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  • 1.
    Aalto, Anders
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap.
    Biodiversity and habitat conditions in reaches with high flow velocity along gradients in hydrological and geomorphological alteration: A study of six rivers in Sweden2021Självständigt arbete på avancerad nivå (masterexamen), 20 poäng / 30 hpStudentuppsats (Examensarbete)
    Abstract [en]

    The vast majority of rivers in the developed world are affected by human alteration, which in turn negatively affects the species that rely on these highly diverse and species rich areas to survive. Homogenization of previously heterogenic areas due to a change in water discharge and the substrate availability in the rivers is often regarded as the main reason for the loss of species richness in rivers and the riparian zone. Because of this, there are a lot of restoration projects which main goal is to increase heterogeneity. The goal of this thesis is to compare hydrology and geomorphology variables between four types of reaches with high flow velocity (rapids in free-flowing reaches, rapids with regulated flow, impounded reaches and reaches in outlet channels below hydropower plants). In this thesis I wanted to find out how changes in geomorphology and hydrology affect fish species richness, riparian vegetation richness and aquatic vascular plants species richness. The result show that both fish species richness and riparian vegetation species richness are negatively affected by the changes in geomorphology and hydrology. There was no significant difference for aquatic vascular plants when comparing the regulation types. The most altered reach type, outlet channels, had significantly fewer fish species compared to the less altered reach type, impounded reaches. Outlet channels also had less riparian vegetation cover compared to all other regulation types, and fewer riparian vegetation species compared to both free-flowing reaches and impounded reaches. In conclusion, hydropower plants and timber floating have both negatively impacted the riverine ecosystem, and in turn caused a decrease in species richness for fish and riparian plants. The reaches studied in this thesis will continue to be altered and the species richness and species composition will change from an ecosystem that relied on the natural flow regime to an ecosystem more used to the flow regime created by the hydropower plants. 

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  • 2. Abafe, Ovokeroye A.
    et al.
    Späth, Jana
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Fick, Jerker
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Jansson, Stina
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Buckley, Chris
    Stark, Annegret
    Pietruschka, Bjoern
    Martincigh, Bice S.
    LC-MS/MS determination of antiretroviral drugs in influents and effluents from wastewater treatment plants in KwaZulu-Natal, South Africa2018Ingår i: Chemosphere, ISSN 0045-6535, E-ISSN 1879-1298, Vol. 200, s. 660-670Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    South Africa has the largest occurrence of the human immune deficiency virus (HIV) in the world but has also implemented the largest antiretroviral (ARV) treatment programme. It was therefore of interest to determine the presence and concentrations of commonly used antiretroviral drugs (ARVDs) and, also, to determine the capabilities of wastewater treatment plants (WWTPs) for removing ARVDs. To this end, a surrogate standard based LC-MS/MS method was optimized and applied for the detection of thirteen ARVDs used in the treatment and management of HIV/acquired immune deficiency syndrome (HIV/AIDS) in two major and one modular WWTP in the eThekwini Municipality in KwaZulu-Natal, South Africa. The method was validated and the detection limits fell within the range of 2–20 ng L−1. The analytical recoveries for the ARVDs were mainly greater than 50% with acceptable relative standard deviations. The concentration values ranged from <LOD – 53000 ng L−1 (influent), <LOD – 34000 ng L−1 (effluent) in a decentralized wastewater treatment facility (DEWATS); <LOD – 24000 ng L−1 (influent), <LOD – 33000 ng L−1 (effluent) in Northern WWTP and 61–34000 ng L−1 (influent), <LOD – 20000 ng L−1 (effluent) in Phoenix WWTP. Whilst abacavir, lamivudine and zidovudine were almost completely removed from the effluents, atazanavir, efavirenz, lopinavir and nevirapine persisted in the effluents from all three WWTPs. To estimate the ecotoxicological risks associated with the discharge of ARVDs, a countrywide survey focussing on the occurrence of ARVDs in WWTPs, surface and fresh water bodies, and aquatic organisms, is necessary.

  • 3. Abalaka, J. L.
    et al.
    Ottosson, Ulf
    Tende, Talatu
    Larson, Keith W.
    Rock Firefinch Lagonosticta sanguinodorsalis in the Mandara Mountains, north-east Nigeria: a new subspecies?2010Ingår i: African Bird Club Bulletin, ISSN 1352-481X, Vol. 17, nr 2, s. 210-211Artikel i tidskrift (Refereegranskat)
    Abstract [fr]

    L’Amarante des rochers Lagonosticta sanguinodorsalis dans les Monts Mandara, Nigeria du sud-est: une nouvelle sous-espèce ? Nous fournissons une description d’un mâle et d’une femelle, ainsi que desphotos d’un mâle, d’un amarante capturé dans les Monts Mandara, au nord-est du Nigeria. Le plumage et le cri de cet amarante sont identiques à ceux de l’Amarante des rochers Lagonosticta sanguinodorsalis, une espèce précédemment rapportée de la zone, excepté que le mâle n’a pas la couronne grise typique de l’espèce. Des travaux supplémentaires sur le terrain sont nécessaires pour déterminer s’il agit d’un individu aberrant ou d’une population de l’Amarante des rochers morphologiquement distincte.

  • 4. Abbasi, Arshad Mehmood
    et al.
    Khan, Mir Ajab
    Khan, Nadeem
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Shah, Munir H
    Ethnobotanical survey of medicinally important wild edible fruits species used by tribal communities of Lesser Himalayas-Pakistan2013Ingår i: Journal of Ethnopharmacology, ISSN 0378-8741, E-ISSN 1872-7573, Vol. 148, nr 2, s. 528-536Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Ethnopharmacological relevance: Present survey was conducted to explore ethnomedicinal uses and cultural importance of wild edible fruits species by the inhabitants of Lesser Himalayas-Pakistan. Materials and methods: Information was obtained through informed consent semi-structured interviews, questionnaires, market survey, focus group conversation, unceremonious dialogue and village walks with key informants. Cultural significance of each species was calculated based on use report by participants at each study site. Results: A total of 35 wild edible fruits belonging to 21 genera and 17 families were used for the treatment of various ailments and consumed. Rosaceae was found dominating family with (8 spp.), followed by Moraceae (6 spp.), Rhamnaceae (5 spp.), Palmae and Vitaceae (2 spp. each) and remaining families were represented by one species each. Fruits (48%) were found highly utilized plant parts, followed by leaves (34%), bark, flowers and seeds (4% each), branches, latex and roots (2% each). Water was used as a medium for preparation while milk, ghee, oil, egg and butter are used for application. Modes of preparation were fall into seven categories like fresh parts eaten raw (38%), powder (24%), decoction (20%), extract (12 %), paste (4%), juice and latex (2% each). Based on cultural important index (CI) Morus nigra was found most significant species within top ten fruit plants followed by Morus alba, Olea ferruginea, Berberis lycium, Pyrus pashia, Ficus carica, Ficus palmata, Ziziphus mauritiana, Diospyros lotus and Ziziphus nummularia. Conclusions: Traditional uses of wild edible plant depend mainly on socio-economic factors rather than climatic conditions or wealth of flora. Use reports and citation demonstrated that there is a common cultural heritage regarding the gathered food plants. Further investigation is required for Antioxidant study, essential and toxic components, pharmacological applications; dietary requirements and biotechnological techniques to improve yields.

    (C) 2013 Elsevier Ireland Ltd. All rights reserved.

  • 5.
    Abdel-Shafi, Seham
    et al.
    Botany and Microbiology Department, Faculty of Science, Zagazig University, Zagazig, Egypt.
    El-Nemr, Mona
    Botany and Microbiology Department, Faculty of Science, Zagazig University, Zagazig, Egypt.
    Enan, Gamal
    Botany and Microbiology Department, Faculty of Science, Zagazig University, Zagazig, Egypt.
    Osman, Ali
    Biochemistry Department, Faculty of Agriculture, Zagazig University, Zagazig, Egypt.
    Sitohy, Basel
    Umeå universitet, Medicinska fakulteten, Institutionen för klinisk mikrobiologi. Umeå universitet, Medicinska fakulteten, Institutionen för strålningsvetenskaper, Onkologi.
    Sitohy, Mahmoud
    Biochemistry Department, Faculty of Agriculture, Zagazig University, Zagazig, Egypt.
    Isolation and characterization of antibacterial conglutinins from Lupine seeds2023Ingår i: Molecules, ISSN 1431-5157, E-ISSN 1420-3049, Vol. 28, nr 1, artikel-id 35Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The main target of this work is to discover new protein fractions from natural resources with high antibacterial action. The 7S and 11S globulin fractions, as well as the basic subunit (BS), were isolated from lupine seeds (Lupinus termis), chemically characterized, and screened for antibacterial activity against seven pathogenic bacteria. SDS-PAGE revealed molecular weights ranging from 55 to 75 kDa for 7S globulin, 20–37 kD for 11S globulin, and 20 kD for the BS. 11S globulin and the BS migrated faster on Urea-PAGE toward the cathode compared to 7S globulin. FTIR and NMR showed different spectral patterns between the 7S and 11S globulins but similar ones between 11S globulin and the BS. The MICs of the BS were in the range of 0.05–2 μg/mL against Listeria monocytogenes, Klebsiella oxytoca, Proteus mirabilis, Staphylococcus aureus, Listeria ivanovii, Salmonella typhimurium, and Pseudomonas aeruginosa compared to higher values for 11S globulin. The BS surpassed 11S globulin in antibacterial action, while 7S globulin showed no effect. The MICs of 11S globulin and the BS represented only 5% and 2.5% of the specific antibiotic against L. monocytogenes, respectively. Scanning electron microscopy (SEM) demonstrated different signs of cellular deformation and decay in the protein-treated bacteria, probably due to interaction with the bacterial cell wall and membranes. 11S globulin and the BS can be nominated as effective food biopreservatives.

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  • 6. Abeli, Thomas
    et al.
    Orsenigo, Simone
    Guzzon, Filippo
    Fae, Matteo
    Balestrazzi, Alma
    Carlsson-Graner, Ulla
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap.
    Mueller, Jonas V.
    Mondoni, Andrea
    Geographical pattern in the response of the arctic-alpine Silene suecica (Cariophyllaceae) to the interaction between water availability and photoperiod2015Ingår i: Ecological research, ISSN 0912-3814, E-ISSN 1440-1703, Vol. 30, nr 2, s. 327-335Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We hypothesized a geographical pattern of the plant performance (seedling development, biomass production, relative water content and chlorophyll content) as a result of response to the interaction between photoperiod and water availability in populations of the arctic-alpine Silene suecica from different latitudes, thus experiencing different photoperiods during the growing season. Particularly, we expected a lower drought sensitivity in northern compared to southern populations as a consequence of harsher conditions experienced by the northern populations in terms of water availability. The experiment was carried out under common garden conditions, manipulating the water availability (wet and dry) and the photoperiod (21 and 16 h). We found an interaction between photoperiod and water availability on plant height, leaves, growth, biomass and total chlorophyll. However, the photoperiod neither counteracted nor intensified the effect of drought. Plants exposed to drought compensated for decreasing water availability by reducing their shoot growth. Changes in the chlorophyll content and chlorophyll a/b ratio were observed. Northern populations showed a higher basal growth performance and a greater response to the changed water regime (from wet to dry) than the southern populations. Southern populations showed a reduced ability to respond to drought, but their low basal performance may be advantageous under low water availability, avoiding water loss. In contrast, northern populations showed a stronger plastic response that limited the negative effects of reduced water availability. This study highlights the possibility that the plant response to environmental constraints (specifically water availability) may follow a geographical pattern.

  • 7.
    Abidine, Yara
    et al.
    Umeå universitet, Medicinska fakulteten, Institutionen för klinisk mikrobiologi. Umeå universitet, Medicinska fakulteten, Wallenberg centrum för molekylär medicin vid Umeå universitet (WCMM).
    Liu, Lifeng
    Umeå universitet, Medicinska fakulteten, Institutionen för klinisk mikrobiologi. Umeå universitet, Medicinska fakulteten, Wallenberg centrum för molekylär medicin vid Umeå universitet (WCMM).
    Wallén, Oskar
    Umeå universitet, Medicinska fakulteten, Institutionen för klinisk mikrobiologi.
    Trybala, Edward
    Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden.
    Olofsson, Sigvard
    Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden.
    Bergström, Tomas
    Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden.
    Bally, Marta
    Umeå universitet, Medicinska fakulteten, Institutionen för klinisk mikrobiologi. Umeå universitet, Medicinska fakulteten, Wallenberg centrum för molekylär medicin vid Umeå universitet (WCMM).
    Cellular Chondroitin Sulfate and the Mucin-like Domain of Viral Glycoprotein C Promote Diffusion of Herpes Simplex Virus 1 While Heparan Sulfate Restricts Mobility2022Ingår i: Viruses, E-ISSN 1999-4915, Vol. 14, nr 8, artikel-id 1836Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The diffusion of viruses at the cell membrane is essential to reach a suitable entry site and initiate subsequent internalization. Although many viruses take advantage of glycosaminoglycans (GAG) to bind to the cell surface, little is known about the dynamics of the virus–GAG interactions. Here, single-particle tracking of the initial interaction of individual herpes simplex virus 1 (HSV-1) virions reveals a heterogeneous diffusive behavior, regulated by cell-surface GAGs with two main diffusion types: confined and normal free. This study reports that different GAGs can have competing influences in mediating diffusion on the cells used here: chondroitin sulfate (CS) enhances free diffusion but hinders virus attachment to cell surfaces, while heparan sulfate (HS) promotes virus confinement and increases entry efficiency. In addition, the role that the viral mucin-like domains (MLD) of the HSV-1 glycoprotein C plays in facilitating the diffusion of the virus and accelerating virus penetration into cells is demonstrated. Together, our results shed new light on the mechanisms of GAG-regulated virus diffusion at the cell surface for optimal internalization. These findings may be extendable to other GAG-binding viruses.

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  • 8. Abraham, Edit
    et al.
    Miskolczi, Pal
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Ayaydin, Ferhan
    Yu, Ping
    Kotogany, Edit
    Bako, Laszlo
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Oetvoes, Krisztina
    Horvath, Gabor V.
    Dudits, Denes
    Immunodetection of retinoblastoma-related protein and its phosphorylated form in interphase and mitotic alfalfa cells2011Ingår i: Journal of Experimental Botany, ISSN 0022-0957, E-ISSN 1460-2431, Vol. 62, nr 6, s. 2155-2168Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Plant retinoblastoma-related (RBR) proteins are primarily considered as key regulators of G(1)/S phase transition, with functional roles in a variety of cellular events during plant growth and organ development. Polyclonal antibody against the C-terminal region of the Arabidopsis RBR1 protein also specifically recognizes the alfalfa 115 kDa MsRBR protein, as shown by the antigen competition assay. The MsRBR protein was detected in all cell cycle phases, with a moderate increase in samples representing G(2)/M cells. Antibody against the human phospho-pRb peptide (Ser807/811) cross-reacted with the same 115 kDa MsRBR protein and with the in vitro phosphorylated MsRBR protein C-terminal fragment. Phospho-MsRBR protein was low in G(1) cells. Its amount increased upon entry into the S phase and remained high during the G(2)/M phases. Roscovitine treatment abolished the activity of alfalfa MsCDKA1;1 and MsCDKB2;1, and the phospho-MsRBR protein level was significantly decreased in the treated cells. Colchicine block increased the detected levels of both forms of MsRBR protein. Reduced levels of the MsRBR protein in cells at stationary phase or grown in hormone-free medium can be a sign of the division-dependent presence of plant RBR proteins. Immunolocalization of the phospho-MsRBR protein indicated spots of variable number and size in the labelled interphase nuclei and high signal intensity of nuclear granules in prophase. Structures similar to phospho-MsRBR proteins cannot be recognized in later mitotic phases. Based on the presented western blot and immunolocalization data, the possible involvement of RBR proteins in G(2)/M phase regulation in plant cells is discussed.

  • 9.
    Abreu, Clare I.
    et al.
    Physics of Living Systems, Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Biology, Stanford University, Stanford, CA, USA.
    Bello, Martina Dal
    Physics of Living Systems, Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA.
    Bunse, Carina
    Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden.
    Pinhassi, Jarone
    Centre for Ecology and Evolution of Microbial Model Systems, Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden.
    Gore, Jeff
    Physics of Living Systems, Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA.
    Warmer temperatures favor slower-growing bacteria in natural marine communities2023Ingår i: Science Advances, E-ISSN 2375-2548, Vol. 9, nr 19, artikel-id eade8352Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Earth’s life-sustaining oceans harbor diverse bacterial communities that display varying composition across time and space. While particular patterns of variation have been linked to a range of factors, unifying rules are lacking, preventing the prediction of future changes. Here, analyzing the distribution of fast- and slow-growing bacteria in ocean datasets spanning seasons, latitude, and depth, we show that higher seawater temperatures universally favor slower-growing taxa, in agreement with theoretical predictions of how temperature-dependent growth rates differentially modulate the impact of mortality on species abundances. Changes in bacterial community structure promoted by temperature are independent of variations in nutrients along spatial and temporal gradients. Our results help explain why slow growers dominate at the ocean surface, during summer, and near the tropics and provide a framework to understand how bacterial communities will change in a warmer world.

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  • 10. Abreu, Ilka N.
    et al.
    Aksmann, Anna
    Bajhaiya, Amit K.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen. Algal Biotechnology Lab, Department of Microbiology, School of Life Sciences, Central University of Tamil Nadu, Thiruvarur, Tamil Nadu, India.
    Benlloch, Reyes
    Giordano, Mario
    Pokora, Wojciech
    Selstam, Eva
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Moritz, Thomas
    Changes in lipid and carotenoid metabolism in Chlamydomonas reinhardtii during induction of CO2-concentrating mechanism: Cellular response to low CO2 stress2020Ingår i: Algal Research, ISSN 2211-9264, Vol. 52, artikel-id 102099Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Photosynthetic organisms strictly depend on CO2 availability and the CO2:O2 ratio, as both CO2/O2 compete for catalytic site of Rubisco. Green alga Chlamydomonas reinhardtii, can overcome CO2 shortage by inducing CO2-concentrating mechanism (CCM). Cells transferred to low-CO2 are subjected to light-driven oxidative stress due to decrease in the electron sink. Response to environmental perturbations is mediated to some extent by changes in the lipid and carotenoid metabolism. We thus hypothesize that when cells are challenged with changes in CO2 availability, changes in the lipidome and carotenoids profile occur. These changes expected to be transient, when CCM is activated, CO2 limitation will be substantially ameliorated. In our experiments, cells were transferred from high (5%) to low (air equilibrium) CO2. qPCR analysis of genes related to CCM and lipid metabolism was carried out. Lipidome was analyzed both in whole cells and in isolated lipid droplets. We characterized the changes in polar lipids, fatty acids and ketocarotenoids. In general, polar lipids significantly and transiently increased in lipid droplets during CCM. Similar pattern was observed for xanthophylls, ketocarotenoids and their esters. The data supports our hypothesis about the roles of lipids and carotenoids in tackling the oxidative stress associated with acclimation to sub-saturating CO2.

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  • 11. Abreu, Ilka N.
    et al.
    Johansson, Annika I.
    Sokolowska, Katarzyna
    Niittylä, Totte
    Sundberg, Björn
    Hvidsten, Torgeir R.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC). Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway.
    Street, Nathaniel R.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Moritz, Thomas
    A metabolite roadmap of the wood-forming tissue in Populus tremula2020Ingår i: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 228, nr 5, s. 1559-1572Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Wood, or secondary xylem, is the product of xylogenesis, a developmental process that begins with the proliferation of cambial derivatives and ends with mature xylem fibers and vessels with lignified secondary cell walls. Fully mature xylem has undergone a series of cellular processes, including cell division, cell expansion, secondary wall formation, lignification and programmed cell death. A complex network of interactions between transcriptional regulators and signal transduction pathways controls wood formation. However, the role of metabolites during this developmental process has not been comprehensively characterized. To evaluate the role of metabolites during wood formation, we performed a high spatial resolution metabolomics study of the wood-forming zone of Populus tremula, including laser dissected aspen ray and fiber cells. We show that metabolites show specific patterns within the wood-forming zone, following the differentiation process from cell division to cell death. The data from profiled laser dissected aspen ray and fiber cells suggests that these two cell types host distinctly different metabolic processes. Furthermore, by integrating previously published transcriptomic and proteomic profiles generated from the same trees, we provide an integrative picture of molecular processes, for example, deamination of phenylalanine during lignification is of critical importance for nitrogen metabolism during wood formation.

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  • 12.
    Abreu, Ilka Nacif
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC). Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    Ahnlund, Maria
    Moritz, Thomas
    Albrectsen, Benedicte R.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    UHPLC-ESI/TOFMS Determination of Salicylate-like Phenolic Gycosides in Populus tremula Leaves2011Ingår i: Journal of Chemical Ecology, ISSN 0098-0331, E-ISSN 1573-1561, Vol. 37, nr 8, s. 857-70Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Associations of salicylate-like phenolic glycosides (PGs) with biological activity have been reported in Salix and Populus trees, but only for a few compounds, and in relation to a limited number of herbivores. By considering the full diversity of PGs, we may improve our ability to recognize genotypes or chemotype groups and enhance our understanding of their ecological function. Here, we present a fast and efficient general method for salicylate determination in leaves of Eurasian aspen that uses ultra-high performance liquid chromatography-electrospray ionization/time-of-flight mass spectrometry (UHPLC-ESI/TOFMS). The time required for the liquid chromatography separations was 13.5 min per sample, compared to around 60 min per sample for most HPLC protocols. In leaf samples from identical P. tremula genotypes with diverse propagation and treatment histories, we identified nine PGs. We found the compound-specific mass chromatograms to be more informative than the UV-visible chromatograms for compound identification and when quantitating samples with large variability in PG content. Signature compounds previously reported for P. tremoloides (tremulacin, tremuloidin, salicin, and salicortin) always were present, and five PGs (2'-O-cinnamoyl-salicortin, 2'-O-acetyl-salicortin, 2'-O-acetyl-salicin, acetyl-tremulacin, and salicyloyl-salicin) were detected for the first time in P. tremula. By using information about the formic acid adduct that appeared for PGs in the LTQ-Orbitrap MS environment, novel compounds like acetyl-tremulacin could be tentatively identified without the use of standards. The novel PGs were consistently either present in genotypes regardless of propagation and damage treatment or were not detectable. In some genotypes, concentrations of 2'-O-acetyl-salicortin and 2'-O-cinnamoyl-salicortin were similar to levels of biologically active PGs in other Salicaceous trees. Our study suggests that we may expect a wide variation in PG content in aspen populations which is of interest both for studies of interactions with herbivores and for mapping population structure.

  • 13. Achouiti, Ahmed
    et al.
    Vogl, Thomas
    Urban, Constantin F
    Umeå universitet, Medicinska fakulteten, Institutionen för klinisk mikrobiologi, Klinisk bakteriologi. Umeå universitet, Medicinska fakulteten, Molekylär Infektionsmedicin, Sverige (MIMS).
    Röhm, Marc
    Umeå universitet, Medicinska fakulteten, Molekylär Infektionsmedicin, Sverige (MIMS). Umeå universitet, Medicinska fakulteten, Institutionen för klinisk mikrobiologi, Klinisk bakteriologi.
    Hommes, Tijmen J
    van Zoelen, Marieke AD
    Florquin, Sandrine
    Roth, Johannes
    van't Veer, Cornelis
    de Vos, Alex F
    van der Poll, Tom
    Myeloid-related protein-14 contributes to protective immunity in gram-negative pneumonia derived sepsis2012Ingår i: PLoS Pathogens, ISSN 1553-7374, Vol. 8, nr 10, s. e1002987-Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Klebsiella (K.) pneumoniae is a common cause of pneumonia-derived sepsis. Myeloid related protein 8 (MRP8, S100A8) and MRP14 (S100A9) are the most abundant cytoplasmic proteins in neutrophils. They can form MRP8/14 heterodimers that are released upon cell stress stimuli. MRP8/14 reportedly exerts antimicrobial activity, but in acute fulminant sepsis models MRP8/14 has been found to contribute to organ damage and death. We here determined the role of MRP8/14 in K. pneumoniae sepsis originating from the lungs, using an established model characterized by gradual growth of bacteria with subsequent dissemination. Infection resulted in gradually increasing MRP8/14 levels in lungs and plasma. Mrp14 deficient (mrp14(-/-)) mice, unable to form MRP8/14 heterodimers, showed enhanced bacterial dissemination accompanied by increased organ damage and a reduced survival. Mrp14(-/-) macrophages were reduced in their capacity to phagocytose Klebsiella. In addition, recombinant MRP8/14 heterodimers, but not MRP8 or MRP14 alone, prevented growth of Klebsiella in vitro through chelation of divalent cations. Neutrophil extracellular traps (NETs) prepared from wildtype but not from mrp14(-/-) neutrophils inhibited Klebsiella growth; in accordance, the capacity of human NETs to kill Klebsiella was strongly impaired by an anti-MRP14 antibody or the addition of zinc. These results identify MRP8/14 as key player in protective innate immunity during Klebsiella pneumonia.

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  • 14.
    Achour, Cyrinne
    Umeå universitet, Medicinska fakulteten, Institutionen för molekylärbiologi (Medicinska fakulteten). Umeå universitet, Medicinska fakulteten, Wallenberg centrum för molekylär medicin vid Umeå universitet (WCMM).
    Canonical and non-canonical functions of METTL3 in breast cancer2022Doktorsavhandling, sammanläggning (Övrigt vetenskapligt)
    Abstract [en]

    Gene expression is spatially and temporally regulated at multiple levels. N6-methyladenosine (m6A) is the most prevalent internal modification in messenger RNA (mRNA) and long noncoding RNA (lncRNAs). m6A plays important roles in multiple cellular processes including stem cell pluripotency, adipogenesis, spermatogenesis, neurogenesis, circadian rhythm and development by modulating RNA splicing, export, stability, degradation and translation. Although aberrant m6A methylation has been reported in various types of cancer, the underlying molecular functions of METTL3, the solely catalytic subunit of the m6A-methylase complex, has yet to be defined.

    m6A has been recently identified in nascent pre-mRNA, and more specifically intronic m6A has been linked to exon skipping events. The occurrence of impaired alternative splicing (AS) is frequently found during the development of cancer. We performed transcriptome wide analysis in breast cancer cell lines and explored AS events. Our results define an AS signature for breast tumorigenesis. We found that METTL3 modulates AS directly through m6A deposition at the intron-exon junctions or indirectly by the m6A deposition in transcripts encoding for splicing factors and transcription factors. In particular, we show that MYC mRNA harbours the m6A mark, suggesting that METTL3 regulates AS indirectly via the regulation of MYC expression. Indeed, the targets of MYC overlapped with METTL3-associated AS events. Importantly, five of the AS events identified and validated in vitro, are linked to a worse prognosis in breast cancer patients. Additionally, we show that METTL3 enhances the breast cancer phenotype through a dual mechanism depending on its sub-cellular localization. We find that the canonical nuclear function of METTL3 decorates transcripts that are involved in cell proliferation and migration. We observe that METTL3 is highly expressed in the cytoplasmic compartment of breast cancer cells from patients. Remarkably, we uncover that the cytoplasmic METTL3 interacts with subunits of the exocyst, whose subunit EXOC7 has been linked to cell adhesion, migration and invasion. Notably, we show that breast cancer cell lines depleted of METTL3 display less gelatinase activity and invadopodia formation, supporting the role of METTL3 in cell invasion via exocytosis.

    m6A is a reversible modification, which can be demethylated by the erasers FTO and ALKBH5. Depletion of FTO has been shown to increase the level of m6A in mRNA, however recent studies have reported that FTO could demethylate N6,2´-O-dimethyladenosine (m6Am), adjacent to the 7-methylguanosine cap on mRNA. In the cellular model of colorectal cancer CRC1, depletion of FTO leads to a cancer stem cell phenotype and confers chemotherapy resistance. By performing m6A-RNA immunoprecipitation followed by sequencing (MeRIP), we show that knockdown of FTO in CRC1 cells does not affect the global level of m6A in mRNA but of m6Am level.

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    Publikationen är tillgänglig i fulltext från 2024-12-13 07:00
  • 15.
    Achour, Cyrinne
    et al.
    Umeå universitet, Medicinska fakulteten, Institutionen för molekylärbiologi (Medicinska fakulteten). Umeå universitet, Medicinska fakulteten, Wallenberg centrum för molekylär medicin vid Umeå universitet (WCMM).
    Bhattarai, Devi Prasad
    Umeå universitet, Medicinska fakulteten, Institutionen för molekylärbiologi (Medicinska fakulteten).
    Esteva-Socias, Margalida
    Umeå universitet, Medicinska fakulteten, Institutionen för molekylärbiologi (Medicinska fakulteten).
    Rodriguez-Barrueco, Ruth
    Malla, Sandhya
    Umeå universitet, Medicinska fakulteten, Institutionen för molekylärbiologi (Medicinska fakulteten). Umeå universitet, Medicinska fakulteten, Wallenberg centrum för molekylär medicin vid Umeå universitet (WCMM).
    Seier, Kerstin
    Umeå universitet, Medicinska fakulteten, Institutionen för klinisk mikrobiologi. Umeå universitet, Medicinska fakulteten, Wallenberg centrum för molekylär medicin vid Umeå universitet (WCMM).
    Marchand, Virginie
    Motorine, Yuri
    Lundin, Eva
    Umeå universitet, Medicinska fakulteten, Institutionen för medicinsk biovetenskap.
    Gilthorpe, Jonathan D.
    Umeå universitet, Medicinska fakulteten, Institutionen för integrativ medicinsk biologi (IMB).
    Marzese, Diego Matias
    Bally, Marta
    Umeå universitet, Medicinska fakulteten, Institutionen för klinisk mikrobiologi. Umeå universitet, Medicinska fakulteten, Wallenberg centrum för molekylär medicin vid Umeå universitet (WCMM).
    Roman, Angel-Carlos
    Pich, Andreas
    Aguilo, Francesca
    Reshaping the role of METTL3 in breast tumorigenesisManuskript (preprint) (Övrigt vetenskapligt)
  • 16.
    Achour, Cyrinne
    et al.
    Umeå universitet, Medicinska fakulteten, Institutionen för molekylärbiologi (Medicinska fakulteten). Umeå universitet, Medicinska fakulteten, Wallenberg centrum för molekylär medicin vid Umeå universitet (WCMM).
    Bhattarai, Devi Prasad
    Umeå universitet, Medicinska fakulteten, Institutionen för molekylärbiologi (Medicinska fakulteten). Umeå universitet, Medicinska fakulteten, Wallenberg centrum för molekylär medicin vid Umeå universitet (WCMM).
    Groza, Paula
    Umeå universitet, Medicinska fakulteten, Institutionen för molekylärbiologi (Medicinska fakulteten). Umeå universitet, Medicinska fakulteten, Wallenberg centrum för molekylär medicin vid Umeå universitet (WCMM).
    Roman, Ángel-Carlos
    Department of Molecular Biology and Genetics, University of Extremadura, Badajoz, Spain.
    Aguilo, Francesca
    Umeå universitet, Medicinska fakulteten, Institutionen för molekylärbiologi (Medicinska fakulteten). Umeå universitet, Medicinska fakulteten, Wallenberg centrum för molekylär medicin vid Umeå universitet (WCMM).
    METTL3 regulates breast cancer-associated alternative splicing switches2023Ingår i: Oncogene, ISSN 0950-9232, E-ISSN 1476-5594, Vol. 42, s. 911-925Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Alternative splicing (AS) enables differential inclusion of exons from a given transcript, thereby contributing to the transcriptome and proteome diversity. Aberrant AS patterns play major roles in the development of different pathologies, including breast cancer. N6-methyladenosine (m6A), the most abundant internal modification of eukaryotic mRNA, influences tumor progression and metastasis of breast cancer, and it has been recently linked to AS regulation. Here, we identify a specific AS signature associated with breast tumorigenesis in vitro. We characterize for the first time the role of METTL3 in modulating breast cancer-associated AS programs, expanding the role of the m6A-methyltransferase in tumorigenesis. Specifically, we find that both m6A deposition in splice site boundaries and in splicing and transcription factor transcripts, such as MYC, direct AS switches of specific breast cancer-associated transcripts. Finally, we show that five of the AS events validated in vitro are associated with a poor overall survival rate for patients with breast cancer, suggesting the use of these AS events as a novel potential prognostic biomarker.

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  • 17. Adeleke, Rasheed
    et al.
    Bello-Akinosho, Maryam
    Maila, Mphekgo
    Lee, Natuschka
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap. Lehrstuhl für Mikrobiologie, Technische Universität München.
    Roles of extremophiles in bioremediation of polycyclic aromatic hydrocarbon contaminated soil environment2020Ingår i: Biotechnological applications of extremophilic microorganisms / [ed] Natuschka M. Lee, Walter de Gruyter, 2020, s. 197-230Kapitel i bok, del av antologi (Refereegranskat)
  • 18.
    Adhikari, Deepak
    Umeå universitet, Medicinska fakulteten, Institutionen för medicinsk kemi och biofysik.
    Signaling pathways in the development of female germ cells2014Doktorsavhandling, sammanläggning (Övrigt vetenskapligt)
    Abstract [en]

    Primordial follicles are the first small follicles to appear in the mammalian ovary. Women are born with a fixed number of primordial follicles in the ovaries. Once formed, the pool of primordial follicles serves as a source of developing follicles and oocytes. The first aim of this thesis was to investigate the functional role of the intra-oocyte signaling pathways, especially the phosphatidylinositol-3 kinase (PI3K) and mammalian target of rapamycin complex 1 (mTORC1) pathways in the regulation of primordial follicle activation and survival. We found that a primordial follicle remains dormant when the PI3K and mTORC1 signaling in its oocyte is activated to an appropriate level, which is just sufficient to maintain its survival, but not sufficient for its growth initiation. Hyperactivation of either of these signaling pathways causes global activation of the entire pool of primordial follicles leading to the exhaustion of all the follicles in young adulthood in mice. Mammalian oocytes, while growing within the follicles, remain arrested at prophase I of meiosis. Oocytes within the fully-grown antral follicles resume meiosis upon a preovulatory surge of leutinizing hormone (LH), which indicates that LH mediates the resumption of meiosis. The prophase I arrest in the follicle-enclosed oocyte is the result of low maturation promoting factor (MPF) activity, and resumption of meiosis upon the arrival of hormonal signals is mediated by activation of MPF. MPF is a complex of cyclin dependent kinase 1 (Cdk1) and cyclin B1, which is essential and sufficient for entry into mitosis. Although much of the mitotic cell cycle machinery is shared during meiosis, lack of Cdk2  in mice leads to a postnatal loss of all oocytes, indicating that Cdk2 is important for oocyte survival, and probably oocyte meiosis also. There have been conflicting results earlier about the role of Cdk2 in metaphase II arrest of Xenopus  oocytes. Thus the second aim of the thesis was to identify the specific Cdk that is essential for mouse oocyte meiotic maturation. We generated mouse models with oocytespecific deletion of Cdk1  or Cdk2  and studied the specific requirements of Cdk1 and Cdk2 during resumption of oocyte meiosis. We found that only Cdk1 is essential and sufficient for the oocyte meiotic maturation. Cdk1 does not only phosphorylate the meiotic phosphoproteins during meiosis resumption but also phosphorylates and suppresses the downstream protein phosphatase 1, which is essential for protecting the Cdk1 substrates from dephosphorylation.

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    Thesis-Deepak Adhikari
  • 19.
    Adhikari, Deepak
    et al.
    Umeå universitet, Medicinska fakulteten, Institutionen för medicinsk kemi och biofysik.
    Flohr, Gilian
    Hogeschool Leiden, Zernikedreef 11,2333 CK Leiden, The Netherlands.
    Gorre, Nagaraju
    Umeå universitet, Medicinska fakulteten, Institutionen för medicinsk kemi och biofysik.
    Shen, Yan
    Umeå universitet, Medicinska fakulteten, Institutionen för medicinsk kemi och biofysik.
    Yang, Hairu
    Umeå universitet, Medicinska fakulteten, Institutionen för medicinsk kemi och biofysik.
    Lundin, Eva
    Umeå universitet, Medicinska fakulteten, Institutionen för medicinsk biovetenskap, Patologi.
    Lan, Zijian
    University of Louisville Health Sciences Center, Louisville, Kentucky, USA.
    Liu, Kui
    Umeå universitet, Medicinska fakulteten, Institutionen för medicinsk kemi och biofysik.
    Disruption of Tsc2 in oocytes leads to overactivation of the entire pool of primordial follicles2009Ingår i: Molecular human reproduction, ISSN 1360-9947, E-ISSN 1460-2407, Vol. 15, nr 12, s. 765-770Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    To maintain the length of reproductive life in a woman, it is essential that most of her ovarian primordial follicles are maintained in a quiescent state to provide a continuous supply of oocytes. However, our understanding of the molecular mechanisms that control the quiescence and activation of primordial follicles is still in its infancy. In this study, we provide some genetic evidence to show that the tumor suppressor tuberous sclerosis complex 2 (Tsc2), which negatively regulates mammalian target of rapamycin complex 1 (mTORC1), functions in oocytes to maintain the dormancy of primordial follicles. In mutant mice lacking the Tsc2 gene in oocytes, the pool of primordial follicles is activated prematurely due to elevated mTORC1 activity in oocytes. This results in depletion of follicles in early adulthood, causing premature ovarian failure (POF). Our results suggest that the Tsc1-Tsc2 complex mediated suppression of mTORC1 activity is indispensable for maintenance of the dormancy of primordial follicles, thus preserving the follicular pool, and that mTORC1 activity in oocytes promotes follicular activation. Our results also indicate that deregulation of Tsc/mTOR signaling in oocytes may cause pathological conditions of the ovary such as infertility and POF.

  • 20.
    Adhikari, Deepak
    et al.
    Umeå universitet, Medicinska fakulteten, Institutionen för medicinsk kemi och biofysik.
    Liu, Kui
    Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden.
    Regulation of quiescence and activation of oocyte growth in primordial follicles2013Ingår i: Oogenesis / [ed] Giovanni Coticchio; David F. Albertini; Lucia De Santis, London: Springer, 2013, 1, s. 49-62Kapitel i bok, del av antologi (Refereegranskat)
    Abstract [en]

    Once formed, the pool of dormant primordial follicles serves as the source of developing follicles and fertilizable ova for the duration of a female’s reproductive life. Depending upon the species, primordial follicles can remain quiescent for months, years, or even decades, and the highly regulated process of primordial follicle activation ensures the availability of growing follicles throughout the reproductive period. We have recently begun to elucidate the molecular mechanisms underlying the maintenance of follicular quiescence and the activation of primordial follicles, mainly through the use of genetically modified mouse models. Both overactivation as well as the failure of activation of primordial follicles can lead to pathological conditions such as premature ovarian failure (POF) in the experimental models. A thorough understanding of the underlying mechanisms that regulate quiescence and activation of oocyte growth in primordial follicles will have important biological and clinical implications.

  • 21. Adkar-Purushothama, Charith Raj
    et al.
    Bolduc, Francois
    Bru, Pierrick
    RNA Group/Groupe ARN, Département de Biochimie, Faculté de Médecine des Sciences de la Santé, Pavillon de Recherche Appliquée au Cancer, Université de Sherbrooke, Sherbrooke, QC, Canada; Present address: Institutionen för Fysiologisk Botanik, Umeå Plant Science Centre, Umeå University, Umeå, Sweden.
    Perreault, Jean-Pierre
    Insights Into Potato Spindle Tuber Viroid Quasi-Species From Infection to Disease2020Ingår i: Frontiers in Microbiology, E-ISSN 1664-302X, Vol. 11, artikel-id 1235Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Viroids are non-coding RNA plant pathogens that are characterized by their possession of a high mutation level. Although the sequence heterogeneity in viroid infected plants is well understood, shifts in viroid population dynamics due to mutations over the course of infection remain poorly understood. In this study, the ten most abundant sequence variants of potato spindle tuber viroid RG1 (PSTVd) expressed at different time intervals in PSTVd infected tomato plants were identified by high-throughput sequencing. The sequence variants, forming a quasi-species, were subjected to both the identification of the regions favoring mutations and the effect of the mutations on viroid secondary structure and viroid derived small RNAs (vd-sRNA). At week 1 of PSTVd infection, 25% of the sequence variants were similar to the "master" sequence (i.e., the sequence used for inoculation). The frequency of the master sequence within the population increased to 70% at week 2 after PSTVd infection, and then stabilized for the rest of the disease cycle (i.e., weeks 3 and 4). While some sequence variants were abundant at week 1 after PSTVd infection, they tended to decrease in frequency over time. For example, the variants with insertions at positions 253 or 254, positions that could affect the Loop E as well as the metastable hairpin I structure that has been shown important during replication and viroid infectivity, resulted in decreased frequency. Data obtained byin silicoanalysis of the viroid derived small RNAs (vd-sRNA) was also analyzed. A few mutants had the potential of positively affecting the viroid's accumulation by inducing the RNA silencing of the host's defense related genes. Variants with mutations that could negatively affect viroid abundance were also identified because their derived vd-sRNA were no longer capable of targeting any host mRNA or of changing its target sequence from a host defense gene to some other non-important host gene. Together, these findings open avenues into understanding the biological role of sequence variants, this viroid's interaction with host components, stable and metastable structures generated by mutants during the course of infection, and the influence of sequence variants on stabilizing viroid population dynamics.

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  • 22. Aeinehband, Shahin
    et al.
    Brenner, Philip
    Stahl, Sara
    Bhat, Maria
    Fidock, Mark D.
    Khademi, Mohsen
    Olsson, Tomas
    Engberg, Goran
    Jokinen, Jussi
    Umeå universitet, Medicinska fakulteten, Institutionen för klinisk vetenskap, Psykiatri.
    Erhardt, Sophie
    Piehl, Fredrik
    Cerebrospinal fluid kynurenines in multiple sclerosis: relation to disease course and neurocognitive symptoms2016Ingår i: Brain, behavior, and immunity, ISSN 0889-1591, E-ISSN 1090-2139, Vol. 51, s. 47-55Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Multiple sclerosis (MS) is a chronic inflammatory and neurodegenerative disease of the central nervous system, with a high rate of neurocognitive symptoms for which the molecular background is still uncertain. There is accumulating evidence for dysregulation of the kynurenine pathway (KP) in different psychiatric and neurodegenerative conditions. We here report the first comprehensive analysis of cerebrospinal fluid (CSF) kynurenine metabolites in MS patients of different disease stages and in relation to neurocognitive symptoms. Levels of tryptophan (TRP), kynurenine (KYN), kynurenic acid (KYNA) and quinolinic acid (QUIN) were determined with liquid chromatography mass spectrometry in cell-free CSF. At the group level MS patients (cohort 1; n = 71) did not differ in absolute levels of TRP, KYN, KYNA or QUIN as compared to non-inflammatory neurological disease controls (n = 20). Stratification of patients into different disease courses revealed that both absolute QUIN levels and the QUIN/KYN ratio were increased in relapsing-remitting MS (RRMS) patients in relapse. Interestingly, secondary progressive MS (SPMS) displayed a trend for lower TRP and KYNA, while primary progressive (PPMS) patients displayed increased levels of all metabolites, similar to a group of inflammatory neurological disease controls (n = 13). In the second cohort (n = 48), MS patients with active disease and short disease duration were prospectively evaluated for neuropsychiatric symptoms. In a supervised multivariate analysis using orthogonal projection to latent structures (OPLS-DA) depressed patients displayed higher KYNA/TRP and KYN/TRP ratios, mainly due to low TRP levels. Still, this model had low predictive value and could not completely separate the clinically depressed patients from the non-depressed MS patients. No correlation was evident for other neurocognitive measures. Taken together these results demonstrate that clinical disease activity and differences in disease courses are reflected by changes in KP metabolites. Increased QUIN levels of RRMS patients in relapse and generally decreased levels of TRP in SPMS may relate to neurotoxicity and failure of remyelination, respectively. In contrast, PPMS patients displayed a more divergent pattern more resembling inflammatory conditions such as systemic lupus erythematosus. The pattern of KP metabolites in RRMS patients could not predict neurocognitive symptoms.

  • 23. Aerts, R.
    et al.
    Callaghan, T. V.
    Dorrepaal, E.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap. Systems Ecology, Department of Ecological Science, VU University Amsterdam, Amsterdam, The Netherlands.
    van Logtestijn, R. S. P.
    Cornelissen, J. H. C.
    Seasonal climate manipulations have only minor effects on litter decomposition rates and N dynamics but strong effects on litter P dynamics of sub-arctic bog species2012Ingår i: Oecologia, ISSN 0029-8549, E-ISSN 1432-1939, Vol. 170, nr 3, s. 809-819Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Litter decomposition and nutrient mineralization in high-latitude peatlands are constrained by low temperatures. So far, little is known about the effects of seasonal components of climate change (higher spring and summer temperatures, more snow which leads to higher winter soil temperatures) on these processes. In a 4-year field experiment, we manipulated these seasonal components in a sub-arctic bog and studied the effects on the decomposition and N and P dynamics of leaf litter of Calamagrostis lapponica, Betula nana, and Rubus chamaemorus, incubated both in a common ambient environment and in the treatment plots. Mass loss in the controls increased in the order Calamagrostis < Betula < Rubus. After 4 years, overall mass loss in the climate-treatment plots was 10 % higher compared to the ambient incubation environment. Litter chemistry showed within each incubation environment only a few and species-specific responses. Compared to the interspecific differences, they resulted in only moderate climate treatment effects on mass loss and these differed among seasons and species. Neither N nor P mineralization in the litter were affected by the incubation environment. Remarkably, for all species, no net N mineralization had occurred in any of the treatments during 4 years. Species differed in P-release patterns, and summer warming strongly stimulated P release for all species. Thus, moderate changes in summer temperatures and/or winter snow addition have limited effects on litter decomposition rates and N dynamics, but summer warming does stimulate litter P release. As a result, N-limitation of plant growth in this sub-arctic bog may be sustained or even further promoted.

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  • 24.
    Afonina, Irina
    et al.
    Singapore Centre for Environmental Life Science Engineering, Nanyang Technological University, 60 Nanyang Drive, Singapore, Singapore; School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, Singapore; Singapore–MIT Alliance for Research and Technology, Antimicrobial Resistance Interdisciplinary Research Group, 1 Create Way, Singapore, Singapore.
    Tien, Brenda
    Singapore Centre for Environmental Life Science Engineering, Nanyang Technological University, 60 Nanyang Drive, Singapore, Singapore; School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, Singapore.
    Nair, Zeus
    Singapore Centre for Environmental Life Science Engineering, Nanyang Technological University, 60 Nanyang Drive, Singapore, Singapore; Interdisciplinary Graduate School, Nanyang Technological University, 61 Nanyang Drive, Singapore, Singapore.
    Matysik, Artur
    Singapore Centre for Environmental Life Science Engineering, Nanyang Technological University, 60 Nanyang Drive, Singapore, Singapore; School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, Singapore.
    Lam, Ling Ning
    Singapore Centre for Environmental Life Science Engineering, Nanyang Technological University, 60 Nanyang Drive, Singapore, Singapore; School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, Singapore.
    Veleba, Mark
    Singapore Centre for Environmental Life Science Engineering, Nanyang Technological University, 60 Nanyang Drive, Singapore, Singapore; School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, Singapore.
    Jie, Augustine Koh Jing
    Singapore Centre for Environmental Life Science Engineering, Nanyang Technological University, 60 Nanyang Drive, Singapore, Singapore; School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, Singapore.
    Rashid, Rafi
    Singapore Centre for Environmental Life Science Engineering, Nanyang Technological University, 60 Nanyang Drive, Singapore, Singapore; Graduate School for Integrative Sciences & Engineering, National University of Singapore, 21 Lower Kent Ridge Rd, Singapore, Singapore.
    Cazenave-Gassiot, Amaury
    Singapore Lipidomics Incubator, National University of Singapore, 28 Medical Dr, Singapore, Singapore; Department of Biochemistry, National University of Singapore, 8 Medical Drive, Block MD7, Singapore, Singapore.
    Wenk, Marcus
    Singapore Lipidomics Incubator, National University of Singapore, 28 Medical Dr, Singapore, Singapore; Department of Biochemistry, National University of Singapore, 8 Medical Drive, Block MD7, Singapore, Singapore; Department of Biological Sciences, Faculty of Science, National University of Singapore, 16 Science Drive 4, Singapore, Singapore.
    Wai, Sun Nyunt
    Umeå universitet, Medicinska fakulteten, Umeå Centre for Microbial Research (UCMR). Umeå universitet, Medicinska fakulteten, Institutionen för molekylärbiologi (Medicinska fakulteten).
    Kline, Kimberly A.
    Singapore Centre for Environmental Life Science Engineering, Nanyang Technological University, 60 Nanyang Drive, Singapore, Singapore; School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, Singapore.
    The composition and function of Enterococcus faecalis membrane vesicles2021Ingår i: MicroLife, E-ISSN 2633-6693, Vol. 2, artikel-id uqab002Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Membrane vesicles (MVs) contribute to various biological processes in bacteria, including virulence factor delivery, antimicrobial resistance, host immune evasion and cross-species communication. MVs are frequently released from the surface of both Gram-negative and Gram-positive bacteria during growth. In some Gram-positive bacteria, genes affecting MV biogenesis have been identified, but the mechanism of MV formation is unknown. In Enterococcus faecalis, a causative agent of life-threatening bacteraemia and endocarditis, neither mechanisms of MV formation nor their role in virulence has been examined. Since MVs of many bacterial species are implicated in host–pathogen interactions, biofilm formation, horizontal gene transfer, and virulence factor secretion in other species, we sought to identify, describe and functionally characterize MVs from E. faecalis. Here, we show that E. faecalis releases MVs that possess unique lipid and protein profiles, distinct from the intact cell membrane and are enriched in lipoproteins. MVs of E. faecalis are specifically enriched in unsaturated lipids that might provide membrane flexibility to enable MV formation, providing the first insights into the mechanism of MV formation in this Gram-positive organism.

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  • 25. Agah, Azin
    et al.
    Kyriakides, Themis R.
    Letrondo, Nikole
    Björkblom, Benny
    Departments of Biochemistry, University of Washington, Seattle, WA, USA.
    Bornstein, P.
    Thrombospondin 2 levels are increased in aged mice: consequences for cutaneous wound healing and angiogenesis2004Ingår i: Matrix Biology, ISSN 0945-053X, E-ISSN 1569-1802, Vol. 22, nr 7, s. 539-547Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The inhibitor of angiogenesis, thrombospondin 2 (TSP2), belongs to a group of matricellular proteins that are induced in response to injury and modulate the healing of dermal wounds. Thus, TSP-2-null mice display abnormal connective tissue architecture and increased angiogenesis in the dermis, and heal wounds at an accelerated rate. In this study, we report that the content of TSP2 is increased in the uninjured skin of aged mice. Furthermore, in primary dermal fibroblasts, TSP2 expression is increased both as a function of the age of the donor and days in culture. To determine the significance of the increased TSP2 in aged mice (two years or older), we performed full-thickness excisional wounds and compared their healing in aged and young (3–4 months) wild-type and TSP2-null mice. Gross morphological examination of wounds indicated that aged TSP2-null mice healed faster than their aged wild-type counterparts, but healing in aged mice was always sub-optimal in comparison to that in young animals. Surprisingly, despite the increase in TSP2, a potent inhibitor of angiogenesis, in wounds in aged mice, the vascular density of these wounds was not reduced in comparison to that in young animals. However, immunohistochemical analysis of healing wounds revealed a shift in the peak content of TSP2, from day 10 in young mice to day 14 or later in aged mice, and there was a corresponding delay in the expected increase in matrix metalloproteinase (MMP) 2 levels in aged TSP2-null mice. We suggest that the delay in expression of TSP2 and MMP2 in the wounds of aged mice could contribute to their impaired rate of wound healing.

  • 26. Agostinelli, Marta
    et al.
    Cleary, Michelle
    Martin, Juan A.
    Albrectsen, Benedicte R.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Witzell, Johanna
    Pedunculate Oaks (Quercus robur L.) Differing in Vitality as Reservoirs for Fungal Biodiversity2018Ingår i: Frontiers in Microbiology, E-ISSN 1664-302X, Vol. 9, artikel-id 1758Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Ecological significance of trees growing in urban and peri-urban settings is likely to increase in future land-use regimes, calling for better understanding of their role as potential reservoirs or stepping stones for associated biodiversity. We studied the diversity of fungal endophytes in woody tissues of asymptomatic even aged pedunculate oak trees, growing as amenity trees in a peri-urban setting. The trees were classified into three groups according to their phenotypic vitality (high, medium, and low). Endophytes were cultured on potato dextrose media from surface sterilized twigs and DNA sequencing was performed to reveal the taxonomic identity of the morphotypes. In xylem tissues, the frequency and diversity of endophytes was highest in oak trees showing reduced vitality. This difference was not found for bark samples, in which the endophyte infections were more frequent and communities more diverse than in xylem. In general, most taxa were shared across the samples with few morphotypes being recovered in unique samples. Leaf phenolic profiles were found to accurately classify the trees according to their phenotypic vitality. Our results confirm that xylem is more selective substrate for endophytes than bark and that endophyte assemblages in xylem are correlated to the degree of host vitality. Thus, high vitality of trees may be associated with reduced habitat quality to wood-associated endophytes.

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  • 27. Aguiar, Francisca C.
    et al.
    Segurado, Pedro
    Martins, Maria Joao
    Bejarano, Maria Dolores
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap.
    Nilsson, Christer
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap.
    Portela, Maria Manuela
    Merritt, David M.
    The abundance and distribution of guilds of riparian woody plants change in response to land use and flow regulation2018Ingår i: Journal of Applied Ecology, ISSN 0021-8901, E-ISSN 1365-2664, Vol. 55, nr 5, s. 2227-2240Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    1. Many riparian ecosystems in Mediterranean Europe are affected by land use and flow alteration by dams. We focused on understanding how these stressors and their components affect riparian forests in the region. We asked the following questions: (1) Are there well‐defined, responsive riparian guilds? (2) Do dam‐induced streamflows determine abundance and distribution of riparian guilds? (3) What are the main drivers governing composition and cover of riparian guilds in regulated rivers?

    2. We inventoried the cover of riparian woody species in free‐flowing rivers and downstream of dams. We performed a cluster analysis and ordination to derive riparian guilds, using abundance data from 66 riparian woody species and 26 functional plant traits. We used a reduced set of principal components for the environment, land use and hydrology, and general linear modelling to explore the effect of these factors (separately and combined) on riparian guilds.

    3. We found that: (1) four dominant guilds are responsive to disturbance in southwestern European streams, namely the obligate riparian, water‐stress tolerant, deciduous competitive and Mediterranean evergreen guilds; (2) a set of land use and hydrological variables differentially affect the diverse co‐occurring riparian guilds; (3) frequency and duration of high flow pulses and the low‐flow conditions were major drivers of change in landscapes dominated by intensive agriculture and forestry; (4) storage reservoirs reduced the cover of obligate riparian and Mediterranean evergreen guilds, and increased the abundance of water‐stress tolerant and deciduous competitive guilds, while run‐of‐river dams, having limited water storage, reduced both obligate and deciduous competitive guilds.

    4. Synthesis and applications. Future research in southwestern Europe should address the resilience of riparian guilds and the effects of interacting landscape factors and stressors on guild distribution. Streamflow regulations downstream of reservoirs should focus on specific flow components, namely the magnitude of flows, and frequency and duration of extreme flow events. For successful mitigation of the dam‐induced effects on riparian vegetation, river management plans must incorporate the environmental and land use site‐specific contexts.

  • 28.
    Aguida, Blanche
    et al.
    Unite Mixed de Recherche (UMR) Centre Nationale de la Recherche Scientifique (CNRS) 8256 (B2A), Institut de Biologie Paris-Seine (IBPS), Sorbonne Université, Paris, France.
    Babo, Jonathan
    Unite Mixed de Recherche (UMR) Centre Nationale de la Recherche Scientifique (CNRS) 8256 (B2A), Institut de Biologie Paris-Seine (IBPS), Sorbonne Université, Paris, France.
    Baouz, Soria
    Unite Mixed de Recherche (UMR) Centre Nationale de la Recherche Scientifique (CNRS) 8256 (B2A), Institut de Biologie Paris-Seine (IBPS), Sorbonne Université, Paris, France.
    Jourdan, Nathalie
    Unite Mixed de Recherche (UMR) Centre Nationale de la Recherche Scientifique (CNRS) 8256 (B2A), Institut de Biologie Paris-Seine (IBPS), Sorbonne Université, Paris, France.
    Procopio, Maria
    Department of Biophysics, Faculty of Arts and Sciences, Johns Hopkins University, MD, Baltimore, United States.
    El-Esawi, Mohamed A.
    Botany Department, Faculty of Science, Tanta University, Tanta, Egypt.
    Engle, Dorothy
    Biology Department, Xavier University, OH, Cincinnati, United States.
    Mills, Stephen
    Chemistry Department, Xavier University, OH, Cincinnati, United States.
    Wenkel, Stephan
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Huck, Alexander
    DTU Physics, Technical University of Denmark, Kongens Lyngby, Denmark.
    Berg-Sørensen, Kirstine
    DTU Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark.
    Kampranis, Sotirios C.
    Biochemical Engineering Group, Plant Biochemistry Section, Department of Plant and Environment Sciences, University of Copenhagen, Frederiksberg, Denmark.
    Link, Justin
    Physics and Engineering Department, OH, Cincinnati, United States.
    Ahmad, Margaret
    Unite Mixed de Recherche (UMR) Centre Nationale de la Recherche Scientifique (CNRS) 8256 (B2A), Institut de Biologie Paris-Seine (IBPS), Sorbonne Université, Paris, France; Biology Department, Xavier University, OH, Cincinnati, United States.
    'Seeing' the electromagnetic spectrum: spotlight on the cryptochrome photocycle2024Ingår i: Frontiers in Plant Science, E-ISSN 1664-462X, Vol. 15, artikel-id 1340304Artikel, forskningsöversikt (Refereegranskat)
    Abstract [en]

    Cryptochromes are widely dispersed flavoprotein photoreceptors that regulate numerous developmental responses to light in plants, as well as to stress and entrainment of the circadian clock in animals and humans. All cryptochromes are closely related to an ancient family of light-absorbing flavoenzymes known as photolyases, which use light as an energy source for DNA repair but themselves have no light sensing role. Here we review the means by which plant cryptochromes acquired a light sensing function. This transition involved subtle changes within the flavin binding pocket which gave rise to a visual photocycle consisting of light-inducible and dark-reversible flavin redox state transitions. In this photocycle, light first triggers flavin reduction from an initial dark-adapted resting state (FADox). The reduced state is the biologically active or ‘lit’ state, correlating with biological activity. Subsequently, the photoreduced flavin reoxidises back to the dark adapted or ‘resting’ state. Because the rate of reoxidation determines the lifetime of the signaling state, it significantly modulates biological activity. As a consequence of this redox photocycle Crys respond to both the wavelength and the intensity of light, but are in addition regulated by factors such as temperature, oxygen concentration, and cellular metabolites that alter rates of flavin reoxidation even independently of light. Mechanistically, flavin reduction is correlated with conformational change in the protein, which is thought to mediate biological activity through interaction with biological signaling partners. In addition, a second, entirely independent signaling mechanism arises from the cryptochrome photocycle in the form of reactive oxygen species (ROS). These are synthesized during flavin reoxidation, are known mediators of biotic and abiotic stress responses, and have been linked to Cry biological activity in plants and animals. Additional special properties arising from the cryptochrome photocycle include responsivity to electromagnetic fields and their applications in optogenetics. Finally, innovations in methodology such as the use of Nitrogen Vacancy (NV) diamond centers to follow cryptochrome magnetic field sensitivity in vivo are discussed, as well as the potential for a whole new technology of ‘magneto-genetics’ for future applications in synthetic biology and medicine.

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  • 29.
    Aguilar, Ximena
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Folding and interaction studies of subunits in protein complexes2014Doktorsavhandling, sammanläggning (Övrigt vetenskapligt)
    Abstract [en]

    Proteins function as worker molecules in the cell and their natural environment is crowded. How they fold in a cell-like environment and how they recognize their interacting partners in such conditions, are questions that underlie the work of this thesis.

    Two distinct subjects were investigated using a combination of biochemical- and biophysical methods. First, the unfolding/dissociation of a heptameric protein (cpn10) in the presence of the crowding agent Ficoll 70. Ficoll 70 was used to mimic the crowded environment in the cell and it has been used previously to study macromolecular crowding effects, or excluded volume effects, in protein folding studies. Second, the conformational changes upon interaction between the Mediator subunit Med25 and the transcription factor Dreb2a from Arabidopsis thaliana. Mediator is a transcriptional co-regulator complex which is conserved from yeast to humans. The molecular mechanisms of its action are however not entirely understood. It has been proposed that the Mediator complex conveys regulatory signals from promoter-bound transcription factors (activators/repressors) to the RNA polymerase II machinery through conformational rearrangements.

    The results from the folding study showed that cpn10 was stabilized in the presence of Ficoll 70 during thermal- and chemical induced unfolding (GuHCl). The thermal transition midpoint increased by 4°C, and the chemical midpoint by 0.5 M GuHCl as compared to buffer conditions. Also the heptamer-monomer dissociation was affected in the presence of Ficoll 70, the transition midpoint was lower in Ficoll 70 (3.1 μM) compared to in buffer (8.1 μM) thus indicating tighter binding in crowded conditions. The coupled unfolding/dissociation free energy for the heptamer increased by about 36 kJ/mol in Ficoll. Altogether, the results revealed that the stability effect on cpn10 due to macromolecular crowding was larger in the individual monomers (33%) than at the monomer-monomer interfaces (8%).

    The results from the interaction study indicated conformational changes upon interaction between the A. thaliana Med25 ACtivator Interaction Domain (ACID) and Dreb2a. Structural changes were probed to originate from unstructured Dreb2a and not from the Med25-ACID. Human Med25-ACID was also found to interact with the plant-specific Dreb2a, even though the ACIDs from human and A. thaliana share low sequence homology. Moreover, the human Med25-interacting transcription factor VP16 was found to interact with A. thaliana Med25. Finally, NMR, ITC and pull-down experiments showed that the unrelated transcription factors Dreb2a and

    VP16 interact with overlapping regions in the ACIDs of A. thaliana and human Med25.

    The results presented in this thesis contribute to previous reports in two different aspects. Firstly, they lend support to the findings that the intracellular environment affects the biophysical properties of proteins. It will therefore be important to continue comparing results between in vitro and cell-like conditions to measure the magnitude of such effects and to improve the understanding of protein folding and thereby misfolding of proteins in cells. Better knowledge of protein misfolding mechanisms is critical since they are associated to several neurodegenerative diseases such as Alzheimer’s and Parkinson's. Secondly, our results substantiate the notion that transcription factors are able to bind multiple targets and that they gain structure upon binding. They also show that subunits of the conserved Mediator complex, despite low sequence homologies, retain a conserved structure and function when comparing evolutionary diverged species.

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  • 30.
    Aguilar, Ximena
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Blomberg, Jeanette
    Umeå universitet, Medicinska fakulteten, Institutionen för medicinsk kemi och biofysik.
    Brännström, Kristoffer
    Umeå universitet, Medicinska fakulteten, Institutionen för medicinsk kemi och biofysik.
    Olofsson, Anders
    Umeå universitet, Medicinska fakulteten, Institutionen för medicinsk kemi och biofysik.
    Schleucher, Jurgen
    Umeå universitet, Medicinska fakulteten, Institutionen för medicinsk kemi och biofysik.
    Björklund, Stefan
    Umeå universitet, Medicinska fakulteten, Institutionen för medicinsk kemi och biofysik.
    Interaction Studies of the Human and Arabidopsis thaliana Med25-ACID Proteins with the Herpes Simplex Virus VP16-and Plant-Specific Dreb2a Transcription Factors2014Ingår i: PLOS ONE, E-ISSN 1932-6203, Vol. 9, nr 5, s. e98575-Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Mediator is an evolutionary conserved multi-protein complex present in all eukaryotes. It functions as a transcriptional coregulator by conveying signals from activators and repressors to the RNA polymerase II transcription machinery. The Arabidopsis thaliana Med25 (aMed25) ACtivation Interaction Domain (ACID) interacts with the Dreb2a activator which is involved in plant stress response pathways, while Human Med25-ACID (hMed25) interacts with the herpes simplex virus VP16 activator. Despite low sequence similarity, hMed25-ACID also interacts with the plant-specific Dreb2a transcriptional activator protein. We have used GST pull-down-, surface plasmon resonance-, isothermal titration calorimetry and NMR chemical shift experiments to characterize interactions between Dreb2a and VP16, with the hMed25 and aMed25-ACIDs. We found that VP16 interacts with aMed25-ACID with similar affinity as with hMed25-ACID and that the binding surface on aMed25-ACID overlaps with the binding site for Dreb2a. We also show that the Dreb2a interaction region in hMed25-ACID overlaps with the earlier reported VP16 binding site. In addition, we show that hMed25-ACID/Dreb2a and aMed25-ACID/Dreb2a display similar binding affinities but different binding energetics. Our results therefore indicate that interaction between transcriptional regulators and their target proteins in Mediator are less dependent on the primary sequences in the interaction domains but that these domains fold into similar structures upon interaction.

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  • 31.
    Aguilera, Anabella
    et al.
    Department of Biology and Environmental Science, Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden.
    Alegria Zufia, Javier
    Department of Biology and Environmental Science, Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden.
    Bas Conn, Laura
    Department of Biology and Environmental Science, Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden.
    Gurlit, Leandra
    Department of Biology and Environmental Science, Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden.
    Śliwińska-Wilczewska, Sylwia
    Mount Allison University, Sackville, New Brunswick, Canada; Laboratory of Marine Plant Ecophysiology, Institute of Oceanography, University of Gdansk, Gdynia, Poland.
    Budzałek, Gracjana
    Laboratory of Marine Plant Ecophysiology, Institute of Oceanography, University of Gdansk, Gdynia, Poland.
    Lundin, Daniel
    Department of Biology and Environmental Science, Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden.
    Pinhassi, Jarone
    Department of Biology and Environmental Science, Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden.
    Legrand, Catherine
    Department of Biology and Environmental Science, Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden; School of Business, Innovation and Sustainability, Halmstad University, Halmstad, Sweden.
    Farnelid, Hanna
    Department of Biology and Environmental Science, Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden.
    Ecophysiological analysis reveals distinct environmental preferences in closely related Baltic Sea picocyanobacteria2023Ingår i: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Cluster 5 picocyanobacteria significantly contribute to primary productivity in aquatic ecosystems. Estuarine populations are highly diverse and consist of many co-occurring strains, but their physiology remains largely understudied. In this study, we characterized 17 novel estuarine picocyanobacterial strains. Phylogenetic analysis of the 16S rRNA and pigment genes (cpcB and cpeBA) uncovered multiple estuarine and freshwater-related clusters and pigment types. Assays with five representative strains (three phycocyanin rich and two phycoerythrin rich) under temperature (10–30°C), light (10–190 μmol photons m−2 s−1), and salinity (2–14 PSU) gradients revealed distinct growth optima and tolerance, indicating that genetic variability was accompanied by physiological diversity. Adaptability to environmental conditions was associated with differential pigment content and photosynthetic performance. Amplicon sequence variants at a coastal and an offshore station linked population dynamics with phylogenetic clusters, supporting that strains isolated in this study represent key ecotypes within the Baltic Sea picocyanobacterial community. The functional diversity found within strains with the same pigment type suggests that understanding estuarine picocyanobacterial ecology requires analysis beyond the phycocyanin and phycoerythrin divide. This new knowledge of the environmental preferences in estuarine picocyanobacteria is important for understanding and evaluating productivity in current and future ecosystems.

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  • 32.
    Aguilo, Francesca
    et al.
    Umeå universitet, Medicinska fakulteten, Wallenberg centrum för molekylär medicin vid Umeå universitet (WCMM). Umeå universitet, Medicinska fakulteten, Institutionen för medicinsk biovetenskap, Patologi. Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
    Walsh, Martin J.
    The N6-Methyladenosine RNA modification in pluripotency and reprogramming2017Ingår i: Current Opinion in Genetics and Development, ISSN 0959-437X, E-ISSN 1879-0380, Vol. 46, s. 77-82Artikel, forskningsöversikt (Refereegranskat)
    Abstract [en]

    Chemical modifications of RNA provide a direct and rapid way to manipulate the existing transcriptome, allowing rapid responses to the changing environment further enriching the regulatory capacity of RNA. N-6-Methyladenosine(m(6)A) has been identified as the most abundant internal modification of messenger RNA in eukaryotes, linking external stimuli to an intricate network of transcriptional, post-transcriptional and translational processes. M(6)A modification affects a broad spectrum of cellular functions, including maintenance of the pluripotency of embryonic stem cells (ESCs) and the reprogramming of somatic cells into induced pluripotent stem cells (iPSCs). In this review, we summarize the most recent findings on m(6)A modification with special focus on the different studies describing how m(6)A is implicated in ESC self-renewal, cell fate specification and iPSC generation.

  • 33.
    Aguilo, Francesca
    et al.
    Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
    Zakirova, Zuchra
    Nolan, Katie
    Wagner, Ryan
    Sharma, Rajal
    Hogan, Megan
    Wei, Chengguo
    Sun, Yifei
    Walsh, Martin J.
    Kelley, Kevin
    Zhang, Weijia
    Ozelius, Laurie J.
    Gonzalez-Alegre, Pedro
    Zwaka, Thomas P.
    Ehrlich, Michelle E.
    THAP1: role in mouse embryonic stem cell survival and differentiation2017Ingår i: Stem Cell Reports, ISSN 2213-6711, Vol. 9, nr 1, s. 92-107Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    THAP1 (THAP [Thanatos-associated protein] domain-containing, apoptosis-associated protein 1) is a ubiquitously expressed member of a family of transcription factors with highly conserved DNA-binding and protein-interacting regions. Mutations in THAP1 cause dystonia, DYT6, a neurologic movement disorder. THAP1 downstream targets and the mechanism via which it causes dystonia are largely unknown. Here, we show that wild-type THAP1 regulates embryonic stem cell (ESC) potential, survival, and proliferation. Our findings identify THAP1 as an essential factor underlying mouse ESC survival and to some extent, differentiation, particularly neuroectodermal. Loss of THAP1 or replacement with a disease-causing mutation results in an enhanced rate of cell death, prolongs Nanog, Prdm14, and/or Rex1 expression upon differentiation, and results in failure to upregulate ectodermal genes. ChIP-Seq reveals that these activities are likely due in part to indirect regulation of gene expression.

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  • 34. Ahad, Abdul
    et al.
    Keech, Olivier
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Sjödin, Andreas
    Lindén, Pernilla
    Brouwer, Bastiaan
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Stenlund, Hans
    Moritz, Thomas
    Jansson, Stefan
    Gardeström, Per
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Comparison between leaves from darkened plants and individually-darkened leaves reveals differential metabolic strategies in response to darknessManuskript (preprint) (Övrigt vetenskapligt)
  • 35.
    Ahlgren, Gunnel
    et al.
    Department of Ecology and Evolution (Limnology), Uppsala University, Uppsala, Sweden.
    Vrede, Tobias
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap.
    Goedkoop, Willem
    Department of Environmental Assessment, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden.
    Fatty Acid Ratios in Freshwater Fish, Zooplankton and Zoobenthos - Are There Specific Optima?2009Ingår i: Lipids in Aquatic Ecosystems / [ed] Martin Kainz, Michael T. Brett, Michael T. Arts, New York: Springer-Verlag New York, 2009, s. 147-178Kapitel i bok, del av antologi (Övrigt vetenskapligt)
    Abstract [en]

    Two groups of polyunsaturated fatty acids (PUFA), termed omega-3 and omega-6 in food (or here as n-3 and n-6 PUFA, respectively), are essential for all vertebrates and probably also for nearly all invertebrates. The absolute concentrations of the different PUFA are important, as is an appropriate balance between the two. The optimal ratio of n-3/n-6 is not known for most organisms but is anticipated to be more or less species-specific (Sargent et al. 1995). The three most important PUFA in vertebrates are eicosapentaenoic acid (EPA, 20:5n-3), docosahexaenoic acid (DHA, 22:6n-3) and arachidonic acid (ARA, 20:4n-6). Both EPA and ARA are precursors for biologically active eicosanoids that are vital components of cell membranes and play many dynamic roles in mediating and controlling a wide array of cellular activities (Crawford et al. 1989; Harrison 1990; Henderson et al. 1996; see Chap. 9). Since n-3 and n-6 PUFA cannot be synthesized de novo by most metazoans, they must be included in the diet, either as EPA, DHA and ARA, or as their precursors, such as α-linolenic acid (ALA, 18:3n-3, precursor of EPA and DHA) and linoleic acid (LIN, 18:2n-6, precursor of ARA) (Bell et al. 1986; Sargent et al. 1995). Both ALA and LIN are produced in the thylacoid membranes of algae and plants with chlorophyll (Sargent at al. 1987).

  • 36.
    Ahlinder, Jon
    et al.
    Division of CBRN Defence and Security, Swedish Defence Research Agency (FOI), Sweden; Department of Tree Breeding, Skogforsk, Sävar, Sweden.
    Eriksson, Karolina Ida Anna
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå marina forskningscentrum (UMF).
    Hellmér, Maria
    Department of Biology, Science Division, Swedish Food Agency, Sweden.
    Salomonsson, Emelie
    Division of CBRN Defence and Security, Swedish Defence Research Agency (FOI), Sweden.
    Granberg, Malin
    Division of CBRN Defence and Security, Swedish Defence Research Agency (FOI), Sweden.
    Dacklin, Ingrid
    Division of CBRN Defence and Security, Swedish Defence Research Agency (FOI), Sweden.
    Elving, Josefine
    Department of Chemistry, Environment and Feed Hygiene, Swedish Veterinary Agency, Sweden.
    Brindefalk, Björn
    Division of CBRN Defence and Security, Swedish Defence Research Agency (FOI), Sweden; Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Sweden.
    Upstream land use with microbial downstream consequences: iron and humic substances link to Legionella spp2024Ingår i: Water Research, ISSN 0043-1354, E-ISSN 1879-2448, Vol. 256, artikel-id 121579Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Intensified land use can disturb water quality, potentially increasing the abundance of bacterial pathogens, threatening public access to clean water. This threat involves both direct contamination of faecal bacteria as well as indirect factors, such as disturbed water chemistry and microbiota, which can lead to contamination. While direct contamination has been well described, the impact of indirect factors is less explored, despite the potential of severe downstream consequences on water supply. To assess direct and indirect downstream effects of buildings, farms, pastures and fields on potential water sources, we studied five Swedish lakes and their inflows. We analysed a total of 160 samples in a gradient of anthropogenic activity spanning four time points, including faecal and water-quality indicators. Through species distribution modelling, Random Forest and network analysis using 16S rRNA amplicon sequencing data, our findings highlight that land use indirectly impacts lakes via inflows. Land use impacted approximately one third of inflow microbiota taxa, in turn impacting ∌20–50 % of lake taxa. Indirect effects via inflows were also suggested by causal links between e.g. water colour and lake bacterial taxa, where this influenced the abundance of several freshwater bacteria, such as Polynucleobacter and Limnohabitans. However, it was not possible to identify direct effects on the lakes based on analysis of physiochemical- or microbial parameters. To avoid potential downstream consequences on water supply, it is thus important to consider possible indirect effects from upstream land use and inflows, even when no direct effects can be observed on lakes. Legionella (a genus containing bacterial pathogens) illustrated potential consequences, since the genus was particularly abundant in inflows and was shown to increase by the presence of pastures, fields, and farms. The approach presented here could be used to assess the suitability of lakes as alternative raw water sources or help to mitigate contaminations in important water catchments. Continued broad investigations of stressors on the microbial network can identify indirect effects, avoid enrichment of pathogens, and help secure water accessibility.

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  • 37.
    Ahlinder, Jon
    et al.
    Division of CBRN Defence and Security, Swedish Defence Research Agency, Umeå, Sweden.
    Giles, Barbara
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap.
    García-Gil, M. Rosario
    Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden.
    Life stage-specific inbreeding depression in long-lived Pinaceae species depends on population connectivity2021Ingår i: Scientific Reports, E-ISSN 2045-2322, Vol. 11, nr 1, artikel-id 8834Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Inbreeding depression (ID) is a fundamental selective pressure that shapes mating systems and population genetic structures in plants. Although it has been shown that ID varies over the life stages of shorter-lived plants, less is known about how the fitness effects of inbreeding vary across life stages in long-lived species. We conducted a literature survey in the Pinaceae, a tree family known to harbour some of the highest mutational loads ever reported. Using a meta-regression model, we investigated distributions of inbreeding depression over life stages, adjusting for effects of inbreeding levels and the genetic differentiation of populations within species. The final dataset contained 147 estimates of ID across life stages from 41 studies. 44 Fst estimates were collected from 40 peer-reviewed studies for the 18 species to aid genetic differentiation modelling. Partitioning species into fragmented and well-connected groups using Fst resulted in the best way (i.e. trade-off between high goodness-of-fit of the model to the data and reduced model complexity) to incorporate genetic connectivity in the meta-regression analysis. Inclusion of a life stage term and its interaction with the inbreeding coefficient (F) dramatically increased model precision. We observed that the correlation between ID and F was significant at the earliest life stage. Although partitioning of species populations into fragmented and well-connected groups explained little of the between-study heterogeneity, the inclusion of an interaction between life stage and population differentiation revealed that populations with fragmented distributions suffered lower inbreeding depression at early embryonic stages than species with well-connected populations. There was no evidence for increased ID in late life stages in well-connected populations, although ID tended to increase across life stages in the fragmented group. These findings suggest that life stage data should be included in inbreeding depression studies and that inbreeding needs to be managed over life stages in commercial populations of long-lived plants.

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  • 38.
    Ahlinder, Jon
    et al.
    Division of CBRN Defence and Security, FOI, Swedish Defence Research Agency, Umeå, Sweden.
    Mathisen, Peter
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap.
    Sjödin, Andreas
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen. Division of CBRN Defence and Security, FOI, Swedish Defence Research Agency, Umeå, Sweden.
    Nilsson, Elin
    Division of CBRN Defence and Security, FOI, Swedish Defence Research Agency, Umeå, Sweden.
    Forsman, Mats
    Division of CBRN Defence and Security, FOI, Swedish Defence Research Agency, Umeå, Sweden.
    Andersson, Agneta
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap.
    Thelaus, Johanna
    Division of CBRN Defence and Security, FOI, Swedish Defence Research Agency, Umeå, Sweden.
    Oligotyping reveals divergent responses of predation resistant bacteria to aquatic productivity and plankton compositionManuskript (preprint) (Övrigt vetenskapligt)
    Abstract [en]

    Predation-resistance has been suggested to be a key for persistence of pathogenic bacteria in aquatic environments. Little is known about driving factors for different types of protozoa resistant bacteria (PRB). We studied if presence of PRB is linked to specific plankton taxa, the aquatic nutrient state, or predation pressure on bacteria. Nineteen freshwater systems were sampled and analyzed for PRB, plankton composition and physicochemical variables. Three PRB genera were identified; Pseudomonas, Mycobacterium and Rickettsia. Use of minimum entropy decomposition algorithm and phylogenetic analysis showed that different nodes (representing OTUs of high taxonomic resolution) matched to environmental isolates of the three genera. Links between the PRB genera and specific plankton taxa were found, but showed different relationships depending on if 18S rRNA OTU or microscopy data were used in the analysis. Mycobacterium spp. was negatively correlated to aquatic nutrient state, while Pseudomonas showed the opposite pattern. Rickettsia spp. was positively related to predation pressure on bacteria. Both Mycobacterium and Rickettsia were more abundant in systems with high eukaryotic diversity, while Pseudomonas occurred abundantly in waters with low prokaryotic diversity. The different drivers may be explained by varying ecological strategies, where Mycobacterium and Rickettsia are slow growing and have an intracellular life style, while Pseudomonas is fast growing and opportunistic. Here we give an insight to the possibilities of newly advanced methods such as sequencing and oligotyping to link potential pathogens with biomarkers. This as a tool to assist predictions of the occurrence and persistence of environmental pathogens.

  • 39.
    Ahlm, Kristoffer
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap.
    Prey specialization and diet of frogs in Borneo2015Självständigt arbete på grundnivå (kandidatexamen), 10 poäng / 15 hpStudentuppsats (Examensarbete)
    Abstract [en]

    Earlier studies of the diet of frogs indicate that most adult frogs are mainly insectivorous. Overall, frogs are viewed more as generalists than specialists in terms of their diet. However, despite earlier studies, there are still gaps in our knowledge regarding what frogs tend to eat and the degree of specialization. The aim of this study was to investigate the diet choice of frogs in a tropical ecosystem. The present study was conducted in a well-known hotspot for frogs with 66 of the 156 known frog species in Borneo found in a protected area comprising of primary rainforest.

     

    Frogs were caught in the field and their stomachs were flushed. The stomach content was retrieved, sorted to prey categories, and the diet analysed. In addition, the frogs were identified to species level. The frogs belonged to five families: Bufonidae, Dicroglossidae, Megophryidae, Microhylidae and Ranidae. My results show that the most common food source was ants, which constituted 63.7 % of the total food for all studied frog families. Termites, beetles and spiders made up 11.7 %, 4.2 % and 2.8 % of the total prey, respectively. The results from the analysis of Shannon’s diversity index supported two diet specialist families, the Bufonidae and Megophridae, which had a significantly lower mean diversity index compared to the generalist Dicroglossidae. To better reveal differences in frog’s diet in this ecosystem, further studies using larger sample size are needed.

     

     

     

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  • 40. Ahlstrand, Tuuli
    et al.
    Tuominen, Heidi
    Beklen, Arzu
    Torittu, Annamari
    Oscarsson, Jan
    Umeå universitet, Medicinska fakulteten, Institutionen för odontologi.
    Sormunen, Raija
    Pöllänen, Marja T.
    Permi, Perttu
    Ihalin, Riikka
    A novel intrinsically disordered outer membrane lipoprotein of Aggregatibacter actinomycetemcomitans binds various cytokines and plays a role in biofilm response to interleukin-1β and interleukin-82017Ingår i: Virulence, ISSN 2150-5594, E-ISSN 2150-5608, Vol. 8, nr 2, s. 115-134Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Intrinsically disordered proteins (IDPs) do not have a well-defined and stable 3-dimensional fold. Some IDPs can function as either transient or permanent binders of other proteins and may interact with an array of ligands by adopting different conformations. A novel outer membrane lipoprotein, bacterial interleukin receptor I (BilRI) of the opportunistic oral pathogen Aggregatibacter actinomycetemcomitans binds a key gatekeeper proinflammatory cytokine interleukin (IL)-1β. Because the amino acid sequence of the novel lipoprotein resembles that of fibrinogen binder A of Haemophilus ducreyi, BilRI could have the potential to bind other proteins, such as host matrix proteins. However, from the tested host matrix proteins, BilRI interacted with neither collagen nor fibrinogen. Instead, the recombinant non-lipidated BilRI, which was intrinsically disordered, bound various pro/anti-inflammatory cytokines, such as IL-8, tumor necrosis factor (TNF)-α, interferon (IFN)-γ and IL-10. Moreover, BilRI played a role in the in vitro sensing of IL-1β and IL-8 because low concentrations of cytokines did not decrease the amount of extracellular DNA in the matrix of bilRI− mutant biofilm as they did in the matrix of wild-type biofilm when the biofilms were exposed to recombinant cytokines for 22 hours. BilRI played a role in the internalization of IL-1β in the gingival model system but did not affect either IL-8 or IL-6 uptake. However, bilRI deletion did not entirely prevent IL-1β internalization, and the binding of cytokines to BilRI was relatively weak. Thus, BilRI might sequester cytokines on the surface of A. actinomycetemcomitans to facilitate the internalization process in low local cytokine concentrations.

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  • 41. Ahlén Bergman, Emma
    et al.
    Hartana, Ciputra Adijaya
    Linton, Ludvig
    Winerdal, Malin E.
    Krantz, David
    Rosenblatt, Robert
    Umeå universitet, Medicinska fakulteten, Institutionen för kirurgisk och perioperativ vetenskap, Urologi och andrologi. Department of Urology, Stockholm South General Hospital, Karolinska Institutet, Stockholm, Sweden.
    Lundgren, Christian
    Marits, Per
    Sherif, Amir
    Umeå universitet, Medicinska fakulteten, Institutionen för kirurgisk och perioperativ vetenskap, Urologi och andrologi.
    Winqvist, Ola
    Epigenetic methylation profiles of CD4 T cell signature loci from patients with urinary bladder cancer2017Ingår i: Scandinavian Journal of Immunology, ISSN 0300-9475, E-ISSN 1365-3083, Vol. 86, nr 4, s. 264-264Artikel i tidskrift (Övrigt vetenskapligt)
    Abstract [en]

    Urinary bladder cancer (UBC) is one of the most frequent cancer diseases with 380 000 new cases diagnosed worldwide and about 150 000 deaths yearly. To dissect the role of T helper (Th) cell responses in UBC we investigate the T helper cell subpopulations; Th1, Th2, Th17 and T regulatory cells (Tregs) and their lineage commitment in draining (sentinel) and non-draining lymph nodes and blood from patients subjected to transurethral resection of the bladder (TUR-B) and/or Cystectomy. By analyzing methylation in signature genes IFNG, IL13, IL17a and FOXP3 we measure the epigenetic stability of these T helper cells.

    In most patients IFNG is more demethylated in sentinel nodes compared to non-sentinel nodes and blood, suggesting a Th1 activation in nodes in contact with the tumor. Aside from that, the distribution of subpopulations in all tissues investigated is highly variable in between patients. All subsets are represented, although there seem to be no or little Th17 cells in nodes. After neoadjuvant treatment (given in between the TUR-B and cystectomy) a temporary increase in methylation of IFNG locus is seen in blood, which could suggest a translocation of activated Th cells from the blood to the tumor area, but also de novo synthesis of Th cells.

    By analyzing the intra-patient variations in distribution and relative amount of Th cell subpopulations in blood and sentinel nodes we hope to draw conclusions on differences in outcome. The long-term goal is to be able to identify which patients could respond well to immune modulatory treatments.

  • 42.
    Ahmad, Irfan
    et al.
    Umeå universitet, Medicinska fakulteten, Institutionen för molekylärbiologi (Medicinska fakulteten). Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.
    Rouf, Syed Fazle
    Sun, Lei
    Cimdins, Annika
    Shafeeq, Sulman
    Le Guyon, Soazig
    Schottkowski, Marco
    Rhen, Mikael
    Romling, Ute
    BcsZ inhibits biofilm phenotypes and promotes virulence by blocking cellulose production in Salmonella enterica serovar Typhimurium2016Ingår i: Microbial Cell Factories, ISSN 1475-2859, E-ISSN 1475-2859, Vol. 15, artikel-id 177Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Background: Cellulose, a 1,4 beta-glucan polysaccharide, is produced by a variety of organisms including bacteria. Although the production of cellulose has a high biological, ecological and economical impact, regulatory mechanisms of cellulose biosynthesis are mostly unknown. Family eight cellulases are regularly associated with cellulose biosynthesis operons in bacteria; however, their function is poorly characterized. In this study, we analysed the role of the cellulase BcsZ encoded by the bcsABZC cellulose biosynthesis operon of Salmonella enterica serovar Typhimurium (S. Typhimurium) in biofilm related behavior. We also investigated the involvement of BcsZ in pathogenesis of S. Typhimurium including a murine typhoid fever infection model. Result: In S. Typhimurium, cellulase BcsZ with a putative periplasmic location negatively regulates cellulose biosynthesis. Moreover, as assessed with a non-polar mutant, BcsZ affects cellulose-associated phenotypes such as the rdar biofilm morphotype, cell clumping, biofilm formation, pellicle formation and flagella-dependent motility. Strikingly, although upregulation of cellulose biosynthesis was not observed on agar plate medium at 37 degrees C, BcsZ is required for efficient pathogen-host interaction. Key virulence phenotypes of S. Typhimurium such as invasion of epithelial cells and proliferation in macrophages were positively regulated by BcsZ. Further on, a bcsZ mutant was outcompeted by the wild type in organ colonization in the murine typhoid fever infection model. Selected phenotypes were relieved upon deletion of the cellulose synthase BcsA and/or the central biofilm activator CsgD. Conclusion: Although the protein scaffold has an additional physiological role, our findings indicate that the catalytic activity of BcsZ effectively downregulates CsgD activated cellulose biosynthesis. Repression of cellulose production by BcsZ subsequently enables Salmonella to efficiently colonize the host.

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  • 43. Ahmad, S.
    et al.
    Zhao, W.
    Renström, F.
    Rasheed, A.
    Zaidi, M.
    Samuel, M.
    Shah, N.
    Mallick, N. H.
    Shungin, Dmitry
    Umeå universitet, Medicinska fakulteten, Institutionen för folkhälsa och klinisk medicin, Medicin. Umeå universitet, Medicinska fakulteten, Institutionen för odontologi.
    Zaman, K. S.
    Ishaq, M.
    Rasheed, S. Z.
    Memon, F-ur-R
    Hanif, B.
    Lakhani, M. S.
    Ahmed, F.
    Kazmi, S. U.
    Deloukas, P.
    Frossard, P.
    Franks, P. W.
    Saleheen, D.
    A novel interaction between theFLJ33534locus and smokingin obesity: a genome-wide study of 14 131 Pakistani adults2016Ingår i: International Journal of Obesity, ISSN 0307-0565, E-ISSN 1476-5497, Vol. 40, nr 1, s. 186-190Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    BACKGROUND: Obesity is a complex disease caused by the interplay of genetic and lifestyle factors, but identification of gene-lifestyle interactions in obesity has remained challenging. Few large-scale studies have reported use of genome-wide approaches to investigate gene-lifestyle interactions in obesity. METHODS: In the Pakistan Risk of Myocardial Infraction Study, a cross-sectional study based in Pakistan, we calculated body mass index (BMI) variance estimates (square of the residual of inverse-normal transformed BMI z-score) in 14 131 participants and conducted genome-wide heterogeneity of variance analyses (GWHVA) for this outcome. All analyses were adjusted for age, age(2), sex and genetic ancestry. RESULTS: The GWHVA analyses identified an intronic variant, rs140133294, in the FLJ33544 gene in association with BMI variance (P-value = 3.1 x 10(-8)). In explicit tests of gene x lifestyle interaction, smoking was found to significantly modify the effect of rs140133294 on BMI (Pinteraction = 0.0005), whereby the minor allele (T) was associated with lower BMI in current smokers, while positively associated with BMI in never smokers. Analyses of ENCODE data at the FLJ33534 locus revealed features indicative of open chromatin and high confidence DNA-binding motifs for several transcription factors, providing suggestive biological support for a mechanism of interaction. CONCLUSIONS: In summary, we have identified a novel interaction between smoking and variation at the FLJ33534 locus in relation to BMI in people from Pakistan.

  • 44. Ahn, Ji Hoon
    et al.
    Schmid, Markus
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    Editorial overview: Growth and development: Change is in the air: how plants modulate development in response to the environment2017Ingår i: Current opinion in plant biology, ISSN 1369-5266, E-ISSN 1879-0356, Vol. 35, s. IV-VIArtikel i tidskrift (Refereegranskat)
  • 45.
    Ahnesjö, Ingrid
    et al.
    Department of Ecology and Genetics/Animal Ecology, Uppsala University, Uppsala, Sweden.
    Brealey, Jaelle C.
    Department of Ecology and Genetics/Animal Ecology, Uppsala University, Uppsala, Sweden.
    Günter, Katerina P.
    Centre for Gender Research, Uppsala University, Uppsala, Sweden.
    Martinossi‑Allibert, Ivain
    Department of Ecology and Genetics/Animal Ecology, Uppsala University, Uppsala, Sweden; Department of Organismal Biology/Systematic Biology, Uppsala University, Uppsala, Sweden.
    Morinay, Jennifer
    Department of Ecology and Genetics/Animal Ecology, Uppsala University, Uppsala, Sweden; Université de Lyon, France.
    Siljestam, Mattias
    Department of Ecology and Genetics/Animal Ecology, Uppsala University, Uppsala, Sweden.
    Stångberg, Josefine
    Department of Ecology and Genetics/Animal Ecology, Uppsala University, Uppsala, Sweden.
    Vasconcelos, Paula
    Department of Ecology and Genetics/Animal Ecology, Uppsala University, Uppsala, Sweden.
    Considering gender‑biased assumptions in evolutionary biology2020Ingår i: Evolutionary biology, ISSN 0071-3260, E-ISSN 1934-2845, Vol. 47, s. 1-5Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Many organisms studied by evolutionary biologists have different sexes, and the evolution of separate sexes and sexual dimorphisms in morphology and behaviour are central questions in evolutionary biology. Considering scientists to be embedded in a social and cultural context, we are also subjected to the risk of gender-biased assumptions and stereotypical thinking to appear when working on topics related to sexual reproduction and sexual dimorphism. Here we present, for continued discussion, a set of good-practice guidelines aimed at (1) helping to improve researchers’ awareness of gender-biased assumptions underlying language use, generalizations, and interpretation of observations; and (2) providing recommendations to increase transparency, avoid problematic terminology, and improve study designs.

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  • 46.
    Aigner, Harald
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Characterization of FtsH proteases in the annual plant Arabidopsis thaliana2012Doktorsavhandling, sammanläggning (Övrigt vetenskapligt)
    Abstract [en]

    Background FtsH is an ATP-dependent membrane-bound metalloprotease. A. thaliana contains 12 FtsH proteases localized in membranes of chloroplasts and mitochondria where they form homo- or hetero-hexameric complexes. FtsH11 – the main subject of this thesis – is located in the chloroplast envelope.

     

    Methods

    • Field studies with A. thaliana to determine Darwinian fitness. A growth under outdoor conditions often allows discovering of phenotypes that are unascertainable in the controlled environment of growth chambers.
    • Proteomic methods to discover fragments of substrate proteins (limited proteolysis) and changes in the proteome of FtsH protease deficient mutants.

     

    Results ftsh11 has increased amount of: RuBisCO activase, several Calvin cycle enzymes, two enzymes involved in starch synthesis and some chaperons. Some of those enzymes have been identified as possible substrates of FtsH11. Under long photoperiods ftsh11 develops a chlorotic phenotype accompanied by decreasing NADP+/NADPH ratio and increase of ROS damaged proteins. 

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    Characterization of FtsH proteases in the annual plant Arabidopsis thaliana
  • 47.
    Aigner, Harald
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Wagner, Raik
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Sjögren, Lars
    Eubel, Holger
    Millar, Harvey
    Clarke, Adrian
    Funk, Christiane
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    FtsH11 protease is required for Arabidopsis thaliana to adapt to gtowth in continuous lightManuskript (preprint) (Övrigt vetenskapligt)
    Abstract [en]

    Continuous light can increase greenhouse food production; however, some of the most important greenhouse horticulture crops are not able to adapt to long photoperiods. Here, we provide evidence that knock-out of the FtsH11 protease causes molecular differences that prevent Arabidopsis thaliana to adapt to prolonged photoperiods. Previously this protease had been shown to be critical for thermotolerance (Chen et al. 2006). We demonstrate that knock-out mutants deficient of FtsH11 develop chlorosis when shifted to continuous light. When grown under normal growth conditions and short days, ftsh11 displayed changes in protein amount of chloroplast proteins involved in the photosynthetic light reaction and the Calvin cycle as well as of the FtsH12 protease. The proteomic changes are accompanied by reduced non-photochemical quenching and faster state transition. A shift to continuous light further enhanced these effects and induced morphological changes of the chloroplast and chlorosis. No changes in the mitochondrial proteome were observed between wild type and ftsh11.

  • 48.
    Ailizati, Aili
    et al.
    Graduate School of Science and Engineering, Saitama University, Saitama, Japan.
    Nagahage, Isura Sumeda Priyadarshana
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    Miyagi, Atsuko
    Graduate School of Science and Engineering, Saitama University, Saitama, Japan.
    Ishikawa, Toshiki
    Graduate School of Science and Engineering, Saitama University, Saitama, Japan.
    Kawai-Yamada, Maki
    Graduate School of Science and Engineering, Saitama University, Saitama, Japan.
    Demura, Taku
    Graduate School of Biological Sciences, Nara Institute of Science and Technology (NAIST), Nara, Japan.
    Yamaguchi, Masatoshi
    Graduate School of Science and Engineering, Saitama University, Saitama, Japan.
    An Arabidopsis NAC domain transcriptional activator VND7 negatively regulates VNI2 expression2021Ingår i: Plant Biotechnology, ISSN 1342-4580, E-ISSN 1347-6114, Vol. 38, nr 4, s. 415-420Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    A NAC domain transcription factor, VND-INTERACTING2 (VNI2) is originally isolated as an interacting protein with another NAC domain transcription factor, VASCULAR-RELATED NAC-DOMAIN7 (VND7), a master regulator of xylem vessel element differentiation. VND7 directly or indirectly induces expression of a number of genes associated with xylem vessel element differentiation, while VNI2 inhibits the transcriptional activation activities of VND7 by forming a protein complex. VNI2 is expressed at an earlier stage of xylem vessel element differentiation than VND7. Here, to investigate whether VND7 also affects VNI2, a transient expression assay was performed. We demonstrated that VND7 downregulated VNI2 expression. Other transcription factors involved in xylem vessel formation did not show the negative regulation of VNI2 expression. Rather, MYB83, a downstream target of VND7, upregulated VNI2 expression. By using the deletion series of the VNI2 promoter, a 400 bp region was identified as being responsible for downregulation by VND7. These data suggested that VND7 and VNI2 mutually regulate each other, and VNI2 expression is both positively and negatively regulated in the transcriptional cascade.

  • 49.
    Ailizati, Aili
    et al.
    Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama, Saitama, Japan.
    Nagahage, Isura Sumeda Priyadarshana
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    Miyagi, Atsuko
    Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama, Saitama, Japan.
    Ishikawa, Toshiki
    Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama, Saitama, Japan.
    Kawai-Yamada, Maki
    Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama, Saitama, Japan.
    Demura, Taku
    Graduate School of Biological Sciences, Nara Institute of Science and Technology (NAIST), 8916-5 Takayama, Nara, Ikoma, Japan.
    Yamaguchi, Masatoshi
    Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama, Saitama, Japan.
    VND-INTERACTING2 effectively inhibits transcriptional activities of VASCULAR-RELATED NAC-DOMAIN7 through a conserved sequence2022Ingår i: Plant Biotechnology, ISSN 1342-4580, E-ISSN 1347-6114, Vol. 39, nr 2, s. 147-153Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    An Arabidopsis NAC domain transcription factor VND-INTERACTING2 (VNI2) was originally isolated as an interacting protein with another NAC domain transcription factor, VASCULAR-RELATED NAC-DOMAIN7 (VND7), a master regulator of xylem vessel element differentiation. VNI2 inhibits transcriptional activation activity of VND7 by forming a protein complex. Here, to obtain insights into how VNI2 regulates VND7, we tried to identify the amino acid region of VNI2 required for inhibition of VND7. VNI2 has an amino acid sequence similar to the ETHYLENE-RESPONSIVE ELEMENT BINDING FACTOR (ERF)-associated amphiphilic repression (EAR) motif, conserved in transcriptional repressors, at the C-terminus. A transient expression assay showed that the EAR-like motif of VNI2 was not required for inhibition of VND7. The C-terminal deletion series of VNI2 revealed that 10 amino acid residues, highly conserved in the VNI2 orthologs contributed to effective repression of the transcriptional activation activity of VND7. Observation of transgenic plants ectopically expressing VNI2 showed that the identified 10 amino acid sequence strongly affected xylem vessel formation and plant growth. These data indicated that the 10 amino acid sequence of VNI2 has an important role in its transcriptional repression activity and negative regulation of xylem vessel formation.

  • 50.
    Aisenbrey, Christopher
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Bechinger, Burkhard
    Gröbner, Gerhard
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Macromolecular Crowding at Membrane Interfaces: Adsorption and Alignment of Membrane Peptides2008Ingår i: Journal of Molecular Biology, ISSN 0022-2836, E-ISSN 1089-8638, Vol. 375, s. 376-385Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Association of proteins to cellular membranes is involved in various biological processes. Various theoretical models have been developed to describe this adsorption mechanism, commonly implying the concept of an ideal solution. However, due to the two-dimensional character of membrane surfaces intermolecular interactions between the adsorbed molecules become important. Therefore previously adsorbed molecules can influence the adsorption behavior of additional protein molecules and their membrane-associated structure. Using the model peptide LAH4, which upon membrane-adsorption can adopt a transmembrane as well as an in-planar configuration, we carried out a systematic study of the correlation between the peptide concentration in the membrane and the topology of this membrane-associated polypeptide. We could describe the observed binding behavior by establishing a concept, which includes intermolecular interactions in terms of a scaled particle theory.

    High surface concentration of the peptide shifts the molecules from an in-planar into a transmembrane conformation, a process driven by the reduction of occupied surface area per molecule. In a cellular context, the crowding-dependent alignment might provide a molecular switch for a cell to sense and control its membrane occupancy. Furthermore, crowding might have pronounced effects on biological events, such as the cooperative behavior of antimicrobial peptides and the membrane triggered aggregation of amyloidogenic peptides.

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