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  • 1101.
    Zubair, Saima
    et al.
    Swedish Univ Agr Sci, SLU Global Bioinformat Ctr, Dept Anim Breeding & Genet, SE-75007 Uppsala, Sweden..
    Fischer, Anne
    Int Livestock Res Inst, Nairobi, Kenya.;Int Ctr Insect Physiol & Ecol, Nairobi, Kenya..
    Liljander, Anne
    Int Livestock Res Inst, Nairobi, Kenya..
    Meens, Jochen
    Univ Vet Med Hannover, Inst Microbiol, Dept Infect Dis, Hannover, Germany..
    Hegerman, Jan
    Hannover Med Sch, Inst Funct & Appl Anat, Hannover, Germany.;Biomed Res Endstage & Obstruct Lung Dis Hannover, Hannover, Germany.;REBIRTH Cluster Excellence, Hannover, Germany..
    Gourle, Hadrien
    Swedish Univ Agr Sci, SLU Global Bioinformat Ctr, Dept Anim Breeding & Genet, SE-75007 Uppsala, Sweden..
    Bishop, Richard P.
    Int Livestock Res Inst, Nairobi, Kenya..
    Roebbelen, Ina
    Int Livestock Res Inst, Nairobi, Kenya..
    Younan, Mario
    Vet Sans Frontieres Germany, Nairobi, Kenya..
    Mustafa, Mudassir Imran
    Uppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Social Sciences, Department of Informatics and Media. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Public Health and Caring Sciences, Clinical Psychology in Healthcare.
    Mushtaq, Mamoona
    Swedish Univ Agr Sci, SLU Global Bioinformat Ctr, Dept Anim Breeding & Genet, SE-75007 Uppsala, Sweden..
    Bongcam-Rudloff, Erik
    Swedish Univ Agr Sci, SLU Global Bioinformat Ctr, Dept Anim Breeding & Genet, SE-75007 Uppsala, Sweden..
    Jores, Joerg
    Int Livestock Res Inst, Nairobi, Kenya..
    Complete genome sequence of Staphylococcus aureus, strain ILRI_Eymole1/1, isolated from a Kenyan dromedary camel2015In: Standards in Genomic Sciences, ISSN 1944-3277, E-ISSN 1944-3277, Vol. 10, 109Article in journal (Refereed)
    Abstract [en]

    We report the genome of a Staphylococcus aureus strain (ILRI_Eymole1/1) isolated from a nasal swab of a dromedary camel (Camelus dromedarius) in North Kenya. The complete genome sequence of this strain consists of a circular chromosome of 2,874,302 bp with a GC-content of 32.88 %. In silico annotation predicted 2755 protein-encoding genes and 76 non-coding genes. This isolate belongs to MLST sequence type 30 (ST30). Phylogenetic analysis based on a subset of 283 core genes revealed that it falls within the human clonal complex 30 (CC30) S. aureus isolate cluster but is genetically distinct. About 79 % of the protein encoding genes are part of the CC30 core genome (genes common to all CC30 S. aureus isolates), similar to 18 % were within the variable genome (shared among multiple but not all isolates) and similar to 3 % were found only in the genome of the camel isolate. Among the 85 isolate-specific genes, 79 were located within putative phages and pathogenicity islands. Protein encoding genes associated with bacterial adhesion, and secretory proteins that are essential components of the type VII secretion system were also identified. The complete genome sequence of S. aureus strain ILRI_Eymole1/1 has been deposited in the European Nucleotide Archive under the accession no LN626917.1.

  • 1102. Zuccolo, Andrea
    et al.
    Scofield, Douglas G.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    De Paoli, Emanuele
    Morgante, Michele
    The Ty1-copia LTR retroelement family PARTC is highly conserved in conifers over 200 MY of evolution2015In: Gene, ISSN 0378-1119, E-ISSN 1879-0038, Vol. 568, no 1, 89-99 p.Article in journal (Refereed)
    Abstract [en]

    Long Terminal Repeat retroelements (LTR-RTs) are a major component of many plant genomes. Although well studied and described in angiosperms, their features and dynamics are poorly understood in gymnosperms. Representative complete copies of a Ty1-copia element isolate in Picea abies and named PARTC were identified in six other conifer species (Picea glauca, Pinus sylvestris, Pinus taeda, Abies sibirica, Taxus baccata and Juniperus communis) covering more than 200 million years of evolution. Here we characterized the structure of this element, assessed its abundance across conifers, studied the modes and timing of its amplification, and evaluated the degree of conservation of its extant copies at nucleotide level over distant species. We demonstrated that the element is ancient, abundant, widespread and its paralogous copies are present in the genera Picea, Pinus and Abies as an LTR-RT family. The amplification leading to the extant copies of PARTC occurred over long evolutionary times spanning 10 s of MY and mostly took place after the speciation of the conifers analyzed. The level of conservation of PARTC is striking and may be explained by low substitution rates and limited removal mechanisms for LTR-RTs. These PARTC features and dynamics are representative of a more general scenario for LTR-RTs in gymnosperms quite different from that characterizing the vast majority of LTR-RT elements in angiosperms. (C) 2015 Elsevier B.V. All rights reserved.

  • 1103. Zulfugarov, Ismayil S.
    et al.
    Tovuu, Altanzaya
    Eu, Young-Jae
    Dogsom, Bolormaa
    Poudyal, Roshan Sharma
    Nath, Krishna
    Hall, Michael
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Banerjee, Mainak
    Yoon, Ung Chan
    Moon, Yong-Hwan
    An, Gynheung
    Jansson, Stefan
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Lee, Choon-Hwan
    Production of superoxide from Photosystem II in a rice (Oryza sativa L.) mutant lacking PsbS2014In: BMC Plant Biology, ISSN 1471-2229, E-ISSN 1471-2229, Vol. 14, 242- p.Article in journal (Refereed)
    Abstract [en]

    Background: PsbS is a 22-kDa Photosystem (PS) II protein involved in non-photochemical quenching (NPQ) of chlorophyll fluorescence. Rice (Oryza sativa L.) has two PsbS genes, PsbS1 and PsbS2. However, only inactivation of PsbS1, through a knockout (PsbS1-KO) or in RNAi transgenic plants, results in plants deficient in qE, the energy-dependent component of NPQ. Results: In studies presented here, under fluctuating high light, growth of young seedlings lacking PsbS is retarded, and PSII in detached leaves of the mutants is more sensitive to photoinhibitory illumination compared with the wild type. Using both histochemical and fluorescent probes, we determined the levels of reactive oxygen species, including singlet oxygen, superoxide, and hydrogen peroxide, in leaves and thylakoids. The PsbS-deficient plants generated more superoxide and hydrogen peroxide in their chloroplasts. PSII complexes isolated from them produced more superoxide compared with the wild type, and PSII-driven superoxide production was higher in the mutants. However, we could not observe such differences either in isolated PSI complexes or through PSI-driven electron transport. Time-course experiments using isolated thylakoids showed that superoxide production was the initial event, and that production of hydrogen peroxide proceeded from that. Conclusion: These results indicate that at least some of the photoprotection provided by PsbS and qE is mediated by preventing production of superoxide released from PSII under conditions of excess excitation energy.

  • 1104. Zulfugarov, Ismayil S.
    et al.
    Tovuu, Altanzaya
    Kim, Chi-Yeol
    Vo, Kieu Thi Xuan
    Ko, Soo Yeon
    Hall, Michael
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Seok, Hye-Yeon
    Kim, Yeon-Ki
    Skogström, Oscar
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Moon, Yong-Hwan
    Jansson, Stefan
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Jeon, Jong-Seong
    Lee, Choon-Hwan
    Enhanced resistance of PsbS-deficient rice (Oryza sativa L.) to fungal and bacterial pathogens2016In: Journal of Plant Biology, ISSN 1226-9239, Vol. 59, no 6, 616-626 p.Article in journal (Refereed)
    Abstract [en]

    The 22-kDa PsbS protein of Photosystem II is involved in nonphotochemical quenching (NPQ) of chlorophyll fluorescence. Genome-wide analysis of the expression pattern in PsbS knockout (KO) rice plants showed that a lack of this protein led to changes in the transcript levels of 406 genes, presumably a result of superoxide produced in the chloroplasts. The top Gene Ontology categories, in which expression was the most differential, included 'Immune response', 'Response to jasmonic acid', and 'MAPK cascade'. From those genes, we randomly selected nine that were up-regulated. Our microarray results were confirmed by quantitative RT-PCR analysis. The KO and PsbS RNAi (knockdown) plants were more resistant to pathogens Magnaporthe oryzae PO6-6 and Xanthomonas oryzae pv. oryzae than either the wild-type plants or PsbS-overexpressing transgenic line. These findings suggest that superoxide production might be the reason that these plants have greater pathogen resistance to fungal and bacterial pathogens in the absence of energy-dependent NPQ. For example, a high level of cell wall lignification in the KO mutants was possibly due to enhanced superoxide production. Our data indicate that certain abiotic stress-induced reactive oxygen species can promote specific signaling pathways, which then activate a defense mechanism against biotic stress in PsbS-KO rice plants.

  • 1105.
    Zwoinska, Martyna K.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology. Univ Lausanne, Dept Ecol & Evolut, CH-1015 Lausanne, Switzerland..
    Maklakov, Alexei A.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Kawecki, Tadeusz J.
    Univ Lausanne, Dept Ecol & Evolut, CH-1015 Lausanne, Switzerland..
    Hollis, Brian
    Univ Lausanne, Dept Ecol & Evolut, CH-1015 Lausanne, Switzerland.;Ecole Polytech Fed Lausanne, Sch Life Sci, Lausanne, Switzerland..
    Experimental evolution of slowed cognitive aging in Drosophila melanogaster2017In: Evolution, ISSN 0014-3820, E-ISSN 1558-5646, Vol. 71, no 3, 662-670 p.Article in journal (Refereed)
    Abstract [en]

    Reproductive output and cognitive performance decline in parallel during aging, but it is unknown whether this reflects a shared genetic architecture or merely the declining force of natural selection acting independently on both traits. We used experimental evolution in Drosophila melanogaster to test for the presence of genetic variation for slowed cognitive aging, and assess its independence from that responsible for other traits' decline with age. Replicate experimental populations experienced either joint selection on learning and reproduction at old age (Old + Learning), selection on late-life reproduction alone (Old), or a standard two-week culture regime (Young). Within 20 generations, the Old + Learning populations evolved a slower decline in learning with age than both the Old and Young populations, revealing genetic variation for cognitive aging. We found little evidence for a genetic correlation between cognitive and demographic aging: although the Old + Learning populations tended to show higher late-life fecundity than Old populations, they did not live longer. Likewise, selection for late reproduction alone did not result in improved late-life learning. Our results demonstrate that Drosophila harbor genetic variation for cognitive aging that is largely independent from genetic variation for demographic aging and suggest that these two aspects of aging may not necessarily follow the same trajectories.

  • 1106.
    Åberg, Karolina
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Lindholm, Eva
    Saetre, Peter
    Wetterberg, Lennart
    Pettersson, Ulf
    Jazin, Elena
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Genome Wide Investigation of an Isolated Schizophrenia Population Using a Dense Map of Microsatellites and SNPs in CombinationManuscript (Other (popular science, discussion, etc.))
  • 1107.
    Åberg, Karolina
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Saetre, Peter
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Lindholm, Eva
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Ekholm, Birgit
    Pettersson, Ulf
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology.
    Adolfsson, Rolf
    Jazin, Elena
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Human QKI, a New Candidate Gene for Schizophrenia Involved in Myelination2005In: American journal of medical genetics. Part B, Neuropsychiatric genetics, ISSN 1552-4841, Vol. 141B, no 1, 84-90 p.Article in journal (Refereed)
    Abstract [en]

    We have previously shown that chromosome 6q25-6q27 includes a susceptibility locus for schizophrenia in a large pedigree from northern Sweden. In this study, we fine-mapped a 10.7 Mb region, included in this locus, using 42 microsatellites or SNP markers. We found a 0.5 Mb haplotype, likely to be inherited identical by decent, within the large family that is shared among the majority of the patients (69%). A gamete competition test of this haplotype in 176 unrelated nuclear families from the same geographical area as the large family showed association to schizophrenia (empirical P-value 0.041). The only gene located in the region, the quaking homolog, KH domain RNA binding (mouse) (QKI), was investigated in human brain autopsies from 55 cases and 55 controls using a high-resolution mRNA expression analysis. Relative mRNA expression levels of two QKI splice variants were clearly downregulated in schizophrenic patients (P-value 0.0004 and 0.03, respectively). The function of QKI has not been studied in humans, but the mouse homolog is involved in neural development and myelination. In conclusion, we present evidence from three unrelated sample-sets that propose the involvement of the QKI gene in schizophrenia. The two family based studies suggest that there may be functional variants of the QKI gene that increase the susceptibility of schizophrenia in northern Sweden, whereas the case-control study suggest that splicing of the gene may be disturbed in schizophrenic patients from other geographical origins. Taken together, we propose QKI as a possible target for functional studies related to the role of myelination in schizophrenia.

  • 1108.
    Åkerström, Tobias
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Surgical Sciences, Endocrine Surgery.
    Carling, T.
    Endocrine Research Unit, Yale University, New Haven, CT, USA..
    Beuschlein, F.
    Medizinische Klinik und Poliklinik IV, Klinikum der Universität München, Munich, Germany..
    Hellman, Per
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Surgical Sciences, Endocrine Surgery.
    Genetics of adrenocortical tumours2016In: Journal of Internal Medicine, ISSN 0954-6820, E-ISSN 1365-2796, Vol. 280, no 6, 540-550 p.Article in journal (Refereed)
    Abstract [en]

    The recently available genomic sequencing techniques have led to breakthroughs in understanding of the underlying genetic mechanisms in adrenocortical tumours. Disease-causing mutations have been described for aldosterone-producing adenomas, cortisol-producing adenomas and adrenocortical carcinomas. Further, knowledge gained from transcriptome analyses and methylation arrays has provided new insights into the development of these tumours. Elucidation of the genomic landscape of adrenocortical tumours and improved techniques may in the future be useful for early diagnosis through the detection of mutated DNA in the circulation. Moreover, compounds that bind specifically to altered proteins may be used as screening targets or therapeutic agents. Regulation of cortisol release by interaction with an altered subunit in adenylate cyclase may be more complex, but may provide a new option for regulating steroid release. Information about derangements in adrenocortical carcinoma is already helpful for determining patient prognosis. With further knowledge, we may be able to identify novel biomarkers that effectively and noninvasively help in differentiating between benign and malignant disease. It is clear that the next few years will provide much novel information that hopefully will aid in the treatment of patients with adrenocortical tumours.

  • 1109.
    Åslund, Sven-Eric
    Umeå University, Faculty of Medicine, Department of Medical Biosciences, Medical and Clinical Genetics.
    Mating behaviour in Drosophila melanogaster and its implication to genetic variation1978Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Not much is known about the mechanisms affecting the genetic composition of populations of different species. To investi­gate one of these potential mechanisms, mating behaviour, the fruit fly Drosophila melanogaster, was chosen as an experimen­tal animal.

    To quantify mating behaviour in easily measurable parameters, it was subdivided into several distinct components; mating activity, mating time, mating competition ability and male mating capacity. As behavioural components to a great extent are influenced by environmental conditions all experiments were performed under controlled temperature and humidity. All components of mating behaviour were estimated by introducing females and males into mating chambers.

    Mating behaviour seems to be one of the major factors affect­ing the genetic composition of Drosophila melanogaster popula­tions. The experiments performed showed that differences in mating properties led to a substantial sexual selection among the genotypes. This selection was of a stabilizing type with regard to characters associated to bristle number and Y chromo­somal chromatin. This selection situation seems to warrant the retention of intermediate phenotypes in a population and will therefore contribute to the genetic variation present. Differences in mating properties were also shown to be able to maintain a balanced polymorphism for allozyme variants in populations. This maintenance was obtained through different forms of balancing selection as heterozygous superiority in sexual activity and balancing selection between female and male genotypes. Heterozygous superiority or overdominance in fitness always leads to balanced polymorphism through segre­gation of individuals with lowered fitness. The balancing selection between the female and male genotypes is best looked upon as a form of marginal overdominance, conferring the aver­aged highest fitness to the heterozygous genotype, thereby maintaining the polymorphism of the population.

  • 1110.
    Ödling, Sara
    Linköping University, Department of Physics, Chemistry and Biology. Linköping University, Faculty of Science & Engineering.
    Is there a correlation between the nutrient content and variation in the HvNAM-2 gene in Hordeum vulgare?2015Independent thesis Basic level (degree of Bachelor), 10,5 credits / 16 HE creditsStudent thesis
    Abstract [en]

    Barley is one of the most important cereal crops in the world and a better understanding of the factors that regulates the nutrient content in the grain is of high interest. The industrial breeding during the last century has led to bigger yield but possibly a decrease in nutrient content. In wheat, the NAM-B1 gene is a well-studied gene that affects the grain protein and micronutrient content. Two orthologue genes in barley HvNAM-1 and HvNAM-2 are candidate genes to play a similar role in the barley senescence process.

    I have looked for a correlation between the diversity in the HvNAM-2 gene and nutrient content in 37 Nordic barley accessions. The samples were sequenced and then aligned and analyzed for variation. I found three haplotypes which were compared in nutrient content and in micronutrient content. No significant difference between the haplotypes was found, which can be due to small sample size or that no correlation exists between the grain protein content and the HvNAM-2 gene variation. Significant correlation was however found between the nitrogen content and the micronutrient contents that indicate that the pathways of all the nutrients’ mobilizations are tightly coupled. For future research a bigger number of accessions, preferably at least 100, need to be analyzed to be able to give any conclusions. The molecular mechanisms in the cells during senescence also need further investigation.

  • 1111. Örmälä-Odegrip, Anni-Maria
    et al.
    Eriksson, Harald
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Mikonranta, Lauri
    Ruotsalainen, Pilvi
    Mattila, Sari
    Hoikkala, Ville
    Nilsson, Anders
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Bamford, Jaana K. H.
    Laakso, Jouni
    Evolution of virulence in Klebsiella pneumoniae treated with phage cocktailsManuscript (preprint) (Other academic)
    Abstract [en]

    The worldwide emergence and spread of multidrug-resistant bacteria is a major concern in modern medicine, and threatens the once established control over bacterial infections. Phage therapy has been suggested as one potential solution to the problem of finding new antibacterial agents. Bacteria are known to evolve resistance against bacteriophages but in many cases phage-resistance comes with a cost on bacterial virulence in multicellular hosts. We investigated how the virulence of a clinical isolate of K. pneumoniae Kpn524 evolves in response to exposure to phage cocktails in the phage-resistant bacteria that would potentially survive the phage treatment. We found that the exposure to multiple phages was linked to lowered virulence in the phage-resistant bacteria, when measured in vivo with Galleria mellonella. However, two phages were found to increase the bacterial virulence when they were administered on the bacteria individually, and this was associated with an increased growth rate. Across all treatments, biofilm production was negatively correlated with virulence, whereas growth rate had a positive correlation with bacterial virulence. Our findings suggest that bacterial virulence is attenuated in the presence of multiple phages, possibly due to a trade-off between phage resistance andrate of replication. However, this is dependent on the composition of the phage cocktail.This is the first study to report increased bacterial virulence associated with exposure tolytic bacteriophages and our results call for meticulous consideration when choosingphages for phage cocktails, as phages with certain identity could have detrimentally adverse effects on the success of the treatment.

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