinska Institutet / Harvard Medical School/MEEI, Boston, Massachusetts, USA.
    Malicki, Jarema J.
    Harvard Medical School/MEEI, Boston, Massachusetts, USA.
    Spatiotemporal Features of Neurogenesis in the Retina of Medaka, Oryzias latipes2008In: Developmental Dynamics, ISSN 1058-8388, E-ISSN 1097-0177, Vol. 237, no 12, p. 3870-3881Article in journal (Refereed)
    Abstract [en]

    The vertebrate retina is very well conserved in evolution. Its structure and functional features are very similar in phyla as different as primates and teleost fish. Here, we describe the spatiotemporal characteristics of neurogenesis in the retina of a teleost, medaka, and compare them with other species, primarily the zebrafish. Several intriguing differences are observed between medaka and zebrafish. For example, photoreceptor differentiation in the medaka retina starts independently in two different areas, and at more advanced stages of differentiation, medaka and zebrafish retinae display obviously different patterns of the photoreceptor cell mosaic. Medaka and zebrafish evolutionary lineages are thought to have separated from each other 110 million years ago, and so the differences between these species are not unexpected, and may be exploited to gain insight into the architecture of developmental pathways. Importantly, this work highlights the benefits of using multiple teleost models in parallel to understand a developmental process.

  • 342.
    Kitambi, Satish S.
    et al.
    Södertörn University, School of Life Sciences. Karolinska Institutet / Harvard Medical School/MEEI, Boston, USA.
    McCulloch, Kyle J.
    Harvard Medical School/MEEI, Boston, USA.
    Peterson, Randall T.
    Massachusetts General Hospital, USA.
    Malicki, Jarema J.
    Harvard Medical School/MEEI, Boston, USA.
    Small molecule screen for compounds that affect vascular development in the zebrafish retina2009In: Mechanisms of Development, ISSN 0925-4773, E-ISSN 1872-6356, Vol. 126, no 5-6, p. 464-477Article in journal (Refereed)
    Abstract [en]

    Blood vessel formation in the vertebrate eye is a precisely regulated process. in the human retina, both an excess and a deficiency of blood vessels may lead to a loss of vision. To gain insight into the molecular basis of vessel formation in the vertebrate retina and to develop pharmacological means of manipulating this process in a living organism, we further characterized the embryonic zebrafish eye vasculature, and performed a small molecule screen for compounds that affect blood vessel morphogenesis. The screening of approximately 2000 compounds revealed four small molecules that at specific concentrations affect retinal vessel morphology but do not produce obvious changes in trunk vessels, or in the neuronal architecture of the retina. Of these, two induce a pronounced widening of vessel diameter without a substantial loss of vessel number, one compound produces a loss of retinal blood vessels accompanied by a mild increase of their diameter, and finally one other generates a severe loss of retinal vessels. This work demonstrates the utility of zebrafish as a screening tool for small molecules that affect eye vasculature and presents several compounds of potential therapeutic importance.

  • 343.
    Kitambi, Satish Srinivas
    Södertörn University, School of Life Sciences. Karolinska Institutet.
    Teleost retina: a model for study neurogenesis and angiogenesis2009Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Teleost models, zebrafish and medaka have become popular models to study various aspects of developmental biology and genetics. The rapid embryonic development, transparent embryos and the availability of many mutants for various developmental and molecular pathways contribute to the usefulness of these models. The availability of various biochemical, molecular and genetic techniques applicable on these models facilitate in dissecting developmental processes. Teleost retina shows very high similarity to that seen in mammalian retina. The arrangement of the six types of neurons and one type of glia is very similar. Zebrafish has been extensively used in gaining insight into the development and functioning of the retina. Medaka, on the other hand has not been so extensively capitalized as zebrafish. The current study characterizes expression of genes mainly from the nuclear receptor family and establishes the role of zebrafish liver x receptor in governing the size, patterning and neurogenesis of the retina in zebrafish. We also establish the time line of the retinal patterning of medaka retina. Zebrafish and medaka retina show both similarity and difference in the developmental events governing the patterning of the retina. In zebrafish, retinal neurogenesis follows a fan gradient pattern starting at the ventro-nasal region. In medaka, neurogenesis starts from the central retina. An additional, second domain of neurogenesis is seen with the patterning of photoreceptors in medaka. This observation highlights the possibility of utilizing these two species as comparative models in gaining rapid understanding of retinal development and function. This study also establishes the time line of vascular development in the zebrafish retina, an important event required for normal function. Similar to neurogenesis, vasculaturedevelops rapidly and this feature was utilized to develop a small molecule-screening assay. The screening resulted in identification of five compounds that produced phenotype ranging from decrease in the number of vessels to loss of vessels specifically in the retina. To gain insight into the mode of action, further analyses of three of the five identified compounds, using either morpholino knockdown or structural similarity search was done. This study highlights the advantage of using zebrafish model to perform medically relevant chemical screen.

  • 344.
    Kitambi, Satish Srinivas
    et al.
    Södertörn University, School of Life Sciences. Karolinska Institutet.
    Archer, Amena
    Karolinska Institutet.
    Hallgren, Stefan
    Södertörn University, School of Life Sciences.
    Olsén, K Håkan
    Södertörn University, School of Life Sciences.
    Gustafsson, Åke
    Karolinska Institutet.
    Mode, Agneta
    Karolinska Institutet.
    The role of liver X receptor (lxr) in the developing eyeManuscript (preprint) (Other academic)
  • 345.
    Kitambi, Satish Srinivas
    et al.
    Södertörn University, School of Life Sciences. Karolinska Institutet.
    Hauptmann, Giselbert
    Södertörn University, School of Life Sciences. Karolinska Institutet.
    The zebrafish orphan nuclear receptor genes nr2e1 and nr2e3 are expressed in developing eye and forebrain2007In: Gene Expression Patterns, ISSN 1567-133X, E-ISSN 1872-7298, Vol. 7, no 4, p. 521-528Article in journal (Refereed)
    Abstract [en]

    Mammalian Nr2e1 (Tailless, Mtll or Tlx) and Nr2e3 (photoreceptor-specific nuclear receptor, Pnr) are highly related orphan nuclear receptors, that are expressed in eye and forebrain-derived structures. In this study, we analyzed the developmental expression patterns of zebrafish nr2e1 and nr2e3. RT-PCR analysis showed that nr2e1 and nr2e3 are both expressed during embryonic and post-embryonic development. To examine the spatial distribution of nr2e1 and nr2e3 during development whole-mount in situ hybridization was performed. At tailbud stage, initial nr2e1 expression was localized to the rostral brain rudiment anterior to pax2.1 and eng2 expression at the prospective midbrain-hindbrain boundary. During Subsequent stages, nr2e1 became widely expressed in fore- and midbrain primordia, eye and olfactory placodes. At 24 hpf, strong nr2e1 expression was detected in telencephalon, hypothalamus, dorsal thalamus, pretectum, midbrain tectum, and retina. At 2 dpf, the initially widespread nr2e1 expression became more restricted to distinct regions within the fore- and midbrain and to the retinal ciliary margin, the germinal zone which gives rise to retina and presumptive iris. Express on of nr2e3 was exclusively found in the developing retina and epiphysis. In both structures, nr2e3 expression was found in photoreceptor cells. The developmental expression profile of zebrafish nr2e1 and nr2e3 is consistent with evolutionary conserved functions in eye and rostral brain structures.

  • 346. Knapp, S
    et al.
    Karshikoff, A
    Berndt, Kurt D
    Karolinska Institutet.
    Christova, P
    Atanasov, B
    Ladenstein, R
    Thermal unfolding of the DNA-binding protein Sso7d from the hyperthermophile Sulfolobus solfataricus1996In: Journal of Molecular Biology, ISSN 0022-2836, E-ISSN 1089-8638, Vol. 264, no 5, p. 1132-1144Article in journal (Refereed)
    Abstract [en]

    Thermal unfolding of the small hyperthermophilic DNA-binding protein Sso7d was studied by circular dichroism spectroscopy and differential scanning calorimetry. The unfolding transition can be described by a reversible two state process. Maximum stability was observed in the region between pH 4.5 and 7.0 where Sso7d unfolds with a melting temperature between 370.8 to 371.9 K and an unfolding enthalpy between 62.9 and 65.4 kcal/mol. The heat capacity differences between the native and the heat denatured states obtained by differential scanning calorimetry (620 cal/(mol K)) and circular dichroism spectroscopy (580 cal/(mol K)) resulted in comparable values. The thermodynamic reason for the high melting temperature of Sso7d is the shallow stability curve with a broad free energy maximum, corresponding to the relatively small heat capacity change which was obtained. The calculated stability curve shows that Sso7d has, despite of its high melting temperature, an only moderate intrinsic stability, which reaches its maximum (approximate to 7 kcal/mol) at 282 K. Sso7d is particularly poorly stabilized (approximate to 1 kcal/mol) at the maximum physiological growth temperature of Sulfolobus solfataricus. Sso7d has furthermore untypically low specific enthalpy (0.99 kcal/(mol residue)) and entropy (2.99 cal/(mol K)) values at convergence temperatures. No significant differences in thermal stability of the partially methylated Sso7d from Sulfolobus solfataricus and the cloned non-methylated form of the protein expressed in Escherichia coli were observed. (C) 1996 Academic Press Limited

  • 347. Knapp, S
    et al.
    Mattson, P T
    Christova, P
    Berndt, Kurt D
    Karolinska Institutet.
    Karshikoff, A
    Vihinen, M
    Smith, C I E
    Ladenstein, R
    Thermal unfolding of small proteins with SH3 domain folding pattern1998In: Proteins: Structure, Function, and Bioinformatics, ISSN 0887-3585, E-ISSN 1097-0134, Vol. 31, no 3, p. 309-319Article in journal (Refereed)
    Abstract [en]

    The thermal unfolding of three SH3 domains of the Tec family of tyrosine kinases was studied by differential scanning calorimetry and CD spectroscopy, The unfolding transition of the three protein domains in the acidic pH region can be described as a reversible two-state process. For all three SH3 domains maximum stability was observed in the pH region 4.5 < pH < 7.0 where these domains unfold at temperatures of 353K (Btk), 342K (Itk), and 344K (Tec), At these temperatures an enthalpy change of 196 kJ/mol, 178 kJ/mol, and 169 kJ/mol was measured for Btk-, Itk-, and Tec-SH3 domains, respectively. The determined changes in heat capacity between the native and the denatured state are in an usual range expected for small proteins. Our analysis revealed that all SH3 domains studied are only weakly stabilized and have free energies of unfolding which do not exceed 12-16 kJ/mol but show quite high melting temperatures. Comparing unfolding free energies measured for eukaryotic SH3 domains with those of the topologically identical Sso7d protein from the hyperthermophile Sulfolobus solfataricus, the increased melting temperature of the thermostable protein is due to a broadening as well as a significant lifting of its stability curve. However, at their physiological temperatures, 310K for mesophilic SH3 domains and 350K for Sso7d, eukaryotic SH3 domains and Sso7d show very similar stabilities. (C) 1998 Wiley-Liss, Inc.

  • 348.
    Kniola, Barbara
    et al.
    Södertörn University, Avdelning Naturvetenskap. Karolinska Institutet.
    O'Toole, E
    McIntosh, J R
    Mellone, B
    Allshire, R
    Mengarelli, S
    Hultenby, K
    Ekwall, Karl
    Södertörn University, Avdelning Naturvetenskap. Karolinska Institutet.
    The domain structure of centromeres is conserved from fission yeast to humans2001In: Molecular Biology of the Cell, ISSN 1059-1524, E-ISSN 1939-4586, Vol. 12, no 9, p. 2767-2775Article in journal (Refereed)
    Abstract [en]

    The centromeric DNA of fission yeast is arranged with a central core flanked by repeated sequences. The centromere-associated proteins, Mis6p and Cnp1p (SpCENP-A), associate exclusively with central core DNA, whereas the Swi6 protein binds the surrounding repeats. Here, electron microscopy and immunofluorescence light microscopy reveal that the central core and flanking regions occupy distinct positions within a heterochromatic domain. An "anchor" structure containing the Ndc80 protein resides between this heterochromatic domain and the spindle pole body. The organization of centromere-associated proteins in fission yeast is reminiscent of the multilayered structures of human kinetochores, indicating that such domain structure is conserved in eukaryotes.

  • 349. Knorpp, Carina
    et al.
    Hugosson, Marie
    Sjöling, Sara
    Eriksson, AnnaCarin
    Glaser, Elzbieta
    Tissue-specific differences of the mitochondrial protein import machinery: in vitro import, processing and degradation of the pre-F1β subunit of the ATP synthase in spinach leaf and root mitochondria1994In: Plant Molecular Biology, ISSN 0167-4412, E-ISSN 1573-5028, Vol. 26, no 2, p. 571-579Article in journal (Refereed)
    Abstract [en]

    In this study we report the first comparison of the mitochondrial protein import and processing events in two different tissues from the same organism. Both spinach leaf and root mitochondria were able to import and process the in vitro transcribed and translated Neurospora crassa F1 subunit of ATP synthase to the mature size product. Temperature optimum for protein import, 20 °C, was considerably lower than that found in other systems. In spinach leaf mitochondria, the processing peptidase has been shown to constitute an integral part of the bc1 complex of the respiratory chain. In accordance with these results, the majority of the processing activity in root mitochondria was also localized in the membrane. However, although the same amount of the processing peptidase was present per mg of membrane protein in both leaf and root mitochondria, as determined immunologically, the specific processing activity was several-fold higher in roots. Furthermore, in contrast to the processing enzyme in leaf, a portion of the processing activity could be disassociated from the root membrane with relatively weak salt treatment. The processing event in both the leaf and root membranes was always accompanied by a degradation of the F1 precursor. The degradation activity was found to be several-fold higher in roots than in leaves and was also partially dissociated from the membrane after salt treatment. Both the processing and degradation activities were inhibited by orthophenanthroline, a known metalloprotease inhibitor. These results show tissue-specific differencies of the processing event catalyzed by the bc1 complex and indicate the presence of two populations of the processing peptidase in root mitochondria.

  • 350.
    Knutsson Jenvert, Rose-Marie
    et al.
    Södertörn University, School of Life Sciences. Stockholm University.
    Holmberg Schiavone, Lovisa
    Södertörn University, School of Life Sciences.
    Characterization of the tRNA and ribosome-dependent pppGpp-synthesis by recombinant stringent factor from Escherichia coli2005In: The FEBS Journal, ISSN 1742-464X, E-ISSN 1742-4658, Vol. 272, no 3, p. 685-695Article in journal (Refereed)
    Abstract [en]

    Stringent factor is a ribosome-dependent ATP:GTP pyrophosphoryl transferase that synthesizes (p)ppGpp upon nutrient deprivation. It is activated by unacylated tRNA in the ribosomal amino-acyl site (A-site) but it is unclear how activation occurs. A His-tagged stringent factor was isolated by affinity-chromatography and precipitation. This procedure yielded a protein of high purity that displayed (a) a low endogenous pyrophosphoryl transferase activity that was inhibited by the antibiotic tetracycline; (b) a low ribosome-dependent activity that was inhibited by the A-site specific antibiotics thiostrepton, micrococcin, tetracycline and viomycin; (c) a tRNA- and ribosome-dependent activity amounting to 4500 pmol pppGpp per pmol stringent factor per minute. Footprinting analysis showed that stringent factor interacted with ribosomes that contained tRNAs bound in classical states. Maximal activity was seen when the ribosomal A-site was presaturated with unacylated tRNA. Less tRNA was required to reach maximal activity when stringent factor and unacylated tRNA were added simultaneously to ribosomes, suggesting that stringent factor formed a complex with tRNA in solution that had higher affinity for the ribosomal A-site. However, tRNA-saturation curves, performed at two different ribosome/stringent factor ratios and filter-binding assays, did not support this hypothesis.

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