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  • 1.
    Ahmed, Engy
    et al.
    Stockholm University, Faculty of Science, Department of Geological Sciences.
    Holmström, Sara
    Stockholm University, Faculty of Science, Department of Geological Sciences.
    Soil Microorganisms and Mineral Weathering: Mechanics of Biotite Dissolution2012Conference paper (Other academic)
    Abstract [en]

    Soil microorganisms play an important role in the environment by contributing to leach and release of essential elements from soil minerals that are required not only for their own nutrition but also for plants growth. This study aims to compare between the mechanisms of different fungal and bacterial species isolated from podzol soil in biotite dissolution. Microplate devices with 6 wells were used for the biological weathering experiments. All of the sterilized microplate wells were filled with 4g/l of biotite followed by 12 ml of an iron free diluted mineral liquid medium. In these conditions, biotite particles are the only source of the essential elements for the microorganisms. To characterize the mechanisms of biotite dissolution, we monitored siderophores production, microbial biomass, pH, exchangeable cations concentration and SEM analysis for mineral surface. There was a significant difference between the behavior of the fungal and bacterial species in dissolution of biotite. This difference may be due to the variation of these microorganisms in their mechanics of interaction with mineral surface. It was observed also that these microorganisms directly and indirectly induce biotite dissolution. Defining soil as a system driven by biological mechanisms rather than chemical processes has major implications for our understanding of how the system functions and how it will respond to changing conditions.

  • 2.
    Ahmed, Engy
    et al.
    Stockholm University, Faculty of Science, Department of Geological Sciences.
    Holmström, Sara
    Stockholm University, Faculty of Science, Department of Geological Sciences.
    THE MICROBE-MINERAL INTERACTIONS IN THE ACIDIC PODZOL SOIL2013In: Mineralogical magazine, ISSN 0026-461X, E-ISSN 1471-8022, Vol. 77, no 5, p. 564-Article in journal (Other (popular science, discussion, etc.))
    Abstract [en]

    Iron is a key component of the chemical architecture of the biosphere. Due to the low bioavailability of iron in the environment, microorganisms have developed specific uptake strategies, like siderophores, which are operationally defined as low-molecular-mass biogenic Fe(III)-binding compounds, that can increase iron’s bioavailability by promoting the dissolution of iron-bearing minerals. In the present study, we aimed to investigate the composition of hydroxamate siderophores in the soil horizons of the acidic podzol, and study how they are affected by the presence of specific mineral types and microbial communities.

     Three different minerals (apatite, biotite and oligioclase) were inserted in the soil horizons (O (organic), E (eluvial), B (upper illuvial), and C (mineral)). After two years, soil samples were collected from both the bulk soil (next to the minerals) and from the soil attached to the mineral surfaces. The concentration of ten different fungal tri-hydroxamates and five bacterial ones were determined by high-performance liquid chromatography coupled to electrospray ionization mass spectrometry (HPLC-ESI-MS). In addition, total microbial composition and diversity were studied.

    Our field experiment succeeded in describing the relationship between the presence of siderophores, soil horizon and mineral type, in addition to understanding the interaction between mineral type and soil microbial composition. A wide range of fungal and bacterial hydroxamates were detected throughout the soil profile. On the other hand, the presence of the minerals completely altered the diversity of siderophores. In addition, each mineral had a unique interaction with hydroxamates in the different soil horizons. There were also a good relationship between the microbial diversity and the siderophore distribution. 

  • 3.
    Ahmed, Engy
    et al.
    Stockholm University, Faculty of Science, Department of Geological Sciences.
    Holmström, Sara
    Stockholm University, Faculty of Science, Department of Geological Sciences.
    The Roles and Applications of Siderophores in Natural Environments2013Conference paper (Other academic)
    Abstract [en]

    Siderophores are organic compounds with low molecular mass that are produced by microorganisms growing under conditions of low iron. The primary function of these compounds is to chelate ferric iron from different terrestrial and aquatic habitats and thereby make it available for microbial cells.

    Siderophores have received much attention in recent years because of their potential roles and applications in various areas of environmental research. For instance, the production of siderophores can provide a quick identification of microbes to the species level that called “siderotyping”. On the other hand, siderophores could also function as biocontrol, biosensor, and bioremediation agents, in addition to their important role in mineral weathering and enhancing plant growth. In the present study, we aimed to investigate the composition of trihydroxamate siderophores in soil samples from different horizons (O (organic), E (eluvial), B (upper illuvial), and C (parent material)) of a podzol soil in Sweden, and study how they are affected by the presence of specific mineral types (apatite, biotite and oligioclase) that were inserted in the soil for two years in a field experiment.

    Our field experiment succeeded in describing the relationship between the presence of siderophores, soil horizons and mineral types. A wide range of fungal and bacterial hydroxamates were detected throughout the soil profile. On the other hand, the presence of the minerals completely altered the diversity of siderophores. In addition, each mineral had a unique interaction with hydroxamates in the different soil horizons. Our next step is to gain greater insight into the siderotyping to illustrate the relationship between the siderophore types that was found throughout the soil profile and on the different mineral surfaces and the microbial diversity by using metagenomic applications.

  • 4.
    Ahmed, Engy
    et al.
    Stockholm University, Faculty of Science, Department of Geological Sciences.
    Holmström, Sara
    Stockholm University, Faculty of Science, Department of Geological Sciences.
    Brüchert, Volker
    Stockholm University, Faculty of Science, Department of Geological Sciences.
    Holm, Nils G.
    Stockholm University, Faculty of Science, Department of Geological Sciences.
    The Role of Microorganisms in the diversity and distribution of siderophores in Podzolic Forest Soil2013In: Mineralogical magazine, ISSN 0026-461X, E-ISSN 1471-8022, Vol. 77, no 2, p. 161--208(48)Article in journal (Other academic)
    Abstract [en]

    Iron is a key component of the chemical architecture of the biosphere. Due to the low bioavailability of iron in the environment, microorganisms have developed specific uptake strategies. The most important one is the production of siderophores, which are operationally defined as low-molecular-mass biogenic Fe (III)-binding compounds which may greatly increase bioavailability of Fe [1]. One of the primary biogeochemical functions of siderophores is therefore to increase Fe bioavailability by promoting the dissolution of iron-bearing minerals [2]. This study aims to understand the role of microorganisms in the chemical diversity and distribution of siderophores in podzol soil and how this diversity can contribute to the bioavailability of Fe in forest soil.Soil samples were collected from an experimental site in the area of Bispgården in central Sweden (63°07′N, 16°70′E) from the O (organic), E (eluvial), B1 (upper illuvial), and C (mineral) horizons. Concentration and chemical composition of dissolved and adsorbed siderophores in the soil samples were determined using colorimetric assays and high-performance liquid chromatography.The highest siderophore concentrations were found in the O layer and thereafter decreased by depth. Concentrations of dissolved hydroxamate, catecholate and carboxylate siderophores were up to 84, 17 and 0.2 nmol/ g soil, respectively. In contrast, concentrations of adsorbed hydroxamates, catecholates and carboxylates were only up to 1.8, 3 and 0.2 nmol/ g soil, respectively.Siderophore-producing microorganisms were isolated from the same soil samples. Viable fungi, bacteria and actinomycete counts ranged from 7 to 300, from 300 to 1800, and from 0 to 5 cfu/gm, respectively. The highest counts were found in the O and E layers. Only the E layer contained the three types of siderophore-producing microorganisms investigated in this study. Siderophores were extracted from culture filtrates of the isolated microorganisms when grown under iron-limited conditions. These extracts varied considerably in siderophore composition. Fungal isolates produced up to 183 μM of hydroxamates, especially those isolated from the O layer, whereas bacteria and actinomycete isolated from the O and E layers of the soil produced high amounts of carboxylate, catecholate and hydroxamate siderophores. Actinomycete produced up to 93 μM of hydroxamates and 47 μM of catecholates, while bacteria produced up to 34 μM of carboxylates and up to 14 μM of catecholates.The depth variability in concentration and chemical composition and the good correlation between abundance of siderophore-producing microorganisms and siderophore soil concentrations strongly suggest that these siderophore-producing microorganisms play an important role in the mobilization of iron in the podzol soil that may be important in iron availability to plants in forest environment.

    [1] Clay et al. (1981) Biochemistry 20, 2432-2436. [2] Duckworth et al. (2009) ChemGeol 260, 149-158.

  • 5.
    Ankarklev, Johan
    et al.
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Lebbad, Marianne
    Einarsson, Elin
    Franzen, Oscar
    Ahola, Harri
    Troell, Karin
    Svard, Staffan G.
    A novel high-resolution multilocus sequence typing of Giardia intestinalis Assemblage A isolates reveals zoonotic transmission, clonal outbreaks and recombination2018In: Infection, Genetics and Evolution, ISSN 1567-1348, E-ISSN 1567-7257, Vol. 60, p. 7-16Article in journal (Refereed)
    Abstract [en]

    Molecular epidemiology and genotyping studies of the parasitic protozoan Giardia intestinalis have proven difficult due to multiple factors, such as low discriminatory power in the commonly used genotyping loci, which has hampered molecular analyses of outbreak sources, zoonotic transmission and virulence types. Here we have focused on assemblage A Giardia and developed a high-resolution assemblage-specific multilocus sequence typing (MLST) method. Analyses of sequenced G. intestinalis assemblage A genomes from different sub-assemblages identified a set of six genetic loci with high genetic variability. DNA samples from both humans (n = 44) and animals (n = 18) that harbored Giardia assemblage A infections, were PCR amplified (557-700 bp products) and sequenced at the six novel genetic loci. Bioinformatic analyses showed five to ten-fold higher levels of polymorphic sites than what was previously found among assemblage A samples using the classic genotyping loci. Phylogenetically, a division of two major clusters in assemblage A became apparent, separating samples of human and animal origin. A subset of human samples (n = 9) from a documented Giardia outbreak in a Swedish day-care center, showed full complementarity at nine genetic loci (the six new and the standard BG, TPI and GDH loci), strongly suggesting one source of infection. Furthermore, three samples of human origin displayed MLST profiles that were phylogenetically more closely related to MLST profiles from animal derived samples, suggesting zoonotic transmission. These new genotyping loci enabled us to detect events of recombination between different assemblage A isolates but also between assemblage A and E isolates. In summary, we present a novel and expanded MLST strategy with significantly improved sensitivity for molecular analyses of virulence types, zoonotic potential and source tracking for assemblage A Giardia.

  • 6. Arroyo, Nina Larissa
    et al.
    Aarnio, Katri
    Olafsson, Emil
    Stockholm University, Faculty of Science, Department of Zoology.
    Interactions between two closely related phytal harpacticoid copepods, asymmetric positive and negative effects2007In: Journal of Experimental Marine Biology and Ecology, ISSN 0022-0981, E-ISSN 1879-1697, Vol. 341, no 2, p. 219-227Article in journal (Refereed)
    Abstract [en]

    Competition for food is generally thought to exert a strong evolutionary pressure, driving trophic niche separation, either by specialization and/or by widening the choice of potential food resources. Harpacticoid copepods are common inhabitants of phytal assemblages, where several closely related species of the so-called phytal dwelling families often co-occur. However, direct competition among phytal harpacticoids has been thought to be unlikely, due to the abundant and continuously available food supplies. We conducted a series of field and laboratory studies to assess the role of competition in the abundance distribution of two closely related harpacticoid species, Mesochra rapiens and M. aestuari. We found that the abundance of both species co-varied on several seaweed species in the northern Baltic Sea, during a 3-month period. Stable isotope ratios in the green alga Cladophora glomerata field samples indicated different resource utilization of the two species, both in fresh and deteriorated C. glomerata, and in drifting algae. We tested in the laboratory if resource utilization was different between the species in sympatry and allopatry. We used enriched stable carbon isotope ratios (C-13/C-12) of the diatom Phaeodactylum tricornutum to trace the uptake in both species. Results from these experiments showed a much higher assimilation by M. aestuari in sympatry with M. rapiens, while the latter species showed a higher assimilation in allopatry. Our results show that while there is no apparent competition for resources between these two species in the field, there seems to be an asymmetric reaction when in sympatry and provided one single resource in the laboratory. We suggest that M. rapiens may facilitate assimilation by M. acstuari and discuss the mechanisms by which this may take place.

  • 7.
    Balk, Lennart
    et al.
    Stockholm University, Faculty of Science, Department of Applied Environmental Science (ITM).
    Hägerroth, Per-Ake
    Stockholm University, Faculty of Science, Department of Applied Environmental Science (ITM).
    Åkerman, Gun
    Stockholm University, Faculty of Science, Department of Applied Environmental Science (ITM).
    Hanson, Marsha
    Stockholm University, Faculty of Science, Department of Applied Environmental Science (ITM).
    Tjärnlund, Ulla
    Stockholm University, Faculty of Science, Department of Applied Environmental Science (ITM).
    Hansson, Tomas
    Stockholm University, Faculty of Science, Department of Applied Environmental Science (ITM).
    Hallgrimsson, Gunnar Thor
    Zebühr, Yngve
    Stockholm University, Faculty of Science, Department of Applied Environmental Science (ITM).
    Broman, Dag
    Stockholm University, Faculty of Science, Department of Applied Environmental Science (ITM).
    Mörner, Torsten
    Sundberg, Henrik
    Wild birds of declining European species are dying from a thiamine deficiency syndrome.2009In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 106, no 29, p. 12001-12006Article in journal (Refereed)
    Abstract [en]

    Wild birds of several species are dying in large numbers from an idiopathic paralytic disease in the Baltic Sea area. Here, we demonstrate strong relationships between this disease, breeding failure, and thiamine (vitamin B(1)) deficiency in eggs, pulli, and full-grown individuals. Thiamine is essential for vertebrates, and its diphosphorylated form functions as a cofactor for several life sustaining enzymes, whereas the triphosphorylated form is necessary for the functioning of neuronal membranes. Paralyzed individuals were remedied by thiamine treatment. Moreover, thiamine deficiency and detrimental effects on thiamine-dependent enzymes were demonstrated in the yolk, liver, and brain. We propose that the mortality and breeding failure are part of a thiamine deficiency syndrome, which may have contributed significantly to declines in many bird populations during the last decades.

  • 8. Barisic, Ivan
    et al.
    Schoenthaler, Silvia
    Ke, Rongqin
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).
    Nilsson, Mats
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).
    Noehammer, Christa
    Wiesinger-Mayr, Herbert
    Multiplex detection of antibiotic resistance genes using padlock probes2013In: Diagnostic microbiology and infectious disease, ISSN 0732-8893, E-ISSN 1879-0070, Vol. 77, no 2, p. 118-125Article in journal (Refereed)
    Abstract [en]

    The elucidation of resistance mechanisms is of central importance to providing and maintaining efficient medical treatment. However, molecular detection methods covering the complete set of resistance genes with a single test are still missing. Here, we present a novel 100-plex assay based on padlock probes in combination with a microarray that allows the simultaneous large-scale identification of highly diverse beta-lactamases. The specificity of the assay was performed using 70 clinical bacterial isolates, recovering 98% of the beta-lactamase nucleotide sequences present. Additionally, the sensitivity was evaluated with PCR products and genomic bacterial DNA, revealing a detection limit of 10(4) DNA copies per reaction when using PCR products as the template. Pre-amplification of genomic DNA in a 25-multiplex PCR further facilitated the detection of beta-lactamase genes in dilutions of 10(7) cells/mL. In summary, we present an efficient, highly specific, and highly sensitive multiplex detection method for any gene.

  • 9.
    Basmarke-Wehelie, Rahma
    et al.
    Stockholm University, Faculty of Science, Department of Genetics, Microbiology and Toxicology.
    Sjölinder, Hong
    Stockholm University, Faculty of Science, Department of Genetics, Microbiology and Toxicology.
    Jurkowski, Wiktor
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Elofsson, Arne
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Arnqvist, Anna
    Umea Univ, Dept Med Biochem & Biophys, Sweden.
    Engstrand, Lars
    Karolinska Inst, Swedish Inst Infect Dis Control, Sweden.
    Hagner, Matthias
    Stockholm University, Faculty of Science, Department of Genetics, Microbiology and Toxicology.
    Wallin, Elin
    Stockholm University, Faculty of Science, Department of Genetics, Microbiology and Toxicology.
    Guan, Na
    Stockholm University, Faculty of Science, Department of Genetics, Microbiology and Toxicology.
    Kuranasekera, Hasanthi
    Stockholm University, Faculty of Science, Department of Genetics, Microbiology and Toxicology.
    Aro, Helena
    Stockholm University, Faculty of Science, Department of Genetics, Microbiology and Toxicology.
    Jonsson, Ann-Beth
    Stockholm University, Faculty of Science, Department of Genetics, Microbiology and Toxicology.
    The complement regulator CD46 is bactericidal to Helicobacter pylori and blocks urease activity2011In: Gastroenterology, ISSN 0016-5085, E-ISSN 1528-0012, Vol. 141, no 3, p. 918-928Article in journal (Refereed)
    Abstract [en]

    BACKGROUND & AIMS: CD46 is a C3b/C4b binding complement regulator and a receptor for several human pathogens. We examined the interaction between CD46 and Helicobacter pylori (a bacterium that colonizes the human gastric mucosa and causes gastritis), peptic ulcers, and cancer.

    METHODS: Using gastric epithelial cells, we analyzed a set of H pylori strains and mutants for their ability to interact with CD46 and/or influence CD46 expression. Bacterial interaction with full-length CD46 and small CD46 peptides was evaluated by flow cytometry, fluorescence microscopy, enzyme-linked immunosorbent assay, and bacterial survival analyses.

    RESULTS: H pylori infection caused shedding of CD46 into the extracellular environment. A soluble form of CD46 bound to H pylori and inhibited growth, in a dose- and time-dependent manner, by interacting with urease and alkyl hydroperoxide reductase, which are essential bacterial pathogenicity-associated factors. Binding of CD46 or CD46-derived synthetic peptides blocked the urease activity and ability of bacteria to survive in acidic environments. Oral administration of one CD46 peptide eradicated H pylori from infected mice.

    CONCLUSIONS: CD46 is an antimicrobial agent that can eradicate H pylori. CD46 peptides might be developed to treat H pylori infection.

  • 10.
    Baumgarten, Thomas
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Protein production in the E. coli cell envelope2018Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Proteins fulfil essential functions in every cell and malfunctioning proteins are often the cause of diseases. On the other hand, proteins like antibody fragments or hormones can be used to treat diseases. Proteins are often produced in the bacterium Escherichia coli so that they can be studied to understand their (mal)function or so that they can be used to treat a disease. Unfortunately, producing proteins in the cell envelope of E. coli, like integral membrane proteins, which are important drug targets, and secretory proteins like antibody fragments and hormones, often results in unsatisfactory yields. Therefore, the objectives of this doctoral thesis were to identify bottlenecks that can limit the production of recombinant proteins in the cell envelope of E. coli and to try to overcome these bottlenecks. In the first study, we isolated and characterized the E. coli membrane protein production strain Mt56(DE3). This strain, in which the target gene expression intensity is strongly reduced, outcompetes the standard E. coli membrane protein production strains for most targets tested. In the second and third study we focused on the production of secretory proteins, i.e., proteins that are translocated across the inner membrane into the periplasm of E. coli. First, we investigated the impact of the targeting pathway used to direct a secretory protein to the translocation machinery on the cell physiology and protein production yields. We found that the co-translational targeting of a produced protein saturates the capacity of the translocation machinery resulting in heavily impaired biomass formation and low protein production yields. In contrast, post-translational targeting of a produced protein did not saturate the capacity of the protein translocation machinery resulting in hardly affected biomass formation and high protein production yields. In the third study we investigated how optimizing the production of a co-translationally targeted protein, by harmonizing its production rate with the capacity of the protein translocation machinery, affects the physiology of the cell. We found that, in stark contrast to the non-optimized condition, the optimized production did not affect the composition of the E. coli proteome. This surprising finding indicates that a protein can be produced efficiently in the periplasm of E. coli without compromising the physiology of the cell. In the last study we aimed at developing an outer membrane vesicle-based tuberculosis vaccine. To this end, an E. coli strain was created that produced outer membrane vesicles coated with different tuberculosis antigens. It was shown that a homogenous population of vesicles was produced, which will hopefully facilitate the isolation of these vesicles on an industrial scale.

  • 11. Bengtsson-Palme, Johan
    et al.
    Angelin, Martin
    Huss, Mikael
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).
    Kjellqvist, Sanela
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).
    Kristiansson, Erik
    Palmgren, Helena
    Larsson, D. G. Joakim
    Johansson, Anders
    The Human Gut Microbiome as a Transporter of Antibiotic Resistance Genes between Continents2015In: Antimicrobial Agents and Chemotherapy, ISSN 0066-4804, E-ISSN 1098-6596, Vol. 59, no 10, p. 6551-6560Article in journal (Refereed)
    Abstract [en]

    Previous studies of antibiotic resistance dissemination by travel have, by targeting only a select number of cultivable bacterial species, omitted most of the human microbiome. Here, we used explorative shotgun metagenomic sequencing to address the abundance of >300 antibiotic resistance genes in fecal specimens from 35 Swedish students taken before and after exchange programs on the Indian peninsula or in Central Africa. All specimens were additionally cultured for extended-spectrum beta-lactamase (ESBL)-producing enterobacteria, and the isolates obtained were genome sequenced. The overall taxonomic diversity and composition of the gut microbiome remained stable before and after travel, but there was an increasing abundance of Proteobacteria in 25/35 students. The relative abundance of antibiotic resistance genes increased, most prominently for genes encoding resistance to sulfonamide (2.6-fold increase), trimethoprim (7.7-fold), and beta-lactams (2.6-fold). Importantly, the increase observed occurred without any antibiotic intake. Of 18 students visiting the Indian peninsula, 12 acquired ESBL-producing Escherichia coli, while none returning from Africa were positive. Despite deep sequencing efforts, the sensitivity of metagenomics was not sufficient to detect acquisition of the low-abundant genes responsible for the observed ESBL phenotype. In conclusion, metagenomic sequencing of the intestinal microbiome of Swedish students returning from exchange programs in Central Africa or the Indian peninsula showed increased abundance of genes encoding resistance to widely used antibiotics.

  • 12.
    Berger, Urs
    et al.
    Stockholm University, Faculty of Science, Department of Applied Environmental Science (ITM).
    Glynn, Anders
    Holmström, Katrin E
    Stockholm University, Faculty of Science, Department of Applied Environmental Science (ITM).
    Berglund, Marika
    Ankarberg, Emma Halldin
    Törnkvist, Anna
    Fish consumption as a source of human exposure to perfluorinated alkyl substances in Sweden: analysis of edible fish from Lake Vättern and the Baltic Sea2009In: Chemosphere, ISSN 0045-6535, E-ISSN 1879-1298, Vol. 76, no 6, p. 799-804Article in journal (Refereed)
    Abstract [en]

    Perfluorinated alkyl substances (PFAS) were analyzed in muscle tissue from edible fish species caught in the second largest freshwater lake in Sweden, Lake Vättern (LV), and in the brackish water Baltic Sea (BS). Perfluorooctane sulfonate (PFOS) was the predominant PFAS found. PFOS concentrations were higher in LV (medians 2.9-12 ng g(-1) fresh weight) than in BS fish (medians 1.0-2.5 ng g(-1) fresh weight). Moreover, LV fish was more contaminated with several other PFAS than BS fish. This may be due to anthropogenic discharges from urban areas around LV. The PFAS pattern differed between LV and BS fish, indicating different sources of contamination for the two study areas. Human exposure to PFOS via fish intake was calculated for three study groups, based on consumption data from literature. The groups consisted of individuals that reported moderate or high consumption of BS fish or high consumption of LV fish, respectively. The results showed that PFOS intake strongly depended on individual fish consumption as well as the fish catchment area. Median PFOS intakes were estimated to 0.15 and 0.62 ng kg(-1) body weight (bw) d(-1) for the consumers of moderate and high amounts of BS fish, respectively. For the group with high consumption of LV fish a median PFOS intake of 2.7 ng kg(-1)bw d(-1) was calculated. Fish consumption varied considerably within the consumer groups, with maximum PFOS intakes of 4.5 (BS fish) or 9.6 ng kg(-1)bw d(-1) (LV fish). Comparison of our results with literature data on PFOS intake from food suggests that fish from contaminated areas may be a significant source of dietary PFOS exposure.

  • 13.
    Bergman, Birgitta
    et al.
    Stockholm University, Faculty of Science, Department of Botany.
    Sandh, Gustaf
    Stockholm University, Faculty of Science, Department of Botany.
    Lin, Senjie
    Larsson, John
    Stockholm University, Faculty of Science, Department of Botany.
    Carpenter, Edward J.
    Trichodesmium - a widespread marine cyanobacterium with unusual nitrogen fixation properties2013In: FEMS Microbiology Reviews, ISSN 0168-6445, E-ISSN 1574-6976, Vol. 37, no 3, p. 286-302Article, review/survey (Refereed)
    Abstract [en]

    The last several decades have witnessed dramatic advances in unfolding the diversity and commonality of oceanic diazotrophs and their N2-fixing potential. More recently, substantial progress in diazotrophic cell biology has provided a wealth of information on processes and mechanisms involved. The substantial contribution by the diazotrophic cyanobacterial genus Trichodesmium to the nitrogen influx of the global marine ecosystem is by now undisputable and of paramount ecological importance, while the underlying cellular and molecular regulatory physiology has only recently started to unfold. Here, we explore and summarize current knowledge, related to the optimization of its diazotrophic capacity, from genomics to ecophysiological processes, via, for example, cellular differentiation (diazocytes) and temporal regulations, and suggest cellular research avenues that now ought to be explored.

  • 14.
    Björnsson, Ásgeir
    Stockholm University, Faculty of Science.
    The influence of codon context on translation termination and messenger RNA levels1994Doctoral thesis, comprehensive summary (Other academic)
  • 15. Buetti-Dinh, Antoine
    et al.
    Dethlefsen, Olga
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).
    Friedman, Ran
    Dopson, Mark
    Transcriptomic analysis reveals how a lack of potassium ions increases Sulfolobus acidocaldarius sensitivity to pH changes2016In: Microbiology, ISSN 1350-0872, E-ISSN 1465-2080, Vol. 162, no 8, p. 1422-1434Article in journal (Refereed)
    Abstract [en]

    Extremely acidophilic microorganisms (optimum growth pH of <= 3) maintain a near neutral cytoplasmic pH via several homeostatic mechanisms, including an inside positive membrane potential created by potassium ions. Transcriptomic responses to pH stress in the thermoacidophilic archaeon, Sulfolobus acidocaldarius were investigated by growing cells without added sodium and/or potassium ions at both optimal and sub-optimal pH. Culturing the cells in the absence of added sodium or potassium ions resulted in a reduced growth rate compared to full-salt conditions as well as 43 and 75 significantly different RNA transcript ratios, respectively. Differentially expressed RNA transcripts during growth in the absence of added sodium ions included genes coding for permeases, a sodium/proline transporter and electron transport proteins. In contrast, culturing without added potassium ions resulted in higher RNA transcripts for similar genes as a lack of sodium ions plus genes related to spermidine that has a general role in response to stress and a decarboxylase that potentially consumes protons. The greatest RNA transcript response occurred when S. acidocaldarius cells were grown in the absence of potassium and/or sodium at a sub-optimal pH. These adaptations included those listed above plus osmoregulated glucans and mechanosensitive channels that have previously been shown to respond to osmotic stress. In addition, data analyses revealed two co-expressed IcIR family transcriptional regulator genes with a previously unknown role in the S. acidocaldarius pH stress response. Our study provides additional evidence towards the importance of potassium in acidophile growth at acidic pH.

  • 16.
    Callac, Nolwenn
    et al.
    Stockholm University, Faculty of Science, Department of Geological Sciences. Université de Brest, France; Ifremer, France; CNRS, France.
    Oger, Philippe
    Lesongeur, Francoise
    Rattray, Jayne E.
    Stockholm University, Faculty of Science, Department of Geological Sciences.
    Vannier, Pauline
    Michoud, Gregoire
    Beauverger, Mickael
    Gayet, Nicolas
    Rouxel, Olivier
    Jebbar, Mohamed
    Godfroy, Anne
    Pyrococcus kukulkanii sp nov., a hyperthermophilic, piezophilic archaeon isolated from a deep-sea hydrothermal vent2016In: International Journal of Systematic and Evolutionary Microbiology, ISSN 1466-5026, E-ISSN 1466-5034, Vol. 66, p. 3142-3149Article in journal (Refereed)
    Abstract [en]

    A novel hyperthermophilic, piezophilic, anaerobic archaeon, designated NCB100(T), was isolated from a hydrothermal vent flange fragment collected in the Guaymas basin at the hydrothermal vent site named 'Rebecca's Roost' at a depth of 1997 m. Enrichment and isolation were performed at 100 degrees C under atmospheric pressure. Cells of strain NCB100(T) were highly motile, irregular cocci with a diameter of -1 mu m. Growth was recorded at temperatures between 70 and 112 degrees C (optimum 105 degrees C) and hydrostatic pressures of 0.1-80 MPa (optimum 40-50 MPa). Growth was observed at pH 3.5-8.5 (optimum pH 7) and with 1.5-7% NaCl (optimum at 2.5-3 %). Strain NCB100(T) was a strictly anaerobic chemo-organoheterotroph and grew on complex proteinaceous substrates such as yeast extract, peptone and tryptone, as well as on glycogen and starch. Elemental sulfur was required for growth and was reduced to hydrogen sulfide. The fermentation products from complex proteinaceous substrates were CO2 and H-2. The G+C content of the genomic DNA was 41.3 %. Phylogenetic analysis of the 16S rRNA gene sequence revealed that strain NCB100(T) belongs to the genus Pyrococcus, showing 99% similarity with the other described species of the genus Pyrococcus. On the basis of physiological characteristics, DNA G+C content, similarity level between ribosomal proteins and an average nucleotide identity value of 79 %, strain NCB100(T) represents a novel species for which the name Pyrococcus kukulkanii sp. nov. is proposed. The type strain is NCB100(T) (=DSM 101590(T) =Souchotheque de Bretagne BG1337(T)).

  • 17.
    Caputo, Andrea
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    Genomic and morphological diversity of marine planktonic diatom-diazotroph associations: a continuum of integration and diversification through geological time2019Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Symbioses between eukaryotes and nitrogen (N2)-fixing cyanobacteria (or diazotrophs) are quite common in the plankton community. A few genera of diatoms (Bacillariophyceae) such as Rhizosolenia, Hemiaulus and Chaetoceros are well known to form symbioses with the heterocystous diazotrophic cyanobacteria Richelia intracellularis and Calothrix rhizosoleniae. The latter are also called diatom-diazotroph associations, or DDAs. Up to now, the prokaryotic partners have been morphologically and genetically characterized, and the phylogenetic reconstruction of the well conserved nifH gene (encodes for the nitrogenase enzyme) placed the symbionts in 3 clusters based on their host-specificity, i.e. het-1 (Rhizosolenia-R. intracellularis), het-2 (Hemiaulus-R. intracellularis), and het-3 (Chaetoceros-C- rhizosoleniae). Conversely, the diatom-hosts, major representative of the phytoplankton community and crucial contributors to the carbon (C) biogeochemical cycle, have been understudied.

    The first aim of this thesis was to genetically and morphologically characterize the diatom-hosts, and to reconstruct the evolutionary background of the partnerships and the symbiont integration in the host. The molecular-clock analysis reconstruction showed the ancient appearance of the DDAs, and the traits characterizing the ancestors. In addition, diatom-hosts bearing internal symbionts (with more eroded draft genomes) appeared earlier than diatom-hosts with external symbionts. Finally a blast survey highlighted a broader distribution of the DDAs than expected.

    The second aim of this thesis was to compare genetic and physiological characteristics of the DDAs symbionts with the other eukaryote-diazotroph symbiosis, i.e. prymnesiophyte-UCYN-A (or Candidatus Atelocyanobacterium thalassa). The genome comparison highlighted more genes for transporters in het-3 (external symbiont) and in the UCYN-A based symbiosis, suggesting that symbiont location might be relevant also for metabolic exchanges and interactions with the host and/or environment. Moreover, a summary of methodological biases that brought to an underestimation of the DDAs is reported.

    The third aim of this thesis was to determine the distribution of the DDAs in the South Pacific Ocean using a quantitative polymerase chain reaction (qPCR) approach and to outline the environmental drivers of such distribution. Among the het-groups, het-1 was the most abundant/detected and co-occurred with the other 2 symbiotic strains, all responding similarly to the influence of abiotic factors, such as temperature and salinity (positive and negative correlation, respectively). Globally, Trichodesmium dominated the qPCR detections, followed by UCYN-B. UCYN-A phylotypes (A-1, A-2) were detected without their proposed hosts, for which new oligonucleotides were designed. The latter suggested a facultative symbiosis. Finally, microscopy observations of the het-groups highlighted a discrepancy with the qPCR counts (i.e. the former were several order of magnitudes lower), leading to the idea of developing a new approach to quantify the DDAs.  

    The fourth aim of this thesis was to develop highly specific in situ hybridization assays (CARD-FISH) to determine the presence of alternative life-stages and/or free-living partners. The new assays were applied to samples collected in the South China Sea and compared with abundance estimates from qPCR assays for the 3 symbiotic strains. Free-living cells were indeed detected along the transect, mainly at deeper depths. Free-living symbionts had two morphotypes: trichomes and single-cells. The latter were interpreted as temporary life-stages. Consistent co-occurrence of the 3 het-groups was also found in the SCS and application of a SEM model predicted positive interactions between the het groups. We interpreted the positive interaction as absence of intra-specific competition, and consistent with the previous study, temperature and salinity were predicted as major drivers of the DDAs distribution.

  • 18. Carlsson, Hans Erik
    Immunological studies in ulcerative colitis1978Doctoral thesis, comprehensive summary (Other academic)
  • 19.
    Celorio-Mancera, Maria de la Paz
    et al.
    Stockholm University, Faculty of Science, Department of Zoology.
    Ahn, Seung-Joon
    Vogel, Heiko
    Heckel, David G.
    Transcriptional responses underlying the hormetic and detrimental effects of the plant secondary metabolite gossypol on the generalist herbivore Helicoverpa armigera2011In: BMC Genomics, ISSN 1471-2164, E-ISSN 1471-2164, Vol. 12, p. 575-Article in journal (Refereed)
    Abstract [en]

    Background: Hormesis is a biphasic biological response characterized by the stimulatory effect at relatively low amounts of chemical compounds which are otherwise detrimental at higher concentrations. A hormetic response in larval growth rates has been observed in cotton-feeding insects in response to increasing concentrations of gossypol, a toxic metabolite found in the pigment glands of some plants in the family Malvaceae. We investigated the developmental effect of gossypol in the cotton bollworm, Helicoverpa armigera, an important heliothine pest species, by exposing larvae to different doses of this metabolite in their diet. In addition, we sought to determine the underlying transcriptional responses to different gossypol doses. Results: Larval weight gain, pupal weight and larval development time were measured in feeding experiments and a hormetic response was seen for the first two characters. On the basis of net larval weight gain responses to gossypol, three concentrations (0%, 0.016% and 0.16%) were selected for transcript profiling in the gut and the rest of the body in a two-color double reference design microarray experiment. Hormesis could be observed at the transcript level, since at the low gossypol dose, genes involved in energy acquisition such as beta-fructofuranosidases were up-regulated in the gut, and genes involved in cell adhesion were down-regulated in the body. Genes with products predicted to be integral to the membrane or associated with the proteasome core complex were significantly affected by the detrimental dose treatment in the body. Oxidoreductase activity-related genes were observed to be significantly altered in both tissues at the highest gossypol dose. Conclusions: This study represents the first transcriptional profiling approach investigating the effects of different concentrations of gossypol in a lepidopteran species. H. armigera's transcriptional response to gossypol feeding is tissue-and dose-dependent and involves diverse detoxifying mechanisms not only to alleviate direct effects of gossypol but also indirect damage such as pH disturbance and oxygen radical formation. Genes discovered through this transcriptional approach may be additional candidates for understanding gossypol detoxification and coping with gossypol-induced stress. In a generalist herbivore that has evolved transcriptionally-regulated responses to a variety of different plant compounds, hormesis may be due to a lower induction threshold of growth-promoting, stress-coping responses and a higher induction threshold of detoxification pathways that are costly and cause collateral damage to the cell.

  • 20.
    Chen, Yunying
    et al.
    Karolinska Institutet.
    Wermeling, Fredrik
    Karolinska Institutet.
    Sundqvist, Johanna
    Karolinska Institutet.
    Jonsson, Ann-Beth
    Stockholm University, Faculty of Science, Department of Genetics, Microbiology and Toxicology.
    Tryggvason, Karl
    Karolinska Institutet.
    Pikkarainen, Timo
    Karolinska Institutet.
    Karlsson, Mikael C I
    Karolinska Institutet.
    A regulatory role for macrophage class A scavenger receptors in TLR4-mediated LPS responses.2010In: European Journal of Immunology, ISSN 0014-2980, E-ISSN 1521-4141, Vol. 40, no 5, p. 1451-60Article in journal (Refereed)
    Abstract [en]

    Recognition of microbial components by TLR, key sensors of infection, leads to induction of inflammatory responses. We found that, in vivo, TLR4 engagement by LPS induces up-regulation of the class A scavenger receptors (SR) macrophage receptor with a collagenous structure (MARCO) and SR-A, which occurs, at least in the case of MARCO, via both MyD88-dependent and -independent pathways. When challenging mice with a low dose of LPS followed by a high dose, class A SR-deficient mice showed a higher survival rate than WT mice. This was paired with increased production of IL-10 and anti-LPS Ab, as well as increased activation status of marginal zone B cells. However, the receptors were not crucial for survival when challenging mice i.p. with Neisseria meningitidis or Listeria monocytogenes, but they were found to contribute to microbial capture and clearance. This indicates physiological significance for the up-regulation of class A SR during early stages of bacterial infection. Thus, we believe that we have revealed a mechanism where SR regulate the activation status of the immune system and are involved in balancing a proper immune response to infection. This regulation could also be important in maintaining tolerance since these receptors have been shown to be involved in regulation of self-reactivity.

  • 21.
    Dahlgren, Ann
    Stockholm University, Faculty of Science, Department of Genetics, Microbiology and Toxicology.
    Function and regulation of release factor one in Escherichia coli2004Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    During translation termination the stop codons UAA and UAG are recognised by release factor one (RF1). RF1 binds to the ribosome and mediates the hydrolysis of the nascent peptide from the peptidyl-tRNA. In this process, RF1 interacts directly or indirectly with several ribosomal proteins (r-proteins). To study this interaction in vivo we have used a mutant allele of RF1, prfA1. The mutation causes a temperature sensitive (Ts) phenotype and increased readthrough of the stop codons. A mutant form of r-protein S4 that suppresses this Ts phenotype was isolated. The S4 mutant also increases the readtrough of UAG caused by prfA1. In the mutated S4 allele, rpsD101, Tyr51 is changed to Asp. That change introduces a negatively charged amino acid in a part of S4 that belongs to the positively charged RNA binding surface. This might affect the binding of S4 to the 16S rRNA, to another r-protein, or to RF1, and in that way influence on the function of RF1.

    One of the few things known about the regulation of RF1 is that expression is decreased with increasing generation time. prfA is the second gene in the hemA-operon located at 27 minutes on the E. coli chromosomal map. We have shown that the growth rate regulation of RF1 is exerted at one of the promoters preceding the hemA gene, PhemA1. The promoter is also growth phase regulated and it is turned off in stationary phase. We have characterised two mutations, asuA1 and asuA2, that increase expression of RF1. The asuA2 mutation is a G to A change one nucleotide downstream of the -10 region of PhemA1. Besides increasing expression of RF1 this mutation also abolishes the growth rate and growth phase regulations we have found. The growth phase regulation is partly dependent on ppGpp. We present two models concerning the effect of ppGpp on PhemA1, and what the asuA2 mutation does to it. The prfA gene has low translation initiation efficiency due to a long spacing between the Shine-Dalgarno (SD) sequence and the start codon. The asuA1 mutation creates a new start codon with a shorter distance to the SD sequence. Most likely this increases the efficiency of translation initiation. That PhemA1 is turned off in stationary phase suggests additional regulation of RF1. Our results indicate a putative promoter for the prfA gene within hemA. This promoter does not seem to be growth rate or growth phase regulated.

  • 22.
    de Klerk, Nele
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Host-bacteria interactions: Host cell responses and bacterial pathogenesis2016Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Helicobacter pylori colonizes the human stomach, where it causes gastritis that may develop into peptic ulcer disease or cancer when left untreated. Neisseria gonorrhoeae colonizes the urogenital tract and causes the sexually transmitted disease gonorrhea. In contrast, Lactobacillus species are part of the human microbiota, which is the resident microbial community, and are considered to be beneficial for health. The first host cell types that bacteria encounter when they enter the body are epithelial cells, which form the border between the inside and the outside, and macrophages, which are immune cells that engulf unwanted material.      

    The focus of this thesis has been the interaction between the host and bacteria, aiming to increase our knowledge of the molecular mechanisms that underlie the host responses and their effects on bacterial pathogenicity. Understanding the interactions between bacteria and the host will hopefully enable the development of new strategies for the treatment of infectious disease.

    In paper I, we investigated the effect of N. gonorrhoeae on the growth factor amphiregulin in cervical epithelial cells and found that the processing and release of amphiregulin changes upon infection. In paper II, we examined the expression of the transcription factor early growth response-1 (EGR1) in epithelial cells during bacterial colonization. We demonstrated that EGR1 is rapidly upregulated by many different bacteria. This upregulation is independent of the pathogenicity, Gram-staining type and level of adherence of the bacteria, but generally requires viable bacteria and contact with the host cell. The induction of EGR1 is mediated primarily by signaling through EGFR, ERK1/2 and β1-integrins. In paper III, we described the interactions of the uncharacterized protein JHP0290, which is secreted by H. pylori, with host cells. JHP0290 is able to bind to several cell types and induces apoptosis and TNF release in macrophages. For both of these responses, signaling through Src family kinases and ERK is essential. Apoptosis is partially mediated by TNF release. Finally, in paper IV, we showed that certain Lactobacillus strains can reduce the colonization of H. pylori on gastric epithelial cells. Lactobacilli decrease the gene expression of SabA and thereby inhibit the binding mediated by this adhesin.

  • 23.
    Diez, Beatriz
    et al.
    Stockholm University, Faculty of Science, Department of Botany.
    Bergman, Birgitta
    Stockholm University, Faculty of Science, Department of Botany.
    Pedros-Alio, Carlos
    Anto, Meritxell
    Snoeijs, Pauline
    Stockholm University, Faculty of Science, Department of Systems Ecology.
    High cyanobacterial nifh gene diversity in arctic seawater and sea ice brine2012In: Environmental Microbiology Reports, ISSN 1758-2229, E-ISSN 1758-2229, Vol. 4, no 3, p. 360-366Article in journal (Refereed)
    Abstract [en]

    Although cyanobacterial diazotrophs are common in Arctic terrestrial and freshwater habitats, they have been assumed to be absent from Arctic marine habitats. We report here a high diversity of cyanobacterial nifH genes in Fram Strait and the Greenland Sea. The nifH gene encodes the iron protein of the nitrogenase enzyme complex, which is essential for biological N2 fixation. Using primers specific for nifH genes we uncovered communities of autotrophic and heterotrophic bacteria in sea ice brine and seawater between latitudes 65 and 81 degrees N. Cyanobacteria (Oscillatoriales and Chroococcales) with known marine planktonic and benthic distributions were distinguished, alongside a mix of metabolically versatile eubacteria (nifH Clusters I and III). Using primers selective for cyanobacterial nifH genes we identified filamentous non-heterocystous Trichodesmium-like and LPP (Leptolyngbya, Phormidium and Plectonema)-like Oscillatoriales, as well as Cyanothece-like Chroococcales in a brine sample from 81 degrees N. The occurrence of Trichodesmium-like cyanobacteria was further confirmed by sequences of the hetR gene of Trichodesmium. Microscopic examinations confirmed the presence of viable filamentous and unicellular cyanobacteria. Our results reveal the potential for microbial N2 fixation in the Arctic seas. However, it is still left to determine if these genes are also metabolically active before any biogeochemical importance of diazotrophy in the polar oceans can be assessed.

  • 24. Dominguez-Escobar, Julia
    et al.
    Beltran, Yislem
    Bergman, Birgitta
    Stockholm University, Faculty of Science, Department of Botany.
    Diez, Beatriz
    Stockholm University, Faculty of Science, Department of Botany.
    Ininbergs, Karolina
    Stockholm University, Faculty of Science, Department of Botany.
    Souza, Valeria
    Falcon, Luisa I.
    Phylogenetic and molecular clock inferences of cyanobacterial strains within Rivulariaceae from distant environments2011In: FEMS Microbiology Letters, ISSN 0378-1097, E-ISSN 1574-6968, Vol. 316, no 2, p. 90-99Article in journal (Refereed)
    Abstract [en]

    Heterocyst-forming cyanobacteria are important players at both evolutionary and ecological scales, but to date it has been difficult to establish their phylogenetic affiliations. We present data from a phylogenetic and molecular clock analysis of heterocystous cyanobacteria within the family Rivulariaceae, including the genera Calothrix, Rivularia, Gloeotrichia and Tolypothrix. The strains were isolated from distant geographic regions including fresh and brackish water bodies, microbial mats from beach rock, microbialites, pebble beaches, plus PCC strains 7103 and 7504. Phylogenetic inferences (distance, likelihood and Bayesian) suggested the monophyly of genera Calothrix and Rivularia. Molecular clock estimates indicate that Calothrix and Rivularia originated similar to 1500 million years ago (MYA) ago and species date back to 400-300 MYA while Tolypothrix and Gloeotrichia are younger genera (600-400 MYA).

  • 25.
    D'Onofrio, Cladio
    et al.
    University of Pisa, Italy.
    Lindberg, Sylvia
    Stockholm University, Faculty of Science, Department of Botany.
    Sodium induces simultaneous changes in cytosolic calcium and pH in salt-tolerant quince protoplasts2009In: Journal of plant physiology (Print), ISSN 0176-1617, E-ISSN 1618-1328, Vol. 166, p. 1755-1763Article in journal (Refereed)
    Abstract [en]

    Previousexperimentswithsalt-resistantquinceBA29(Cydonia oblonga cv.Mill.) have shownthatthiscultivartakesupsodiumtransientlyintothecytosolofshoot protoplasts onlyintheabsenceofcalciumchloride,orat o1mMcalciumchloride. Addition ofNaClZ100mMtosingleprotoplastsfrom in vitro-cultivated quinceinthe presence of1.0mMcalciuminducedinstantchangesinthecytosolicconcentrations of calciumandprotons.Thesechangeswereinvestigatedbyuseoftetra [acetoxymethyl] estersofthefluorescentstilbenechromophoresFura2andbis- carboxyethyl-carboxyfluorescein (BCECF),respectively.ThecytosolicCa2+ dynamics in theprotoplastsweredependentontheconcentrationofNaCladded.Thechanges in calciumdifferedinamplitudeandfinalconcentrationandwerecorrelatedintime mainly withchangesinpH.Additionof100–400mMNaCltotheprotoplastscausedan oscillating increaseinthecytosoliclevelofcalcium,andthenadecrease.Addition of mannitol,ofequiosmolarconcentrationtoNaCl,didnotincreasethecytosolic calcium concentration.Moreover,therewasnoincreaseincytosoliccalciumwhen NaCl wasaddedinthepresenceofcalciumbindingethyleneglycol-bis(beta- aminoethylether)-N,N,N0,N0-tetra aceticacid(EGTA),orlantanorverapamil,two inhibitors ofplasmamembranecalciumchannels.Therefore,weconcludethat,in salt-resistant quince,sodiuminducesaninfluxofcalciumintothecytosolbyplasma membrane calciumchannels,andasimultaneousincreaseincytosolicpH.Because these changeswereobtainedinthepresenceof1mMcalciuminthemedium,they were notduetosodiumuptakeintothecytosol.

  • 26.
    Dou, Dan
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Influenza A Virus: Spatial analysis of influenza genome trafficking and the evolution of the neuraminidase protein2019Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Influenza A viruses (IAVs) are a common infectious agent that seasonally circulates within the human population that causes mild to severe acute respiratory infections. The severity of the infection is often related to how the virus has evolved with respect to the pre-existing immunity in the population. For IAVs, the most common mechanisms to avoid the immune response are to vary the surface antigens, hemagglutinin (HA) and neuraminidase (NA), by processes known as antigenic drift and shift.

    Antigenic drift refers to point mutations that accumulate in HA and NA as a result of the antibody-mediated selection pressure that exists in the population. The majority of the changes attributed to antigenic drift localize to HA and NA surface exposed regions, however this does not exclude that drift can also result in the selection of residues that are not exposed. One region where non-exposed residues have potentially been selected for is the NA transmembrane domain (TMD) of human H1N1 IAVs, where a temporal bias exists for the accumulation of polar residues. By examining these sequence changes in the NA TMD, we found that the polar residues contribute to the amphipathic characteristic of the NA TMD, which mediates the oligomerization of the N-terminus. As more polar residues became incorporated, the strength of the TMD-TMD interaction increased, presumably to benefit the NA head domain assembly into a functional tetramer. We determined that the amphiphilic drift in the NA TMD is able to bypass the strict hydrophobicity required for membrane insertion at the endoplasmic reticulum because it can utilize the co-translational translocation process to facilitate the insertion and inversion of its non-ideal TMD. The contribution of the TMD to proper NA assembly was traced to the formation of the Ca2+ binding pocket that is located at the center of the tetrameric assembly, as this pocket lies above the stalk linker regions and must be occupied for NA to function.

    In addition to antigenic drift, NA and HA can also undergo antigenic shift. Antigenic shift occurs when either of the gene segments encoding NA or HA are exchanged with ones from another IAV encoding another subtype of NA or HA. Different from antigenic drift, antigenic shift can only occur when a cell is co-infected and most investigations on the process of reassortment have been made at the protein level due to the methodological issues for labeling the RNA genome in situ. To overcome these technical limitations, we developed an in situ RNA labeling approach that provides highly specific spatial resolution of the IAV genome throughout the infection process. By applying this approach to temporally analyze the co-infection process, we found that the entry of a second IAV is stalled in the cytoplasm if another IAV has begun to replicate. Together, these results provide insight into the low frequency of antigenic shift in nature and provide evidence that non-exposed residues may make an underappreciated contribution to NA antigenic drift in human H1N1 viruses.

  • 27. Downing, Simone
    et al.
    Scott, Laura Louise
    Zguna, Nadezda
    Stockholm University, Faculty of Science, Department of Environmental Science and Analytical Chemistry.
    Downing, Timothy Grant
    Human Scalp Hair as an Indicator of Exposure to the Environmental Toxin -N-Methylamino-l-alanine2018In: Toxins, ISSN 2072-6651, E-ISSN 2072-6651, Vol. 10, no 1, article id 14Article in journal (Refereed)
    Abstract [en]

    Dietary or aerosol exposure to the environmental neurotoxin -N-methylamino-l-alanine (BMAA) is a putative risk factor for the development of sporadic neurodegenerative disease. There are many potential sources of BMAA in the environment, but BMAA presence and quantities are highly variable. It has been suggested that BMAA in human hair may serve as an indicator of exposure. We sought to evaluate the use of the BMAA content of human scalp hair as an indicator of exposure, as well as the correlation between specific lifestyle or dietary habits, reported as hypothesised exposure risk factors, and BMAA in hair. Scalp hair samples and questionnaires were collected from participants in a small residential village surrounding a freshwater impoundment renowned for toxic cyanobacterial blooms. Data suggested a positive correlation between hair BMAA content and consumption of shellfish, and possibly pork. No statistically significant correlations were observed between hair BMAA content and residential proximity to the water or any other variable. Hair BMAA content was highly variable, and in terms of exposure, probably reflects primarily dietary exposure. However, the BMAA content of human hair may be affected to a great extent by several other factors, and as such, should be used with caution when evaluating human BMAA exposure, or correlating exposure to neurodegenerative disease incidence.

  • 28.
    Edberg, Frida
    et al.
    Stockholm University, Faculty of Science, Department of Applied Environmental Science (ITM).
    Andersson, Anders F.
    Holmström, Sara J. M.
    Stockholm University, Faculty of Science, Department of Geological Sciences.
    Bacterial community composition in the water column of a lake formed by a former uranium open pit mine2012In: Microbial Ecology, ISSN 0095-3628, E-ISSN 1432-184X, Vol. 64, no 4, p. 870-880Article in journal (Refereed)
    Abstract [en]

    Mining of pyrite minerals is a major environmental issue involving both biological and geochemical processes. Here we present a study of an artificial lake of a former uranium open pit mine with the aim to connect the chemistry and bacterial community composition (454-pyrosequencing of 16S rRNA genes) in the stratified water column. A shift in the water chemistry from oxic conditions in the epilimnion to anoxic, alkaline, and metal and sulfide-rich conditions in the hypolimnion was corresponded by a strong shift in the bacterial community, with few shared operational taxonomic units (OTU) between the water layers. The epilimnetic bacterial community of the lake (similar to 20 years old) showed similarities to other temperate freshwater lakes, while the hypolimnetic bacterial community showed similarity to extreme chemical environments. The epilimnetic bacterial community had dominance of Actinobacteria and Betaproteobacteria. The hypolimnion displayed a higher bacterial diversity and was dominated by the phototrophic green sulphur bacterium of the genus Chlorobium (ca. 40 % of the total community). Deltaproteobacteria were only represented in the hypolimnion and the most abundant OTUs were affiliated with ferric iron and sulfate reducers of the genus Geobacter and Desulfobulbus, respectively. The chemistry is clearly controlling, especially the hypolimnetic, bacterial community but the community composition also indicates that the bacteria are involved in metal cycling in the lake.

  • 29.
    Envall, Ida
    et al.
    Stockholm University, Faculty of Science, Department of Zoology.
    Gustavsson, Lena M.
    Swedish Museum of Natural History.
    Erséus, Christer
    University of Gothenburg.
    Genetic and morphological variation in “cosmopolitan” Nais worms (Annelida, Clitellata, Naididae): species diversity beyond that of current taxonomyManuscript (Other academic)
  • 30.
    Eriksson, Harald
    et al.
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Berta, David
    Örmälä-Odegrip, Anni-Maria
    Giske, Christian G.
    Nilsson, Anders S.
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    A novel phage cocktail inhibiting the growth of 99 β-lactamase carrying Klebsiella pneumoniae clinical isolates in vitroManuscript (preprint) (Other academic)
    Abstract [en]

    Klebsiella pneumoniae is a gram-negative bacterial pathogen, accountable for a variety of nosocomial infections in immunocompromised patients, open-wound infections and community-acquired pneumonia in elderly. K. pneumoniae strains harboring plasmid-mediated extended spectrum β-lactamase enzymes (ESBL) are resistant to all penicillin and cephalosoprins, whereas bacteria capable of producing carbapenemase enzymes (e.g. NDM, KPC and VIM) are resistant to virtually all β-lactam group antibiotics. The use of bacterial viruses lysing bacterial hosts (phage therapy) has been suggested as an alternative in fighting bacterial infections resistant to known antibiotics. In this study, we assembled a phage cocktail consisting of 6 novel lytic bacteriophages infecting K. pneumoniae. The phage cocktail was tested against 125 β-lactamase producing clinical isolates of K. pneumoniae and we found that at high titres, the cocktail was able to lyse 99 of these isolates in vitro.

  • 31.
    Eriksson, Jens
    Stockholm University, Faculty of Science, Department of Genetics, Microbiology and Toxicology.
    Virulence Factors and Motility Mechanisms of Pathogenic Neisseria2012Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Neisseria gonorrhoeae and Neisseria meningitidis are two closely related human specific pathogens. Neisseria gonorrhoeae is the causative agent for the sexually transmitted disease gonorrhea and often causes asymptomatic infections in women which is a cause of infertility. Neisseria meningitidis is a major cause of mortality world-wide through bacterial meningitis and septicemia. The severity of meningococcal disease, especially in sub-Saharan Africa warrants development of effective vaccines against serogroups that currently lack them. Here, Neisseria host-pathogen interactions and common virulence factors that may prove useful in vaccine development and in understanding disease caused by pathogenic Neisseria are reviewed and investigated. The aim of this thesis is to investigate the virulence-associated properties of the universally expressed N. meningitidis proteins NhhA, NafA, PilU and PilT, as well as to characterize the twitching motility of the pathogenic Neisseria. The conserved autotransporter adhesin NhhA has in Paper I of this thesis been investigated in a murine model of meningococcemia and found to be important for intranasal colonization and disease outcome of N. meningitidis in CD46 transgenic mice. NafA has in Paper II of this thesis been named and identified as a novel anti-aggregation factor that impacts both pilus bundling and the virulence potential of N. meningitidis. The ATPases, PilU and PilT, which are involved in the functionality of pili were studied in Paper III of this thesis. PilU and PilT were found to modulate Neisseria microcolony formation, host cell adhesion, pilus retraction, serum resistance, as well as mortality in a mouse model of meningococcal disease. Finally, Paper IV of this thesis also provides novel insights into the nature of twitching motility in pathogenic Neisseria. By live-cell microscopy and automated particle tracking coupled with visualization of pili in motile bacteria we found that N. meningitidis strains, on average, move faster and utilizes more pili then N. gonorrhoeae. In summary, this thesis investigates Neisseria virulence factors in general, type IV pili in particular and characterizes the roles of several virulence-associated proteins and twitching motility in the pathogenic Neisseria.

  • 32.
    Eriksson, Jens
    et al.
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Eriksson, Olaspers Sara
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Maudsdotter, Lisa
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Palm, Oskar
    Institutionen för teoretisk fysik, KTH.
    Sarkissian, Tim
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Aro, Helena
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Wallin, Mats
    Institutionen för teoretisk fysik, KTH.
    Jonsson, Ann-Beth
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Characterization of motility and piliation in pathogenic NeisseriaManuscript (preprint) (Other academic)
  • 33.
    Eriksson, Jens
    et al.
    Stockholm University, Faculty of Science, Department of Genetics, Microbiology and Toxicology.
    Eriksson, Olaspers Sara
    Stockholm University, Faculty of Science, Department of Genetics, Microbiology and Toxicology.
    Palm, Oscar
    KTH.
    Sarkissian, Tim
    Stockholm University, Faculty of Science, Department of Genetics, Microbiology and Toxicology.
    Wallin, Mats
    KTH.
    Jonsson, Ann-beth
    Stockholm University, Faculty of Science, Department of Genetics, Microbiology and Toxicology.
    Difference in twitching motility between Neisseria meningitidis and Neisseria gonorrhoeae and its relation to pilus dynamicsManuscript (preprint) (Other academic)
    Abstract [en]

    Type IV pili of pathogenic Neisseria, i. e. Neisseria gonorrhoeae and Neisseria meningitidis, are essential for initial attachment to host cells, induction of signal transduction cascades and disease development. A characteristic feature of type IV pili is their ability to retract, which generates forces that move bacteria over surfaces. However, the relation between bacterial motility and pilus dynamics remains poorly understood. In this work we analyzed bacterial motility and monitored movement of fluorescently labeled pili by live cell imaging. We found that movement of N. meningitidis occurred at higher speed and with a larger number of retracting pili than for N. gonorrhoeae. Analysis of time-lapse images suggested that N. gonorrhoeae most often moved using one retracting pilus, whereas N. meningitidis most often used four pili. There were no differences in the membrane distribution of PilT among strains. However, we found significantly higher levels of PilT in N. gonorrhoeae than in N. meningitidis. This produces a higher retraction probability, which could contribute to explaining the lower number of pili observed in N. gonorrhoeae. Finally, we propose a mechanism for how the speed of bacterial movement on a surface depends on the number of retracting pili.

  • 34.
    Eriksson, Olaspers Sara
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Pathogenic Neisseria: Single cell motility, multicellular dynamics and antimicrobial susceptibility2014Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Neisseria meningitidis and Neisseria gonorrhoeae can colonize humans without causing any symptoms. However, gonorrhea and invasive meningococcal disease are serious health concerns. An essential virulence factor for neisserial adhesion to host cells, twitching motility and microcolony formation/aggregation is the retractile type IV pili (Tfp). The scope of this thesis stretches from the motility of single Neisseria cells, via the multicellular dynamics of N. meningitidis microcolonies, to the bactericidal and endotoxin-inhibiting activity of a novel anti-meningococcal peptide. The Tfp machinery in pathogenic Neisseria is highly conserved. Nevertheless, our data demonstrate species-specific expression levels of the Tfp retraction ATPase PilT. By using live-cell microscopy and particle tracking together with visualization of pili, differences between N. gonorrhoeae and N. meningitidis were also observed in piliation and twitching motility speed. However, these differences could not be attributed to the contrasting PilT expressions per se (Paper I). The importance of PilT for pilus dynamics is well established in the literature while comprehensive knowledge of the paralog PilU is lacking. In Paper II, results suggest that PilU promotes timely formation of microcolonies. Furthermore, both PilU and PilT were required for full virulence of meningococci in vivo. The meningococcal response upon adhesion to host cells includes upregulation of the novel virulence factor Neisseria anti-aggregation factor A (NafA). Our data indicate that NafA limits microcolony formation by preventing excessive formation of Tfp bundles (Paper III). Microcolony dispersal is a prerequisite for close adhesion and mucosal invasion. Dispersal progressed rapidly on host cells and upon induction with host cell-conditioned medium (Paper IV). The dispersal phase was not altered in NafA-deficient meningococci. However, NafA may be important after microcolony dispersal on host cells for maintaining bacteria in a single cell state (Paper IV). In Paper V, a screen of cell-penetrating peptides for antimicrobial activity towards meningococci demonstrated that transportan-10 (TP10) exhibited rapid membrane-disruptive and bactericidal activity. TP10 also decreased bacteraemia levels in a murine model of meningococcal disease. Furthermore, TP10 reduced the proinflammatory effect of endotoxin on macrophages. Thus, TP10 displays two properties that may be utilized for the development of a peptide-based treatment against pathogens.

  • 35.
    Eriksson, Olaspers Sara
    et al.
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Sigurlásdóttir, Sara
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Jonsson, Ann-Beth
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    A host cell-derived factor induces the dispersal of Neisseria meningitidis microcoloniesManuscript (preprint) (Other academic)
  • 36. Falcon, Luisa I
    et al.
    Lindwall, Susanne
    Stockholm University, Faculty of Science, Department of Botany. Växtfysiologi.
    Bauer, Karolina
    Stockholm University, Faculty of Science, Department of Botany. Växtfysiologi.
    Bergman, Birgitta
    Stockholm University, Faculty of Science, Department of Botany. Växtfysiologi.
    Carpenter, Edward C
    Ultrastructure of unicellular N-2 fixing cyanobacteria from the tropical North Atlantic and subtropical North Pacific Oceans2004In: Journal of Phycology, Vol. 40, no 6, p. 1074-1078Article in journal (Refereed)
    Abstract [en]

    Abstract: Nitrogen fixing unicellular marine cyanobacteria may have a major role in the global biogeochemistry of N; nevertheless, little is known about their phylogeny and morphology. We isolated N-2 fixing unicellular cyanobacteria from the tropical North Atlantic and subtropical North Pacific Oceans and examined ultrastructural dynamics during dark:light cycles when grown in incubators. The isolate from the subtropical North Pacific was larger and showed a size variation from 3 to 7 mum but had similar morphology and cell division-plane characteristics as the isolate from the North Atlantic (2.5 mum). Nitrogen fixation only occurred during the dark phase, and ultrastructural analysis demonstrated changes in the appearance and quantity of large carbohydrate-like granules present in the cells. To verify the composition of these carbohydrate-like granules, staining with periodic acid, thioacetic acid, and silver was carried out, and a positive reaction was obvious in all cells. The cells from the Atlantic seemed to empty their polysaccharide granules during the night, whereas those from the Pacific showed a decrease in the number of their granules. Our work suggests that phylogenetically related strains of unicellular N-2 fixing cyanobacteria from different oceans showed similar carbohydrate-like granules that could be used to fuel N-2 fixation during darkness.

  • 37.
    Faxén, Margareta
    Stockholm University, Faculty of Science, Department of Microbiology.
    Studies of translation in E. coli1993Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    A cis-acting translational mutation in the beginning of the glnS gene was analyzed; this mutation creates a extra base pair to a proposed extended ribosome binding site. When increasing the complementarity to this extended ribosome binding site, it was demonstrated that the expression increased; correspondingly, when complementarity was decreasd the expression went down. It was also shown that the presence of rare codons near the beginning of the gene can affect expression.

    Studies of a S13 mutant (rpsM413) revealed that the mutant allele is associated with slow growth rate and slow elongation rate. The 30S subunit showed a reduced sedimentation coefficient but was able to form apparently normal 70S ribosomes.

    Investigations to see whether ribosomal mutants are able to affect proofreading in vivo found that the missense and nonsense suppressors are affected by rpsD mutations in a rather unpredictable manner. It was shown that the ribosome allele, the nature of the suppressor tRNA, the codon context, and the structure of the anticodon loop are the determinig factors. rpsL mutations decrease the nonsense suppression, in accordance with their restrictive effect on translational error formation.

    Streptomycin, which is known to increase translational error in vitro, did not increase efficiency of nonsense suppressor tRNAs in strains with normal or rpsL ribosomes. It did so only in combination with one rpsL mutation which is associated with streptomycin pseudodependence.

    The presence or absence of the modification ms2i6A37 in the tRNA was found to be a determining factor in the functional response to the ribosomal mutations. These effects strongly indicate that tRNA is directly involved in this phenomena.

    The role of ppGpp was investigated, and the results suggest that it affects transcription efficiency, but not translation. ppGpp seems to play a role in the tuning of the coupling between transcription and translation.

  • 38. Fuchslueger, Lucia
    et al.
    Wild, Birgit
    Stockholm University, Faculty of Science, Department of Environmental Science and Analytical Chemistry. University of Vienna, Austria.
    Mooshammer, Maria
    Takriti, Mounir
    Kienzl, Sandra
    Knoltsch, Anna
    Hofhansl, Florian
    Bahn, Michael
    Richter, Andreas
    Microbial carbon and nitrogen cycling responses to drought and temperature in differently managed mountain grasslands2019In: Soil Biology and Biochemistry, ISSN 0038-0717, E-ISSN 1879-3428, Vol. 135, p. 144-153Article in journal (Refereed)
    Abstract [en]

    Grassland management can modify soil microbial carbon (C) and nitrogen (N) cycling, affecting the resistance to extreme weather events, which are predicted to increase in frequency and magnitude in the near future. However, effects of grassland management on microbial C and N cycling and their responses to extreme weather events, such as droughts and heatwaves, have rarely been tested in a combined approach. We therefore investigated whether grassland management affects microbial C and N cycling responses to drought and temperature manipulation. We collected soils from in situ drought experiments conducted in an extensively managed and an abandoned mountain grassland and incubated them at two temperature levels. We measured microbial respiration and substrate incorporation, as well as gross rates of organic and inorganic N cycling to estimate microbial C and N use efficiencies (CUE and NUE). The managed grassland was characterized by lower microbial biomass, lower fungi to bacteria ratio, and higher microbial CUE, but only slightly different microbial NUE. At both sites drought induced a shift in microbial community composition driven by an increase in Gram-positive bacterial abundance. Drought significantly reduced C substrate respiration and incorporation by microbes at both sites, while microbial CUE remained constant. In contrast, drought increased gross rates of N mineralization at both sites, whereas gross amino acid uptake rates only marginally changed. We observed a significant direct, as well as interactive effect between land management and drought on microbial NUE. Increased temperatures significantly stimulated microbial respiration and reduced microbial CUE independent of drought or land management. Although microbial N processing rates showed no clear response, microbial NUE significantly decreased at higher temperatures. In summary in our study, microbial CUE, in particular respiration, is more responsive to temperature changes. Although N processing rates were stronger responding to drought than to temperature microbial NUE was affected by both drought and temperature increase. We conclude that direct effects of drought and heatwaves can induce different responses in soil microbial C and N cycling similarly in the studied land management systems.

  • 39.
    Garpe, Kajsa C
    et al.
    Stockholm University, Faculty of Science, Department of Zoology.
    Öhman, Marcus C
    Stockholm University, Faculty of Science, Department of Zoology, Animal Ecology.
    Non-random habitat use by coral reef fish recruits in Mafia Island Marine Park, Tanzania2007In: African Journal of Marine Science, ISSN 1814-232X, Vol. 29, no 2, p. 187-199Article in journal (Refereed)
    Abstract [en]

    The habitat use by nearly 3 000 reef fish recruits, comprising 56 taxa, at seven sites in Mafia Island Marine Park, Tanzania, were examined. The study was carried out following the 1998 global coral bleaching event and all sites but one were dominated by dead coral and rubble. Mean recruit densities ranged between 0.1 m-2 and 0.7 m-2 among sites. Although live coral represented only 15% of the overall substrate composition, almost half of all observed recruits were found associated with this substrate. Pooled across all sites, 46% of the recruits used live coral cover in disproportion to availability. Principal component analyses were applied to explore microhabitat use by the 11 most common recruit taxa in comparison to availability. Among these taxa, 10 exhibited nonrandom microhabitat use and six associated with live coral in disproportion to availability. A comparison with the adult fish community revealed that adult abundances of four of the six coral selective recruit taxa were significantly correlated with live coral. The study demonstrated that reef fish recruits use microhabitats non-randomly and that a substantial proportion is selective towards live coral.

  • 40.
    Geörg, Miriam
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Antimicrobial peptides and virulence factors in meningococcal colonisation and disease2014Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The Gram-negative bacterium Neisseria meningitidis is a transient commensal of the human nasopharynx, but occasionally causes life-threatening disease. During colonisation of its niche, N. meningitidis has to overcome innate immune defences, including the expression of antimicrobial peptides (AMPs). Meningococcal resistance to the host defence peptide LL-37 was investigated in Papers I and II. The polysaccharide capsule and lipopolysaccharide (LPS) were found to increase LL-37 resistance by inhibiting peptide binding to the bacteria. Further, N. meningitidis responded to sub-lethal doses of LL-37 by an increase in capsule biosynthesis. Intriguingly, adhesion to epithelial cells and tissues protected N. meningitidis from physiological concentrations of LL-37 and two other helical peptides. The protective effect was mediated by RhoA- and Cdc42-dependent host cell signalling and cholesterol-rich membrane microdomains. The host epithelium thus seems to play an active role in AMP resistance.

    Cell-penetrating peptides (CPPs) are structurally related to AMPs, but are primarily employed for the delivery of membrane-impermeable molecules in vitro and in vivo. In Paper III, several of these peptides were screened for antimicrobial activity against N. meningitidis. The best candidate, transportan-10 (TP10), exhibited membrane-disruptive, bactericidal activity and decreased bacteraemia levels in a mouse model of meningococcal disease. Additionally, TP10 inhibited binding of LPS to macrophages, thereby neutralising its inflammatory effect. These dual effects of TP10 may potentially be harnessed for the treatment of invasive disease.

    The role of the N. meningitidis polynucleotide phosphorylase (PNPase) homologue in pathogenesis was studied in Paper IV. PNPase-deficient meningococci were hyper-aggregative and resistant to normal human serum, and these phenotypes were associated with an accumulation of extracellular DNA on the pili and surface of the bacteria. Wild-type meningococci differentially regulated PNPase expression in contact with epithelial cells and in human serum, suggesting the dynamic regulation of PNPase levels during pathogenesis.

  • 41.
    Geörg, Miriam
    et al.
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Maudsdotter, Lisa
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Tavares, Raquel
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Jonsson, Ann-Beth
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Meningococcal resistance to antimicrobial peptides is mediated by bacterial adhesion and host cell RhoA and Cdc42 signalling2013In: Cellular Microbiology, ISSN 1462-5814, E-ISSN 1462-5822, Vol. 15, no 11, p. 1938-1954Article in journal (Refereed)
    Abstract [en]

    Antimicrobial peptides (AMPs) constitute an essential part of the innate immune defence. Pathogenic bacteria have evolved numerous strategies to withstand AMP-mediated killing. The influence of host epithelia on bacterial AMP resistance is, however, still largely unknown. We found that adhesion to pharyngeal epithelial cells protected Neisseria meningitidis, a leading cause of meningitis and sepsis, from the human cathelicidin LL-37, the cationic model amphipathic peptide (MAP) and the peptaibol alamethicin, but not from polymyxin B. Adhesion to primary airway epithelia resulted in a similar increase in LL-37 resistance. The inhibition of selective host cell signalling mediated by RhoA and Cdc42 was found to abolish the adhesion-induced LL-37 resistance by a mechanism unrelated to the actin cytoskeleton. Moreover, N. meningitidis triggered the formation of cholesterol-rich membrane microdomains in pharyngeal epithelial cells, and host cell cholesterol proved to be essential for adhesion-induced resistance. Our data highlight the importance of Rho GTPase-dependent host cell signalling for meningococcal AMP resistance. These results indicate that N. meningitidis selectively exploits the epithelial microenvironment in order to protect itself from LL-37.

  • 42. Giha, H. A.
    et al.
    Nasr, A. A.
    Stockholm University, Faculty of Science, The Wenner-Gren Institute .
    Iriemenam, N. C.
    Stockholm University, Faculty of Science, The Wenner-Gren Institute .
    Berzins, Klavs
    Stockholm University, Faculty of Science, The Wenner-Gren Institute .
    Troye-Blomberg, Marita
    Stockholm University, Faculty of Science, The Wenner-Gren Institute .
    Arnot, D. E.
    ElGhazali, G.
    A malaria serological map indicating the intersection between parasite antigenic diversity and host antibody repertoires2012In: European Journal of Clinical Microbiology and Infectious Diseases, ISSN 0934-9723, E-ISSN 1435-4373, Vol. 31, no 11, p. 3117-3125Article in journal (Refereed)
    Abstract [en]

    A malaria vaccine targeting Plasmodium falciparum remains a strategic goal for malaria control. If a polyvalent vaccine is to be developed, its subunits would probably be chosen based on immunogenicity (concentration of elicited antibodies) and associations of selected antigens with protection. We propose an additional possible selection criterion for the inclusion of subunit antigens; that is, coordination between elicited antibodies. For the quantitative estimation of this coordination, we developed a malaria serological map (MSM). Construction of the MSM was based on three categories of variables: (i) malaria antigens, (ii) total IgG and IgG subclasses, (iii) different sources of plasma. To validate the MSM, in this study, we used four malaria antigens (AMA1, MSP2-3D7, MSP2-FC27 and Pf332-C231) and re-grouped the plasma samples into five pairs of subsets based on age, gender, residence, HbAS and malaria morbidity in 9 years. The plasma total IgG and IgG subclasses to the test antigens were measured, and the whole material was used for the MSM construction. Most of the variables in the MSM were previously tested and their associations with malaria morbidity are known. The coordination of response to each antigens pair in the MSM was quantified as the correlation rate (CR = overall number of significant correlations/total number of correlations x 100 %). Unexpectedly, the results showed that low CRs were mostly associated with variables linked with malaria protection and the antigen eliciting the least CRs was the one associated with protection. The MSM is, thus, of potential value for vaccine design and understanding of malaria natural immunity.

  • 43. Giha, Hayder A.
    et al.
    Nasr, Amre
    Iriemenam, Nnaemeka C.
    Troye-Blomberg, Marita
    Stockholm University, Faculty of Science, The Wenner-Gren Institute , Immunology.
    Berzins, Klavs
    Stockholm University, Faculty of Science, The Wenner-Gren Institute , Immunology.
    ElGhazali, Gehad
    Lack of significant influence for Fc gamma RIIa-RH131 or hemoglobin AA/AS polymorphisms on immunity and susceptibility to uncomplicated malaria and existence of marked linkage between the two polymorphisms in Daraweesh2012In: Microbes and infection, ISSN 1286-4579, E-ISSN 1769-714X, Vol. 14, no 6, p. 537-544Article in journal (Refereed)
    Abstract [en]

    Malaria signature on human genome is marked by several gene polymorphisms. HemoglobinAS (HbAS) is known to protect against severe malaria, but barely proved to protect against uncomplicated malaria (UM). Similarly, the influence of Fc gamma RIIa-RH131 polymorphism on malaria is controversial. Polymorphisms in both genes were examined and levels of IgG subclasses against four malaria antigens were measured for 250 Fulani's from Daraweesh, eastern Sudan. Morbidity data for up to nine years was available for 214 donors. Number of malaria episodes experienced by each individual during the study period was used as indicator for susceptibility to UM. PCR and RFLP were used for donors DNA genotyping and ELISA for antibodies measurement. Results revealed that neither Fc gamma RIIa-RH131 alleles/genotypes nor HbAA/AS was significantly associated with malaria morbidity or with levels of IgG to test antigens. Both polymorphisms were in Hardy-Weinberg Equilibrium, interestingly, there was strong association between the two polymorphisms (linkage disequilibrium - LD) with D' = 0.89. The association between the two polymorphisms was confirmed by analysis of independent material from a neighboring village. In conclusion, in Daraweesh both Fc gamma RIIa-RH131 and HbAA/AS genotypes, independently or together, were not major markers for UM susceptibility, however, marked LD was observed between the two polymorphisms.

  • 44. Gioti, Anastasia
    et al.
    Nystedt, Björn
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).
    Li, Wenjun
    Xu, Jun
    Andersson, Anna
    Averette, Anna F.
    Muench, Karin
    Wang, Xuying
    Kappauf, Catharine
    Kingsbury, Joanne M.
    Kraak, Bart
    Walker, Louise A.
    Johansson, Henrik J.
    Holm, Tina
    Lehtio, Janne
    Stajich, Jason E.
    Mieczkowski, Piotr
    Kahmann, Regine
    Kennell, John C.
    Cardenas, Maria E.
    Lundeberg, Joakim
    Saunders, Charles W.
    Boekhout, Teun
    Dawson, Thomas L.
    Munro, Carol A.
    de Groot, Piet W. J.
    Butler, Geraldine
    Heitman, Joseph
    Scheynius, Annika
    Genomic Insights into the Atopic Eczema-Associated Skin Commensal Yeast Malassezia sympodialis2013In: mBio, ISSN 2161-2129, E-ISSN 2150-7511, Vol. 4, no 1, p. e00572-12-Article in journal (Refereed)
    Abstract [en]

    Malassezia commensal yeasts are associated with a number of skin disorders, such as atopic eczema/dermatitis and dandruff, and they also can cause systemic infections. Here we describe the 7.67-Mbp genome of Malassezia sympodialis, a species associated with atopic eczema, and contrast its genome repertoire with that of Malassezia globosa, associated with dandruff, as well as those of other closely related fungi. Ninety percent of the predicted M. sympodialis protein coding genes were experimentally verified by mass spectrometry at the protein level. We identified a relatively limited number of genes related to lipid biosynthesis, and both species lack the fatty acid synthase gene, in line with the known requirement of these yeasts to assimilate lipids from the host. Malassezia species do not appear to have many cell wall-localized glycosylphosphatidylinositol (GPI) proteins and lack other cell wall proteins previously identified in other fungi. This is surprising given that in other fungi these proteins have been shown to mediate interactions (e. g., adhesion and biofilm formation) with the host. The genome revealed a complex evolutionary history for an allergen of unknown function, Mala s 7, shown to be encoded by a member of an amplified gene family of secreted proteins. Based on genetic and biochemical studies with the basidiomycete human fungal pathogen Cryptococcus neoformans, we characterized the allergen Mala s 6 as the cytoplasmic cyclophilin A. We further present evidence that M. sympodialis may have the capacity to undergo sexual reproduction and present a model for a pseudobipolar mating system that allows limited recombination between two linked MAT loci. IMPORTANCE Malassezia commensal yeasts are associated with a number of skin disorders. The previously published genome of M. globosa provided some of the first insights into Malassezia biology and its involvement in dandruff. Here, we present the genome of M. sympodialis, frequently isolated from patients with atopic eczema and healthy individuals. We combined comparative genomics with sequencing and functional characterization of specific genes in a population of clinical isolates and in closely related model systems. Our analyses provide insights into the evolution of allergens related to atopic eczema and the evolutionary trajectory of the machinery for sexual reproduction and meiosis. We hypothesize that M. sympodialis may undergo sexual reproduction, which has important implications for the understanding of the life cycle and virulence potential of this medically important yeast. Our findings provide a foundation for the development of genetic and genomic tools to elucidate host-microbe interactions that occur on the skin and to identify potential therapeutic targets.

  • 45.
    Granbom, Malena
    et al.
    Stockholm University, Faculty of Science, Department of Botany.
    Lopes, Patricia F.
    Pedersen, Marianne
    Stockholm University, Faculty of Science, Department of Botany.
    Colepicolo, Pio
    Nitrate reductase in the marine macroalga Kappaphycus alvarezii (Rhodophyta): oscillation due to the protein level2007In: Botanica Marina, ISSN 0006-8055, E-ISSN 1437-4323, Vol. 50, no 2, p. 106-112Article in journal (Refereed)
    Abstract [en]

    Nitrate reductase, (NR; EC 1.6.6.1) of the marine red macroalga Kappaphycus alvarezii was examined in algae maintained under L:D and constant light conditions. Undenaturated protein had a molecular mass of about 210 kD (+/- 23 kD); based on sodium dodecyl sulfate-polyacrylamide gel electrophoresis and immunoblotting techniques, the enzyme appears to be composed of two possibly identical subunits of 100 kD. The NR of K alvarezii was recognized by 10 out of 17 monoclonal antibodies raised against the NR from the red alga Porphyra yezoensis. Basal parts of the algal thallus had higher NR protein content, although the highest activity of NR has been located previously in the apical thallus parts, suggesting a post-translational regulation. The cellular expression of NR exhibits a daily rhythm. In extracts of algae grown under either constant light or a light:dark cycle, staining with antibodies NR 6 and NR 10 showed that the amount of protein varied by a factor of about 2, with the maximum occurring in the early day phase.

  • 46.
    Gubanova, Evgenia
    et al.
    Stockholm University, Faculty of Science, Department of Genetics, Microbiology and Toxicology.
    Brown, Brandee
    Ivanov, Sergei V.
    Helleday, Thomas
    Mills, Gordon B.
    Yarbrough, Wendell G.
    Issaeva, Natalia
    Downregulation of SMG-1 in HPV-Positive Head and Neck Squamous Cell Carcinoma Due to Promoter Hypermethylation Correlates with Improved Survival2012In: Clinical Cancer Research, ISSN 1078-0432, E-ISSN 1557-3265, Vol. 18, no 5, p. 1257-1267Article in journal (Refereed)
    Abstract [en]

    Purpose: Human papillomavirus (HPV) is linked with a subset of head and neck squamous cell carcinomas (HNSCC). HPV-positive HNSCCs show a better prognosis than HPV-negative HNSCCs, which may be explained by sensitivity of the HPV-positive HNSCCs to ionizing radiation (IR). Although the molecular mechanism behind sensitivity to IR in HPV-positive HNSCCs is unresolved, DNA damage response (DDR) might be a significant determinant of IR sensitivity. An important player in the DDR, SMG-1 (suppressor with morphogenetic effect on genitalia), is a potential tumor suppressor and may therefore be deregulated in cancer. No studies have yet been conducted linking defects in SMG-1 expression with cancer. We investigated whether deregulation of SMG-1 could be responsible for defects in the DDR in oropharyngeal HNSCC. Experimental Design: Expression and promoter methylation status of SMG-1 were investigated in HNSCCs. To identify a functional link between HPV infection and SMG-1, we transfected the HPV-negative cells with an E6/E7 expression construct. SMG-1 short hairpin RNAs were expressed in HPV-negative cells to estimate survival upon IR. Results: Forced E6/E7 expression in HPV-negative cells resulted in SMG-1 promoter hypermethylation and decreased SMG-1 expression. Due to promoter hypermethylation, HPV-positive HNSCC cells and tumors express SMG-1 at lower levels than HPV-negative SCCs. Depletion of SMG-1 in HPV-negative HNSCC cells resulted in increased radiation sensitivity, whereas SMG-1 overexpression protected HPV-positive tumor cells from irradiation. Conclusions: Levels of SMG-1 expression negatively correlated with HPV status in cancer cell lines and tumors. Diminished SMG-1 expression may contribute to the enhanced response to therapy exhibited by HPV-positive HNSCCs. 

  • 47.
    Gustafsson, Robert
    et al.
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Zhang, Sicai
    Masuyer, Geoffrey
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Dong, Min
    Stenmark, Pål
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Crystal Structure of Botulinum Neurotoxin A2 in Complex with the Human Protein Receptor SV2C Reveals Plasticity in Receptor Binding2018In: Toxins, ISSN 2072-6651, E-ISSN 2072-6651, Vol. 10, no 4, article id 153Article in journal (Refereed)
    Abstract [en]

    Botulinum neurotoxins (BoNTs) are a family of highly dangerous bacterial toxins, with seven major serotypes (BoNT/A-G). Members of BoNTs, BoNT/A1 and BoNT/B1, have been utilized to treat an increasing number of medical conditions. The clinical trials are ongoing for BoNT/A2, another subtype of BoNT/A, which showed promising therapeutic properties. Both BoNT/A1 and BoNT/A2 utilize three isoforms of synaptic vesicle protein SV2 (SV2A, B, and C) as their protein receptors. We here present a high resolution (2.0 angstrom) co-crystal structure of the BoNT/A2 receptor-binding domain in complex with the human SV2C luminal domain. The structure is similar to previously reported BoNT/A-SV2C complexes, but a shift of the receptor-binding segment in BoNT/A2 rotates SV2C in two dimensions giving insight into the dynamic behavior of the interaction. Small differences in key residues at the binding interface may influence the binding to different SV2 isoforms, which may contribute to the differences between BoNT/A1 and BoNT/A2 observed in the clinic.

  • 48. Guðmundsson, Guðmundur H.
    Structure and expression of the cecropin locus in the moth Hyalophora cecropia1992Doctoral thesis, comprehensive summary (Other academic)
  • 49. Haeuser, Roman
    et al.
    Blasche, Sonja
    Dokland, Terje
    Haggård-Ljungquist, Elisabeth
    Stockholm University, Faculty of Science, Department of Genetics, Microbiology and Toxicology.
    von Brunn, Albrecht
    Salas, Margarita
    Casjens, Sherwood
    Molineux, Ian
    Uetz, Peter
    Bacteriophage Protein-Protein Interactions2012In: Advances in virus research, vol 83: Bacteriophages, pt B, ELSEVIER ACADEMIC PRESS , 2012, p. 219-298Chapter in book (Refereed)
    Abstract [en]

    Bacteriophages T7, lambda, P22, and P2/P4 (from Escherichia coli), as well as phi 29 (from Bacillus subtilis), are among the best-studied bacterial viruses. This chapter summarizes published protein interaction data of intraviral protein interactions, as well as known phage-host protein interactions of these phages retrieved from the literature. We also review the published results of comprehensive protein interaction analyses of Pneumococcus phages Dp-1 and Cp-1, as well as coliphages lambda and T7. For example, the approximate to 55 proteins encoded by the T7 genome are connected by approximate to 43 interactions with another approximate to 15 between the phage and its host. The chapter compiles published interactions for the well-studied phages lambda (33 intra-phage/22 phage-host), P22 (38/9), P2/P4 (14/3), and phi 29 (20/2). We discuss whether different interaction patterns reflect different phage lifestyles or whether they may be artifacts of sampling. Phages that infect the same host can interact with different host target proteins, as exemplified by E. coli phage lambda and T7. Despite decades of intensive investigation, only a fraction of these phage interactomes are known. Technical limitations and a lack of depth in many studies explain the gaps in our knowledge. Strategies to complete current interactome maps are described. Although limited space precludes detailed overviews of phage molecular biology, this compilation will allow future studies to put interaction data into the context of phage biology.

  • 50.
    Hallgren, Stefan
    Stockholm University, Faculty of Science, Department of Zoology.
    Brain Aromatase in the guppy, Poecilia reticulata: Distribution, control and role in behaviour2009Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Oestrogens are produced by aromatisation of androgens by the aromatase enzyme. In the vertebrate brain this synthesis has vital functions in nerve protection, cell proliferation and nerve development during injury respectively brain development. Brain oestrogens are also crucial in activating certain reproductive and aggressive behaviours in mammals and birds. Teleosts have remarkably high activity of brain aromatase (bAA) compared to mammals and birds; 100-1000 times higher in brain regions like the hypothalamus, pre-optic area and optic tectum. The role of brain oestrogens in teleost behaviour is, however, less clear than in e.g. songbirds and rodents. This thesis studies the potential role of brain aromatase and brain oestrogens in the reproductive behaviour of the guppy male (Poecilia reticulata), how guppy brain aromatase responds to steroids and is distributed in the adult brain.

    The thesis shows that male behaviour can be affected by brain aromatase. Reduction of bAA by aromatase inhibitor treatment reduced the sexual behaviours sigmoid display and gonopodium swinging (I) and oestrogen receptor blocking with an oestrogen antagonist reduced the number of successful mating attempts (II). The anatomical study (IV) showed that brain aromatase is distributed in areas of the adult guppy brain that are connected to reproductive control and behaviour in vertebrates.

    Guppy bAA is stimulated by both androgens and oestrogens (III) but is more sensitive to oestrogens, especially in males, and could thus be used as an indicator of endocrine disruption at low concentrations found in the environment.

    The thesis can also conclude that females possess more brain aromatase than males, and that although it is expressed in the same pattern throughout the brain in both genders the enzymatic activity is differently distributed between the sexes.

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