Change search
Refine search result
123 1 - 50 of 123
CiteExportLink to result list
Permanent link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf
Rows per page
  • 5
  • 10
  • 20
  • 50
  • 100
  • 250
Sort
  • Standard (Relevance)
  • Author A-Ö
  • Author Ö-A
  • Title A-Ö
  • Title Ö-A
  • Publication type A-Ö
  • Publication type Ö-A
  • Issued (Oldest first)
  • Issued (Newest first)
  • Created (Oldest first)
  • Created (Newest first)
  • Last updated (Oldest first)
  • Last updated (Newest first)
  • Disputation date (earliest first)
  • Disputation date (latest first)
  • Standard (Relevance)
  • Author A-Ö
  • Author Ö-A
  • Title A-Ö
  • Title Ö-A
  • Publication type A-Ö
  • Publication type Ö-A
  • Issued (Oldest first)
  • Issued (Newest first)
  • Created (Oldest first)
  • Created (Newest first)
  • Last updated (Oldest first)
  • Last updated (Newest first)
  • Disputation date (earliest first)
  • Disputation date (latest first)
Select
The maximal number of hits you can export is 250. When you want to export more records please use the Create feeds function.
  • 1. Acevedo, Nathalie
    et al.
    Bornacelly, Adriana
    Mercado, Dilia
    Unneberg, Per
    Stockholm University, Science for Life Laboratory (SciLifeLab). Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Mittermann, Irene
    Valenta, Rudolf
    Kennedy, Malcolm
    Scheynius, Annika
    Caraballo, Luis
    Genetic Variants in CHIA and CHI3L1 Are Associated with the IgE Response to the Ascaris Resistance Marker ABA-1 and the Birch Pollen Allergen Bet v 12016In: plos one, ISSN 1932-6203, Vol. 11, no 12, article id e0167453Article in journal (Refereed)
    Abstract [en]

    Helminth infections and allergic diseases are associated with IgE hyperresponsiveness but the genetics of this phenotype remain to be defined. Susceptibility to Ascaris lumbricoides infection and antibody levels to this helminth are associated with polymorphisms in locus 13q33-34. We aimed to explore this and other genomic regions to identify genetic variants associated with the IgE responsiveness in humans. Forty-eight subjects from Cartagena, Colombia, with extreme values of specific IgE to Ascaris and ABA-1, a resistance marker of this nematode, were selected for targeted resequencing. Burden analyses were done comparing extreme groups for IgE values. One-hundred one SNPs were genotyped in 1258 individuals of two well-characterized populations from Colombia and Sweden. Two low-frequency coding variants in the gene encoding the Acidic Mammalian Chitinase (CHIA rs79500525, rs139812869, tagged by rs10494133) were found enriched in high IgE responders to ABA-1 and confirmed by genetic association analyses. The SNP rs4950928 in the Chitinase 3 Like 1 gene (CHI3L1) was associated with high IgE to ABA-1 in Colombians and with high IgE to Bet v 1 in the Swedish population. CHIA rs10494133 and ABDH13 rs3783118 were associated with IgE responses to Ascaris. SNPs in the Tumor Necrosis Factor Superfamily Member 13b gene (TNFSF13B) encoding the cytokine B cell activating Factor were associated with high levels of total IgE in both populations. This is the first report on the association between low-frequency and common variants in the chitinases- related genes CHIA and CHI3L1 with the intensity of specific IgE to ABA-1 in a population naturally exposed to Ascaris and with Bet v 1 in a Swedish population. Our results add new information about the genetic influences of human IgE responsiveness; since the genes encode for enzymes involved in the immune response to parasitic infections, they could be helpful for understanding helminth immunity and allergic responses. We also confirmed that TNFSF13B has an important and conserved role in the regulation of total IgE levels, which supports potential evolutionary links between helminth immunity and allergic response.

  • 2.
    Ahlgren Berg, Alexandra
    Stockholm University, Faculty of Science, Department of Genetics, Microbiology and Toxicology.
    Developmental switches in a family of temperate phages2005Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    P2 is the prototype phage of the non-lambdoid P2 family of temperate phages. A developmental switch determines whether a temperate phage will grow lytically or form lysogeny after infection. P2 related phages have two face-to-face located promoters controlling the lysogenic and the lytic operon respectively, and two repressors. The immunity C repressor of P2 is the first gene of the lysogenic operon and it represses the lytic promoter. The Cox protein, the first gene of the lytic operon, is multifunctional. It represses the lysogenic promoter, acts as a directionality factor in site-specific recombination and activates the PLL promoter of satellite phage P4.

    This thesis focuses on comparisons between the developmental switches of P2 and the two heteroimmune family members, P2 Hy dis and WΦ. A characterization of the developmental switch region of P2 Hy dis identifies a directly repeated sequence which is important for C repression. P2 Hy dis Cox can substitute for P2 Cox in repression of the P2 lysogenic promoter, excision of a P2 prophage and activation of P4 PLL. The P4 ε protein can derepress the developmental switch of P2 Hy dis.

    Functional characterizations of the C repressors and Cox proteins of P2 and WΦ show that both C repressors induce bending of their respective DNA targets. WΦ C, like P2 C, has a strong dimerization activity in vivo, but there are no indications of higher oligomeric forms. Despite the high degree of identity in the C-terminus, required for dimerization in P2 C, they seem to be unable to form heterodimers. The two Cox proteins are predicted to have identical secondary structures containing a helix-turn-helix motif believed to be involved in DNA binding. It is, however, not possible to change the DNA specificity of P2 Cox to that of WΦ Cox by swapping the presumed recognition helix. P2 Cox recognizes a sequence repeated at least six times in the different targets, while WΦ Cox seems to recognize a single direct repeat. In contrast to P2 Cox, WΦ Cox binds with a stronger affinity to the switch region than to the attachment site (attP). The Cox proteins induce a strong bend in their DNA targets, strengthening the hypothesis that they have a structural role at site-specific recombination. Both proteins show a capacity to oligomerize, but P2 Cox has a higher tendency to form oligomers than WΦ Cox.

    The P2 integrase mediates site-specific recombination leading to integration or excision of the P2 genome in or out of the host chromosome. P2 Cox controls the direction by inhibiting integration and promoting excision. In this work it is shown that Cox and Int bind cooperatively to attP.

  • 3.
    Allentoft, Morten E.
    et al.
    University of Copenhagen, Denmark.
    Pokutta, Dalia
    Gothenburg University, Sweden.
    Willerslev, Eske
    University of Copenhagen, Denmark.
    Bronze Age population dynamics and its impact on modern Eurasian genetic structure2015In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 522, p. 167-172Article in journal (Refereed)
    Abstract [en]

    The Bronze Age of Eurasia (around 3000–1000 BC) was a period of major cultural changes. However, there is debate about whether these changes resulted from the circulation of ideas or from human migrations, potentially also facilitating the spread of languages and certain phenotypic traits. We investigated this by using new, improved methods to sequence low-coverage genomes from 101 ancient humans from across Eurasia. We show that the Bronze Age was a highly dynamic period involving large-scale population migrations and replacements, responsible for shaping major parts of present-day demographic structure in both Europe and Asia. Our findings are consistent with the hypothesized spread of Indo-European languages during the Early Bronze Age. We also demonstrate that light skin pigmentation in Europeans was already present at high frequency in the Bronze Age, but not lactose tolerance, indicating a more recent onset of positive selection on lactose tolerance than previously thought.

  • 4. André, Carl
    et al.
    Larsson, Lena C
    Stockholm University, Faculty of Science, Department of Zoology.
    Laikre, Linda
    Stockholm University, Faculty of Science, Department of Zoology.
    Bekkevold, D
    Brigham, J
    Carvalho, GR
    Dahlgren, TG
    Hutchinson, WF
    Mariani, S
    Mudde, K
    Ruzzante, DE
    Ryman, Nils
    Stockholm University, Faculty of Science, Department of Zoology.
    Detecting population structure in a high gene-flow species, Atlantic herring (Clupea harengus): direct, simultaneous evaluation of neutral vs putatively selected loci2011In: Heredity, ISSN 0018-067X, E-ISSN 1365-2540, Vol. 106, no 2, p. 270-280Article in journal (Refereed)
    Abstract [en]

    In many marine fish species, genetic population structure is typically weak because populations are large, evolutionarily young and have a high potential for gene flow. We tested whether genetic markers influenced by natural selection are more efficient than the presumed neutral genetic markers to detect population structure in Atlantic herring (Clupea harengus), a migratory pelagic species with large effective population sizes. We compared the spatial and temporal patterns of divergence and statistical power of three traditional genetic marker types, microsatellites, allozymes and mitochondrial DNA, with one microsatellite locus, Cpa112, previously shown to be influenced by divergent selection associated with salinity, and one locus located in the major histocompatibility complex class IIA (MHC-IIA) gene, using the same individuals across analyses. Samples were collected in 2002 and 2003 at two locations in the North Sea, one location in the Skagerrak and one location in the low-saline Baltic Sea. Levels of divergence for putatively neutral markers were generally low, with the exception of single outlier locus/sample combinations; microsatellites were the most statistically powerful markers under neutral expectations. We found no evidence of selection acting on the MHC locus. Cpa112, however, was highly divergent in the Baltic samples. Simulations addressing the statistical power for detecting population divergence showed that when using Cpa112 alone, compared with using eight presumed neutral microsatellite loci, sample sizes could be reduced by up to a tenth while still retaining high statistical power. Our results show that the loci influenced by selection can serve as powerful markers for detecting population structure in high gene-flow marine fish species.

  • 5.
    Appelgren, Henrik
    Stockholm University.
    Spontaneous and induced mutations at the human minisatellite MS32 in yeast1999Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Tandem repetitive DNA including minisatellites make up a large part of eukaryotic genomes, and some tandem repetitive loci are associated with human disease. Little is known about the functions and dynamics of these sequences. Hypervariable minisatellites are used as naturally occurring genetic markers and form the basis of DNA fingerprinting. Studies in human have shown that minisatellite alleles frequently mutate to new lengths by recombination-based mechanisms that operate in the germline, possibly in meiosis. In addition to the variability in length, all hypervariable minisatellites characterised to date also show variation in the DNA sequence of repeat units. The order of variant repeat units can be revealed by MVR-PCR (Minisatellite Variant Repeat mapping by PCR), and this has greatly contributed to mutation analysis by comparing structures of alleles before and after mutation. Certain aspects of minisatellite mutation and general eukaryotic meiotic recombination, cannot be studies in human or any other mammalian system. It was therefore necessary to develop a manipulable eukaryotic model system in the yeast Saccharomyces cerevisiae. The best characterised human minisatellite MS32 was integrated in the vicinity of a hotspot for meiotic recombination in chromosome III. This thesis presents the construction of the model system and analyses of MS32 mutation in yeast.

    The results proved that MS32 mutation is induced in meiosis. Mutant structures were strikingly similar to mutant structures seen in man. Tetrad analysis demonstrated that gene conversion is the major pathway leading to interallelic exchanges. The data also suggested that a hyper-recombinogenic state is formed, and it was shown that entire alleles can be transferred from a chromatid to another. An allele that displays reduced mutation rate in man showed a reduced mutation rate also in yeast. The results have implications for general eukaryotic meiotic recombination. Mutations at MS32 were induced in meiosis by PCB, suggesting that the model system can be used as an in vitro bioassay for the screening of environmental contaminants capable of inducing genomic damage in meiosis. It is concluded that the yeast model constitute a suitable system for the molecular dissection of pathways in spontaneous and induced minisatellite mutations and for elucidating general eukaryotic meiotic recombination mechanisms.

  • 6.
    Arefin, Md. Badrul
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute. Stockholm University.
    Molecular characterization of the Drosophila responses towards nematodes2016Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    A sophisticated evolutionary conserved innate immune system has evolved in insects to fight pathogens and to restrict damage in harmful (danger) situations including cancer. A significant amount of knowledge about different infection models in Drosophila has been generated in past decades, which revealed functional resemblances and implications for vertebrate systems. However, how Drosophila responds towards multicellular parasitic nematodes and in danger situations is still little understood. Therefore, the aim of the thesis was to characterize multiple aspects of the host defense in the two important contexts mentioned above.

    We analyzed the transcriptome profiles of nematode-infected Drosophila larvae with uninfected samples. For this we employed the entomopathogenic nematode Heterorhabditis bacteriophora with its symbiont Photorhabdus luminescence to infect Drosophila larvae. We found 642 genes were differentially regulated upon infection. Among them a significant portion belonged to immune categories. Further functional analysis identified a thioester containing protein TEP3, a recognition protein GNBP-like 3, the basement membrane component protein Glutactin and several other small peptides. Upon loss or reduced expression of these genes hosts showed mortality during nematode infections. This study uncovers a novel function for several of the genes in immunity.

    Furthermore, we investigated the cellular response towards nematodes. When we eliminated hemocytes genetically (referred to as hml-apo) in Drosophila, we found hml-apo larvae are resistant to nematodes. Subsequent characterization of hml-apo larvae showed massive lamellocyte differentiation (another blood cell type which is rare in naïve larvae), emergence of melanotic masses, up- and down-regulation of Toll and Imd signaling respectively suggesting a pro-inflammatory response. Moreover, a striking defective leg phenotype in adult escapers from pupal lethality was observed. We identified nitric oxide (NO) as a key regulator of these processes. We also showed that imaginal disc growth factors 3 (IDGF3): (a) protects hosts against nematodes, (b) is a clotting component and (c) negatively regulates Wnt and JAK/STAT signaling. To follow larval behavior in the presence or absence of nematodes we monitored Drosophila larval locomotion behaviors using FIMtrack (a recently devised automated method) to elucidate evasive strategies of hosts. Finally, we characterized host defenses in three Drosophila leukemia models with and without nematode infection. Taken together, these studies shed light on host responses in two crucial circumstances, nematode infections and danger situations.

  • 7.
    Arnaudeau, Catherine
    Stockholm University.
    Mitotic recombination in mammalian cells2000Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Recombination is usually defined as the exchange of genetic material between two strands or regions of nucleic acids. This process occurs in all known organisms and is highly conserved, especially among higher eukaryotes. Various types of recombination, involving homologous or non-homologous nucleic acid sequences, are known to exist. Recombination is a double-edged sword that may be beneficial or harmful for the cell. On one hand, it fulfills essential functions in connection with, e.g., repair of DNA double- strand breaks and maintenance of genomic stability; but, at the same time, this process is also partly responsible for, among other things, error prone repair and genomic instability, which can lead to cancer.

    The aim of the present study has been to investigate molecular mechanisms underlying spontaneous and induced mitotic recombination in mammalian cells and, in particular, to characterize the role of the RAD51 protein in these processes. For this purpose, V79 Chinese hamster cell lines containing spontaneous partial duplications of the hprt gene were employed. A new approach to investigate homologous recombination, which offers the unique possibility of determining the type of homologous recombination involved, was developed. This assay procedure was compared to other systems used previously for detection of induced recombination. Use of this newly developed method to characterize mechanisms underlying induction of homologous recombination revealed that inhibition of DNA synthesis is a potent pathway for such induction.

    Subsequently, the effect of overexpressing RAD51 on two different assays for recombination was determined. Our findings suggest that the RAD51 protein supports spontaneous homologous recombination via an exchange mechanism, as well as being involved in spontaneous non-homologous recombination, possibly with respect to class switch recombination. However, RAD51 was found not to affect induced non-homologous recombination, suggesting that this protein might not be involved in repairing DNA damage via non-homologous end-joining.

    Finally, the repair of DNA double-strand breaks induced in the S phase of the cell cycle was examined. Our observations in this case suggest that homologous recombination by strand invasion, employing an exchange mechanism, is a major feature of such repair and, furthermore, that a functional pathway for recombination is essential for the survival of cells in which DNA double-strand breaks have occurred.

    In summary, the work described here improves our understanding of the molecular mechanisms underlying spontaneous and induced recombination, as well as the repair of DNA double-strand breaks in mammalian cells.

  • 8.
    Asgard, Rikard
    et al.
    Uppsala Univ, Dept Pharmaceut Biosci., Uppsala, Sweden.
    Haghdoost, Siamak
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Golkar, Siv Osterman
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Hellman, Bjorn
    Uppsala Univ, Dept Pharmaceut Biosci., Uppsala, Sweden.
    Czene, Stefan
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Evidence for different mechanisms of action behind the mutagenic effects of 4-NOPD and OPD: the role of DNA damage, oxidative stress and an imbalanced nucleotide pool2013In: Mutagenesis, ISSN 0267-8357, E-ISSN 1464-3804, Vol. 28, no 6, p. 637-644Article in journal (Refereed)
    Abstract [en]

    The mutagenicity of 4-nitro-o-phenylenediamine (4-NOPD) and o-phenylenediamine (OPD) was compared using the Mouse Lymphoma Assay (MLA) with or without metabolic activation (S9). As expected, OPD was found to be a more potent mutagen than 4-NOPD. To evaluate possible mechanisms behind their mutagenic effects, the following end points were also monitored in cells that had been exposed to similar concentrations of the compounds as in the MLA: general DNA damage (using a standard protocol for the Comet assay); oxidative DNA damage (using a modified procedure for the Comet assay in combination with the enzyme hOGG1); reactive oxygen species (ROS; using the CM-H(2)DCFDA assay); and the balance of the nucleotide pool (measured after conversion to the corresponding nucleosides dC, dT, dG and dA using high-performance liquid chromatography). Both compounds increased the level of general DNA damage. Again, OPD was found to be more potent than 4-NOPD (which only increased the level of general DNA damage in the presence of S9). Although less obvious for OPD, both compounds increased the level of oxidative DNA damage. However, an increase in intracellular ROS was only observed in cells exposed to 4-NOPD, both with and without S9 (which in itself induced oxidative stress). Both compounds decreased the concentrations of dA, dT and dC. A striking effect of OPD was the sharp reduction of dA observed already at very low concentration, both with and without S9 (which in itself affected the precursor pool). Taken together, our results indicate that indirect effects on DNA, possibly related to an unbalanced nucleotide pool, mediate the mutagenicity and DNA-damaging effects of 4-NOPD and OPD to a large extent. Although induction of intracellular oxidative stress seems to be a possible mechanism behind the genotoxicity of 4-NOPD, this pathway seems to be of less importance for the more potent mutagen OPD.

  • 9.
    Assefaw-Redda, Yohannes
    Stockholm University, Faculty of Science, Department of Genetics, Microbiology and Toxicology.
    Hemolin expression during Cecropia development and its effect on malaria parasites2005Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Hemolin is a lepidopteran member of the immunoglobulin superfamily, initially isolated from the giant silkmoth Hyalophora cecropia. Hemolin is also induced by stimulation with microbial cell wall components and was recently shown to be strongly upregulated by baculovirus and double stranded RNA. An interesting characteristic of the protein is that it is not only highly expressed during infection but also during development.

    The work presented in this thesis investigated the expression of hemolin during oogenesis and embryogenesis in H. cecropia. Vitellogenic follicles from ovaries were analysed for the presence of the protein by immunohistochemistry in whole-mount preparations and in cryosections. PCR was used to show the presence of Hemolin transcripts throughout vitellogenesis and choriogenesis and in fertilized and unfertilized mature eggs and Western blots showed the protein in unfertilized eggs, yolk cells and embryo.

    Injection of the moulting hormone 20-hydroxyecdysone (20E) into hibernating diapausing pupae (low metabolic state), upregulates Hemolin. When diapausing pupae were treated with 20E and the protein synthesis inhibitor cycloheximide, its expression stayed low. This shows that the hormone indirectly regulates Hemolin by some factor(s) induced by 20E. When both bacteria and 20E were injected into diapausing pupae, an enhanced induction of hemolin gene expression occurred. Despite the seemingly indirect 20E regulation, several putative hormone responsive elements were found in the upstream region of the Hemolin (HRE-IR, HRE-M and MRE). When these elements were analysed by gel electrophoresis mobility shift assays (EMSA) to investigate their binding to nuclear factors, all the sites resulted in specific retarded bands. The HRE-IR binding factor was clearly increased by ecdysone. Last but not least we have investigated the effect of Hemolin on development of the malaria parasite Plasmodium falciparum in the midgut of the Anopheles mosquitoes. Hemolin completely inhibits the development of the parasite into its final transmission stage, the sporozoite. A future goal is to generate para-transgenic mosquitoes, enforced by hemolin, to stop malaria transmission. Importantly, hemolin did not affect the mosquito fecundity when fed to the mosquito. We are currently constructing truncated forms of hemolin to gain insight into which parts are important for its effect on the parasite.

  • 10.
    Bajinskis, Ainars
    et al.
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Natarajan, Adayapalam T.
    Erixon, Klaus
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Harms-Ringdahl, Mats
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    DNA double strand breaks induced by the indirect effect of radiation are more efficiently repaired by non-homologous end joining compared to homologous recombination repair2013In: Mutation research. Genetic toxicology and environmental mutagenesis, ISSN 1383-5718, E-ISSN 1879-3592, Vol. 756, no 1-2, p. 21-29Article in journal (Refereed)
    Abstract [en]

    The aim of this study was to investigate the relative involvement of three major DNA repair pathways, i.e., non-homologous end joining (NHEJ), homologous recombination (HRR) and base excision (BER) in repair of DNA lesions of different complexity induced by low- or high-LET radiation with emphasis on the contribution of the indirect effect of radiation for these radiation qualities. A panel of DNA repair-deficient CHO cell lines was irradiated by Cs-137 gamma-rays or radon progeny alpha-particles. Irradiation was also performed in the presence of 2 M DMSO to reduce the indirect effect of radiation and the complexity of the DNA damage formed. Clonogenic survival and micronucleus assays were used to estimate efficiencies of the different repair pathways for DNA damages produced by direct and indirect effects. Removal of the indirect effect of low-LET radiation by DMSO increased clonogenic survival and decreased MN formation for all cell lines investigated. A direct contribution of the indirect effect of radiation to DNA base damage was suggested by the significant protection by DMSO seen for the BER deficient cell line. Lesions formed by the indirect effect are more readily repaired by the NHEJ pathway than by HRR after irradiation with gamma-rays or alpha-particles as evaluated by cell survival and the yields of MN. The results obtained with BER- and NHEJ-deficient cells suggest that the indirect effect of radiation contributes significantly to the formation of repair substrates for these pathways.

  • 11.
    Belotserkovsky, Jaroslav
    Stockholm University, Faculty of Science, Department of Genetics, Microbiology and Toxicology.
    Studies on the functional interaction of translation initiation factor IF1 with ribosomal RNA2012Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Translation initiation factor IF1 is a small, essential and ubiquitous protein factor encoded by a single infA gene in bacteria. Although several important functions have been attributed to IF1, the precise reason for its indispensability is yet to be defined. It is known that IF1 binds to the ribosomal A-site during initiation, where it primarily contacts ribosomal RNA (rRNA) and induces large scale conformational changes in the small ribosomal subunit. To shed more light on the function of IF1 and its interaction with the ribosome, we have employed a genetic approach to elucidate structure-function interactions between IF1 and rRNA. A selection has been used to isolate second site suppressor mutations in rRNA that restore the growth of a cold sensitive mutant IF1 with an arginine to leucine substitution in position 69 (R69L).  This yielded two classes of suppressors – one class that mapped to the processing stem of 23S rRNA – a transient structure important for proper maturation of 23S rRNA; and the other class to the functional sequence of 16S rRNA. Suppressor mutations in the processing stem of 23S rRNA were shown to disrupt efficient processing of 23S rRNA. In addition, we report that at least one of the manifestations of cold sensitivity associated with the mutant IF1 is at the level of ribosomal subunit association. These results led to a model whereby the cold sensitive R69L mutant IF1 results in aberrant ribosomal subunit association properties, while the 23S processing stem mutations indirectly suppress this effect by decreasing the pool of mature 50S subunits available for association.  Spontaneous suppressor mutations in 16S rRNA were diverse in position and phenotypic properties, but all mutations affected ribosomal subunit association, in most cases by directly decreasing the affinity of the 30S for 50S subunits. Site directed mutagenesis of select positions in 16S rRNA yielded additional suppressor mutations that were localized to the mRNA and streptomycin binding sites on the small ribosomal subunit. We suggest that the 16S rRNA suppressors occur in positions that affect the conformational dynamics brought about by IF1. Taken together, this work indicates that the major function of IF1 is the modulation of ribosomal subunit association brought about through conformational changes of the 30S subunit.

  • 12.
    Belotserkovsky, Jaroslav
    et al.
    Stockholm University, Faculty of Science, Department of Genetics, Microbiology and Toxicology.
    Isaksson, Leif
    Stockholm University, Faculty of Science, Department of Genetics, Microbiology and Toxicology.
    Mutations in the streptomycin and mRNA binding sites on 16S rRNA suppress a cold sensitive initiation factor IF1Manuscript (preprint) (Other academic)
  • 13.
    Belotserkovsky, Jaroslav M.
    et al.
    Stockholm University, Faculty of Science, Department of Genetics, Microbiology and Toxicology.
    Dabbs, Eric R.
    Isaksson, Leif A.
    Stockholm University, Faculty of Science, Department of Genetics, Microbiology and Toxicology.
    Mutations in 16S rRNA that suppress cold-sensitive initiation factor 1 affect ribosomal subunit association2011In: The FEBS Journal, ISSN 1742-464X, E-ISSN 1742-4658, Vol. 278, no 18, p. 3508-3517Article in journal (Refereed)
    Abstract [en]

    A mutation in the infA gene encoding initiation factor 1 (IF1) gives rise to a cold-sensitive phenotype. An Escherichia coli strain with this mutation was used as a tool to select for second-site suppressors that compensate for the cold sensitivity and map specifically to rRNA. Several suppressor mutants with altered 16S rRNA that partially restore growth of an IF1 mutant strain in the cold were isolated and characterized. Suppressor mutations were found in helix (h) 18, h32, h34 and h41 in 16S rRNA. These mutations are not clustered to any particular region in 16S rRNA and none overlap previously reported sites of interaction with IF1. While the isolated suppressors are structurally diverse, they are functionally related because all affect ribosomal subunit association in vivo. Furthermore, in vitro subunit-association experiments indicate that most of the suppressor mutations directly influence ribosomal subunit association even though none of these are confined to any of the known intersubunit bridges. These results are consistent with the model that IF1 is an rRNA chaperone that induces large-scale conformational changes in the small ribosomal subunit, and as a consequence modulates initiation of translation by affecting subunit association.

  • 14.
    Belotserkovsky, Jaroslav M.
    et al.
    Stockholm University, Faculty of Science, Department of Genetics, Microbiology and Toxicology.
    Isak, Georgina I.
    Stockholm University, Faculty of Science, Department of Genetics, Microbiology and Toxicology.
    Isaksson, Leif A.
    Stockholm University, Faculty of Science, Department of Genetics, Microbiology and Toxicology.
    Suppression of a cold-sensitive mutant initiation factor 1 by alterations in the 23S rRNA maturation region2011In: The FEBS Journal, ISSN 1742-464X, E-ISSN 1742-4658, Vol. 278, no 10, p. 1745-1756Article in journal (Refereed)
    Abstract [en]

    Genetic selection has been used to isolate second-site suppressors of a defective cold-sensitive initiation factor I (IF1) R69L mutant of Escherichia coli. The suppressor mutants specifically map to a single rRNA operon on a plasmid in a strain with all chromosomal rRNA operons deleted. Here, we describe a set of suppressor mutations that are located in the processing stem of precursor 23S rRNA. These mutations interfere with processing of the 23S rRNA termini. A lesion of RNase III also suppresses the cold sensitivity. Our results suggest that the mutant IF1 strain is perturbed at the level of ribosomal subunit association, and the suppressor mutations partially compensate for this defect by disrupting rRNA maturation. These results support the notion that IF1 is an RNA chaperone and that translation initiation is coupled to ribosomal maturation.

  • 15. Berg, Ingrid
    Instability of the human minisatellite MS1 in yeast and man2003Doctoral thesis, comprehensive summary (Other academic)
  • 16. Bergman, Ingvar
    et al.
    Almkvist, Ove
    Stockholm University, Faculty of Social Sciences, Department of Psychology.
    The effect of age on fluid intelligence is fully mediated by physical health2013In: Archives of gerontology and geriatrics (Print), ISSN 0167-4943, E-ISSN 1872-6976, Vol. 57, no 1, p. 100-109Article in journal (Refereed)
    Abstract [en]

    The present study investigated the extent to which the effect of age on cognitive ability is predicted by individual differences in physical health. The sample consisted of 118 volunteer subjects who were healthy and ranging in age from 26 to 91. The examinations included a clinical investigation, magnetic resonance imaging (MRI) brain neuroimaging, and a comprehensive neuropsychological assessment. The effect of age on fluid IQ with and without visual spatial praxis and on crystallized IQ was tested whether being fully-, partially-or non-mediated by physical health. Structural equation analyses showed that the best and most parsimonious fit to the data was provided by models that were fully mediated for fluid IQ without praxis, non-mediated for crystallized IQ and partially mediated for fluid IQ with praxis. The diseases of the circulatory and nervous systems were the major mediators. It was concluded from the pattern of findings that the effect of age on fluid intelligence is fully mediated by physical health, while crystallized intelligence is non-mediated and visual spatial praxis is partially mediated, influenced mainly by direct effects of age. Our findings imply that improving health by acting against the common age-related circulatory-and nervous system diseases and risk factors will oppose the decline in fluid intelligence with age.

  • 17. Bertrand, Yann
    et al.
    Topel, Mats
    Elvang, Annelie
    Melik, Wessam
    Stockholm University, Faculty of Science, Department of Genetics, Microbiology and Toxicology.
    Johansson, Magnus
    First Dating of a Recombination Event in Mammalian Tick-Borne Flaviviruses2012In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 7, no 2, p. e31981-Article in journal (Refereed)
    Abstract [en]

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

  • 18.
    Bettencourt, Raul
    Stockholm University, Faculty of Science, Department of Genetics, Microbiology and Toxicology.
    Hemolin, a versatile immune protein from the Cecropia moth1999Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Insects have become useful models for the study of innate immune mechanisms, due to their lack of antibodies and receptors involved in adaptive immune response. However, the molecules and mechanisms involved in primordial immune recognition are still poorly understood. Hemolin, originally cloned from Hyalophora cecropia, is a soluble and membrane associated Ig-related molecule which meets the criteria for a pattern recognition molecule. It is constitutively expressed in the hemolymph and up-regulated after bacterial injection. It was shown to bind specifically to the Lipid A moiety of LPS from bacteria and to associate with aggregates formed by hemocytes and bacteria. The aim of the present studies was to characterize the binding of hemolin to insect cells and further investigate the mechanisms behind. Earlier results shown in Manduca sexta were confirmed and it was shown that soluble hemolin has a deaggregating effect on naive hemocytes of H. cecropia. Moreover, hemolin increases phagocytic activity of hemocytes, especially when combined with LPS. This enhanced phagocytosis was correlated to the activity of protein kinase C and tyrosine phosphorylation. We revealed a number of cell adhesion characteristics of hemolin 1) a membrane associated form, (2) Ca2+-dependent homophilic binding, (3) glycosylation (4) importance of Ca2+ and carbohydrates on the binding to hemocytes. Based on our present results and the hemolin crystal structure, we have proposed a model for the interactions between soluble hemolin and its membrane form. The close relatedness to NCAMs prompted us to investigate its expression in other tissues than those originally described. It was found that hemolin is present in the retinal eye discs of pupae, in developing follicles during oogenesis and in embryos of H. cecropia. It was inferred that hemolin has a role in developmental processes in addition to its putative immune functions in insects. From a phylogenetic point of view, hemolin function is consistent with the assumption that non-self recognition molecules of the IgSF arose from cell-adhesion molecules with multiple functions.

  • 19.
    Brehwens, Karl
    et al.
    Stockholm University, Faculty of Science, Department of Genetics, Microbiology and Toxicology.
    Bajinskis, Ainars
    Stockholm University, Faculty of Science, Department of Genetics, Microbiology and Toxicology.
    Staaf, Elina
    Stockholm University, Faculty of Science, Department of Genetics, Microbiology and Toxicology.
    Haghdoost, Siamak
    Stockholm University, Faculty of Science, Department of Genetics, Microbiology and Toxicology.
    Cederwall, Bo
    Wojcik, Andrzej
    Stockholm University, Faculty of Science, Department of Genetics, Microbiology and Toxicology.
    A NEW DEVICE TO EXPOSE CELLS TO CHANGING DOSE RATES OF IONISING RADIATION2012In: Radiation Protection Dosimetry, ISSN 0144-8420, E-ISSN 1742-3406, Vol. 148, no 3, p. 366-371Article in journal (Refereed)
    Abstract [en]

    In many exposure scenarios to ionising radiation, the dose rate is not constant. Despite this, most in vitro studies aimed at investigating the effects of ionising radiation are carried out exposing samples at constant dose rates. Consequently, very little data exist on the biological effects of exposures to changing dose rates. This may be due to technical limitations of standard irradiation facilities, but also to the fact that the importance of research in this area has not been appreciated. We have recently shown that cells exposed to a decreasing dose rate suffer higher levels of cytogenetic damage than do cells exposed to an increasing or a constant dose rate. To further study the effects of changing dose rates, a new device was constructed that permits the exposure of cell samples in tubes, flasks or Petri dishes to changing dose rates of X-rays. This report presents the technical data, performance and dosimetry of this novel device.

  • 20.
    Cardoso Palacios, Carlos
    Stockholm University, Faculty of Science, Department of Genetics, Microbiology and Toxicology.
    Site-specific recombination in P2-like coliphages2009Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The scope of these studies has been to investigate the site-specific recombination systems of P2-like coliphages, both in an evolutionary perspective by a comparative analysis of related phages as well as in a functional perspective.

    Surveys of P2-like phages in Escherichia coli isolated from nature reveal the existence of seven discrete immunity classes and three integration sites, one of them previously unknown. Phylogenetic analysis of the repressor proteins and other analyses show that homologous recombination plays a role in the appearance of new immunities. Other studies of P2-like prophages from sequenced genomes from public databases show that the P2-like phages grow in different γ-proteobacteria. Based on the type of immunity and site-specific recombination system they can be roughly subdivided in two distinct subgroups and some new host integration sites could be identified. Some of the host attachment sites have a high identity to the sequences in the human genome, making them interesting as potential tools for targeted gene insertions into unmodified human cells.

    The functional studies have been focused on the identification of the determinants for site specificity, which is important for the use of the enzyme for targeted gene insertions into unmodified genomes. Two approaches have been used. In one, we have performed a structure-function analysis of P2 Int that has identified several presumptive residues involved in specific binding to the core sequence, all of them located in the same alpha-helix. This knowledge could be a base for an in vitro evolution of the integrase to enable it to accept new DNA targets with a high affinity. With respect to the excisionases from P2-like coliphages integrating in different sites, we found that they share some common features when they bind and bend to their DNA targets, but there are also significant differences, especially those related to the number of binding sites and the distribution of these and the IHF binding sites in the attP regions. In the other approach we have started to characterize the site-specific recombination system of another P2-like phage, ΦD145, that has a host target with a high identity to a site in the human genome. This looks promising since the human sequence can be used in vivo in E. coli with a rather high efficiency.

  • 21.
    Cardoso-Palacios, Carlos
    et al.
    Stockholm University, Faculty of Science, Department of Genetics, Microbiology and Toxicology.
    Sylwan, Lina
    Stockholm University, Faculty of Science, Department of Genetics, Microbiology and Toxicology.
    Mandali, Sridhar
    Stockholm University, Faculty of Science, Department of Genetics, Microbiology and Toxicology.
    Frumerie, Clara
    Stockholm University, Faculty of Science, Department of Molecular Biology and Functional Genomics.
    Haggård-Ljungquist, Elisabeth
    Stockholm University, Faculty of Science, Department of Genetics, Microbiology and Toxicology.
    A structure-function analysis of P2 integraseManuscript (preprint) (Other academic)
    Abstract [en]

    Bacteriophage P2 integrase catalyzes site-specific recombination between the phage DNA and the host chromosome thereby promoting integration or excision of the phage genome. P2 integrase belongs to the large tyrosine family of integrases that shows little sequence identity besides some conserved boxes and patches in the catalytic domain. However, the overall structure of the tyrosine family of integrases seems to be similar. Phage integrases have the potential as tools for site-specific gene insertions into eukaryotic genomes provided that target sequences are available. To elucidate the possibility of evolving the P2 integrase to accept new targets, we have in this work initiated a structure-function analysis of the P2 integrase using two approaches based on a comparison of the predicted secondary structure of P2 integrase with that determined for the lambda integrase. First, we have made hybrids between P2 integrase and the related WΦ integrase that has a different host DNA target, to locate the region promoting specificity between the integrases. This, however, has not been possible, the N-terminal domains can be exchanged without losing biological activity and this will not affect the specificity. All other hybrids made were biological inactive. Next we have made an alanine scanning of the alpha helices believed to be involved in specific interactions with the target, and four amino acids have been identified as candidates for sequence-specific interactions with the core.

  • 22.
    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.

  • 23.
    Daniel, Chammiran
    et al.
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Silberberg, Gilad
    Behm, Mikaela
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Öhman, Marie
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Alu elements shape the primate transcriptome by cis-regulation of RNA editing2014In: Genome Biology, ISSN 1465-6906, E-ISSN 1474-760X, Vol. 15, no 2, article id R28Article in journal (Refereed)
    Abstract [en]

    Background: RNA editing by adenosine to inosine deamination is a widespread phenomenon, particularly frequent in the human transcriptome, largely due to the presence of inverted Alu repeats and their ability to form double-stranded structures - a requisite for ADAR editing. While several hundred thousand editing sites have been identified within these primate-specific repeats, the function of Alu-editing has yet to be elucidated. Results: We show that inverted Alu repeats, expressed in the primate brain, can induce site-selective editing in cis on sites located several hundred nucleotides from the Alu elements. Furthermore, a computational analysis, based on available RNA-seq data, finds that site-selective editing occurs significantly closer to edited Alu elements than expected. These targets are poorly edited upon deletion of the editing inducers, as well as in homologous transcripts from organisms lacking Alus. Sequences surrounding sites near edited Alus in UTRs, have been subjected to a lesser extent of evolutionary selection than those far from edited Alus, indicating that their editing generally depends on cis-acting Alus. Interestingly, we find an enrichment of primate-specific editing within encoded sequence or the UTRs of zinc finger-containing transcription factors. Conclusions: We propose a model whereby primate-specific editing is induced by adjacent Alu elements that function as recruitment elements for the ADAR editing enzymes. The enrichment of site-selective editing with potentially functional consequences on the expression of transcription factors indicates that editing contributes more profoundly to the transcriptomic regulation and repertoire in primates than previously thought.

  • 24. Dessimoz, Christophe
    et al.
    Gabaldón, Toni
    Roos, David S
    Sonnhammer, Erik L L
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Herrero, Javier
    Toward community standards in the quest for orthologs.2012In: Bioinformatics (Oxford, England), ISSN 1367-4811, Vol. 28, no 6, p. 900-4Article in journal (Refereed)
    Abstract [en]

    The identification of orthologs-genes pairs descended from a common ancestor through speciation, rather than duplication-has emerged as an essential component of many bioinformatics applications, ranging from the annotation of new genomes to experimental target prioritization. Yet, the development and application of orthology inference methods is hampered by the lack of consensus on source proteomes, file formats and benchmarks. The second 'Quest for Orthologs' meeting brought together stakeholders from various communities to address these challenges. We report on achievements and outcomes of this meeting, focusing on topics of particular relevance to the research community at large. The Quest for Orthologs consortium is an open community that welcomes contributions from all researchers interested in orthology research and applications.

  • 25.
    Dinca, Vlad
    et al.
    Stockholm University, Faculty of Science, Department of Zoology.
    Wiklund, Christer
    Stockholm University, Faculty of Science, Department of Zoology.
    Lukhtanov, V. A.
    Kodandaramaiah, U.
    Norén, Karin
    Stockholm University, Faculty of Science, Department of Zoology.
    Dapporto, L.
    Wahlberg, N.
    Vila, R.
    Friberg, Mange
    Stockholm University, Faculty of Science, Department of Zoology.
    Reproductive isolation and patterns of genetic differentiation in a cryptic butterfly species complex2013In: Journal of Evolutionary Biology, ISSN 1010-061X, E-ISSN 1420-9101, Vol. 26, no 10, p. 2095-2106Article in journal (Refereed)
    Abstract [en]

    Molecular studies of natural populations are often designed to detect and categorize hidden layers of cryptic diversity, and an emerging pattern suggests that cryptic species are more common and more widely distributed than previously thought. However, these studies are often decoupled from ecological and behavioural studies of species divergence. Thus, the mechanisms by which the cryptic diversity is distributed and maintained across large spatial scales are often unknown. In 1988, it was discovered that the common Eurasian Wood White butterfly consisted of two species (Leptidea sinapis and Leptidea reali), and the pair became an emerging model for the study of speciation and chromosomal evolution. In 2011, the existence of a third cryptic species (Leptidea juvernica) was proposed. This unexpected discovery raises questions about the mechanisms preventing gene flow and about the potential existence of additional species hidden in the complex. Here, we compare patterns of genetic divergence across western Eurasia in an extensive data set of mitochondrial and nuclear DNA sequences with behavioural data on inter- and intraspecific reproductive isolation in courtship experiments. We show that three species exist in accordance with both the phylogenetic and biological species concepts and that additional hidden diversity is unlikely to occur in Europe. The Leptidea species are now the best studied cryptic complex of butterflies in Europe and a promising model system for understanding the formation of cryptic species and the roles of local processes, colonization patterns and heterospecific interactions for ecological and evolutionary divergence.

  • 26.
    Domingo Prim, Judit
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    The exosome and the maintenance of genome integrity2016Licentiate thesis, comprehensive summary (Other academic)
    Abstract [en]

    The RNA exosome acts on different RNA substrates and plays important roles in RNA metabolism. The fact that short non-coding RNAs are involved in the DNA damage response led us to investigate whether the exosome plays a role in DNA repair. We have shown that the exosome catalytic subunit RRP6/EXOSC10 is recruited to DNA double-strand breaks (DSBs) in Drosophila S2 cells and human HeLa cells exposed to either ionizing radiation or I-PpoI endonuclease cleavage. DIS3, the other catalytic subunit of the nuclear exosome, is also recruited to DSBs, whereas the exosome core subunit EXOSC7 is not. Depletion of different exosome subunits does not interfere with the phosphorylation of the histone variants H2Av (Drosophila) or H2AX (humans), but depletion of RRP6/EXOSC10 impairs the recruitment of the homologous recombination factor RAD51 to the damaged sites, without affecting RAD51 levels. The recruitment of RAD51 to DSBs in S2 cells is also inhibited by overexpression of RRP6-Y361A–V5, a catalytically inactive RRP6 mutant. Furthermore, cells depleted of RRP6 or EXOSC10 are more sensitive to radiation, which is consistent with RRP6/EXOSC10 playing a role in DNA repair. RRP6/EXOSC10 can be co-immunoprecipitated with RAD51, which links RRP6/EXOSC10 to the homologous recombination pathway in animal cells. Taken together, our results suggest that a 3’-5’ ribonucleolytic activity is required for efficient DNA repair. 

  • 27.
    Ellencrona, Karin
    Stockholm University, Faculty of Science, Department of Genetics, Microbiology and Toxicology.
    Functional characterization of interactions between the flavivirus NS5 protein and PDZ proteins of the mammalian host2009Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Flaviviruses are found all over the world and affect and infect millions of people every year. Flavivirus infection can lead to severe clinical outcomes resulting in neuronal damages e.g. Tick-borne encephalitis virus (TBEV), or severe hemorrhagic fevers e.g. Dengue virus (DENV). In order to effectively treat infected patients and to prevent these diseases we must understand how these viruses work and how they interfere with the mammalian host. This thesis is focusing on interactions between the virus protein NS5 and human host cell proteins. The interactions presented here might be key factors for out-come of viral disease. NS5 is the largest of the non-structural proteins and is essential for the replication and the capping as it contains both RNA dependent RNA polymerase and Methyltransferase domains. We found that TBEV NS5 interacts with human PDZ domain protein Scribble, a polarization protein important e.g. in regulating membrane trafficking. We determined that the interaction depend on a novel internal motif in TBEVNS5. This interaction could be correlated to NS5s ability to interfere with the immune system as absence of Scribble prevented NS5 from blocking phosphorylation of STAT upon Interferon induction. The role of NS5 in human PDZ domain targeting was addressed further by using a PDZ array system. Both TBEVNS5 and DENVNS5 bind additional PDZ domains using the internal motif. The tight junction protein ZO-1 binds both DENVNS5 and TBEVNS5. DENVNS5 is mainly present in the nucleus and co-localize with ZO-1 in un-polarized cells. In polarized cells TBEVNS5 and ZO-1 co-localize at the plasmamembrane. Putative C-terminal PDZ binding motifs of TBEVNS5 and WNVNS5 were characterized using the PDZ array system. This detected four novel binding partners of TBEVNS5 but numerous of potential WNVNS5 binding partners. We found that TBEVNS5 co-localizes with ZO-2 in the cellular membrane. Further, we found that TBEVNS5 induce the AP-1 by a 2 fold over the control.

  • 28.
    Emma, Lind
    et al.
    Stockholm University, Faculty of Science, Department of Zoology. Södertörns högskola.
    Ohlin, Helena
    Mälardalens högskola.
    Grahn, Mats
    Södertörns högskola.
    Fine scale genetic structure in Thresspine sticklback (Gasterosteus aculeatus) along Sweden's coastManuscript (preprint) (Other academic)
    Abstract [en]

    There are three basic types of population structures in marine environments; populations that are distinct, with a continuous change and without any differentiation. In each type the population units are characterized by groups of individuals with panmixia within groups and site fidelity to a limited geographic area. Earlier studies of the population genetic structure on sticklebacks in the Baltic Sea have shown none or only little structure. We have sampled 8 sites (253 individuals) along Sweden’s coast to estimate the genetic structure, using five microsatellites and 173 Amplified Fragment Length Polymorphism (AFLP) markers and detected a fine scale genetic structure (AFLP FST= 25%, microsatellites FST = 2.7%). With AFLPs the observed variation followed isolation by distance model (but not with microsatellites). Even sites separated by only 2 km of water are significantly separated. Both Bayesian clustering analysis and Capscale separated populations and identified populations from Gulf of Bothnia (4 psu) and from the west coast (20 psu) as genetically distinctly different from Baltic populations (about 7-8 psu).  In conclusion, gene flow is limited between sampled sites, and since no geographic barriers can be distinguished the population structure is likely caused by the sticklebacks’ behavior. Hence, we have probably sampled either stationary populations of marine sticklebacks, or homing sticklebacks. In this study AFLP and microsatellites did not give congruent results; with AFLPs we got high separation, and genetic variation followed isolation by distance model and supported the continuous change type of population structure.

  • 29.
    Eriksson, Harald
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Bacterial viruses targeting multi-resistant Klebsiella pneumoniae and Escherichia coli2015Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The global increase in antibiotic resistance levels in bacteria is a growing concern to our society and highlights the need for alternative strategies to combat bacterial infections. Bacterial viruses (phages) are the natural predators of bacteria and are as diverse as their hosts, but our understanding of them is limited. The current levels of knowledge regarding the role that phage play in the control of bacterial populations are poor, despite the use of phage therapy as a clinical therapy in Eastern Europe.

    The aim of this doctoral thesis is to increase knowledge of the diversity and characteristics of bacterial viruses and to assess their potential as therapeutic agents towards multi-resistant bacteria.

    Paper I is the product of de novo sequencing of newly isolated phages that infect and kill multi-resistant Klebsiella pneumoniae. Based on similarities in gene arrangement, lysis cassette type and conserved RNA polymerase, the creation of a new phage genus within Autographivirinae is proposed.

    Paper II describes the genomic and proteomic analysis of a phage of the rare C3 morphotype, a Podoviridae phage with an elongated head that uses multi-resistant Escherichia coli as its host.

    Paper III describes the study of a pre-made phage cocktail against 125 clinical K. pneumoniae isolates. The phage cocktail inhibited the growth of 99 (79 %) of the bacterial isolates tested. This study also demonstrates the need for common methodologies in the scientific community to determine how to assess phages that infect multiple serotypes to avoid false positive results.

    Paper IV studies the effects of phage predation on bacterial virulence: phages were first allowed to prey on a clinical K. pneumoniae isolate, followed by the isolation of phage-resistant bacteria. The phage resistant bacteria were then assessed for their growth rate, biofilm production in vitro. The virulence of the phage resistant bacteria was then assessed in Galleria mellonella. In the single phage treatments, two out of four phages showed an increased virulence in the in G. mellonella, which was also linked to an increased growth rate of the phage resistant bacteria. In multi-phage treatments however, three out of five phage cocktails decreased the bacterial virulence in G. mellonella compared to an untreated control.

  • 30.
    Eriksson, Harald
    et al.
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Maciejewska, Barbara
    Latka, Agnieszka
    Majkowska-Skrobek, Grazyna
    Hellstrand, Marios
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Melefors, Öjar
    Wang, Jin-Town
    Kropinski, Andrew M.
    Drulis-Kawa, Zuzanna
    Nilsson, Anders S.
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    A suggested new bacteriophage genus, “Kp34likevirus”, within the Autographivirinae subfamily of Podoviridae2015In: Viruses, ISSN 1999-4915, E-ISSN 1999-4915, Vol. 7, no 4, p. 1804-1822Article, review/survey (Refereed)
    Abstract [en]

    Klebsiella pneumoniae phages vB_KpnP_SU503 (SU503) and vB_KpnP_SU552A (SU552A) are virulent viruses belonging to theAutographivirinae subfamily of Podoviridae that infect and kill multi-resistant K. pneumoniae isolates. Phages SU503 and SU552A show high pairwise nucleotide identity to Klebsiella phages KP34 (NC_013649), F19 (NC_023567) and NTUH-K2044-K1-1 (NC_025418). Bioinformatic analysis of these phage genomes show high conservation of gene arrangement and gene content, conserved catalytically active residues of their RNA polymerase, a common and specific lysis cassette, and form a joint cluster in phylogenetic analysis of their conserved genes. Also, we have performed biological characterization of the burst size, latent period, host specificity (together with KP34 and NTUH-K2044-K1-1), morphology, and structural genes as well as sensitivity testing to various conditions. Based on the analyses of these phages, the creation of a new phage genus is suggested within the Autographivirinae, called “Kp34likevirus” after their type phage, KP34. This genus should encompass the recently genome sequenced Klebsiella phages KP34, SU503, SU552A, F19 and NTUH-K2044-K1-1.

  • 31.
    Eriksson, Jesper
    Stockholm University, Faculty of Science, Department of Genetics, Microbiology and Toxicology.
    Structure-Function Studies of Bacteriophage P2 Integrase and Cox protein2005Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Probably no group of organisms has been as important as bacteriophages when it comes to the understanding of fundamental biological processes like transcriptional control, DNA replication, site-specific recombination, e.t.c.

    The work presented in this thesis is a contribution towards the complete understanding of these organisms. Two proteins, integrase, and Cox, which are important for the choice of the life mode of bacteriophage P2, are investigated. P2 is a temperate phage, i.e. it can either insert its DNA into the host chromosome (by site-specific recombination) and wait (lysogeny), or it can produce new progeny with the help of the host protein machinery and thereafter lyse the cell (lytic cycle). The integrase protein is necessary for the integration and excision of the phage genome. The Cox protein is involved as a directional factor in the site-specific recombination, where it stimulates excision and inhibits integration. It has been shown that the Cox protein also is important for the choice of the lytic cycle. The choice of life mode is regulated on a transcriptional level, where two mutually exclusive promoters direct whether the lytic cycle (Pe) or lysogeny (Pc) is chosen. The Cox pro-tein has been shown to repress the Pc promoter and thereby making tran-scription from the Pe promoter possible, leading to the lytic cycle. Further, the Cox protein can function as a transcriptional activator on the parasite phage, P4. P4 has gained the ability to adopt the P2 protein machinery to its own purposes.

    In this work the importance of the native size for biologically active integrase and Cox proteins has been determined. Further, structure-function analyses of the two proteins have been performed with focus on the protein-protein interfaces. In addition it is shown that P2 Cox and the P2 relative Wphi Cox changes the DNA topology upon specific binding. From the obtained results a mechanism for P2 Cox-DNA interaction is discussed.

    The results from this thesis can be used in the development of a gene delivery system based on the P2 site-specific recombination system.

  • 32.
    Fotouhi, Asal
    et al.
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Cornella, Nicola
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Ramezani, Mehrafarin
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Wojcik, Andrzej
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Haghdoost, Siamak
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Investigation of micronucleus induction in MTH1 knockdown cells exposed to UVA, UVB or UVC2015In: Mutation research. Genetic toxicology and environmental mutagenesis, ISSN 1383-5718, E-ISSN 1879-3592, Vol. 793, no SI, p. 161-165Article in journal (Refereed)
    Abstract [en]

    The longer wave parts of UVR can increase the production of reactive oxygen species (ROS) which can oxidize nucleotides in the DNA or in the nucleotide pool leading to mutations. Oxidized bases in the DNA are repaired mainly by the DNA base excision repair system and incorporation of oxidized nucleotides into newly synthesized DNA can be prevented by the enzyme MTH1. Here we hypothesize that the formation of several oxidized base damages (from pool and DNA) in close proximity, would cause a high number of base excision repair events, leading to DNA double strand breaks (DSB) and therefore giving rise to cytogenetic damage. If this hypothesis is true, cells with low levels of MTH1 will show higher cytogenetic damage after the longer wave parts of UVR. We analyzed micronuclei induction (MN) as an endpoint for cytogenetic damage in the human lymphoblastoid cell line, TK6, with a normal and a reduced level of MTH1 exposed to UVR. The results indicate a higher level of micronuclei at all incubation times after exposure to the longer wave parts of UVR. There is no significant difference between wildtype and MTH1-knockdown TK6 cells, indicating that MTH1 has no protective role in UVR-induced cytogenetic damage. This indicates that DSBs induced by UV arise from damage forms by direct interaction of UV or ROS with the DNA rather than through oxidation of dNTP.

  • 33. Freimann, Krista
    et al.
    Kurrikoff, Kaido
    Langel, Ülo
    Stockholm University, Faculty of Science, Department of Neurochemistry. University of Tartu, Estonia.
    Galanin receptors as a potential target for neurological disease2015In: Expert opinion on therapeutic targets, ISSN 1472-8222, E-ISSN 1744-7631, Vol. 19, no 12, p. 1665-1676Article in journal (Refereed)
    Abstract [en]

    INTRODUCTION: Galanin is a 29/30 amino acid long neuropeptide that is widely expressed in the brains of many mammals. Galanin exerts its biological activities through three different G protein-coupled receptors, GalR1, GalR2 and GalR3. The widespread distribution of galanin and its receptors in the CNS and the various physiological and pharmacological effects of galanin make the galanin receptors attractive drug targets.

    AREAS COVERED: This review provides an overview of the role of galanin and its receptors in the CNS, the involvement of the galaninergic system in various neurological diseases and the development of new galanin receptor-specific ligands.

    EXPERT OPINION: Recent advances and novel approaches in migrating the directions of subtype-selective ligand development and chemical modifications of the peptide backbone highlight the importance of the galanin neurochemical system as a potential target for drug development.

  • 34. Friedlaender, Jonathan S
    et al.
    Hunley, Keith
    University of New Mexico.
    Dunn, Michael
    Radboud University; Max Planck Institute for Psycholinguistics.
    Terrill, Angela
    Radboud University.
    Lindström, Eva
    Stockholm University, Faculty of Humanities, Department of Linguistics, General Linguistics.
    Friedlaender, Françoise
    Linguistics More Robust Than Genetics: (Letter to the editors)2009Other (Refereed)
  • 35. Gaulton, Kyle J.
    et al.
    Ferreira, Teresa
    Lee, Yeji
    Raimondo, Anne
    Maegi, Reedik
    Reschen, Michael E.
    Mahajan, Anubha
    Locke, Adam
    Rayner, N. William
    Robertson, Neil
    Scott, Robert A.
    Prokopenko, Inga
    Scott, Laura J.
    Green, Todd
    Sparso, Thomas
    Thuillier, Dorothee
    Yengo, Loic
    Grallert, Harald
    Wahl, Simone
    Frånberg, Mattias
    Stockholm University, Faculty of Science, Numerical Analysis and Computer Science (NADA). Stockholm University, Science for Life Laboratory (SciLifeLab). Karolinska Institutet, Sweden.
    Strawbridge, Rona J.
    Kestler, Hans
    Chheda, Himanshu
    Eisele, Lewin
    Gustafsson, Stefan
    Steinthorsdottir, Valgerdur
    Thorleifsson, Gudmar
    Qi, Lu
    Karssen, Lennart C.
    van Leeuwen, Elisabeth M.
    Willems, Sara M.
    Li, Man
    Chen, Han
    Fuchsberger, Christian
    Kwan, Phoenix
    Ma, Clement
    Linderman, Michael
    Lu, Yingchang
    Thomsen, Soren K.
    Rundle, Jana K.
    Beer, Nicola L.
    van de Bunt, Martijn
    Chalisey, Anil
    Kang, Hyun Min
    Voight, Benjamin F.
    Abecasis, Goncalo R.
    Almgren, Peter
    Baldassarre, Damiano
    Balkau, Beverley
    Benediktsson, Rafn
    Blueher, Matthias
    Boeing, Heiner
    Bonnycastle, Lori L.
    Bottinger, Erwin P.
    Burtt, Noel P.
    Carey, Jason
    Charpentier, Guillaume
    Chines, Peter S.
    Cornelis, Marilyn C.
    Couper, David J.
    Crenshaw, Andrew T.
    van Dam, Rob M.
    Doney, Alex S. F.
    Dorkhan, Mozhgan
    Edkins, Sarah
    Eriksson, Johan G.
    Esko, Tonu
    Eury, Elodie
    Fadista, Joao
    Flannick, Jason
    Fontanillas, Pierre
    Fox, Caroline
    Franks, Paul W.
    Gertow, Karl
    Gieger, Christian
    Gigante, Bruna
    Gottesman, Omri
    Grant, George B.
    Grarup, Niels
    Groves, Christopher J.
    Hassinen, Maija
    Have, Christian T.
    Herder, Christian
    Holmen, Oddgeir L.
    Hreidarsson, Astradur B.
    Humphries, Steve E.
    Hunter, David J.
    Jackson, Anne U.
    Jonsson, Anna
    Jorgensen, Marit E.
    Jorgensen, Torben
    Kao, Wen-Hong L.
    Kerrison, Nicola D.
    Kinnunen, Leena
    Klopp, Norman
    Kong, Augustine
    Kovacs, Peter
    Kraft, Peter
    Kravic, Jasmina
    Langford, Cordelia
    Leander, Karin
    Liang, Liming
    Lichtner, Peter
    Lindgren, Cecilia M.
    Lindholm, Eero
    Linneberg, Allan
    Liu, Ching-Ti
    Lobbens, Stephane
    Luan, Jian'an
    Lyssenko, Valeriya
    Mannisto, Satu
    McLeod, Olga
    Meyer, Julia
    Mihailov, Evelin
    Mirza, Ghazala
    Muehleisen, Thomas W.
    Mueller-Nurasyid, Martina
    Navarro, Carmen
    Noethen, Markus M.
    Oskolkov, Nikolay N.
    Owen, Katharine R.
    Palli, Domenico
    Pechlivanis, Sonali
    Peltonen, Leena
    Perry, John R. B.
    Platou, Carl G. P.
    Roden, Michael
    Ruderfer, Douglas
    Rybin, Denis
    van der Schouw, Yvonne T.
    Sennblad, Bengt
    Sigurdsson, Gunnar
    Stancakova, Alena
    Steinbach, Gerald
    Storm, Petter
    Strauch, Konstantin
    Stringham, Heather M.
    Sun, Qi
    Thorand, Barbara
    Tikkanen, Emmi
    Tonjes, Anke
    Trakalo, Joseph
    Tremoli, Elena
    Tuomi, Tiinamaija
    Wennauer, Roman
    Wiltshire, Steven
    Wood, Andrew R.
    Zeggini, Eleftheria
    Dunham, Ian
    Birney, Ewan
    Pasquali, Lorenzo
    Ferrer, Jorge
    Loos, Ruth J. F.
    Dupuis, Josee
    Florez, Jose C.
    Boerwinkle, Eric
    Pankow, James S.
    van Duijn, Cornelia
    Sijbrands, Eric
    Meigs, James B.
    Hu, Frank B.
    Thorsteinsdottir, Unnur
    Stefansson, Kari
    Lakka, Timo A.
    Rauramaa, Rainer
    Stumvoll, Michael
    Pedersen, Nancy L.
    Lind, Lars
    Keinanen-Kiukaanniemi, Sirkka M.
    Korpi-Hyovalti, Eeva
    Saaristo, Timo E.
    Saltevo, Juha
    Kuusisto, Johanna
    Laakso, Markku
    Metspalu, Andres
    Erbel, Raimund
    Joecke, Karl-Heinz
    Moebus, Susanne
    Ripatti, Samuli
    Salomaa, Veikko
    Ingelsson, Erik
    Boehm, Bernhard O.
    Bergman, Richard N.
    Collins, Francis S.
    Mohlke, Karen L.
    Koistinen, Heikki
    Tuomilehto, Jaakko
    Hveem, Kristian
    Njolstad, Inger
    Deloukas, Panagiotis
    Donnelly, Peter J.
    Frayling, Timothy M.
    Hattersley, Andrew T.
    de Faire, Ulf
    Hamsten, Anders
    Illig, Thomas
    Peters, Annette
    Cauchi, Stephane
    Sladek, Rob
    Froguel, Philippe
    Hansen, Torben
    Pedersen, Oluf
    Morris, Andrew D.
    Palmer, Collin N. A.
    Kathiresan, Sekar
    Melander, Olle
    Nilsson, Peter M.
    Groop, Leif C.
    Barroso, Ines
    Langenberg, Claudia
    Wareham, Nicholas J.
    O'Callaghan, Christopher A.
    Gloyn, Anna L.
    Altshuler, David
    Boehnke, Michael
    Teslovich, Tanya M.
    McCarthy, Mark I.
    Morris, Andrew P.
    Genetic fine mapping and genomic annotation defines causal mechanisms at type 2 diabetes susceptibility loci2015In: Nature Genetics, ISSN 1061-4036, E-ISSN 1546-1718, Vol. 47, no 12, p. 1415-+Article in journal (Refereed)
    Abstract [en]

    We performed fine mapping of 39 established type 2 diabetes (T2D) loci in 27,206 cases and 57,574 controls of European ancestry. We identified 49 distinct association signals at these loci, including five mapping in or near KCNQ1. 'Credible sets' of the variants most likely to drive each distinct signal mapped predominantly to noncoding sequence, implying that association with T2D is mediated through gene regulation. Credible set variants were enriched for overlap with FOXA2 chromatin immunoprecipitation binding sites in human islet and liver cells, including at MTNR1B, where fine mapping implicated rs10830963 as driving T2D association. We confirmed that the T2D risk allele for this SNP increases FOXA2-bound enhancer activity in islet- and liver-derived cells. We observed allele-specific differences in NEUROD1 binding in islet-derived cells, consistent with evidence that the T2D risk allele increases islet MTNR1B expression. Our study demonstrates how integration of genetic and genomic information can define molecular mechanisms through which variants underlying association signals exert their effects on disease.

  • 36.
    Ghirlanda, Stefano
    et al.
    Stockholm University, Faculty of Humanities, Centre for the Study of Cultural Evolution. Brooklyn College, USA.
    Enquist, Magnus
    Stockholm University, Faculty of Science, Department of Zoology. Stockholm University, Faculty of Humanities, Centre for the Study of Cultural Evolution.
    Lind, Johan
    Stockholm University, Faculty of Science, Department of Zoology. Stockholm University, Faculty of Humanities, Centre for the Study of Cultural Evolution.
    Coevolution of intelligence, behavioral repertoire, and lifespan2014In: Theoretical Population Biology, ISSN 0040-5809, E-ISSN 1096-0325, Vol. 91, p. 44-49Article in journal (Refereed)
    Abstract [en]

    Across many taxa, intriguing positive correlations exist between intelligence (measured by proxy as encephalization), behavioral repertoire size, and lifespan. Here we argue, through a simple theoretical model, that such correlations arise from selection pressures for efficient learning of behavior sequences. We define intelligence operationally as the ability to disregard unrewarding behavior sequences, without trying them out, in the search for rewarding sequences. We show that increasing a species' behavioral repertoire increases the number of rewarding behavior sequences that can be performed, but also the time required to learn such sequences. This trade-off results in an optimal repertoire size that decreases rapidly with increasing sequence length. Behavioral repertoire size can be increased by increasing intelligence or lengthening the lifespan, giving rise to the observed correlations between these traits.

  • 37.
    Ghirlanda, Stefano
    et al.
    Stockholm University, Faculty of Humanities, Centre for the Study of Cultural Evolution. Brooklyn College, USA.
    Enquist, Magnus
    Stockholm University, Faculty of Science, Department of Zoology. Stockholm University, Faculty of Humanities, Centre for the Study of Cultural Evolution.
    Lind, Johan
    Stockholm University, Faculty of Science, Department of Zoology. Stockholm University, Faculty of Humanities, Centre for the Study of Cultural Evolution.
    Corrigendum to "Coevolution of intelligence, behavioral repertoire, and lifespan" [Theoret. Popul. Biol. 91 (2014) 44–49]2014In: Theoretical Population Biology, ISSN 0040-5809, E-ISSN 1096-0325, Vol. 97, p. 57-57Article in journal (Other academic)
  • 38.
    Golkar, Siv Österman
    et al.
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Czene, Stefan
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute. AstraZeneca R&D, Safety Assessment, Dept Genet Toxicol, AstraZeneca, Södertälje, Sweden.
    Gokarakonda, Amulya
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Haghdoost, Siamak
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Intracellular deoxyribonucleotide pool imbalance and DNA damage in cells treated with hydroxyurea, an inhibitor of ribonucleotide reductase2013In: Mutagenesis, ISSN 0267-8357, E-ISSN 1464-3804, Vol. 28, no 6, p. 653-660Article in journal (Refereed)
    Abstract [en]

    Imbalance in the nucleotide pool of mammalian cells has been shown to result in genotoxic damage. The goal of this study was to devise a sensitive, reproducible and simple method for detection of nucleotide pool changes in mammalian cells that could be used for problem-solving activities in drug development, e.g. mechanistic explanation of a positive response in a mammalian in vitro genotoxicity test. The method evaluated in this study is based on ethanol extraction of the total nucleotide pool, heat treatment and filtration, treatment with calf intestine alkaline phosphatase to convert nucleotides to nucleosides and analysis of the nucleosides by high-performance liquid chromatography with ultraviolet detection. The method was applied to measure the intracellular levels of deoxyribonucleotides in mouse lymphoma (ML) L5178Y cells treated with various concentrations of a model compound, hydroxyurea (HU), a ribonucleotide reductase inhibitor. DNA strand breakage and micronuclei formation were assessed in the same experiments. Imbalance of nucleotide pool (i.e. changes in the relative ratios between individual nucleotide pools) in HU-treated ML cells has been observed already at a concentration of 0.01 mmol/l, whereas genotoxic effects became apparent only at higher concentrations of HU (i.e. 0.25 mmol/l and higher) as indicated by formation of DNA strand breaks and micronuclei.

  • 39.
    Groth, Petra
    Stockholm University, Faculty of Science, Department of Genetics, Microbiology and Toxicology.
    Replication Dynamics in the DNA Damage Response2011Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Faithful DNA replication is essential and the induction of replication stress may have profound effects on genomic integrity. This is demonstrated by the formation of DNA double strand breaks (DSBs), considered to be the most toxic DNA lesions, at stalled replication forks. Homologous recombination (HR) has been shown to be involved in the replication stress response and has been suggested for stabilisation, restart and repair of stalled replication forks. However, the HR mechanisms induced by replication stress are still, to a major part, unknown. The present thesis focuses on investigating replication patterns following the induction of replication stress. Further, the consequences of stressed replication are studied by detection of DSB formation and characterisation of HR in mammalian cells.

    Here, we have identified WEE1, a regulator of mitotic entry, as a factor required to maintain correct replication. Depletion of WEE1 results in the formation of DSBs specifically in newly replicated DNA, as visualised in a modified pulse field electrophoresis assay. We were also able to detect formation of replication-associated secondary DSBs following treatment with ionizing radiation (IR). These DSBs were further demonstrated as major substrates for IR induced HR.

    Using the DNA fibre technique we investigated the effect of DNA alkylating agents on replication. We found that DNA methylations pose direct physical blocks to progressing replication forks causing them to stall in a checkpoint independent manner. Furthermore, we studied restart kinetics following methylation blocked replication and identified a distinct restart mechanism for blocked replication forks independent of new origin firing and HR.

    In conclusion, our findings increase the knowledge of replication dynamics following perturbed replication and further clarify the role of HR following IR induced damage and DNA alkylation.

  • 40.
    Hambäck, Peter A.
    et al.
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    Weingartner, Elisabet
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    Ericson, Lars
    Fors, Lisa
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    Cassel-Lundhagen, Anna
    Stenberg, Johan A.
    Bergsten, Johannes
    Bayesian species delimitation reveals generalist and specialist parasitic wasps on Galerucella beetles (Chrysomelidae): sorting by herbivore or plant host2013In: BMC Evolutionary Biology, ISSN 1471-2148, E-ISSN 1471-2148, Vol. 13, article id 92Article in journal (Refereed)
    Abstract [en]

    Background: To understand the ecological and evolutionary consequences of species interactions in food webs necessitates that interactions are properly identified. Genetic analyses suggest that many supposedly generalist parasitoid species should rather be defined as multiple species with a more narrow diet, reducing the probability that such species may mediate indirect interactions such as apparent competition among hosts. Recent studies showed that the parasitoid Asecodes lucens mediate apparent competition between two hosts, Galerucella tenella and G. calmariensis, affecting both interaction strengths and evolutionary feedbacks. The same parasitoid was also recorded from other species in the genus Galerucella, suggesting that similar indirect effects may also occur for other species pairs. Methods: To explore the possibility of such interactions, we sequenced mitochondrial and nuclear genetic markers to resolve the phylogeny of both host and parasitoid and to test the number of parasitoid species involved. We thus collected 139 Galerucella larvae from 8 host plant species and sequenced 31 adult beetle and 108 parasitoid individuals. Results: The analysis of the Galerucella data, that also included sequences from previous studies, verified the five species previously documented as reciprocally monophyletic, but the Bayesian species delimitation for A. lucens suggested 3-4 cryptic taxa with a more specialised host use than previously suggested. The gene data analyzed under the multispecies coalescent model allowed us to reconstruct the species tree phylogeny for both host and parasitoid and we found a fully congruent coevolutionary pattern suggesting that parasitoid speciation followed upon host speciation. Conclusion: Using multilocus sequence data in a Bayesian species delimitation analysis we propose that hymenopteran parasitoids of the genus Asecodes that infest Galerucella larvae constitute at least three species with narrow diet breath. The evolution of parasitoid Asecodes and host Galerucella show a fully congruent coevolutionary pattern. This finding strengthens the hypothesis that the parasitoid in host search uses cues of the host rather than more general cues of both host and plant.

  • 41. Hasmats, Johanna
    et al.
    Gréen, Henrik
    Orear, Cedric
    Validire, Pierre
    Huss, Mikael
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).
    Käller, Max
    Lundeberg, Joakim
    Assessment of Whole Genome Amplification for Sequence Capture and Massively Parallel Sequencing2014In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 9, no 1, article id e84785Article in journal (Refereed)
    Abstract [en]

    Exome sequence capture and massively parallel sequencing can be combined to achieve inexpensive and rapid global analyses of the functional sections of the genome. The difficulties of working with relatively small quantities of genetic material, as may be necessary when sharing tumor biopsies between collaborators for instance, can be overcome using whole genome amplification. However, the potential drawbacks of using a whole genome amplification technology based on random primers in combination with sequence capture followed by massively parallel sequencing have not yet been examined in detail, especially in the context of mutation discovery in tumor material. In this work, we compare mutations detected in sequence data for unamplified DNA, whole genome amplified DNA, and RNA originating from the same tumor tissue samples from 16 patients diagnosed with non-small cell lung cancer. The results obtained provide a comprehensive overview of the merits of these techniques for mutation analysis. We evaluated the identified genetic variants, and found that most (74%) of them were observed in both the amplified and the unamplified sequence data. Eighty-nine percent of the variations found by WGA were shared with unamplified DNA. We demonstrate a strategy for avoiding allelic bias by including RNA-sequencing information.

  • 42.
    Huminiecki, Lukasz
    et al.
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Conant, Gavin C
    Polyploidy and the evolution of complex traits.2012In: International journal of evolutionary biology, ISSN 2090-052X, Vol. 2012, p. 292068-(12 pp.)Article, review/survey (Refereed)
    Abstract [en]

    We explore how whole-genome duplications (WGDs) may have given rise to complex innovations in cellular networks, innovations that could not have evolved through sequential single-gene duplications. We focus on two classical WGD events, one in bakers' yeast and the other at the base of vertebrates (i.e., two rounds of whole-genome duplication: 2R-WGD). Two complex adaptations are discussed in detail: aerobic ethanol fermentation in yeast and the rewiring of the vertebrate developmental regulatory network through the 2R-WGD. These two examples, derived from diverged branches on the eukaryotic tree, boldly underline the evolutionary potential of WGD in facilitating major evolutionary transitions. We close by arguing that the evolutionary importance of WGD may require updating certain aspects of modern evolutionary theory, perhaps helping to synthesize a new evolutionary systems biology.

  • 43.
    Hunley, Keith
    et al.
    University of New Mexico.
    Dunn, Michael
    Max Planck Institute for Psycholinguistics.
    Lindström, Eva
    Stockholm University, Faculty of Humanities, Department of Linguistics, General Linguistics.
    Reesink, Ger
    Terrill, Angela
    Radboud University.
    Inferring Prehistory from Genetic, Linguistic, and Geographic Variation2007In: Genes, Language, and Culture History in the Southwest Pacific / [ed] Friedlaender, Jonathan S, New York: Oxford University Press , 2007, p. 141-154Chapter in book (Other academic)
  • 44.
    Jansson, Mija
    et al.
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Amundin, Mats
    Linköpings Universitet.
    Laikre, Linda
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Supportive release from a zoo population by cross-fostering can significantly increase genetic variation in the highly inbred wild Swedish wolf populationManuscript (preprint) (Other academic)
    Abstract [en]

    The wild wolf population (Canis lupus) in Sweden is classified as Endangered and descends from only five individuals. The population is isolated and highly inbred; individuals are on average more related to each other than siblings. Inbreeding depression expressed as reduced litter size and a high frequency of spinal disorders have been reported. Management goals include reducing levels of inbreeding, and one suggestion to achieve this is through crossfostering release of pups from a zoo conservation breeding program into wild dens. We used pedigree data of the wild and zoo populations, respectively, to evaluate to what extent the zoo population can support the wild one with respect to increased genetic variation and reduction of inbreeding. The results show a potential to almost double genetic variation measured as founder alleles from 11.2 to 21.1, despite the fact that the two populations have three common founders. Potentially, the number of founder genome equivalents can be increased from present 1.8 to around 3.2. However, to achieve maximum genetic support, almost 50 percent of the wild population gene pool must consist of genes from the zoo population. Average kinship in the joint population of zoo and wild wolves is 0.15, thus release of zoo wolves cannot in itself be expected to reduce average inbreeding below the management target of 0.1. We conclude that releases from the zoo can support but not resolve the genetically precarious situation of the wild Swedish wolf population.

  • 45.
    Jansson, Mija
    et al.
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Laikre, Linda
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Monitoring rate of inbreeding and loss of genetic variation in traditional Swedish dog breeds of conservation concern using pedigree dataManuscript (preprint) (Other academic)
    Abstract [en]

    Increasing conservation genetic focus is directed towards domestic animal populations because: 1) domestic animals are of direct socio-economic importance to humans, and 2) strong selective breeding for a single or a few traits are considered to rapidly deplete the genetic variability of many domestic animal populations. International policy work within the Convention on Biological Diversity identifies strategies for minimizing genetic erosion of domesticated animals as one of the key biodiversity targets for 2010-2020. We investigated recent rate of inbreeding and loss of genetic variation in 12 traditional Swedish dog breeds, 10 of which have been identified as of conservation concern by the Swedish Board of Agriculture. We used studbook data provided by the Swedish Kennel Club with pedigrees dating back to the mid 20th century and comprising 5-10 generations with 350-60,000 individuals per pedigree. We assessed levels of inbreeding and loss of genetic variation measured in relation to the number of founding animals (founder alleles) among live animals at five points in time (1980, 1990, 2000, 2006, and 2012). We found average inbreeding coefficients among breeds to double over our period of monitoring, from an average of 0.03 over breeds in 1980 to 0.07 in 2012. This is in spite of the majority of breeds being large with pedigrees comprising thousands of individuals. The loss of genetic variation is extensive with an average of 70 percent loss of founder alleles over the study period, and the proportion of founder genome equivalents in relation to the number of founders is on average only 0.09. This is comparable to previously published rates of genetic variability loss in dog breeds, indicating that the explicit conservation goals for these traditional Swedish breeds is not yet reflected in conservation genetic status. One of the breeds is particularly threatened - the Gotland hound with less than 150 living individuals, but this breed also shows comparably larger retention of genetic variation.

  • 46.
    Jansson, Mija
    et al.
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Laikre, Linda
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Recent breeding history of dog breeds in Sweden: modest ratesof inbreeding, extensive loss of genetic diversity and lack ofcorrelation between inbreeding and health2014In: Journal of Animal Breeding and Genetics, ISSN 0931-2668, E-ISSN 1439-0388, Vol. 131, no 2, p. 153-162Article in journal (Refereed)
    Abstract [en]

    One problem in modern dogs is a high occurrence of physical diseases,defects and disorders. Many breeds exhibit physical problems that affectindividual dogs throughout life. A potential cause of these problems isinbreeding that is known to reduce the viability of individuals. We investigatedthe possible correlation between recent inbreeding and health problemsin dogs and used studbook data from 26 breeds provided by theSwedish Kennel Club for this purpose. The pedigrees date back to themid-20th century and comprise 5–10 generations and 1 000–50 000 individualsper pedigree over our study period of 1980–2010. We comparedlevels of inbreeding and loss of genetic variation measured in relation tothe number of founding animals during this period in the investigated dogbreeds that we classified as ‘healthy’ (11 breeds) or ‘unhealthy’ (15) basedon statistics on the extent of veterinary care obtained from Sweden’sfour largest insurance companies for pets. We found extensive loss ofgenetic variation and moderate levels of recent inbreeding in all breedsexamined, but no strong indication of a difference in these parametersbetween healthy versus unhealthy breeds over this period. Thus, recentbreeding history with respect to rate of inbreeding does not appear to be amain cause of poor health in the investigated dog breeds in Sweden. Weidentified both strengths and weaknesses of the dog pedigree data importantto consider in future work of monitoring and conserving geneticdiversity of dog breeds.

  • 47.
    Johansson, Ann-Louise
    et al.
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Collins, Ruairi
    Arner, Elias S. J.
    Brzezinski, Peter
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Högbom, Martin
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Biochemical Discrimination between Selenium and Sulfur 2: Mechanistic Investigation of the Selenium Specificity of Human Selenocysteine Lyase2012In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 7, no 1, p. e30528-Article in journal (Refereed)
    Abstract [en]

    Selenium is an essential trace element incorporated into selenoproteins as selenocysteine. Selenocysteine (Sec) lyases (SCLs) and cysteine (Cys) desulfurases (CDs) catalyze the removal of selenium or sulfur from Sec or Cys, respectively, and generally accept both substrates. Intriguingly, human SCL (hSCL) is specific for Sec even though the only difference between Sec and Cys is a single chalcogen atom. The crystal structure of hSCL was recently determined and gain-of-function protein variants that also could accept Cys as substrate were identified. To obtain mechanistic insight into the chemical basis for its substrate discrimination, we here report time-resolved spectroscopic studies comparing the reactions of the Sec-specific wild-type hSCL and the gain-of-function D146K/H389T variant, when given Cys as a substrate. The data are interpreted in light of other studies of SCL/CD enzymes and offer mechanistic insight into the function of the wild-type enzyme. Based on these results and previously available data we propose a reaction mechanism whereby the Sec over Cys specificity is achieved using a combination of chemical and physico-mechanical control mechanisms.

  • 48.
    Kamat, Nasir K.
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Genotoxic effects of systemic chemotherapy in cancer patients, with special focus on the relation between MSI, LOH and development of secondary cancers2013Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Systemic chemotherapy results in both phenotypic and genotypic side effects. Genotoxicity posed by chemotherapy is a major concern since it induces DNA damage and instability in the patients’ genome. Chemotherapy-related genetic instability is thought to be the cause of some secondary tumors especially the acute myeloid leukemia and/or myelodysplasia, which affect 2-15% of patients receiving chemotherapy. Microsatellites are polymorphic repetitive DNA sequences that undergo changes in their length due to instability. Microsatellite instability (MSI) and loss of heterozygosity (LOH) are the main features of chemotherapy-related genotoxicity.

    Using a panel of five and ten microsatellite markers, MSI and LOH were evident in blood specimens collected from patients with breast cancer or other solid tumors, respectively. In addition, the expression of mismatch repair (MMR) proteins was analyzed in tumor tissues using immunohistochemistry. The results showed a decreased expression of the following proteins, human mutL homolog 1 (hMLH1), human mutS homolog 2 (hMSH2), human mutS homolog 6 (hMSH6), human post-meiotic segregation increased 2 (hPMS2), and p53 tumor suppressor protein (p53) after completion of chemotherapy. The clinical complications resistance to chemotherapy, recurrence of primary tumor, and development of secondary tumors were also studied. Incidence of MSI and LOH detected in Tp53-Alu, the marker related to the TP53 tumor suppressor gene, was noticeable compared to the other studied microsatellites. Statistical analysis showed a significant correlation between alterations in microsatellites in blood specimens (MSI and LOH) and MMR expression in tumor tissues. Another strong correlation observed was between MSI, LOH and MMR and the recurrence of primary tumor and/or development of secondary cancers.

    The findings support the hypothesis that MSI and LOH play an important role in tumorigenesis of primary and secondary tumors, and that MSI and LOH may be used as screening tools for early prediction of chemotherapy-related side effects, especially resistance to treatment, recurrence of primary cancer and generation of secondary tumors.

  • 49.
    Kamat, Nasir
    et al.
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Khidhir, Mohammed A.
    Alashari, Mouied M.
    Rannug, Ulf
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Microsatellite instability and loss of heterozygosity detected in middle-aged patients with sporadic colon cancer: A retrospective study2013In: Oncology Letters, ISSN 1792-1074, E-ISSN 1792-1082, Vol. 6, no 5, p. 1413-1420Article in journal (Refereed)
    Abstract [en]

    Microsatellite instability (MSI) is a mutator phenotype that results from a defective mismatch repair (MMR) pathway. The present study examined the incidence of MSI and loss of heterozygosity (LOH) according to five markers from the panel of the National Cancer Institute (NCI) in 38 colorectal cancer (CRC) patients from the United Arab Emirates (UAE). MSI and LOH were analyzed using fragment analyses in a multiplex PCR setting on a capillary array electrophoresis platform. The expression of the MMR proteins, hMLH1 and hMSH2, was analyzed using immunohistochemistry. The cohort consisted of 17 females (44.7%) and 21 males (55.3%) with mean ages of 59.9 and 63.3 years, respectively. The overall MSI incidence was 31.3% (95% CI, 16.1-50.0), and included three patients with high MSI (MSI-H; 9.4%; 95% CI, 2.0-25.0) and seven patients with low MSI (MSI-L; 21.9%; 95% CI, 10.7-39). LOH was detected in three patients, while the remaining 25 patients (65.8%) showed no instability and were therefore classified as microsatellite stable (MSS). MSI was detected in the following screened markers: Bat25 in seven patients, Bat26 in three patients, adenomatous polyposis coli (APC; D5S346) in five patients, AFM093xh3 (D2S123) in two patients and Mfd15 (D17S250) in three patients. Of the five MSI-positive patients, four (80%) were evidently younger, aged 38, 48, 49 and 59 years, respectively. The MSI-H incidence (9.4%) was lower compared with that of other ethnic groups. In terms of the MMR proteins, hMLH1 expression was deficient in seven patients, of whom three were MSI-H patients, and hMSH2 was deficient in three patients. Fisher's exact test showed significant associations between hMLH1 and MSI when classified as MSS, MSI-L or MSI-H (P=0.0003). No such association was observed with abnormal MMR protein expression, age, cancer stage or gender.

  • 50.
    Kamat, Nasir
    et al.
    Stockholm University, Faculty of Science, Department of Genetics, Microbiology and Toxicology.
    Khidhir, Mohammed A.
    Jaloudi, Mohammed
    Hussain, Sabir
    Alashari, Mouied M.
    Al Qawasmeh, Khaled H.
    Rannug, Ulf
    Stockholm University, Faculty of Science, Department of Genetics, Microbiology and Toxicology.
    High incidence of microsatellite instability and loss of heterozygosity in three loci in breast cancer patients receiving chemotherapy: a prospective study2012In: BMC Cancer, ISSN 1471-2407, E-ISSN 1471-2407, Vol. 12, p. 373-Article in journal (Refereed)
    Abstract [en]

    Background: The aim of the study was to evaluate potential chemotherapy-induced microsatellite instability, loss of heterozygosity, loss of expression in mismatch repair proteins and associations with clinical findings in breast cancer patients, especially resistance to chemotherapy and/or development of other tumors in the four years following chemotherapy treatment. Methods: A comprehensive study of chemotherapy-related effects with a follow-up period of 48 months post treatment was conducted. A total of 369 peripheral blood samples were collected from 123 de novo breast cancer patients. Microsatellite instability and loss of heterozygosity in five commonly used marker loci (including Tp53-Alu of the tumor suppressor gene TP53) were analyzed in blood samples. Sampling was conducted on three occasions; 4-5 weeks prior to the first chemotherapy session (pre-treatment), to serve as a baseline, followed by two consecutive draws at 12 weeks intervals from the first collection. Mismatch repair protein expression was evaluated in cancer tissues using immunohistochemistry for three mismatch-repair related proteins. Results: A total of 70.7% of the patients showed microsatellite instability for at least one locus, including 18.6% marked as high-positive and 52.1% as low-positive; 35.8% showed loss of heterozygosity in addition to microsatellite instability, while 29.3% exhibited microsatellite stability. The following incidence rates for microsatellite instability and loss of heterozygosity were detected: 39.1% positive for Tp53-Alu, 31.1% for locus Mfd41, and 25.3% for locus Mfd28. A higher occurrence of loss of heterozygosity was noted with alleles 399 and 404 of Tp53-Alu. The mismatch repair protein expression analysis showed that the chemotherapy caused a loss of 29.3% in hMLH1 expression, and 18.7% and 25.2% loss in hMSH2 and P53 expression, respectively. A strong correlation between low or deficient hMSH2 protein expression and occurrence of mismatch repair/loss of heterozygosity events in Mfd41, Tp53-Alu, and Mfd28 was evident. A significant association between mismatch repair/loss of heterozygosity and incidence of secondary tumors was also established. Conclusion: Our results suggest that microsatellite instability, loss of heterozygosity, and deficiency in mismatch repair may serve as early prognostic factors for potential chemotherapy-related side effects in breast cancer patients.

123 1 - 50 of 123
CiteExportLink to result list
Permanent link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf