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  • 951.
    Zhou, Xiangzhi
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Westlund, Per-Olof
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    1H NMRD profiles and ESR lineshapes of Gd(III) complexes: a comparison between the generalized SBM and the stochastic Liouville approach2005In: Journal of magnetic resonance, ISSN 1090-7807, E-ISSN 1096-0856, Vol. 173, no 1, p. 75-83Article in journal (Refereed)
    Abstract [en]

    A complete description of the T1-NMRD profiles and the ESR lineshape of Gd(III) complexes (S = 7/2) was presented using second-order perturbation theory (GSBM) by Zhou et al. [J. Magn. Reson. 167 (2004) 147]. This report compares the GSBM with the stochastic Liouville approach (SLA) to determine the validity of the closed analytical expressions of NMRD and the ESR lineshape functions. Both approaches give the same results at high fields while a very small divergence is observed for X- and W-band ESR lineshapes when the magnitude of the perturbation term times the correlation time approaches the limit of the perturbation regime, ΔZFSτf ≈ 0.1. There was a clear discrepancy between the theoretical GSBM X-band spectrum and the recorded ESR spectrum of the Gd(III) MS-325 + HSA complex. This is probably due to a slow-motion effect caused by a slow modulation of the ZFS interaction. The characteristic correlation time of this slow modulation is in the range of 150 ps, which therefore cannot be due to the reorientational motion of the whole MS-325 + HSA complex.

  • 952.
    Zhou, Yang
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology).
    Regulation of pre-mRNA splicing and mRNA degradation in Saccharomyces cerevisiae2017Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Messenger RNAs are transcribed and co-transcriptionally processed in the nucleus, and transported to the cytoplasm. In the cytoplasm, mRNAs serve as the template for protein synthesis and are eventually degraded. The removal of intron sequences from a precursor mRNA is termed splicing and is carried out by the dynamic spliceosome. In this thesis, I describe the regulated splicing of two transcripts in Saccharomyces cerevisiae. I also describe a study where the mechanisms that control the expression of magnesium transporters are elucidated.

    The pre-mRNA retention and splicing (RES) complex is a spliceosome-associated protein complex that promotes the splicing and nuclear retention of a subset of pre-mRNAs. The RES complex consists of three subunits, Bud13p, Snu17p and Pml1p. We show that the lack of RES factors causes a decrease in the formation of N4-acetylcytidine (ac4C) in tRNAs. This phenotype is caused by inefficient splicing of the pre-mRNA of the TAN1 gene, which is required for the formation of ac4C in tRNAs. The RES mutants also show growth defects that are exacerbated at elevated temperatures. We show that the temperature sensitive phenotype of the bud13Δ and snu17Δ cells is caused by the inefficient splicing of the MED20 pre-mRNA. The MED20 gene encodes a subunit of the Mediator complex. Unspliced pre-mRNAs that enter the cytoplasm are usually degraded by the nonsense-mediated mRNA decay (NMD) pathway, which targets transcripts that contain premature translation termination codons. Consistent with the nuclear retention function of the RES complex, we find that NMD inactivation in the RES mutants leads to the accumulation of both TAN1 and MED20 pre-mRNAs. We also show that the cis-acting elements that promote RES-dependent splicing are different between the TAN1 and MED20 pre-mRNAs.

    The NMD pathway also targets transcripts with upstream ORFs (uORFs) for degradation. The ALR1 gene encodes the major magnesium importer in yeast, and its expression is controlled by the NMD pathway via a uORF in the 5’ untranslated region. We show that the ribosome reaches the downstream main ORF by a translation reinitiation mechanism. The NMD pathway was shown to control cellular Mg2+ levels by regulating the expression of the ALR1 gene. We further show that the NMD pathway targets the transcripts of the vacuolar Mg2+ exporter Mnr2p and the mitochondrial Mg2+ exporter Mme1p for degradation.

    In summary, we conclude that the RES complex has a role in the splicing regulation of a subset of transcripts. We also suggest a regulatory role for the NMD pathway in maintaining the cellular Mg2+ concentration by controlling the expression of Mg2+ transporters.

  • 953.
    Zhou, Yang
    et al.
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology).
    Johansson, Marcus
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology).
    The nonsense-mediated mRNA decay pathway controls the expression of magnesium transporters in Saccharomyces cerevisiaeManuscript (preprint) (Other academic)
  • 954.
    Zhou, Yang
    et al.
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology).
    Johansson, Marcus J O
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology). BRF Krutet, Norra Majorsgatan, Umea, Sweden; University of Tartu, Institute ofTechnology, Nooruse, Tartu, Estonia.
    The pre-mRNA retention and splicing complex controls expression of the Mediator subunit Med202017In: RNA Biology, ISSN 1547-6286, E-ISSN 1555-8584, Vol. 14, no 10, p. 1411-1417Article in journal (Refereed)
    Abstract [en]

    The heterotrimeric pre-mRNA retention and splicing (RES) complex, consisting of Bud13p, Snu17p and Pml1p, promotes splicing and nuclear retention of a subset of intron-containing pre-mRNAs. Yeast cells deleted for individual RES genes show growth defects that are exacerbated at elevated temperatures. Although the growth phenotypes correlate to the splicing defects in the individual mutants, the underlying mechanism is unknown. Here, we show that the temperature sensitive (Ts) growth phenotype of bud13Δ and snu17Δ cells is a consequence of inefficient splicing of MED20 pre-mRNA, which codes for a subunit of the Mediator complex; a co-regulator of RNA polymerase II transcription. The MED20 pre-mRNA splicing defect is less pronounced in pml1Δ cells, explaining why they grow better than the other 2 RES mutants at elevated temperatures. Inactivation of the cytoplasmic nonsense-mediated mRNA decay (NMD) pathway in the RES mutants leads to accumulation of MED20 pre-mRNA, indicating that inefficient nuclear retention contributes to the growth defect. Further, the Ts phenotype of bud13Δ and snu17Δ cells is partially suppressed by the inactivation of NMD, showing that the growth defects are augmented by the presence of a functional NMD pathway. Collectively, our results demonstrate an important role of the RES complex in maintaining the Med20p levels.

  • 955. Zhou, Yizhou
    et al.
    Smith, Daniel
    Leong, Bryan J
    Brännström, Kristoffer
    Umeå University, Faculty of Medicine, Department of Medical Biochemistry and Biophysics.
    Almqvist, Fredrik
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Umeå University, Faculty of Medicine, Umeå Centre for Microbial Research (UCMR).
    Chapman, Matthew R
    Umeå University, Faculty of Medicine, Umeå Centre for Microbial Research (UCMR).
    Promiscuous cross-seeding between bacterial amyloids promotes interspecies biofilms2012In: Journal of Biological Chemistry, ISSN 0021-9258, E-ISSN 1083-351X, Vol. 287, no 42, p. 35092-35103Article in journal (Refereed)
    Abstract [en]

    Amyloids are highly aggregated proteinaceous fibers historically associated with neurodegenerative conditions including Alzheimer's, Parkinson's and prion-based encephalopathies. Polymerization of amyloidogenic proteins into ordered fibers can be accelerated by preformed amyloid aggregates derived from the same protein in a process called seeding. Seeding of disease-associated amyloids and prions is highly specific and cross-seeding is usually limited or prevented. Here we describe the first study on the cross-seeding potential of bacterial functional amyloids. Curli are produced on the surface of many Gram-negative bacteria where they facilitate surface attachment and biofilm development. Curli fibers are composed of the major subunit CsgA and the nucleator CsgB, which templates CsgA into fibers. Our results showed that curli subunit homologs from Escherichia coli, Salmonella typhimurium LT2 and Citrobacter koseri were able to cross-seed in vitro. The polymerization of E. coli CsgA was also accelerated by fibers derived from a distant homolog in Shewanella oneidensis that shares less than 30% identity in primary sequence. Cross-seeding of curli proteins was also observed in mixed colony biofilms with E. coli and S. typhimurium. CsgA secreted from E. coli csgB- mutants assembled into fibers on adjacent S. typhimurium that presented CsgB on its surfaces. Similarly, CsgA secreted by S. typhimurium csgB- mutants formed curli on CsgB-presenting E. coli. This interspecies curli assembly enhanced bacterial attachment to agar surfaces and supported pellicle biofilm formation. Collectively, this work suggests that the seeding specificity among curli homologs is relaxed and that heterogeneous curli fibers can facilitate multispecies biofilm development.

  • 956.
    Zou, Xiaozhou
    et al.
    State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, Donghua University, Shanghai, China; China-Sweden Associated Research Laboratory in Industrial Biotechnology, College of Chemistry, Chemical Engineering and Biotechnology, Donghua University, Shanghai, China; Group of Microbiological Engineering and Industrial Biotechnology, College of Chemistry, Chemical Engineering and Biotechnology, Donghua University, Shanghai, China.
    Wu, Guochao
    Umeå University, Faculty of Science and Technology, Department of Chemistry. China-Sweden Associated Research Laboratory in Industrial Biotechnology, College of Chemistry, Chemical Engineering and Biotechnology, Donghua University, Shanghai, China.
    Stagge, Stefan
    Umeå University, Faculty of Science and Technology, Department of Chemistry. China-Sweden Associated Research Laboratory in Industrial Biotechnology, College of Chemistry, Chemical Engineering and Biotechnology, Donghua University, Shanghai, China.
    Chen, Lin
    Jönsson, Leif J.
    Umeå University, Faculty of Science and Technology, Department of Chemistry. China-Sweden Associated Research Laboratory in Industrial Biotechnology, College of Chemistry, Chemical Engineering and Biotechnology, Donghua University, Shanghai, China.
    Hong, Feng F.
    Comparison of tolerance of four bacterial nanocellulose-producing strains to lignocellulose-derived inhibitors2017In: Microbial Cell Factories, ISSN 1475-2859, E-ISSN 1475-2859, Vol. 16, article id 229Article in journal (Refereed)
    Abstract [en]

    Background: Through pretreatment and enzymatic saccharification lignocellulosic biomass has great potential as a low-cost feedstock for production of bacterial nanocellulose (BNC), a high value-added microbial product, but inhibitors formed during pretreatment remain challenging. In this study, the tolerance to lignocellulose-derived inhibitors of three new BNC-producing strains were compared to that of Komagataeibacter xylinus ATCC 23770. Inhibitors studied included furan aldehydes (furfural and 5-hydroxymethylfurfural) and phenolic compounds (coniferyl aldehyde and vanillin). The performance of the four strains in the presence and absence of the inhibitors was assessed using static cultures, and their capability to convert inhibitors by oxidation and reduction was analyzed.

    Results: Although two of the new strains were more sensitive than ATCC 23770 to furan aldehydes, one of the new strains showed superior resistance to both furan aldehydes and phenols, and also displayed high volumetric BNC yield (up to 14.78 ± 0.43 g/L) and high BNC yield on consumed sugar (0.59 ± 0.02 g/g). The inhibitors were oxidized and/or reduced by the strains to be less toxic. The four strains exhibited strong similarities with regard to predominant bioconversion products from the inhibitors, but displayed different capacity to convert the inhibitors, which may be related to the differences in inhibitor tolerance.

    Conclusions: This investigation provides information on different performance of four BNC-producing strains in the presence of lignocellulose-derived inhibitors. The results will be of benefit to the selection of more suitable strains for utilization of lignocellulosics in the process of BNC-production.

  • 957. Zou, Zhen
    et al.
    Evans, Jay
    Lu, Zhiqiang
    Zhao, Picheng
    Williams, Michael
    Umeå University, Faculty of Medicine, Umeå Centre for Molecular Pathogenesis (UCMP) (Faculty of Medicine).
    Sumathipala, Niranji
    Hetru, Charles
    Hultmark, Dan
    Umeå University, Faculty of Medicine, Umeå Centre for Molecular Pathogenesis (UCMP) (Faculty of Medicine).
    Jiang, Haobo
    Comparative genomic analysis of the Tribolium immune system.2007In: Genome Biol, ISSN 1465-6914, Vol. 8, no 8, p. R177.1-16Article in journal (Refereed)
    Abstract [en]

    BACKGROUND: Tribolium castaneum is a species of Coleoptera, the largest and most diverse order of all eukaryotes. Components of the innate immune system are hardly known in this insect, which is in a key phylogenetic position to inform us about genetic innovations accompanying the evolution of holometabolous insects. We have annotated immunity-related genes and compared them with homologous molecules from other species. RESULTS: Around 300 candidate defense proteins are identified based on sequence similarity to homologs known to participate in immune responses. In most cases, paralog counts are lower than those of Drosophila melanogaster or Anopheles gambiae but are substantially higher than Apis mellifera. The genome contains probable orthologs for nearly all members of the Toll, IMD, and JAK/STAT pathways. While total numbers of the clip-domain serine proteinases are approximately equal in the fly (29), mosquito (32) and beetle (30), lineage-specific expansion of the family is discovered in all three species. Sixteen of the thirty-one serpin genes form a large cluster in a 50 kb region resulted from extensive gene duplications. Among the nine Toll-like proteins, four are orthologous to Drosophila Toll. The presence of scavenger receptors and other related proteins indicates a role of cellular responses in the entire system. The structures of some antimicrobial peptides drastically differ from those in other orders of insects. CONCLUSIONS: A framework of information on Tribolium immunity is established, which may serve as a stepping stone for future genetic analyses of defense responses in a nondrosophiline genetic model insect.

  • 958.
    Ådén, Jörgen
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Wittung-Stafshede, Pernilla
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Folding of an unfolded protein by macromolecular crowding in vitro2014In: Biochemistry, ISSN 0006-2960, E-ISSN 1520-4995, Vol. 53, no 14, p. 2271-2277Article in journal (Refereed)
    Abstract [en]

    Protein folding in vivo takes place in a highly crowded environment. The resulting excluded volume forces are thought to stabilize folded forms of proteins. In agreement, many in vitro studies have shown that the presence of macromolecular crowding agents increases the stability of folded proteins but often by only a few kJ per mol. Although it should not matter at what position in the transition between folded and unfolded forms the effect of crowding is employed, there have been no studies assessing whether excluded volume forces alone can correctly fold polypeptides that are mostly unfolded. However, some studies have indicated that the effect of crowding becomes larger the more destabilized the protein is (but still being folded), suggesting that the crowding effect may be exaggerated for unfolded proteins. To address this question directly, we turned to a destabilized mutant of protein L that is mostly unfolded in water but can be folded upon addition of salt. We find that the effect of 200 mg/mL Dextran 20 on the folding equilibrium constant for unfolded protein L (ΔΔGU ≈ 2 kJ mol(-1)) matches the crowding effects found on the folded wild type protein and the mutant when prefolded by salt. This result indicates that the excluded volume effect is independent of starting protein stability and that crowding can shift the reaction toward the folded form when the polypeptide is in the transition region between folded and unfolded states.

  • 959.
    Åström, Stefan U
    et al.
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology).
    Byström, Anders S
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology).
    Rit1, a tRNA backbone-modifying enzyme that mediates initiator and elongator tRNA discrimination1994In: Cell, ISSN 0092-8674, E-ISSN 1097-4172, Vol. 79, no 3, p. 535-546Article in journal (Refereed)
    Abstract [en]

    Using a genetic screen in yeast aimed at identifying cellular factors involved in initiator and elongator methionine tRNA discrimination in the translational process, we have identified a mutation that abolish the requirement for elongator methionine tRNA. The gene affected, which we call the ribosylation of the initiator tRNA gene or RIT1, encodes a 2'-O-ribosyl phosphate transferase. This enzyme modifies exclusively the initiator tRNA in position 64 using 5'-phosphoribosyl-1'-pyrophosphate as the modification donor. As the initiator tRNA participates both in the initiation and elongation of translation in a rit1 strain, we conclude that the 2'-O-ribosyl phosphate modification discriminates the initiator tRNAs from the elongator tRNAs during protein synthesis. The modification enzyme was shown to recognize the stem-loop IV region that is unique in eukaryotic cytoplasmic initiator tRNAs.

  • 960. Ögren, Erling
    et al.
    Öquist, Gunnar
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Photoinhibition of photosynthesis in Lemna gibba as induced by the interaction between light and temperature. II. Photosynthetic electron transport1984In: Physiologia Plantarum: An International Journal for Plant Biology, ISSN 0031-9317, E-ISSN 1399-3054, Vol. 62, no 2, p. 187-192Article in journal (Refereed)
    Abstract [en]

    Photoinhibition of photosynthesis in Lemna gibba L. was induced by exposing intact plants to a high photosynthetic photon flux density of 1 750 μmol m−2 s−1 at a low temperature of 3°C. Subsequently isolated chloroplasts showed pronounced reductions in the capacity of whole chain electron transport, measured as Hill activity, and in the efficiency of electron transport to the primary electron acceptor Q of photosystem II, measured as variable chlorophyll fluorescence at 20°C. These changes proceeded with similar kinetics (probably of the first-order reaction), suggesting that the site of photoinhibition is in the electron transfer to Q. A partial uncoupling of the whole chain electron transport also occured. The capacity of electron transport mediated by photosystem I was unaffected. The extent of photoinhibition of photosynthetic electron transport, as produced by a 2 h exposure of L. gibba to three different combinations of photon flux density and temperature was studied. It was shown that intrinsically similar states of photoinhibition, on the evidence of their time courses of recovery, were induced by either a high photon flux density and 25°C or by a moderate photon flux density and 3°C.

  • 961. Ögren, Erling
    et al.
    Öquist, Gunnar
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Photoinhibition of photosynthesis in lemna-gibba as induced by the interaction between light and temperature .3. Chlorophyll fluorescence at 77-K1984In: Physiologia Plantarum: An International Journal for Plant Biology, ISSN 0031-9317, E-ISSN 1399-3054, Vol. 62, no 2, p. 193-200Article in journal (Refereed)
    Abstract [en]

    Photoinhibition in Lemna gibba L. was studied by interpreting chlorophyll fluorescence characteristics at 77 K on the basis of the bipartite model of Butler and co-workers (Butler 1978). Application of this analysis to chloroplasts (isolated from plants before and after exposure to a photosynthetic photon flux density of 1 750 μmol m−2 s−1 at 3°C for 2 h) revealed that photoinhibition had the following effect on primary events in photosynthesis. Firstly, the fluorescence of PS II increased (44%) in the state of open traps (Fo) and decreased (32%) in the state of closed traps (Fm). It is suggested, that the Fo-decrease reflects increased quenching by radiationless decay, both effects occurring at PS II reaction centers. Secondly, the rate constant for transfer of excitation energy from PS II to PS I (kT(μ→J)) increased by 34%. However, in the state of closed traps, the flux of excitation energy via this transfer process decreased, most likely because of increased quenching by radiationless decay at PS II reaction centers. Thirdly, the probability for fluorescence from PS I decreased (19%). This indicates increased quenching by radiationless decay.

  • 962.
    Önskog, Jenny
    et al.
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Freyhult, Eva
    Umeå University, Faculty of Medicine, Department of Clinical Microbiology, Clinical Bacteriology.
    Landfors, Mattias
    Umeå University, Faculty of Science and Technology, Department of Mathematics and Mathematical Statistics. Umeå University, Faculty of Medicine, Department of Clinical Microbiology, Clinical Bacteriology.
    Rydén, Patrik
    Umeå University, Faculty of Science and Technology, Department of Mathematics and Mathematical Statistics.
    Hvidsten, Torgeir R
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Classification of microarrays: synergistic effects between normalization, gene selection and machine learning2011In: BMC Bioinformatics, ISSN 1471-2105, E-ISSN 1471-2105, Vol. 12, no 1, article id 390Article in journal (Refereed)
    Abstract [en]

    BACKGROUND: Machine learning is a powerful approach for describing and predicting classes in microarray data. Although several comparative studies have investigated the relative performance of various machine learning methods, these often do not account for the fact that performance (e.g. error rate) is a result of a series of analysis steps of which the most important are data normalization, gene selection and machine learning.

    RESULTS: In this study, we used seven previously published cancer-related microarray data sets to compare the effects on classification performance of five normalization methods, three gene selection methods with 21 different numbers of selected genes and eight machine learning methods. Performance in term of error rate was rigorously estimated by repeatedly employing a double cross validation approach. Since performance varies greatly between data sets, we devised an analysis method that first compares methods within individual data sets and then visualizes the comparisons across data sets. We discovered both well performing individual methods and synergies between different methods.

    CONCLUSION: Support Vector Machines with a radial basis kernel, linear kernel or polynomial kernel of degree 2 all performed consistently well across data sets. We show that there is a synergistic relationship between these methods and gene selection based on the T-test and the selection of a relatively high number of genes. Also, we find that these methods benefit significantly from using normalized data, although it is hard to draw general conclusions about the relative performance of different normalization procedures.

  • 963.
    Öquist, Gunnar
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Effects of low temperature on photosynthesis1983In: Plant, Cell and Environment, ISSN 0140-7791, E-ISSN 1365-3040, Vol. 6, no 4, p. 281-300Article, review/survey (Refereed)
  • 964.
    Österberg, Sofia
    et al.
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology).
    del Peso-Santos, Teresa
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology).
    Shingler, Victoria
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology).
    Regulation of alternative sigma factor use2011In: Annual Review of Microbiology, ISSN 0066-4227, E-ISSN 1545-3251, Vol. 65, p. 37-55Article in journal (Refereed)
    Abstract [en]

    Alternative bacterial sigma factors bind the catalytic core RNA polymerase to confer promoter selectivity on the holoenzyme. The different holoenzymes are thus programmed to recognize the distinct promoter classes in the genome to allow coordinated activation of discrete sets of genes needed for adaptive responses. To form the holoenzymes, the different sigma factors must be available to compete for their common substrate (core RNA polymerase). This review highlights (a) the roles of antisigma factors in controlling the availability of alternative sigma factors and (b) the involvement of diverse regulatory molecules that promote the use of alternative sigma factors through subversion of the domineering housekeeping σ(70). The latter include the nucleotide alarmone ppGpp and small proteins (DksA, Rsd, and Crl), which directly target the transcriptional machinery to mediate their effects.

  • 965.
    Östman, J.
    et al.
    Umeå University, Faculty of Medicine, Department of Molecular Biology (Faculty of Medicine).
    Lundgren, E.
    Caspase independent cytotoxicity induced by oligomeric TTR- mutants in neuroblastoma cellsManuscript (Other academic)
  • 966.
    Överby Wernstedt, Anna
    et al.
    Umeå University, Faculty of Medicine, Department of Clinical Microbiology.
    Weber, Friedemann
    Hiding from intracellular pattern recognition receptors, a passive strategy of flavivirus immune evasion2011Conference paper (Refereed)
17181920 951 - 966 of 966
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