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  • 301. Hurme, R
    et al.
    Berndt, Kurt D
    Karolinska Institutet.
    Namork, E
    Rhen, M
    DNA binding exerted by a bacterial gene regulator with an extensive coiled-coil domain1996Inngår i: Journal of Biological Chemistry, ISSN 0021-9258, E-ISSN 1083-351X, Vol. 271, nr 29, s. 12626-12631Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Although quite common in the eukaryotic cell, bacterial proteins with an extensive coiled-coil domain are still relatively rare. One of the few thus far documented examples, TlpA from Salmonella typhimurium, is characterized by a remarkably long (250 amino acids) alpha-helical coiled-coil domain. Herein, we demonstrate that TlpA is a novel, sequence-specific DNA-binding protein. Several tlpA deletion mutants have been constructed, and their corresponding protein products were purified and tested for DNA binding. Two of the mutant proteins were shown to be deficient in DNA binding. Both mutants were analyzed by circular dichroism and electron microscopy, supporting the notion that mutant proteins were largely intact despite lacking the amino acid residues necessary for DNA binding. In vivo studies with transcriptional tlpA-lacZ fusions demonstrated that TlpA acts as a repressor. Using the repressor phenotype as a readout, the chain exchange previously described in vitro could also be confirmed in vivo. We believe the coiled-coil domain acts not only as a dimerization interface but could also serve a role as a flexible modulator of the protein-DNA interaction.

  • 302. Hurme, R
    et al.
    Berndt, Kurt D
    Karolinska Institutet.
    Normark, S J
    Rhen, M
    A proteinaceous gene regulatory thermometer in Salmonella1997Inngår i: Cell, ISSN 0092-8674, E-ISSN 1097-4172, Vol. 90, nr 1, s. 55-64Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Novel utilization of the coiled-coil motif is presented that enables TlpA, an autoregulatory repressor protein in Salmonella, to sense temperature shifts directly and thereby to modulate the extent of transcription repression. Salmonella cells shifted to higher temperatures, such as those encountered at host entry, showed derepressed tlpA activity. tlpA::lacZ fusions indicated that the promoter itself is insensitive to thermal shifts and that transcription control was exerted by the autorepressor TlpA only. In vitro studies with highly purified TlpA showed concentration and temperature dependence for both fully folded conformation and function, indicating that the thermosensing in TlpA is based on monomer-to-coiled-coil equilibrium.

  • 303.
    Hårdeman, Fredrik
    Södertörns högskola, Institutionen för livsvetenskaper.
    Exploring the metagenome of the Baltic Sea sediment2008Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    Environmental microorganisms are fundamental to ecosystem function, acting as drivers in processes such as primary production, organic matter remineralisation, pollution remediation and global biogeochemical cycling. However, the study of the bacterial communities requires the application of advanced culture-independent methods considering that only a small fraction of the community is otherwise accessed. The goal of this thesis was to investigate the bacterial community structures and functions of Baltic Sea coastal sediments. To assess the distribution and identity of metabolically active bacteria along a vertical redox gradient, a polyphasic method was applied including: reverse transcriptase-PCR (transcription) and bromodeoxyuridine immunocapture (replication) for 16S rRNA gene analyses through both clone library sequence analysis and terminal restriction fragment length polymorphism (T-RFLP). It was demonstrated that the bacterial communities were highly diverse and significantly different at different redox layers. Phylogenetic analysis identified several novel bacterial groups, some with potentially important ecological roles, notably the first genetic evidence of active anammox bacteria, demonstrating that the bacterial community of the Baltic Sea sediment includes several largely unexplored groups. A metagenomic approach was used to access the bacterial diversity. Considering that the Baltic Sea sediment contained a diverse and largely unexplored bacterial community and also represent a permanently cold environment. This community is likely to harbor bacteria with enzymes adapted to low temperatures that would have a potential biotechnological value. The capacity of functional metagenomics for bioprospecting was demonstrated though the construction of a fosmid library of the prokaryotic genomic pool and expression screening, which enabled the identification of several novel lipolytical enzymes. A novel lipase, h1Lip1 (DQ118648) was isolated, overexpressed, purified and characterized for catalytic activity, substrate specificity, apparent temperature optimum and thermo-stability, demonstrating that the enzyme was low temperature active. 3D protein structure modelling of the lipase supported the presence of an alpha/beta-hydrolase fold, a catalytic triad and a lid structure, covering the active site. Comparative structure analyses and site directed-mutagenesis further showed the importance of a region within the N-terminal and lid for substrate affinity and thermal stability. In conclusion, these targeted molecular strategies demonstrate that the Baltic Sea sediments contain a highly diverse and unique bacterial community that also represents a useful source of biotechnologically interesting molecules.

  • 304.
    Hårdeman, Fredrik
    et al.
    Södertörns högskola, Institutionen för livsvetenskaper. Karolinska Institutet.
    Pérez-Bercoff, Åsa
    University of Dublin, Dublin, Ireland.
    Sjöling, Sara
    Södertörns högskola, Institutionen för livsvetenskaper.
    Comparative structure modelling and mutational analysis of the low-temperature-active metagenomically derived lipase h1Lip1Manuskript (preprint) (Annet vitenskapelig)
  • 305.
    Hårdeman, Fredrik
    et al.
    Södertörns högskola, Institutionen för livsvetenskaper. Karolinska Institute.
    Sjöling, Sara
    Södertörns högskola, Institutionen för livsvetenskaper.
    Metagenomic approach for the isolation of a novel low-temperature-active lipase from uncultured bacteria of marine sediment2007Inngår i: FEMS Microbiology Ecology, ISSN 0168-6496, E-ISSN 1574-6941, Vol. 59, nr 2, s. 524-534Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    A novel lipase was isolated from a metagenomic library of Baltic Sea sediment bacteria. Prokaryotic DNA was extracted and cloned into a copy control fosmid vector (pCC1FOS) generating a library of > 7000 clones with inserts of 24-39 kb. Screening for clones expressing lipolytic activity based on the hydrolysis of tributyrin and p-nitrophenyl esters, identified 1% of the fosmids as positive. An insert of 29 kb was fragmented and subcloned. Subclones with lipolytic activity were sequenced and an open reading frame of 978 bp encoding a 35.4-kDa putative lipase/esterase h1Lip1 (DQ118648) with 54% amino acid similarity to a Pseudomomas putida esterase (BAD07370) was identified. Conserved regions, including the putative active site, GDSAG, a catalytic triad (Ser148, Glu242 and His272) and a HGG motif, were identified. The h1Lip1 lipase was over expressed, (pGEX-6P-3 vector), purified and shown to hydrolyse p-nitrophenyl esters of fatty acids with chain lengths up to C-14. Hydrolysis of the triglyceride derivative 1,2-di-O-lauryl-rac-glycero-3-glutaric acid 6'-methylresorufin ester (DGGR) confirmed that h1Lip1 was a lipase. The apparent optimal temperature for h1Lip1, by hydrolysis of p-nitrophenyl butyrate, was 35 degrees C. Thermal stability analysis showed that h1Lip1 was unstable at 25 degrees C and inactivated at 40 degrees C with t(1/2) < 5 min.

  • 306. Högbom, M.
    et al.
    Collins, R.
    van den Berg, S.
    Jenvert, Rose-Marie
    Södertörns högskola, Institutionen för livsvetenskaper.
    Karlberg, T.
    Kotenyova, T.
    Flores, A.
    Hedestam, G. B. K.
    Schiavone, L. H.
    Crystal Structure of Conserved Domains 1 and 2 of the Human DEAD-box Helicase DDX3X in Complex with the Mononucleotide AMP2007Inngår i: Journal of Molecular Biology, ISSN 0022-2836, E-ISSN 1089-8638, Vol. 372, nr 1, s. 150-159Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    DExD-box helicases are involved in all aspects of cellular RNA metabolism. Conserved domains 1 and 2 contain nine signature motifs that are responsible for nucleotide binding, RNA binding and ATP hydrolysis. The human DEAD-box helicase DDX3X has been associated with several different cellular processes, such as cell-growth control, mRNA transport and translation, and is suggested to be essential for the export of unspliced/partially spliced HIV mRNAs from the nucleus to the cytoplasm. Here, the crystal structure of conserved domains 1 and 2 of DDX3X, including a DDX3-specific insertion that is not generally found in human DExD-box helicases, is presented. The N-terminal domain 1 and the C-terminal domain 2 both display RecA-like folds comprising a central β-sheet flanked by α-helices. Interestingly, the DDX3X-specific insertion forms a helical element that extends a highly positively charged sequence in a loop, thus increasing the RNA-binding surface of the protein. Surprisingly, although DDX3X was crystallized in the presence of a large excess of ADP or the slowly hydrolyzable ATP analogue ATPγS the contaminant AMP was seen in the structure. A fluorescent-based stability assay showed that the thermal stability of DDX3X was increased by the mononucleotide AMP but not by ADP or ATPγS, suggesting that DDX3X is stabilized by AMP and elucidating why AMP was found in the nucleotide-binding pocket.

  • 307. Högstrand, K.
    et al.
    Böhme, Jan
    Södertörns högskola, Avdelning Naturvetenskap. Karolinska Institute.
    DNA damage caused by etoposide and γ-irradiation induces gene conversion of the MHC in a mouse non-germline testis cell line1999Inngår i: Mutation research, ISSN 0027-5107, E-ISSN 1873-135X, Vol. 423, nr 1-2, s. 155-169Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We have explored the effects of γ-irradiation and etoposide on the gene conversion frequency between the endogenous major histocompatibility complex class II genes Abk and Ebd in a mouse testis cell line of non-germline origin with a polymerase chain reaction assay. Both γ-rays and etoposide were shown to increase the gene conversion frequency with up to 15-fold compared to untreated cells. Etoposide, which is an agent that stabilise a cleavable complex between DNA and DNA topoisomerase II, shows an increased induction of gene conversion events with increased dose of etoposide. Cells treated with γ-rays, which induce strand breaks, had an increased gene conversion frequency when they were subjected to low doses of irradiation, but increasing doses of irradiation did not lead to an increase of gene conversion events, which might reflect differences in the repair process depending on the extent and nature of the DNA damage. These results where DNA damage was shown to be able to induce gene conversion of endogenous genes in mouse testis cells suggests that the DNA repair system could be involved in the molecular genetic mechanism that results in gene conversion in higher eukaryotes like mammals.

  • 308. Högstrand, K
    et al.
    Böhme, Jan
    Södertörns högskola, Avdelning Naturvetenskap. Karolinska Institute / Stockholm University.
    Gene conversion of major histocompatibility complex genes in the mouse spermatogenesis is a premeiotic event1997Inngår i: Molecular Biology of the Cell, ISSN 1059-1524, E-ISSN 1939-4586, Vol. 8, nr 12, s. 2511-2517Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The molecular genetic mechanism of gene conversion in higher eukaryotes remains unknown. We find it of considerable interest to determine when during spermatogenesis gene conversion occurs. We have therefore purified pachytene spermatocytes and haploid spermatocytes from adult mice and analyzed these fractions for the presence of gene conversion products resulting from the transfer between the major histocompatibility complex class II genes Ebd and Abk in a polymerase chain reaction assay. We have further isolated spermatogenic cells from prepubescent mice and analyzed them for the presence of the same gene conversion products. We can detect gene conversion products in testis cells as early as in 8-d-old mice where the only existing spermatogenic cells are spermatogonia. The frequency of gene conversion products remains the same as the cells reach meiosis in 18-d-old mice, and is unchanged after meiosis is completed in haploid spermatocytes. Gene conversion of this specific fragment therefore appears to be a premeiotic event and, consequently, relies on genetic mechanisms other than normal meiotic recombination.

  • 309. Högstrand, K.
    et al.
    Böhme, Jan
    Södertörns högskola, Avdelning Naturvetenskap. Karolinska Institute.
    Gene conversion of major histocompatibility complex genes is associated with CpG-rich regions1999Inngår i: Immunogenetics, ISSN 0093-7711, E-ISSN 1432-1211, Vol. 49, nr 5, s. 446-455Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We examined 32 DNA sequences of mouse and human major histocompatibility complex (MHC) genes believed to have been subjected to gene conversion events. All regions of the mouse H2 genes as well as the human HLA genes which have been implied to be involved in gene conversion events had elevated levels of CpG dinucleotides, whereas the rest of the genes showed extensive CpG suppression. Mouse MHC genes which have been suspected but not directly implied to be involved in gene conversion events also showed elevated levels of CpG dinucleotides. Moreover, both mouse and human MHC genes which have never been suspected of undergoing gene conversion had low levels of CpG throughout the genes. These results indicate that high CpG levels are correlated with gene conversion rather than with polymorphism, as non-polymorphic genes that have been implicated as gene conversion donors also have elevated levels of CpG dimers in the involved regions whereas polymorphic genes which have never been considered to undergo gene conversion events have a low level of CpG dinucleotides. We also studied the methylation pattern of CpG dimers in the Abk gene by restriction enzyme digestion of mouse testis DNA followed by Southern blot and hybridization to an Abk-specific probe. The examined CpG dimers in prepubescent mice, where the latest germline stages are spermatogonia, leptene, or pachytene, are respectively non-methylated. Accordingly, the CpG dimers appear to be non-methylated in germline DNA from the testis of prepubescent mice, where gene conversions have been reported to occur.

  • 310.
    Imreh, Gabriela
    Södertörns högskola, Avdelning Naturvetenskap. Stockholms universitet.
    Distribution and dynamics of a nuclear pore membrane protein2002Doktoravhandling, med artikler (Annet vitenskapelig)
  • 311.
    Imreh, Gabriela
    et al.
    Stockhlms univeristet.
    Beckman, M.
    Stockholms universitet.
    Iverfeldt, K.
    Stockholms universitet.
    Hallberg, Einar
    Stockholms universitet.
    Noninvasive monitoring of apoptosis versus necrosis in a neuroblastoma cell line expressing a nuclear pore protein tagged with the green fluorescent protein1998Inngår i: Experimental Cell Research, ISSN 0014-4827, E-ISSN 1090-2422, Vol. 238, nr 2, s. 371-376Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    A fusion chimera between the integral nuclear pore membrane protein POM121 and GFP (green fluorescent protein) has been shown to correctly target to the nuclear pores when transiently expressed in a number of mammalian cell types. POM121-GFP is therefore an excellent marker for the noninvasive studies of the nuclear pores in living cells using fluorescence microscopy. We have established a line of neuroblastoma cells stably expressing the POM121-GFP fusion protein. We also monitored the nuclear envelope in living cells after induction of apoptosis or necrosis using 1 μM staurosporine or 100 μM p-benzoquinone, respectively. Interestingly, the POM121-GFP fluorescence was weaker or missing in the apoptotic cells. The disappearance of the nuclear pore marker accompanied apoptotic progression as judged by the degree of chromatin condensation and DNA fragmentation as analyzed by DNA staining and TUNEL assay, respectively. In contrast, the intensity of the nuclear rim fluorescence was unaffected in necrotic cells displaying an abnormal morphology with tilted nuclei. Thus, it was possible to distinguish between apoptotic and necrotic development in living cells using fluorescence microscopy. This cell line provides a fast and convenient model for screening suspected toxic xenobiotics.

  • 312.
    Imreh, Gabriela
    et al.
    Södertörns högskola, Avdelning Naturvetenskap. Stockholms unviersitet.
    de Monvel, J. B
    Karolinska universitetssjukhuset.
    Branden, L.
    Karolinska institutet.
    Hallberg, Einar
    Södertörns högskola, Avdelning Naturvetenskap.
    ER retention may play a role in sorting of the nuclear pore membrane Protein POM121 towards the NPCManuskript (preprint) (Annet vitenskapelig)
  • 313.
    Imreh, Gabriela
    et al.
    Södertörns högskola, Avdelning Naturvetenskap. Stockholm University.
    Hallberg, Einar
    Södertörns högskola, Avdelning Naturvetenskap.
    An integral membrane protein from the nuclear pore complex is also present in the annulate lamellae: Implications for annulate lamella formation2000Inngår i: Experimental Cell Research, ISSN 0014-4827, E-ISSN 1090-2422, Vol. 259, nr 1, s. 180-190Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Annulate lamellae (AL) are cytoplasmic arrays of stacked membrane cisternae containing densely packed pore complexes which are similar in structure to the nuclear pore complexes (NPCs) and thus referred to as annulate lamella pore complexes (ALPCs). We have recently shown that the integral nuclear pore membrane protein POM121 tagged with green fluorescent protein was correctly targeted to the nuclear pores (H. Soderqvist et al., 1997, fur. J. Biochem. 250, 808-813). Here we have investigated if POM121 fused to three tandem molecules of yellow fluorescent protein YFP) (POM121-YFP3,) also was able to distribute in the extensive and well-characterized Al; of RC37 and BMGE cells. Transfected RC37 or BMGE cells displayed YFP fluorescence around the nuclear envelope, as well. as in the cytoplasmic AL structures. The YFP fluorescence colocalized perfectly with immunostaining using antibodies specific for different NPC proteins. The AL of both transfected and untransfected BMGE cells resisted extractions with Tx-100 and 250 mM NaCl, but were completely solubilized at 450 mM NaCl. Loss of YFP fluorescence and immunostaining for other NPC proteins correlated under all extraction conditions tested, suggesting that overexpressed POM121-YFP3, had become an integrated part both of the NPCs and of the ALPCs. Furthermore, we have generated a stable BHK cell line expressing POM121YFP(3,) located exclusively at the nuclear pores. Treatment with vinblastine sulfate, which induces formation of Al; in a variety of cells, resulted in distribution of POM121-YFP3, into cytoplasmic foci colocalizing with immunostaining for peripheral NPC proteins. Taken together, the results show that YFP-tagged POM121 is able to distribute in drug-induced or naturally occurring AL, suggesting that POM121 is a natural constituent of ALPCs. In COS cells, which normally lack or have very little AT-I, YFP-tagged POM121 distributed in the nuclear pores when expressed at low levels. However, at high expression levels the YFP fluorescence also distributed in a number of brightly fluorescing cytoplasmic dots or foci, which were not present in untransfected cells. This was also true for untagged POM121. The cytoplasmic foci varied in size from 0.1 to 2 mu m and were distinctly located in the immediate vicinity of ER cisternae (without colocalizing) and also contained other nuclear pore proteins, indicating that they may represent cytoplasmic AL. This idea is supported by time-lapse studies of postmitotic assembly of these structures. This raises the question of the role of POM121 in ALPC and NPC biogenesis.

  • 314.
    Imreh, Gabriela
    et al.
    Södertörns högskola, Avdelning Naturvetenskap. Stockholm University.
    Maksel, Danuta
    Södertörns högskola, Avdelning Naturvetenskap.
    de Monvel, J B
    Branden, L
    Hallberg, Einar
    Södertörns högskola, Avdelning Naturvetenskap.
    ER retention may play a role in sorting of the nuclear pore membrane protein POM1212003Inngår i: Experimental Cell Research, ISSN 0014-4827, E-ISSN 1090-2422, Vol. 284, nr 2, s. 173-184Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Integral membrane proteins of the nuclear envelope (NE) are synthesized on the rough endoplasmic reticulum (ER) and following free diffusion in the continuous ER/NE membrane system are targeted to their proper destinations due to interactions of specific domains with other components of the NE. By studying the intracellular distribution and dynamics of a deletion mutant of an integral membrane protein of the nuclear pores, POM121, which lacks the pore-targeting domain, we investigated if ER retention plays a role in sorting of integral membrane proteins to the nuclear envelope. A nascent membrane protein lacking sorting determinants is believed to diffuse laterally in the continuous ER/NE lipid bilayer and expected to follow vesicular traffic to the plasma membrane. The GFP-tagged deletion mutant, POM121(1-129)-GFP, specifically distributed within the ER membrane, but was completely absent from the Golgi compartment and the plasma membrane. Experiments using fluorescence recovery after photobleaching (FRAP) and fluorescence loss in photobleaching (FLIP) demonstrated that despite having very high mobility within the whole ER network (D = 0.41 +/- 0.11 mum(2)/s) POM121(1-129)-GFP was unable to exit the ER. It was also not detected in post-ER compartments of cells incubated at 15degreesC. Taken together, these experiments show that amino acids 1-129 of POM121 are able to retain GFP in the ER membrane and suggest that this retention occurs by a direct mechanism rather than by a retrieval mechanism. Our data suggest that ER retention might be important for sorting of POM121 to the nuclear pores.

  • 315.
    Imreh, Gabriela
    et al.
    Stockholms unviersitet.
    Söderqvist, H
    Stockholms universitet.
    Kihlmark, Madeleine
    Hallberg, Einar
    Stockholms universitet.
    GFP as a marker for a nuclear pore complex protein1997Inngår i: Bioluminescence and chemiluminescence: proceedings of the 9th International Symposium on Bioluminescence and Chemiluminescence at Woods Hole, Massachusetts, October 1996 / [ed] J.W. Hastings, L.J. kricka & P.E. Stanley, Sussex: John Wiley & Sons, 1997Konferansepaper (Annet vitenskapelig)
  • 316.
    Inganni, Johan
    Södertörns högskola, Institutionen för livsvetenskaper.
    Nitric Oxide in Primary Ciliary Dyskinesia: Missing in action?2008Independent thesis Basic level (professional degree), 20 poäng / 30 hpOppgave
    Fulltekst (pdf)
    FULLTEXT01
  • 317. Isaac, Sara
    et al.
    Walfridsson, Julian
    Södertörns högskola, Institutionen för livsvetenskaper. Karolinska Institute.
    Zohar, Tal
    Lazar, David
    Kahan, Tamar
    Ekwall, Karl
    Södertörns högskola, Institutionen för livsvetenskaper. Karolinska Institute.
    Cohen, Amikam
    Interaction of Epe1 with the heterochromatin assembly pathway in Schizosaccharomyces pombe2007Inngår i: Genetics, ISSN 0016-6731, E-ISSN 1943-2631, Vol. 175, nr 4, s. 1549-1560Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Epe1 is a JmjC domain protein that antagonizes heterochromatization in Schizosaccharomyces pombe. Related JmjC domain proteins catalyze a histone demethylation reaction that depends on Fe(II) and alpha-ketoglutarate. However, no detectable demethylase activity is associated with Epe1, and its JmjC domain lacks conservation of Fe(II)-binding residues. We report that Swi6 recruits Epe1 to heterochromatin and that overexpression of epe1(+), like mutations in silencing genes or overexpression of swi6(+), upregulates expression of certain genes. A significant overlap was observed between the lists of genes that are upregulated by overexpression of epe1(+) and those that are upregulated by mutations in histone deacetylase genes. However, most of the common genes are not regulated by Clr4 histone methyltransferase. This suggests that Epe1 interacts with the heterochromatin assembly pathway at the stage of histone deacetylation. Mutational inactivation of Epe1 downregulates similar to 12% of S. pombe genes, and the list of these genes overlaps significantly with the lists of genes that are upregulated by mutations in silencing genes and genes that are hyperacetylated at their promoter regions in clr6-1 mutants. We propose that an interplay between the repressive HDACs activity and Epe1 helps to regulate gene expression in S. pombe.

  • 318.
    Ismail, R. O.
    et al.
    Stockholm University, Sweden; University of Dar es Salaam, Tanzania.
    Asplund, M. E.
    University of Gothenburg, Sweden.
    Gullström, Martin
    Södertörns högskola, Institutionen för naturvetenskap, miljö och teknik, Miljövetenskap.
    George, R.
    Stockholm University, Sweden; Tanzania Fisheries Research Institute (TAFIRI), Tanzania.
    Dahl, Martin
    Södertörns högskola, Institutionen för naturvetenskap, miljö och teknik, Miljövetenskap.
    Buriyo, A. S.
    University of Dar es Salaam, Tanzania.
    Mtolera, M. S. P.
    University of Dar es Salaam, Tanzania.
    Björk, M.
    Stockholm University, Sweden.
    Effects of calcification on air-water CO2 fluxes in tropical seagrass meadows: A mesocosm experiment2023Inngår i: Journal of Experimental Marine Biology and Ecology, ISSN 0022-0981, E-ISSN 1879-1697, Vol. 561, artikkel-id 151864Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Seagrass meadows deliver a range of ecosystem services, where one of the more important is the capacity to store carbon and serve as sinks for atmospheric carbon dioxide. The capacity of seagrass meadows for carbon storage might, however, be modified and complicated by several factors; one important factor is the possible effects of calcification within the meadows. In tropical areas, seagrass meadows can contain high proportions of calcareous organisms, which through their calcification may cause release of CO2. To study this aspect of the CO2 balance within tropical seagrass systems, we investigated the air-water CO2 flux in seagrass mesocosms with different plant community compositions, i.e. mixtures of seagrass and calcifying macroalgae, having similar overall photosynthetic oxygen evolution rates. The measured CO2 fluxes changed both in rate and direction over the day and were significantly related to plant community composition. Downward fluxes of CO2 were found only over vegetation with high proportion of seagrass and in the afternoon, whereas occurrence of calcifying algae appeared to reverse the flow. A partial least squares (PLS) regression model indicated that pH, pCO2 and dissolved inorganic carbon (DIC) were the primary environmental variables predicting the CO2 fluxes. Our findings show that algal calcification might partly counteract the carbon sequestration in seagrass meadows.

  • 319. Ivanova, Natalia
    et al.
    Lindell, Magnus
    Pavlov, Michael
    Holmberg Schiavone, Lovisa
    Södertörns högskola, Institutionen för livsvetenskaper.
    Wagner, E. Gerhart H.
    Ehrenberg, Mans
    Structure probing of tmRNA in distinct stages of trans-translation2007Inngår i: RNA: A publication of the RNA Society, ISSN 1355-8382, E-ISSN 1469-9001, Vol. 13, nr 5, s. 713-722Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Ribosomes stalled on problematic mRNAs in bacterial cells can be rescued by transfer-messenger RNA ( tmRNA), its helper protein ( small protein B, SmpB), and elongation factor Tu (EF-Tu) through a mechanism called trans-translation. In this work we used lead(II) footprinting to probe the interactions of tmRNA with SmpB and other components of the translation machinery at different steps of the trans-translation cycle. Ribosomes with a short nascent peptide stalled on a truncated mRNA were reacted with Ala-tmRNAdEF-TudGTP, SmpB, and other translation components to initiate and execute trans-translation. Free tmRNA was probed with lead( II) acetate with and without SmpB, and ribosome bound tmRNA was probed in one of four different trans-translation states stabilized by antibiotic addition or selective exclusion of translation components. For comparison, we also analyzed lead( II) cleavage patterns of tmRNA in vivo in a wild-type as well as in an SmpB-deficient Escherichia coli strain. We observed some specific cleavages/protections in tmRNA for the individual steps of trans-translation, but the overall tmRNA conformation appeared to be similar in the stages analyzed. Our findings suggest that, in vivo, a dominant fraction of tmRNA is in complex with SmpB and that, in vitro, SmpB remains tmRNA bound at the initial steps of trans-translation.

  • 320. Ivanova, Natalia
    et al.
    Pavlov, Michael Y
    Bouakaz, Elli
    Ehrenberg, Måns
    Holmberg Schiavone, Lovisa
    Södertörns högskola, Institutionen för livsvetenskaper.
    Mapping the interaction of SmpB with ribosomes by footprinting of ribosomal RNA2005Inngår i: Nucleic Acids Research, ISSN 0305-1048, E-ISSN 1362-4962, Vol. 33, nr 11, s. 3529-3539Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    In trans-translation transfer messenger RNA (tmRNA) and small protein B (SmpB) rescue ribosomes stalled on truncated or in other ways problematic mRNAs. SmpB promotes the binding of tmRNA to the ribosome but there is uncertainty about the number of participating SmpB molecules as well as their ribosomal location. Here, the interaction of SmpB with ribosomal subunits and ribosomes was studied by isolation of SmpB containing complexes followed by chemical modification of ribosomal RNA with dimethyl sulfate, kethoxal and hydroxyl radicals. The results show that SmpB binds 30S and 50S subunits with 1:1 molar ratios and the 70S ribosome with 2:1 molar ratio. SmpB-footprints are similar on subunits and the ribosome. In the 30S subunit, SmpB footprints nucleotides that are in the vicinity of the P-site facing the E-site, and in the 50S subunit SmpB footprints nucleotides that are located below the L7/L12 stalk in the 3D structure of the ribosome. Based on these results, we suggest a mechanism where two molecules of SmpB interact with tmRNA and the ribosome during trans-translation. The first SmpB molecule binds near the factor-binding site on the 50S subunit helping tmRNA accommodation on the ribosome, whereas the second SmpB molecule may functionally substitute for a missing anticodon stem-loop in tmRNA during later steps of trans-translation.

  • 321. Jacobson, Therese
    et al.
    Prevodnik, Andreas
    Södertörns högskola, Institutionen för livsvetenskaper.
    Sundelin, Brita
    Combined effects of temperature and a pesticide on the Baltic amphipod Monoporeia affinis2008Inngår i: Aquatic Biology, ISSN 1864-7782, E-ISSN 1864-7790, Vol. 1, nr 3, s. 269-276Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Effects of elevated temperature, in combination with exposure to the fungicide fenarimol, on reproduction in the deposit-feeding Baltic amphipod Monoporeia affinis were investigated. Previously, fenarimol was found to cause endocrine disruption in other crustacean species, via the ecdysteroid system. M. affinis were exposed to elevated temperature and/or fenarimol in soft-bottom microcosms during sexual maturation and mating. Elevated temperature and fenarimol (0.7 mg l(-1)) acted synergistically and increased the number of females with dead eggs, with a more than 4-fold incidence compared to exposure to one of the stressors (24 vs. < 5 %). Exposure to both stressors also resulted in a negative intrinsic rate of increase, which might indicate a population decline in the field. Elevated temperature impaired sexual maturation in males and females, lowered the number of fertilised females, reduced fecundity and altered embryogenesis. Exposure to fenarimol resulted in a 40 % decrease in ecdysteroid levels in sexually mature males and an increase in heat shock protein 60 expression. Ecdysteroid levels were not affected by temperature in either sex or stage of sexual maturation. Our results suggest that increase in the water temperature due to, e.g., global warming would impair reproduction and possibly increase the sensitivity of M affinis to toxicants.

  • 322.
    Jaensson, Alia
    Södertörns högskola, Institutionen för livsvetenskaper.
    Effects of glyphosate on olfactory mediated endorcine responses to female odours and reproductive behaviour in male brown trout (slamo trutta)Inngår i: Ecotoxicology, ISSN 0963-9292, E-ISSN 1573-3017Artikkel i tidsskrift (Fagfellevurdert)
  • 323. Jaensson, Alia
    et al.
    Olsén, K Håkan
    Södertörns högskola, Institutionen för livsvetenskaper, Miljövetenskap. Södertörns högskola, Institutionen för livsvetenskaper, Biologi.
    Effects of copper on olfactory-mediated endocrine responses and reproductive behaviour in mature male brown trout Salmo trutta parr to conspecific females2010Inngår i: Journal of Fish Biology, ISSN 0022-1112, E-ISSN 1095-8649, Vol. 76, nr 4, s. 800-817Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    In the present study, the effects of copper (CuSO4) on the ability of mature male brown trout Salmo trutta parr to detect and react both physiologically and behaviourally to female pheromones were studied. The study was composed of two parts. In the first experiment, priming effects of the female pheromone prostaglandin F-2 alpha (PGF(2 alpha)) were evaluated by determining the amount of milt produced and the blood plasma levels of 11-ketotestosterone (11-KT) and 17 alpha,20 beta-dihydroxy-4-pregnen-3-one (17,20 beta-P) after the PGF(2 alpha) exposure. In the second experiment, male parr were placed in a large stream tank together with a group of adult males and ovulated females and their individual behaviours were recorded. In the priming experiment, the amount of expressible milt was significantly lower, less than half, in groups exposed during 4 days to 10 or 100 mu g l-1 copper compared with control parr only exposed to water. No significant differences were observed in plasma levels of 11-KT and 17, 20 beta-P. During the behavioural experiment, exposed parr spent less time with the female and had a lower number of courting events. Blood plasma levels of 11-KT were, however, significantly higher in the group exposed to 100 mu g l-1 copper compared with the control group. Furthermore, the exposed group spent significantly less time swimming upstream than did the control group. The present study demonstrates that exposure to copper affects reproductive behaviours and endocrinology of S. trutta male parr.

  • 324.
    Jaensson, Alia
    et al.
    Södertörns högskola, Institutionen för livsvetenskaper.
    Olsén, K. Håkan
    Södertörns högskola, Institutionen för livsvetenskaper.
    Prolonged cypermthrin exposure increases sex steroid plasma hormone levels in mature male brown trout (Salmo trutta) parr in spawning groupsInngår i: Aquatic Toxicology, ISSN 0166-445X, E-ISSN 1879-1514Artikkel i tidsskrift (Fagfellevurdert)
  • 325.
    Jahnke, Marlene
    et al.
    University of Gothenburg / University of Groningen, Groningen, Netherlands.
    Gullström, Martin
    Stockholm University / University of Gothenburg.
    Larsson, Josefine
    Södertörns högskola, Institutionen för naturvetenskap, miljö och teknik, Miljövetenskap.
    Asplund, Maria E.
    Stockholm University / University of Gothenburg.
    Mgeleka, Said
    Stockholm University / Tanzania Fisheries Research Institute (TAFIRI), Dar es Salaam, Tanzania.
    Silas, Mathew Ogalo
    Stockholm University / Tanzania Fisheries Research Institute (TAFIRI), Dar es Salaam, Tanzania.
    Hoamby, Arielle
    Institut Halieutique et des Science Marine Toliara (IH.SM), Toliara, Madagascar.
    Mahafina, Jamal
    Institut Halieutique et des Science Marine Toliara (IH.SM), Toliara, Madagascar.
    Nordlund, Lina Mtwana
    Stockholm University / Uppsala University.
    Population genetic structure and connectivity of the seagrass Thalassia hemprichii in the Western Indian Ocean is influenced by predominant ocean currents2019Inngår i: Ecology and Evolution, E-ISSN 2045-7758, Vol. 9, nr 16, s. 8953-8964Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    This study is the first large-scale genetic population study of a widespread climax species of seagrass, Thalassia hemprichii, in the Western Indian Ocean (WIO). The aim was to understand genetic population structure and connectivity of T. hemprichii in relation to hydrodynamic features. We genotyped 205 individual seagrass shoots from 11 sites across the WIO, spanning over a distance of similar to 2,700 km, with twelve microsatellite markers. Seagrass shoots were sampled in Kenya, Tanzania (mainland and Zanzibar), Mozambique, and Madagascar: 4-26 degrees S and 33-48 degrees E. We assessed clonality and visualized genetic diversity and genetic population differentiation. We used Bayesian clustering approaches (TESS) to trace spatial ancestry of populations and used directional migration rates (DivMigrate) to identify sources of gene flow. We identified four genetically differentiated groups: (a) samples from the Zanzibar channel; (b) Mozambique; (c) Madagascar; and (d) the east coast of Zanzibar and Kenya. Significant pairwise population genetic differentiation was found among many sites. Isolation by distance was detected for the estimated magnitude of divergence (D-EST), but the three predominant ocean current systems (i.e., East African Coastal Current, North East Madagascar Current, and the South Equatorial Current) also determine genetic connectivity and genetic structure. Directional migration rates indicate that Madagascar acts as an important source population. Overall, clonality was moderate to high with large differences among sampling sites, indicating relatively low, but spatially variable sexual reproduction rates. The strongest genetic break was identified for three sites in the Zanzibar channel. Although isolation by distance is present, this study suggests that the three regionally predominant ocean current systems (i.e., East African Coastal Current, North East Madagascar Current, and the South Equatorial Current) rather than distance determine genetic connectivity and structure of T. hemprichii in the WIO. If the goal is to maintain genetic connectivity of T. hemprichii within the WIO, conservation planning and implementation of marine protection should be considered at the regional scale-across national borders.

    Fulltekst (pdf)
    fulltext
  • 326.
    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 metronidazoleManuskript (preprint) (Annet vitenskapelig)
  • 327.
    Janson, Sven
    et al.
    Södertörns högskola, Institutionen för naturvetenskap, miljö och teknik.
    Wouters, Johanna
    Södertörns högskola, Institutionen för naturvetenskap, miljö och teknik, Biologi.
    Bonow, Madeleine
    Södertörns högskola, Institutionen för naturvetenskap, miljö och teknik, Geografi.
    Svanberg, Ingvar
    Uppsala University.
    Olsén, K. Håkan
    Södertörns högskola, Institutionen för naturvetenskap, miljö och teknik, Biologi.
    Population genetic structure of crucian carp (Carassius carassius) in man-made ponds and wild populations in Sweden2015Inngår i: Aquaculture International, ISSN 0967-6120, E-ISSN 1573-143X, Vol. 23, nr 1, s. 359-368Artikkel i tidsskrift (Annet vitenskapelig)
    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.

    Fulltekst (pdf)
    fulltext
  • 328.
    Janzén, Therese
    Södertörns högskola, Institutionen för naturvetenskap, miljö och teknik, Miljövetenskap.
    Hammer, Monica
    Södertörns högskola, Institutionen för naturvetenskap, miljö och teknik, Miljövetenskap.
    Dinnétz, Patrik
    Södertörns högskola, Institutionen för naturvetenskap, miljö och teknik, Miljövetenskap.
    Factors responsible for Ixodes ricinus presence and abundance across a natural-urban gradient2023Dataset
    Abstract [en]

    In 2017, ticks and field data were collected from 12 different sites in Stockholm County originally chosen as random controls for another study but was never used. In 2019, we collected ticks and field data at 35 randomly selected sites along the natural-urban gradient. To calculate and urbanization index, we used the proportion of artificial surfaces surrounding each site. All sampling sites were visited once with a total of 295 sampling plots inventoried for ticks and field data. For each sampling plot, we recorded date, time, temperature, weather conditions, number of ticks, vegetation height and tree stem density surrounding the inventory plot. To retrieve large landscape characteristics, we established 10 buffer zones ranging from 100m to 1000m around each sampling site in GIS using satellite land cover maps (retrieved from: https://www.naturvardsverket.se/verktyg-och-tjanster/kartor-och-karttjanster/nationella-marktackedata/ladda-ner-nationella-marktackedata/). These maps have a spatial resolution of 10m and include the following main categories 1) Forest and seminatural areas, 2) Open areas, 3) Arable land, 4) Wetlands, 5) Artificial surfaces and 6) Inland and marine water. These main categories are further divided into subcategories with detailed information regarding the different land cover classes. In the analyses, we used the main categories, with the exception of Forest and seminatural areas where we included eight individual forest types: Pine forest, Spruce forest, Mixed coniferous forest, Mixed forest, Broadleaved forest, Broadleaved hardwood forest, Broadleaved forest with hardwood forest and Temporarily non-forest. To calculate landscape configuration metrics at each sampling site, we used land cover data from the GIS buffers with a 1000m radius, exported to GeoTIFF format and analyzed them with FRAGSTATS version 4. For landscape heterogeneity we used Shannons’ diversity index (SHDI) and to measure the aggregation of landscape attributes we used Contagion (CONTAG). As measures of forest configuration, we used percent of forest cover (PLAND) and total forest edge length (TE). All statistical analyses were performed with R version 4.0.3. To analyze the effect of possible risk factors for tick abundance in different greenspaces across the natural-urban gradient, we used generalized linear mixed models assuming Poisson distributed residuals. As the data contained a larger proportion of zeros than would be expected according to a Poisson or a negative binomial distribution causing overdispersion, we fitted zero-inflated Poisson models using the package glmmTMB (generalized linear mixed models using Template Model Builder).

  • 329.
    Janzén, Thérese
    Södertörns högskola, Institutionen för naturvetenskap, miljö och teknik, Miljövetenskap. Södertörns högskola, Centrum för Östersjö- och Östeuropaforskning (CBEES), Baltic & East European Graduate School (BEEGS).
    Ticks - ecology, new hazards, and relevance for public health2024Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    Ticks and tick-borne diseases are ranking second only to mosquitoes as vectors of pathogens responsible for diseases in both humans and domestic animals. In the countries around the Baltic Sea, two medically important tick species are increasing both in range and abundance, and the public health threat posed by tick-borne diseases in this area is steadily growing. The aim of this thesis was to study the eco-epidemiological dynamics and mechanisms of ticks and bacterial tick-borne pathogens along the natural-urban gradient.

    Green spaces have become important intersections between humans, domestic animals, ticks, and tick-borne pathogens. Along the natural-urban gradient in Stockholm County, Sweden, we examined the impact of green space characteristics on tickabundance and pathogens prevalence. In this study all questing ticks were molecularly identified as Ixodes ricinus. Questing ticks were abundant in natural and seminatural habitats, but also present in urbanized parks. Important drivers of tickabundance included significant negative effects of local vegetation height and positiveeffects of mixed coniferous forests in the surrounding landscape.

    The prevalence of Borrelia burgdorferi sensu lato was 24% and that of Anaplasma phagocytophilum 7.5%. B. miyamotoi was found at a few sites with a prevalence of 0.9%. The dominant B. burgdorferi (s.l.) genospecies was B. afzelii. Tree stem density had a significant positive effect on B. burgdorferi (s.l.) prevalence. Broadleaved forests and total forest edge had significant positive effects on A. phagocytophilum prevalence, persisting even in highly urbanized areas. The tick-borne disease equine granulocytic anaplasmosis (EGA) significant increased from 2002 to 2015, with a yearly peak in late summer and early fall.

    The public health risk for tick-borne diseases in an urban green space was estimated from hazard data on tick abundances and pathogen prevalence combined with exposure data using residential population densities and green space visitor numbers. The results indicated a medium to high risk of tick-borne diseases at most sites. Structured interviews with visitors showed that even if visitors showed a high tick awareness and attempted to avoid ticks, most protective measures were only practiced during specific recreational activities.

    The findings from this doctoral project show a notable risk of encountering ticks and tick-borne pathogens along the entire natural-urban gradient, even in highly urbanized areas traditionally perceived as having a low risk. The information on the eco-epidemiological drivers of EGA is important also for the medical health field since the agent causing EGA is identical to the agent causing human disease. Despite ticks and their pathogens green spaces still continue to play a vital role in public health, but the omnipresent risk of tick-borne diseases highlights the need for public health initiatives to mitigate this risk. 

    Fulltekst (pdf)
    Ticks: ecology, new hazards and relevance for public health
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  • 330.
    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
    Södertörns högskola, Institutionen för naturvetenskap, miljö och teknik, Biologi.
    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, L2016Inngår i: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 25, nr 13, s. 2997-3018Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 331. Jensen, Lasse Dahl Ejby
    et al.
    Cao, Renhai
    Hedlund, Eva-Maria
    Söll, Iris
    Södertörns högskola, Institutionen för livsvetenskaper, Molekylärbiologi.
    Lundberg, Jon O.
    Hauptmann, Giselbert
    Södertörns högskola, Institutionen för livsvetenskaper, Molekylärbiologi.
    Steffensen, John Fleng
    Cao, Yihai
    Nitric oxide permits hypoxia-induced lymphatic perfusion by controlling arterial-lymphatic conduits in zebrafish and glass catfish2009Inngår i: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 106, nr 43, s. 18408-18413Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 332.
    Jenvert, Rose-Marie
    Södertörns högskola, Institutionen för livsvetenskaper. Stockholms universitet.
    The ribosome, stringent factor and the bacterial stringent response2007Doktoravhandling, med artikler (Annet vitenskapelig)
    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.

  • 333.
    Jenvert, Rose-Marie
    et al.
    Södertörns högskola, Institutionen för livsvetenskaper. Stockholms universitet.
    Holmberg Schiavone, Lovisa
    Södertörns högskola, Institutionen för livsvetenskaper. Karolinska institutet.
    Mapping the interaction between stringent factor and the ribosome by footprinting of ribosomal RNAManuskript (preprint) (Annet vitenskapelig)
  • 334.
    Jenvert, Rose-Marie
    et al.
    Södertörns högskola, Institutionen för livsvetenskaper. Stockholm University.
    Holmberg Schiavone, Lovisa
    Södertörns högskola, Institutionen för livsvetenskaper.
    The flexible n-terminal domain of ribosomal protein L11 from Escherichia coli is necessary for the activation of stringent factor2007Inngår i: Journal of Molecular Biology, ISSN 0022-2836, E-ISSN 1089-8638, Vol. 365, nr 3, s. 764-772Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 335.
    Jernberg, Cecilia
    Södertörns högskola, Institutionen för livsvetenskaper. Karolinska Institutet.
    Use of microbiomics to study human impacts on complex microbial communities2006Doktoravhandling, med artikler (Annet vitenskapelig)
    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.

  • 336.
    Jernberg, Cecilia
    et al.
    Södertörns högskola, Avdelning Naturvetenskap. Karolinska Institutet.
    Jansson, Janet K
    Södertörns högskola, Avdelning Naturvetenskap.
    Impact of 4-chlorophenol contamination and/or inoculation with the 4-chlorophenol-degrading strain, Arthrobacter chlorophenolicus A6L, on soil bacterial community structure2002Inngår i: FEMS Microbiology Ecology, ISSN 0168-6496, E-ISSN 1574-6941, Vol. 42, nr 3, s. 387-97Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 337.
    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 microbiota2007Inngår i: The ISME Journal, ISSN 1751-7362, E-ISSN 1751-7370, Vol. 1, nr 1, s. 56-66Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 338.
    Jernberg, Cecilia
    et al.
    Södertörns högskola, Institutionen för kemi, biologi, geografi och miljövetenskap. Karolinska Institute.
    Sullivan, A
    Karolinska Institute.
    Edlund, Charlotta
    Södertörns högskola, Institutionen för kemi, biologi, geografi och miljövetenskap. 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 polymorphism2005Inngår i: Applied and Environmental Microbiology, ISSN 0099-2240, E-ISSN 1098-5336, Vol. 71, nr 1, s. 501-506Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 339. Jimenez, A
    et al.
    Johansson, C
    Ljung, J
    Sagemark, Johan
    Södertörns högskola, Avdelning Naturvetenskap. Karolinska Institutet.
    Berndt, Kurt D
    Södertörns högskola, 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 activity2002Inngår i: FEBS Letters, ISSN 0014-5793, E-ISSN 1873-3468, Vol. 530, nr 1-3, s. 79-84Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 340. Johannesson, Kerstin
    et al.
    Smolarz, Katarzyna
    Södertörns högskola, Centrum för Östersjö- och Östeuropaforskning (CBEES).
    Grahn, Mats
    Södertörns högskola, Institutionen för livsvetenskaper, Miljövetenskap. Södertörns högskola, Institutionen för livsvetenskaper, Biologi.
    André, Carl
    The future of Baltic Sea populations: local extinction or evolutionary rescue?2011Inngår i: Ambio, ISSN 0044-7447, E-ISSN 1654-7209, Vol. 40, nr 2, s. 179-190Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 341.
    Johansson, Ambjörn
    Södertörns högskola, Institutionen för livsvetenskaper.
    Evolution toward pollution-resistant ecotypes of Baltic threespine stickleback, Gasterosteus aculeatus, suggested by AFLP markers2008Independent thesis Basic level (degree of Bachelor), 10 poäng / 15 hpOppgave
    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.

    Fulltekst (pdf)
    FULLTEXT01
  • 342. 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-371998Inngår i: Journal of Biological Chemistry, ISSN 0021-9258, E-ISSN 1083-351X, Vol. 273, nr 6, s. 3718-3724Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 343. Johansson, Victor
    et al.
    Bergman, Karl-Olof
    Lättman, Håkan
    Södertörns högskola, Institutionen för livsvetenskaper, Biologi. Södertörns högskola, Institutionen för livsvetenskaper, Miljövetenskap.
    Milberg, Per
    Tree and site quality preferences of six epiphytic lichens growing on oaks in southeastern Sweden2009Inngår i: Annales Botanici Fennici, ISSN 0003-3847, E-ISSN 1797-2442, Vol. 46, nr 6, s. 496-506Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 344.
    Johnsson, Anna
    Södertörns högskola, Institutionen för livsvetenskaper, Molekylärbiologi. Karolinska Institutet.
    Characterization of Gcn5 histone acetyltransferase in Schizosaccharomyces pombe2009Doktoravhandling, med artikler (Annet vitenskapelig)
    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.

  • 345.
    Johnsson, Anna
    et al.
    Södertörns högskola, Institutionen för livsvetenskaper, Molekylärbiologi. Karolinska Institutet.
    Durand-Dubief, Mickael
    Karolinska Intitutet.
    Xue-Franzen, Yongtao
    Södertörns högskola, Institutionen för livsvetenskaper, Molekylärbiologi. Karolinska Institutet.
    Rönnerblad, Michelle
    Karolinska Institutet.
    Ekwall, Karl
    Södertörns högskola, Institutionen för livsvetenskaper, Molekylärbiologi. Karolinska Institutet.
    Wright, Anthony P. H.
    Södertörns högskola, Institutionen för livsvetenskaper, Molekylärbiologi. Karolinska Institutet.
    HAT-HDAC interplay modulates global histone H3K14 acetylation in gene-coding regions during stress2009Inngår i: EMBO Reports, ISSN 1469-221X, E-ISSN 1469-3178, Vol. 10, nr 9, s. 1009-1014Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 346.
    Johnsson, Anna E.
    et al.
    Södertörns högskola, Institutionen för livsvetenskaper, Molekylärbiologi.
    Wright, Anthony P. H.
    Södertörns högskola, Institutionen för livsvetenskaper, Molekylärbiologi.
    The role of specific HAT-HDAC interactions in transcriptional elongation2010Inngår i: Cell Cycle, ISSN 1538-4101, E-ISSN 1551-4005, Vol. 9, nr 3, s. 467-471Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 347.
    Johnsson, Anna
    et al.
    Södertörns högskola, Institutionen för livsvetenskaper, Molekylärbiologi. Karolinska Institutet.
    Xue-Franzen, Yongtao
    Södertörns högskola, Institutionen för livsvetenskaper, Molekylärbiologi. Karolinska Intitutet.
    Lundin, Maria
    Södertörns högskola, Institutionen för livsvetenskaper, Molekylärbiologi. Karolinska Institutet.
    Wright, Anthony P. H.
    Södertörns högskola, Institutionen för livsvetenskaper, Molekylärbiologi. Karolinska Institutet.
    Stress-specific role of fission yeast Gcn5 histone acetyltransferase in programming a subset of stress response genes2006Inngår i: Eukaryotic Cell, ISSN 1535-9778, E-ISSN 1535-9786, Vol. 5, nr 8, s. 1337-1346Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 348.
    Jonsson, Magnus
    et al.
    Södertörns högskola, Institutionen för livsvetenskaper.
    Bertilsson, Maria
    Ehrlén, Johan
    Lönn, Mikael
    Södertörns högskola, Institutionen för livsvetenskaper.
    Genetic divergence of climatically marginal populations of Vicia pisiformis on the Scandinavian Peninsula2008Inngår i: Hereditas, ISSN 0018-0661, E-ISSN 1601-5223, Vol. 145, nr 1, s. 1-8Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 349. Juntti-Berggren, L
    et al.
    Webb, D L
    Arkhammar, P O G
    Schultz, V
    Schweda, Elke K H
    Södertörns högskola, 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 glucose2003Inngår i: Journal of Biological Chemistry, ISSN 0021-9258, E-ISSN 1083-351X, Vol. 278, nr 42, s. 40710-40716Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 350.
    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
    Södertörns högskola, Institutionen för naturvetenskap, miljö och teknik, Biologi. Karolinska Institute.
    Pujol, Nathalie
    Aix-Marseille Université, Marseille, France.
    Niklaus, Gisela
    Universität Basel, Basel, Switzerland.
    Bürglin, Thomas R.
    Södertörns högskola, Institutionen för naturvetenskap, miljö och teknik, Biologi. Karolinska Institute / Universität Basel, Basel, Switzerland.
    The LIM homeobox gene ceh-14 is required for phasmid function and neurite outgrowth2013Inngår i: Developmental Biology, ISSN 0012-1606, E-ISSN 1095-564X, Vol. 380, nr 2, s. 314-323Artikkel i tidsskrift (Fagfellevurdert)
    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.

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