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  • 1. Abafe, Ovokeroye A.
    et al.
    Späth, Jana
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Fick, Jerker
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Jansson, Stina
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    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 Africa2018In: Chemosphere, ISSN 0045-6535, E-ISSN 1879-1298, Vol. 200, p. 660-670Article in journal (Refereed)
    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.

  • 2. 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?2010In: African Bird Club Bulletin, ISSN 1352-481X, Vol. 17, no 2, p. 210-211Article in journal (Refereed)
    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.

  • 3. Abbasi, Arshad Mehmood
    et al.
    Khan, Mir Ajab
    Khan, Nadeem
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Shah, Munir H
    Ethnobotanical survey of medicinally important wild edible fruits species used by tribal communities of Lesser Himalayas-Pakistan2013In: Journal of Ethnopharmacology, ISSN 0378-8741, E-ISSN 1872-7573, Vol. 148, no 2, p. 528-536Article in journal (Refereed)
    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.

  • 4. Abeli, Thomas
    et al.
    Orsenigo, Simone
    Guzzon, Filippo
    Fae, Matteo
    Balestrazzi, Alma
    Carlsson-Graner, Ulla
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Mueller, Jonas V.
    Mondoni, Andrea
    Geographical pattern in the response of the arctic-alpine Silene suecica (Cariophyllaceae) to the interaction between water availability and photoperiod2015In: Ecological research, ISSN 0912-3814, E-ISSN 1440-1703, Vol. 30, no 2, p. 327-335Article in journal (Refereed)
    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.

  • 5. Abraham, Edit
    et al.
    Miskolczi, Pal
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Ayaydin, Ferhan
    Yu, Ping
    Kotogany, Edit
    Bako, Laszlo
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, 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 cells2011In: Journal of Experimental Botany, ISSN 0022-0957, E-ISSN 1460-2431, Vol. 62, no 6, p. 2155-2168Article in journal (Refereed)
    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.

  • 6.
    Abreu, Ilka Nacif
    et al.
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Ahnlund, Maria
    Moritz, Thomas
    Albrectsen, Benedicte R.
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    UHPLC-ESI/TOFMS Determination of Salicylate-like Phenolic Gycosides in Populus tremula Leaves2011In: Journal of Chemical Ecology, ISSN 0098-0331, E-ISSN 1573-1561, Vol. 37, no 8, p. 857-70Article in journal (Refereed)
    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.

  • 7. Achouiti, Ahmed
    et al.
    Vogl, Thomas
    Urban, Constantin F
    Umeå University, Faculty of Medicine, Department of Clinical Microbiology, Clinical Bacteriology. Umeå University, Faculty of Medicine, Molecular Infection Medicine Sweden (MIMS).
    Röhm, Marc
    Umeå University, Faculty of Medicine, Molecular Infection Medicine Sweden (MIMS). Umeå University, Faculty of Medicine, Department of Clinical Microbiology, Clinical Bacteriology.
    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 sepsis2012In: PLoS Pathogens, ISSN 1553-7374, Vol. 8, no 10, p. e1002987-Article in journal (Refereed)
    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.

  • 8.
    Adhikari, Deepak
    Umeå University, Faculty of Medicine, Department of Medical Biochemistry and Biophysics.
    Signaling pathways in the development of female germ cells2014Doctoral thesis, comprehensive summary (Other academic)
    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.

  • 9.
    Adhikari, Deepak
    et al.
    Umeå University, Faculty of Medicine, Department of Medical Biochemistry and Biophysics.
    Flohr, Gilian
    Hogeschool Leiden, Zernikedreef 11,2333 CK Leiden, The Netherlands.
    Gorre, Nagaraju
    Umeå University, Faculty of Medicine, Department of Medical Biochemistry and Biophysics.
    Shen, Yan
    Umeå University, Faculty of Medicine, Department of Medical Biochemistry and Biophysics.
    Yang, Hairu
    Umeå University, Faculty of Medicine, Department of Medical Biochemistry and Biophysics.
    Lundin, Eva
    Umeå University, Faculty of Medicine, Department of Medical Biosciences, Pathology.
    Lan, Zijian
    University of Louisville Health Sciences Center, Louisville, Kentucky, USA.
    Liu, Kui
    Umeå University, Faculty of Medicine, Department of Medical Biochemistry and Biophysics.
    Disruption of Tsc2 in oocytes leads to overactivation of the entire pool of primordial follicles2009In: Molecular human reproduction, ISSN 1360-9947, E-ISSN 1460-2407, Vol. 15, no 12, p. 765-770Article in journal (Refereed)
    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.

  • 10. Aeinehband, Shahin
    et al.
    Brenner, Philip
    Stahl, Sara
    Bhat, Maria
    Fidock, Mark D.
    Khademi, Mohsen
    Olsson, Tomas
    Engberg, Goran
    Jokinen, Jussi
    Umeå University, Faculty of Medicine, Department of Clinical Sciences, Psychiatry.
    Erhardt, Sophie
    Piehl, Fredrik
    Cerebrospinal fluid kynurenines in multiple sclerosis: relation to disease course and neurocognitive symptoms2016In: Brain, behavior, and immunity, ISSN 0889-1591, E-ISSN 1090-2139, Vol. 51, p. 47-55Article in journal (Refereed)
    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.

  • 11. Aerts, R.
    et al.
    Callaghan, T. V.
    Dorrepaal, E.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. 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 species2012In: Oecologia, ISSN 0029-8549, E-ISSN 1432-1939, Vol. 170, no 3, p. 809-819Article in journal (Refereed)
    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.

  • 12. Agostinelli, Marta
    et al.
    Cleary, Michelle
    Martin, Juan A.
    Albrectsen, Benedicte R.
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Witzell, Johanna
    Pedunculate Oaks (Quercus robur L.) Differing in Vitality as Reservoirs for Fungal Biodiversity2018In: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 9, article id 1758Article in journal (Refereed)
    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.

  • 13. Aguiar, Francisca C.
    et al.
    Segurado, Pedro
    Martins, Maria Joao
    Bejarano, Maria Dolores
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Nilsson, Christer
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Portela, Maria Manuela
    Merritt, David M.
    The abundance and distribution of guilds of riparian woody plants change in response to land use and flow regulation2018In: Journal of Applied Ecology, ISSN 0021-8901, E-ISSN 1365-2664, Vol. 55, no 5, p. 2227-2240Article in journal (Refereed)
    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.

  • 14.
    Aguilar, Ximena
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Folding and interaction studies of subunits in protein complexes2014Doctoral thesis, comprehensive summary (Other academic)
    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.

  • 15.
    Aguilar, Ximena
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Blomberg, Jeanette
    Umeå University, Faculty of Medicine, Department of Medical Biochemistry and Biophysics.
    Brännström, Kristoffer
    Umeå University, Faculty of Medicine, Department of Medical Biochemistry and Biophysics.
    Olofsson, Anders
    Umeå University, Faculty of Medicine, Department of Medical Biochemistry and Biophysics.
    Schleucher, Jurgen
    Umeå University, Faculty of Medicine, Department of Medical Biochemistry and Biophysics.
    Björklund, Stefan
    Umeå University, Faculty of Medicine, Department of Medical Biochemistry and Biophysics.
    Interaction Studies of the Human and Arabidopsis thaliana Med25-ACID Proteins with the Herpes Simplex Virus VP16-and Plant-Specific Dreb2a Transcription Factors2014In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 9, no 5, p. e98575-Article in journal (Refereed)
    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.

  • 16.
    Aguilo, Francesca
    et al.
    Umeå University, Faculty of Medicine, Department of Medical Biosciences. Umeå University, Faculty of Medicine, Wallenberg Centre for Molecular Medicine at Umeå University (WCMM). 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 reprogramming2017In: Current Opinion in Genetics and Development, ISSN 0959-437X, E-ISSN 1879-0380, Vol. 46, p. 77-82Article, review/survey (Refereed)
    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.

  • 17.
    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 Differentiation2017In: Stem Cell Reports, ISSN 2213-6711, Vol. 9, no 1, p. 92-107Article in journal (Refereed)
    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.

  • 18. Ahad, Abdul
    et al.
    Keech, Olivier
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Sjödin, Andreas
    Lindén, Pernilla
    Brouwer, Bastiaan
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Stenlund, Hans
    Moritz, Thomas
    Jansson, Stefan
    Gardeström, Per
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Comparison between leaves from darkened plants and individually-darkened leaves reveals differential metabolic strategies in response to darknessManuscript (preprint) (Other academic)
  • 19.
    Ahlgren, Gunnel
    et al.
    Department of Ecology and Evolution (Limnology), Uppsala University, Uppsala, Sweden.
    Vrede, Tobias
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    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?2009In: Lipids in Aquatic Ecosystems / [ed] Martin Kainz, Michael T. Brett, Michael T. Arts, New York: Springer-Verlag New York, 2009, p. 147-178Chapter in book (Other academic)
    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).

  • 20.
    Ahlinder, Jon
    et al.
    Division of CBRN Defence and Security, FOI, Swedish Defence Research Agency, Umeå, Sweden.
    Mathisen, Peter
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Sjödin, Andreas
    Umeå University, Faculty of Science and Technology, Department of Chemistry. 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 University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    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 compositionManuscript (preprint) (Other academic)
    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.

  • 21.
    Ahlm, Kristoffer
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Prey specialization and diet of frogs in Borneo2015Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    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.

     

     

     

  • 22. Ahlstrand, Tuuli
    et al.
    Tuominen, Heidi
    Beklen, Arzu
    Torittu, Annamari
    Oscarsson, Jan
    Umeå University, Faculty of Medicine, Department of Odontology.
    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-82017In: Virulence, ISSN 2150-5594, E-ISSN 2150-5608, Vol. 8, no 2, p. 115-134Article in journal (Refereed)
    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.

  • 23.
    Ahmad, Irfan
    et al.
    Umeå University, Faculty of Medicine, Department of Molecular Biology (Faculty of Medicine). 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 Typhimurium2016In: Microbial Cell Factories, ISSN 1475-2859, E-ISSN 1475-2859, Vol. 15, article id 177Article in journal (Refereed)
    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.

  • 24. Ahmad, S.
    et al.
    Zhao, W.
    Renström, F.
    Rasheed, A.
    Zaidi, M.
    Samuel, M.
    Shah, N.
    Mallick, N. H.
    Shungin, Dmitry
    Umeå University, Faculty of Medicine, Department of Public Health and Clinical Medicine, Medicine. Umeå University, Faculty of Medicine, Department of Odontology.
    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 adults2016In: International Journal of Obesity, ISSN 0307-0565, E-ISSN 1476-5497, Vol. 40, no 1, p. 186-190Article in journal (Refereed)
    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.

  • 25. Ahn, Ji Hoon
    et al.
    Schmid, Markus
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Editorial overview: Growth and development: Change is in the air: how plants modulate development in response to the environment2017In: Current opinion in plant biology, ISSN 1369-5266, E-ISSN 1879-0356, Vol. 35, p. IV-VIArticle in journal (Refereed)
  • 26.
    Aigner, Harald
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Characterization of FtsH proteases in the annual plant Arabidopsis thaliana2012Doctoral thesis, comprehensive summary (Other academic)
    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. 

  • 27.
    Aigner, Harald
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Wagner, Raik
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Sjögren, Lars
    Eubel, Holger
    Millar, Harvey
    Clarke, Adrian
    Funk, Christiane
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    FtsH11 protease is required for Arabidopsis thaliana to adapt to gtowth in continuous lightManuscript (preprint) (Other academic)
    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.

  • 28.
    Ajaikumar, Samikannu
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Ahlkvist, Johan
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Larsson, William
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Shchukarev, Andrey
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Kordas, K
    Mikkola, Jyri-Pekka
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Laboratory of Industrial Chemistry and Reaction Engineering, Process Chemistry Centre, Åbo Akademi University, Piispankatu 8, FIN-20500, Turku/Åbo, Finland.
    Oxidation of α-pinene over gold containing bimetallic nanoparticles supported on reducible TiO2 by DPU method2011In: Applied Catalysis A: General, ISSN 0926-860X, E-ISSN 1873-3875, Vol. 392, no 1-2, p. 11-18Article in journal (Refereed)
    Abstract [en]

    A series of bimetallic catalysts Au–M (where M = Cu, Co and Ru) were supported on a reducible TiO2 oxide via deposition-precipitation (DP) method with a slow decomposition of urea as the precipitating agent. The characteristic structural features of the prepared materials were characterized by various physico-chemical techniques such as X-ray photoelectron spectroscopy (XPS), and transmission electron microscopy (TEM). XPS results indicated the formation of alloyed bimetallic particles on the TiO2 support. TEM results confirmed the fine dispersion of metal nanoparticles on the support with an average particle size in the range of 3–5 nm. An industrially important process, oxy-functionalization of α-pinene was carried out over the prepared bimetallic heterogeneous catalysts under liquid phase conditions. Reaction parameters such as the reaction time, temperature, and the effect of solvent were studied for optimal conversion of α-pinene into verbenone. The major products obtained were verbenone, verbenol, α-pinene oxide and alkyl-pinene peroxide. The activity of the catalysts followed the order; AuCu/TiO2 > AuCo/TiO2 > Cu/TiO2 > Au/TiO2 > AuRu/TiO2. Upon comparison of the various catalysts, AuCu/TiO2 was found to be an active and selective catalyst towards the formation of verbenone. The temperature, nature of the catalysts and the choice of solvents greatly influenced the reaction rate.

  • 29.
    Akram, Neelam
    Linnéuniversitetet, Institutionen för biologi och miljö (BOM).
    From genes to ecological function in marine bacteria2013Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Bacteria in the sea are constantly exposed to environmental challenges (e.g. variations in nutrient concentrations, temperature and light conditions), and therefore appropriate gene expression response strategies to cope with them efficiently are evolved. This thesis investigates some interconnected questions regarding such adaptive strategies employed by marine bacteria.

    The recently discovered ability of bacteria to use the membrane protein proteorhodopsin (PR) to harvest light energy for cell metabolism were investigated in Vibrio sp. AND4 and Dokdonia sp. MED134. PR phototrophy in AND4 promoted survival during starvation, the molecular basis for which were the upregulation of the PR gene by nutrient limitation rather than light. MED134, in contrast, uses PR phototrophy to grow better, and we discovered that the light-stimulated growth was stronger in seawater with the single carbon compound alanine compared to a mixture of complex organic matter. Thus, differences between bacteria in PR gene expression regulation in response to light, nutrients or organic matter quality critically determine the ecological role of PR phototrophy in the sea.

    Current observations that membrane transporters (including PR) are highly expressed in seawater inspired a comparative analysis of transporter distributions in marine bacteria. Totally, 192 transporter families were found in 290 genome-sequenced strains. Consistent differences, but also similarities, in the number of transporters were found between major bacterial groups. Interestingly, sodium transporters were found to be more abundant in PR-containing SAR11. These findings suggest that bacteria have inherently distinctive potentials to adapt to resource variations in the sea.

    To examine links between transcriptional responses and growth of bacteria under controlled environmental settings, a mesocosm phytoplankton bloom experiment was performed. Transcriptional analysis of the microbial community (i.e. metatranscriptomics) revealed 2800 categories of functional genes (SEED functions), of which around 10% were overrepresented in either the bloom mesocosms or the controls. Importantly, these functions indicated potential metabolic mechanisms (e.g. TonB mediated nutrient transport) by which bacteria took advantage of the bloom conditions.

    This thesis combines analyses of model organisms with community analysis and highlights the possibilities to identify important mechanisms that underlie the ecological success of different bacteria in the marine environment. 

  • 30. Aksmann, Anna
    et al.
    Shutova, Tatiana
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Samuelsson, Göran
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Tukaj, Zbigniew
    The mechanism of anthracene interaction with photosynthetic apparatus: A study using intact cells, thylakoid membranes and PS II complexes isolated from Chlamydomonas reinhardtii2011In: Aquatic Toxicology, ISSN 0166-445X, E-ISSN 1879-1514, Vol. 104, no 3-4, p. 205-210Article in journal (Refereed)
    Abstract [en]

    Intact cells of Chlamydomonas reinhardtii as well as isolated thylakoid membranes and photosystem II complexes were used to examine a possible mechanism of anthracene (ANT) interaction with the photosynthetic apparatus. Since ANT concentrations above 1 mM were required to significantly inhibit the rate of oxygen evolution in PS II membrane fragments it may indicate that the toxicant did not directly interact with this photosystem. On the other hand, stimulation of oxygen uptake by ANT-treated thylakoids suggested that ANT could either act as an artificial electron acceptor in the photosynthetic electron transport chain or function as an uncoupler. Electron transfer from excited chlorophyll to ANT is impossible due to the very low reduction potential of ANT and therefore we propose that toxic concentrations of ANT increase the thylakoid membrane permeability and thereby function as an uncoupler, enhancing electron transport in vitro. Hence, its unspecific interference with photosynthetic membranes in vitro suggests that the inhibitory effect observed on intact cell photosynthesis is caused by uncoupling of phosphorylation. 

  • 31.
    Alakpa, Enateri V.
    et al.
    Umeå University, Faculty of Medicine, Department of Integrative Medical Biology (IMB).
    Saeed, Anwer
    Chung, Peter
    Riehle, Mathis O.
    Gadegaard, Nikolaj
    Dalby, Matthew J.
    Cusack, Maggie
    The Prismatic Topography of Pinctada maxima Shell Retains Stem Cell Multipotency and Plasticity In Vitro2018In: Advanced Biosystems, ISSN 2366-7478, Vol. 2, no 6, article id 1800012Article in journal (Refereed)
    Abstract [en]

    The shell of the bivalve mollusc Pinctada maxima is composed of the calcium carbonate polymorphs calcite and aragonite (nacre). Mother-of-pearl, or nacre, induces vertebrate cells to undergo osteogenesis and has good osteointegrative qualities in vivo. The calcite counterpart, however, is less researched in terms of the response of vertebrate cells. This study shows that isolation of calcite surface topography from the inherent chemistry allows viable long-term culture of bone marrow derived mesenchymal stem cells (MSCs). Self-renewal is evident from the increased gene expression of the self-renewal markers CD63, CD166, and CD271 indicating that cells cultured on the calcite topography maintain their stem cell phenotype. MSCs also retain their multipotency and can undergo successful differentiation into osteoblasts and adipocytes. When directed to adipogenesis, MSCs cultured on prism replicas are more amenable to differentiation than MSCs cultured on tissue culture polystyrene indicating a higher degree of plasticity in MSCs growing on calcite P. maxima prismatic topography. The study highlights the potential of the calcite topography of P. maxima as a biomimetic design for supporting expansion of MSC populations in vitro, which is of fundamental importance if it meets the demands for autologous MSCs for therapeutic use.

  • 32.
    Alanentalo, Tomas
    Umeå University, Faculty of Medicine, Umeå Centre for Molecular Medicine (UCMM).
    Optical projection tomography based 3D-spatial and quantitative assessments of the diabetic pancreas2008Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The gastrointestinal tract comprises a number of digestive organs including the stomach and pancreas. The stomach is involved in the digestion and short term storage of food while the pancreas is a mixed endocrine and exocrine gland which provides the body with hormones and enzymes essential for nutritional utilisation. The pancreas consists of three different cell lineages, acinar, ductal and endocrine cells. The endocrine cells, organised in the islets of Langerhans, are scattered throughout the exocrine parenchyma and regulate blood glucose levels by production of hormones such as glucagon and insulin.

    The Nkx family of homeodomain proteins controls numerous processes during development. Previous studies have identified two members belonging to the Nkx6 subfamily of Nkx proteins, Nkx6.1 and Nkx6.2. We have described the cloning and embryonic expression pattern of Nkx6.3. All three members of the Nkx6 gene family were shown to be expressed in partially overlapping domains during the development of the gastrointestinal tract and the central nervous system. Nkx6.2 was also identified as a transient marker for pancreatic exocrine cells.

    Analysing gene expression patterns and morphological features in tissues and organs is often performed by stereologic sampling which is a labour-intensive two dimensional approach that rely on certain assumptions when calculating e.g. β-cell mass and islet number in the pancreas. By combined improvements in immunohistochemical protocols, computational processing and tomographic scanning, we have developed a methodology based on optical projection tomography (OPT) allowing for 3D visualisation and quantification of specifically labelled objects within intact adult mouse organs. In the pancreas, this technique allows for spatial and quantitative measurements of total islet number and β-cell mass. We have further developed a protocol allowing for high resolution regional analyses based on global OPT assessments of the pancreatic constitution. This methodology is likely to facilitate detailed cellular and molecular analysis of user defined regions of interest in the pancreas, at the same time providing information on the overall disease state of the gland.

    Type 1 diabetes mellitus (T1D) can occur at any age and is characterized by the marked inability of the pancreas to secrete insulin due to an autoimmune destruction of the insulin producing β-cells. Information on the key cellular and molecular events underlying the recruitment of lymphocytes, their infiltration of the islets of Langerhans and consequent β-cell destruction is essential for understanding the pathogenesis of T1D. Using the developed methodology we have recorded the spatial and quantitative distribution of islet β-cells and infiltrating lymphocytes in the non obese diabetic (NOD) mouse model for T1D. This study shows that the smaller islets, which are predominantly organised in the periphery of the organ, are the first to disappear during the progression of T1D. The larger islets appear more resistant and our data suggest that a compensatory proliferative process is going on side by side with the autoimmune-induced β-cell destruction. Further, the formation of structures resembling tertiary lymphoid organs (TLOs) in areas apparently unaffected by insulitis suggests that local factors may provide cues for the homing of these lymphocytes back to the pancreas.

  • 33. Al-Behadili, Ali
    et al.
    Uhler, Jay P.
    Berglund, Anna-Karin
    Peter, Bradley
    Doimo, Mara
    Umeå University, Faculty of Medicine, Department of Medical Biochemistry and Biophysics.
    Reyes, Aurelio
    Wanrooij, Sjoerd
    Umeå University, Faculty of Medicine, Department of Medical Biochemistry and Biophysics.
    Zeviani, Massimo
    Falkenberg, Maria
    A two-nuclease pathway involving RNase H1 is required for primer removal at human mitochondrial OriL2018In: Nucleic Acids Research, ISSN 0305-1048, E-ISSN 1362-4962, Vol. 46, no 18, p. 9471-9483Article in journal (Refereed)
    Abstract [en]

    The role of Ribonuclease H1 (RNase H1) during primer removal and ligation at the mitochondrial origin of light-strand DNA synthesis (OriL) is a key, yet poorly understood, step in mitochondrial DNA maintenance. Here, we reconstitute the replication cycle of L-strand synthesis in vitro using recombinant mitochondrial proteins and model OriL substrates. The process begins with initiation of DNA replication at OriL and ends with primer removal and ligation. We find that RNase H1 partially removes the primer, leaving behind the last one to three ribonucleotides. These 5′-end ribonucleotides disturb ligation, a conclusion which is supported by analysis of RNase H1-deficient patient cells. A second nuclease is therefore required to remove the last ribonucleotides and we demonstrate that Flap endonuclease 1 (FEN1) can execute this function in vitro. Removal of RNA primers at OriL thus depends on a two-nuclease model, which in addition to RNase H1 requires FEN1 or a FEN1-like activity. These findings define the role of RNase H1 at OriL and help to explain the pathogenic consequences of disease causing mutations in RNase H1.

  • 34.
    Albertsson, Jan
    Umeå University, Faculty of Science and Technology, Umeå Marine Sciences Centre (UMF).
    Trophic interactions involving mysid shrimps (Mysidacea) in the near-bottom habitat in the Baltic Sea2004In: Aquatic Ecology, ISSN 1386-2588, E-ISSN 1573-5125, Vol. 38, no 3, p. 457-469Article in journal (Refereed)
    Abstract [en]

    In a six month mesocosm tank experiment, hypotheses were tested concerning the role of benthopelagic mysid shrimps (Mysidacea) in the near-bottom food web of the Bothnian Sea, in the northern Baltic Sea. The first hypothesis tested was that the mysids interact, through predation, with benthic deposit-feeding Monoporeia affinis amphipods. A second hypothesis tested was that the sediment type is important for the overwintering success of the mysids. Changes in abundance and mass were recorded for M. affinis and mysids when separate and when coexisting, in two sediment types differing in organic content (food level); soft muddy clay (rich) and fine sand (poor). Despite the fact that newborn M. affinis offspring, a plausible target for predation by mysids, were present in substantial numbers in the tanks, no consistent evidence for any interaction between these taxa was found. The biomass of mysids was slightly higher in the muddy clay than in the sand tanks, and the mechanism behind this substrate effect is discussed. A third hypothesis, that the mysids interact with near-bottom zooplankton, was investigated. The tanks were continually supplied with in situ near-bottom sea-water containing a seminatural assemblage of near-bottom plankton. As a result of mysid predation, tanks with mysids had lower abundance and biomass of cyclopoid copepods than tanks without mysids. Thus, the major interaction found was predation on near-bottom zooplankton by mysids and it is suggested that this interaction could potentially be an important food link, especially during periods with low food availability in the pelagic system.

  • 35.
    Albertsson, Jan
    Umeå University, Faculty of Science and Technology, Umeå Marine Sciences Centre (UMF).
    Uppföljning av naturtypen 1140 blottade ler- och sandbottnar i Bottenviken och Södra Östersjön: En pilotstudie2016Report (Other (popular science, discussion, etc.))
  • 36.
    Albertsson, Jan
    et al.
    Umeå University, Faculty of Science and Technology, Umeå Marine Sciences Centre (UMF).
    Leonardsson, K
    Deposit-feeding amphipods (Monoporeia affinis) reduce the recruitment of copepod nauplii from benthic resting eggs in the northern Baltic Sea2001In: Marine Biology, ISSN 0025-3162, E-ISSN 1432-1793, Vol. 138, no 4, p. 793-801Article in journal (Refereed)
    Abstract [en]

    We experimentally investigated the effect of different densities of the burrowing, deposit-feeding amphipod Monoporeia affinis on the recruitment of zooplankton from benthic resting eggs. Intact sediment cores with in situ density and species composition of zooplankton resting eggs and benthic fauna were collected in the northern Bothnian Sea, part of the Baltic Sea. We removed as many M, affinis as possible from the cores and then added different numbers of ill. affinis to the cores to generate a range of densities. The cores were exposed to different densities of M. affinis for either 3 or 40 days, after which the hatched zooplankton was registered. One subset of the cores were initially incubated under low temperature (2-3 degreesC, to prevent hatching) for 37 days (the resting phase), to allow for effects of M. affinis on unhatched resting eggs. These cores were then incubated under higher temperature (13 degreesC) for 3 days (the hatching phase), to induce hatching and allow for effects on hatching or hatched specimens. In a second subset of cores with the same time and temperature schedule, the M. affinis density was experimentally reduced at the start of the hatching phase, to evaluate the effect of M. affinis during the hatching phase. To a third subset of cores, we immediately initiated the hatching phase, without an experimental resting phase, to evaluate the effects induced during the resting phase. The most common zooplankton species that hatched was Eurytemora affinis (Copepoda), followed by Bosmina longispina maritima (Cladocera). In all cores that were subjected to a resting phase, the numbers of hatched E. affinis were log-linearly negatively related to density of M. affinis. An increase of M. affinis density from 1,000 to 5,000 individuals m(-2), normal field densities, reduced the hatching by 60-70%. The negative impact was mainly exerted during the hatching phase, suggesting predation on, burial of or physical injury of hatching nauplii or eggs in a late development stage as likely mechanisms. Also, the number of B. longispina maritima that hatched was reduced by M. affinis during the hatching phase, but no clear relation to density of M. affinis could be identified. The results show that M. affinis can reduce recruitment to zooplankton from benthic resting eggs. Such impact by the benthos on resting stages of zooplankton is therefore a potentially significant link between the benthic and pelagic systems.

  • 37.
    Albertsson, Jan
    et al.
    Umeå University, Faculty of Science and Technology, Umeå Marine Sciences Centre (UMF).
    Leonardsson, K
    Impact of a borrowing deposit-feeder, Monoporeia affinis, on viable zooplankton resting eggs in the northern Baltic Sea2000In: Marine Biology, ISSN 0025-3162, E-ISSN 1432-1793, Vol. 136, no 4, p. 611-619Article in journal (Refereed)
    Abstract [en]

    We investigated the effect of different densities of the burrowing deposit-feeding amphipod Monoporeia affinis on the potential for recruitment of zooplankton from benthic resting eggs. Hatching of resting eggs was induced in the laboratory on sliced and resuspended 1-cm depth-sections of sediment cores, collected at six stations ill an archipelago area of the Gulf of Bothnia, Baltic Sea. The uppermost 5 cm of the sediment was studied. The most common species that hatched was Eurytemor affinis (Copepoda). Individuals from another copepod genus, Acartia, hatched in significant numbers only in the cores from two stations with low amphipod abundance. Cores from stations with high amphipod densities showed a deeper distribution of emerging E. affinis nauplii compared with stations with few amphipods: the oxidised sediment layer was also deeper at high M. affinis densities than at low. Total (0 to 5 cm strata pooled) number of hatched E. affinis nauplii was independent of amphipod density. This indicates that the effect of M. affinis on E. affinis eggs involves deeper burial due to bioturbation, rather than predation. Decreased benthic recruitment of zooplankton at localities with high M. affinis density is suggested, since more deeply positioned eggs are less likely to hatch. When hatching was induced in intact, non-sliced cores from one station, the number of E. affinis nauplii that hatched was on average 43% of the number that hatched in the upper centimetre of the sliced cores from the same station. This fraction (43%), if applied to the other stations, implied a potential for benthic recruitment of up to 80000 ind m(-2) for E. affinis. Due to its high abundance, M. affinis is likely to greatly reduce benthic recruitment of zooplankton in this system.

  • 38.
    Albrectsen, Benedicte Riber
    et al.
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Siddique, Abu Bakar
    Decker, Vicki Huizu Guo
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Unterseher, Martin
    Robinson, Kathryn M
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Both plant genotype and herbivory shape aspen endophyte communities2018In: Oecologia, ISSN 0029-8549, E-ISSN 1432-1939, Vol. 187, no 2, p. 535-545Article in journal (Refereed)
    Abstract [en]

    Salicinoid phenolic glycosides are common defence substances in salicaceous trees and specialist leaf beetles use these compounds for their own defence against predators. Salicinoids vary qualitatively and qualitatively in aspen (Populus tremula) and this variation has a genetic basis. The foliar endophyte mycobiome is plentiful and we hypothesised that it is related to plant genotype, potentially mediated by salicinoid composition, and that interactions with the leaf beetle Chrysomela tremula may alter this relationship. We studied these three-way interactions in controlled greenhouse experiments. Endophytic fungi were isolated from sterilised leaf tissues with and without beetle damage, and from beetles. We confirmed that endophyte composition was influenced by host genotype. Beetle activity added generalist morphs to the mycobiome that overrode the initial host association. Yeast-like genera (Cryptococcus and Rhodotorula) were isolated only from beetle-damaged tissues and from beetles, whereas fast-growing filamentous fungi dominated beetle-free control plants. Competition experiments between filamentous fungi of plant origin and beetle-related yeasts suggested interaction of both stimulating and inhibiting modes of action amongst the fungi. As a result, we detected examples of amensalism, commensalism, parasitism and competition between the morphs tested, but we found no evidence of mutualism, and consequently no co-evolutionary relationship could be demonstrated, between yeasts carried by beetles, host genotype and associated filamentous morphs. Endophyte studies are method-dependent and high-throughput sequencing technology best define the fungal mycobiome, culturing however continues to be a cheap way to provide fundamental ecological insights and it is also required for experimental studies.

  • 39. Alcocer, M. J. C.
    et al.
    Murtagh, G. J.
    Mirotti, L.
    Brans, A.
    Harnett, W.
    Rundqvist, Louise
    Umeå University, Faculty of Medicine, Department of Medical Biochemistry and Biophysics.
    Larsson, Göran
    Umeå University, Faculty of Medicine, Department of Medical Biochemistry and Biophysics.
    The allergenicity of 2S plant albumins2011In: Clinical and Experimental Allergy, ISSN 0954-7894, E-ISSN 1365-2222, Vol. 41, no 12, p. 1827-1827Article in journal (Refereed)
  • 40. Alekeyenko, Artyom A.
    et al.
    Ho, Joshua W. K.
    Peng, Shouyong
    Gelbart, Marnie
    Tolstorukov, Michael Y.
    Plachetka, Annette
    Kharchenko, Peter V.
    Jung, Youngsook L.
    Gorchakov, Andrey A.
    Larschan, Erica
    Gu, Tingting
    Minoda, Aki
    Riddle, Nicole C.
    Schwartz, Yuri B.
    Umeå University, Faculty of Medicine, Department of Molecular Biology (Faculty of Medicine).
    Elgin, Sarah C. R.
    Karpen, Gary H.
    Pirrotta, Vincenzo
    Kuroda, Mitzi I.
    Park, Peter J.
    Sequence-Specific Targeting of Dosage Compensation in Drosophila Favors an Active Chromatin Context2012In: PLoS Genetics, ISSN 1553-7390, Vol. 8, no 4, p. e1002646-Article in journal (Refereed)
    Abstract [en]

    The Drosophila MSL complex mediates dosage compensation by increasing transcription of the single X chromosome in males approximately two-fold. This is accomplished through recognition of the X chromosome and subsequent acetylation of histone H4K16 on X-linked genes. Initial binding to the X is thought to occur at "entry sites" that contain a consensus sequence motif ("MSL recognition element" or MRE). However, this motif is only similar to 2 fold enriched on X, and only a fraction of the motifs on X are initially targeted. Here we ask whether chromatin context could distinguish between utilized and non-utilized copies of the motif, by comparing their relative enrichment for histone modifications and chromosomal proteins mapped in the modENCODE project. Through a comparative analysis of the chromatin features in male S2 cells (which contain MSL complex) and female Kc cells (which lack the complex), we find that the presence of active chromatin modifications, together with an elevated local GC content in the surrounding sequences, has strong predictive value for functional MSL entry sites, independent of MSL binding. We tested these sites for function in Kc cells by RNAi knockdown of Sxl, resulting in induction of MSL complex. We show that ectopic MSL expression in Kc cells leads to H4K16 acetylation around these sites and a relative increase in X chromosome transcription. Collectively, our results support a model in which a pre-existing active chromatin environment, coincident with H3K36me3, contributes to MSL entry site selection. The consequences of MSL targeting of the male X chromosome include increase in nucleosome lability, enrichment for H4K16 acetylation and JIL-1 kinase, and depletion of linker histone H1 on active X-linked genes. Our analysis can serve as a model for identifying chromatin and local sequence features that may contribute to selection of functional protein binding sites in the genome.

  • 41.
    Alenius, Mattias
    et al.
    Umeå University, Faculty of Medicine, Department of Molecular Biology (Faculty of Medicine). Umeå University.
    Bohm, Staffan
    Umeå University, Faculty of Medicine, Department of Molecular Biology (Faculty of Medicine). Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology).
    Identification of a novel neural cell adhesion molecule-related gene with a potential role in selective axonal projection1997In: Journal of Biological Chemistry, ISSN 0021-9258, E-ISSN 1083-351X, Vol. 272, no 42, p. 26083-26086Article in journal (Refereed)
    Abstract [en]

    We describe here the cloning of mouse complementary DNAs encoding a novel protein, Rb-8 neural cell adhesion molecule (RNCAM), with a predicted extracellular region of five immunoglobulin Ca-type domains followed by two fibronectin type III domains, Alternative splicing is likely to generate two RNCAM isoforms, which are differently attached to the cell membrane, These structural features and overall sequence identity identify this protein as a novel member of a cell adhesion molecule subgroup together with vertebrate neural cell adhesion molecule, Aplysia cell adhesion molecule, and Drosophila fasciclin II, In insects, fasciclin II is present on a restricted subset of embryonic central nervous system axons where it controls selective axon fasciculation. Intriguingly, RNCAM likewise is expressed in subsets of olfactory and vomeronasal neurons with topographically defined axonal projections, The spatial expression RNCAM corresponds precisely to that of certain odorant receptor expression zones of the olfactory epithelium. These expression patterns thus render RNCAM the first described cell adhesion molecule with a potential regulatory role in formation of selective axonal projections important for olfactory sensory information coding.

  • 42.
    Alewell, C
    et al.
    Institute of Environmental Geosciences, University of Basel, Switzerland.
    Giesler, Reiner
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Klaminder, Jonatan
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Leifeld, J
    Agroscope Reckenholz-Tänikon Research Station ART, Switzerland.
    Rollog, M
    Institute of Environmental Geosciences, University of Basel, Switzerland.
    Stable carbon isotopes as indicators for micro-geomorphic changes in palsa peats2011In: Biogeoscience Discussions, ISSN 1810-6277, Vol. 8, no 1, p. 527-548Article in journal (Refereed)
    Abstract [en]

    Palsa peats are unique northern ecosystems formed under an arctic climate and characterizedby an unique biodiversity and ecology. The stability of the palsas are seriouslythreatened by climate warming which will change the permafrost dynamic and5 results in degradation of the mires. We used stable carbon isotope depth profiles intwo palsa mires of Northern Sweden to track environmental change during the formationof the mires. Carbon isotope (13C) depth profile of the yet undisturbed mireStorflaket indicated very low to no degradation of the peat in the water saturated depressions(hollows) but increased rates of anaerobic degradation at the Stordalen site.10 The latter might be induced by degradation of the permafrost cores in the uplifted areas(hummocks) and subsequent braking and submerging of the hummock peat intothe hollows due to climate warming. Carbon isotope depth profiles of hummocks indicateda turn from aerobic mineralisation to anaerobic degradation at a peat depthbetween 4 to 25 cm. The age of these turning point was 14C dated between 150 and15 670 years and could thus not be caused by anthropogenically induced climate change.We found the uplifting of the hummocks due to permafrost heave the most likely explanationfor our findings. We thus concluded that differences in carbon isotope profiles ofthe hollows might point to the disturbance of the mires due to climate warming or dueto differences in hydrology. The characteristic profiles of the hummocks are indicators20 for micro-geomorphic change during permafrost up heaving.

  • 43.
    Alexeyev, O. A.
    et al.
    Umeå University, Faculty of Medicine, Department of Medical Biosciences, Pathology.
    Jahns, A. C.
    Umeå University, Faculty of Medicine, Department of Medical Biosciences, Pathology.
    Sampling and detection of skin Propionibacterium acnes: Current status2012In: Anaerobe, ISSN 1075-9964, E-ISSN 1095-8274, Vol. 18, no 5, p. 479-483Article, review/survey (Refereed)
    Abstract [en]

    A connection between acne vulgaris and Propionibacterium acnes has long been suggested. Over the years, several human skin microbiota sampling methods have been evolved and applied, e.g. swab, scrape, extraction techniques including cyanoacrylate gel sampling as well as punch biopsy. Collected samples have been processed following various methodologies ranging from culture studies to probe labelling and molecular analysis. Direct visualization techniques have recently shown the existence of anatomically distinct skin P acnes populations: epidermal and follicular. P. acnes biofilms appear to be a common phenomenon. Current sampling approaches target different skin populations of P. acnes and the presence of microbial biofilms can influence the retrieval of P. acnes. The anatomical considerations must be taken into account while interpreting microbiological data. (C) 2012 Elsevier Ltd. All rights reserved.

  • 44.
    Alfredsson, Jessica
    Umeå University, Faculty of Social Sciences, Department of Psychology.
    INNOVATIVE TOOL-MODIFICATIONS AND TOOL SELECTIVITY IN NEW CALEDONIAN CROWS (CORVUS MONEDULOIDES)2012Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Tool-use and tool-manufacture are thought to require high cognitive skills and have been considered as an exclusive attribute to primates. Recent observations of New Caledonian crows (NCCs) challenge this assumption. In this study 13 NCCs were tested with two different tool production tasks. The NCC either had to straighten a hook or bend a stick to retrieve food from two different kinds of tree trunks. The result showed that 3/5 birds bent sticks and used them to retrieve food and 1/5 birds straightened hooks to retrieve food. The birds managed to solve both tasks but not the birds in the control group. This indicates that NCC's tool making is a flexible innovative act and not just an innate predisposition to bend flexible material. This finding is interesting given that recent studies on human children show that below 8 years of age children fail in similar innovative tool making tasks.

  • 45.
    Al-Furoukh, Natalie
    et al.
    Umeå University, Faculty of Medicine, Department of Medical Biochemistry and Biophysics.
    Ianni, Alessandro
    Nolte, Hendrik
    Hölper, Soraya
    Krüger, Marcus
    Wanrooij, Sjoerd
    Umeå University, Faculty of Medicine, Department of Medical Biochemistry and Biophysics.
    Braun, Thomas
    ClpX stimulates the mitochondrial unfolded protein response (UPRmt) in mammalian cells2015In: Biochimica et Biophysica Acta. Molecular Cell Research, ISSN 0167-4889, E-ISSN 1879-2596, Vol. 1853, no 10, p. 2580-2591Article in journal (Refereed)
    Abstract [en]

    Proteostasis is crucial for life and maintained by cellular chaperones and proteases. One major mitochondrial protease is the ClpXP complex, which is comprised of a catalytic ClpX subunit and a proteolytic ClpP subunit. Based on two separate observations, we hypothesized that ClpX may play a leading role in the cellular function of ClpXP. Therefore, we analyzed the effect of ClpX overexpression on a myoblast proteome by quantitative proteomics. ClpX overexpression results in the upregulation of markers of the mitochondria( proteostasis pathway, known as the "mitochondrial unfolded protein response" (UPRmt). Although this pathway is described in detail in Caenorhabditis elegans, it is not clear whether it is conserved in mammals. Therefore, we compared features of the classical nematode UPRmt with our mammalian ClpX-triggered UPRmt dataset. We show that they share the same retrograde mitochondria-to-nucleus signaling pathway that involves the key UPRmt transcription factor CHOP (also known as Ddit3, CEBPZ or GADD153). In conclusion, our data confirm the existence of a mammalian UPRmt that has great similarity to the C elegans pathway. Furthermore, our results illustrate that ClpX overexpression is a good and simple model to study the underlying mechanisms of the UPRmt in mammalian cells.

  • 46. Ali, Qasim
    et al.
    Haider, Muhammad Zulqurnain
    Iftikhar, Wasif
    Jamil, Sidra
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Department of Botany, Faculty of Science and Technology, Government College University, Faisalabad, Pakistan.
    Javed, M. Tariq
    Noman, Ali
    Iqbal, Muhammad
    Perveen, Rashida
    Drought tolerance potential of Vigna mungo L. lines as deciphered by modulated growth, antioxidant defense, and nutrient acquisition patterns2016In: Revista Brasileira de Botânica, ISSN 0100-8404, E-ISSN 1806-9959, Vol. 39, no 3, p. 801-812Article in journal (Refereed)
    Abstract [en]

    Water shortage is one of the major environmental constraints that hamper the crop productivity worldwide. The present study was aimed to examine the drought tolerance potential of seven cultivars/lines of Vigna mungo L. depending upon their germination behavior, seedling growth, antioxidative defense mechanism, and nutrient acquisition. An experiment was conducted in the growth chamber using petri-plates and laid out in a completely randomized design (CRD). Hoagland's nutrient solution supplemented with 12 % PEG-8000 (drought treatment) or without PEG-800 (control) was used. Drought stress significantly altered the germination attributes as well as biomass production of all the studied cultivars/lines. Least adversative effects of drought stress were recorded in lines M-01001-1 and M-6036-21, respectively. The studied cultivars/lines exhibited differential response for various biochemical attributes under drought stress. The maximum increase in MDA and SOD activities and protein content was recorded in line M-603621, while the maximum AsA was recorded in line M-01001-1. Drought stress resulted in a significant reduction of plant N, P, K, Ca, and Mg contents, while the plant iron (Fe) contents remained unaffected. Results revealed that cultivars/lines M-01001-1 and M-6036-21 exhibited enhanced performance in terms of nutrient acquisition when stressed by drought. Based upon seed germination behavior, plant biomass production, biochemical attributes and mineral elements, the cultivars/lines M-01001-1 and M-6036-21 were identified as drought tolerant, while M-97 and Arroj-II were identified as drought sensitive.

  • 47. Aljetlawi, A A
    et al.
    Albertsson, Jan
    Umeå University, Faculty of Science and Technology, Umeå Marine Sciences Centre (UMF).
    Leonardsson, K
    Effect of food and sediment pre-treatment in experiments with a deposit-feeding amphipod, Monoporeia affinis2000In: Journal of Experimental Marine Biology and Ecology, ISSN 0022-0981, E-ISSN 1879-1697, Vol. 249, no 2, p. 263-280Article in journal (Refereed)
    Abstract [en]

    We experimentally investigated the effects of different pre-treatments of the sediment, and the effect of daily addition of fresh phytoplankton, on the growth and survival of 1-year-old (1 +) individuals of the deposit feeder Monoporeia affinis (Amphipoda). We used three different types of sieved sediment: pre-frozen muddy clay, non-pre-frozen muddy clay, and fine sand. The muddy clay contained phytoplankton originating from the surface sediment sampled in the field during the late spring bloom. No phytoplankton was initially present in sand. The experiment lasted for 18 days. M. affinis responded to the daily phytoplankton addition by increasing growth. Phytoplankton addition had no significant effects on the survival of M. affinis. Upon phytoplankton addition, the sandy and non-frozen muddy clay gave similar growth and survival responses. In contrast, the pre-frozen sediment resulted in significantly lower growth and survival. The growth was negative in all treatments without phytoplankton. Thus, the high initial chlorophyll content in the muddy clay was not of sufficient quality or concentration to allow a positive growth response in M. affinis. The growth of M. affinis was significantly correlated with the reduction of the chlorophyll. Our results indicated that M. affinis is capable of assimilating settled phytoplankton with no, or only a few days' time delay. (C) 2000 Elsevier Science BN: All rights reserved.

  • 48.
    Alkhori, Liza
    et al.
    Linköpings universitet, Avdelningen för cellbiologi.
    Öst, Anita
    Linköpings universitet, Avdelningen för cellbiologi.
    Alenius, Mattias
    Linköpings universitet, Avdelningen för cellbiologi.
    The corepressor Atrophin specifies odorant receptor expression in Drosophila2014In: The FASEB Journal, ISSN 0892-6638, E-ISSN 1530-6860, Vol. 28, no 3, p. 1355-1364Article in journal (Refereed)
    Abstract [en]

    In both insects and vertebrates, each olfactory sensory neuron (OSN) expresses one odorant receptor (OR) from a large genomic repertoire. How a receptor is specified is a tantalizing question addressing fundamental aspects of cell differentiation. Here, we demonstrate that the corepressor Atrophin (Atro) segregates OR gene expression between OSN classes in Drosophila. We show that the knockdown of Atro result in either loss or gain of a broad set of ORs. Each OR phenotypic group correlated with one of two opposing Notch fates, Notch responding, Nba (N(on)), and nonresponding, Nab (N(off)) OSNs. Our data show that Atro segregates ORs expressed in the Nba OSN classes and helps establish the Nab fate during OSN development. Consistent with a role in recruiting histone deacetylates, immunohistochemistry revealed that Atro regulates global histone 3 acetylation (H3ac) in OSNs and requires Hdac3 to segregate OR gene expression. We further found that Nba OSN classes exhibit variable but higher H3ac levels than the Nab OSNs. Together, these data suggest that Atro determines the level of H3ac, which ensures correct OR gene expression within the Nba OSNs. We propose a mechanism by which a single corepressor can specify a large number of neuron classes.-Alkhori, L., Öst, A., Alenius, M. The corepressor Atrophin specifies odorant receptor expression in Drosophila.

  • 49. Allakhverdiev, Suleyman I.
    et al.
    Zharmukhamedov, Sergey K.
    Rodionova, Margarita V.
    Shuvalov, Vladimir A.
    Dismukes, Charles
    Shen, Jian-Ren
    Barber, James
    Samuelsson, Göran
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Govindjee,
    Vyacheslav (Slava) Klimov (1945-2017): A scientist par excellence, a great human being, a friend, and a Renaissance man2018In: Photosynthesis Research, ISSN 0166-8595, E-ISSN 1573-5079, Vol. 136, no 1, p. 1-16Article in journal (Other academic)
    Abstract [en]

    Vyacheslav Vasilevich (V.V.) Klimov (or Slava, as most of us called him) was born on January 12, 1945 and passed away on May 9, 2017. He began his scientific career at the Bach Institute of Biochemistry of the USSR Academy of Sciences (Akademy Nauk (AN) SSSR), Moscow, Russia, and then, he was associated with the Institute of Photosynthesis, Pushchino, Moscow Region, for about 50 years. He worked in the field of biochemistry and biophysics of photosynthesis. He is known for his studies on the molecular organization of photosystem II (PSII). He was an eminent scientist in the field of photobiology, a well-respected professor, and, above all, an outstanding researcher. Further, he was one of the founding members of the Institute of Photosynthesis in Pushchino, Russia. To most, Slava Klimov was a great human being. He was one of the pioneers of research on the understanding of the mechanism of light energy conversion and of water oxidation in photosynthesis. Slava had many collaborations all over the world, and he is (and will be) very much missed by the scientific community and friends in Russia as well as around the World. We present here a brief biography and some comments on his research in photosynthesis. We remember him as a friendly and enthusiastic person who had an unflagging curiosity and energy to conduct outstanding research in many aspects of photosynthesis, especially that related to PSII.

  • 50. Allan, Mohammed
    et al.
    Le Roux, Gael
    De Vleeschouwer, Francois
    Bindler, Richard
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Blaauw, Maarten
    Piotrowska, Natalia
    Sikorski, Jaroslaw
    Fagel, Nathalie
    High-resolution reconstruction of atmospheric deposition of trace metals and metalloids since AD 1400 recorded by ombrotrophic peat cores in Hautes-Fagnes, Belgium2013In: Environmental Pollution, ISSN 0269-7491, E-ISSN 1873-6424, Vol. 178, p. 381-394Article in journal (Refereed)
    Abstract [en]

    The objective of our study was to determine the trace metal accumulation rates in the Misten bog, Hautes-Fagnes, Belgium, and assess these in relation to established histories of atmospheric emissions from anthropogenic sources. To address these aims we analyzed trace metals and metalloids (Pb, Cu, Ni, As, Sb, Cr, Co, V, Cd and Zn), as well as Pb isotopes, using XRF, Q-ICP-MS and MC-ICP-MS, respectively in two 40-cm peat sections, spanning the last 600 yr. The temporal increase of metal fluxes from the inception of the Industrial Revolution to the present varies by a factor of 5-50, with peak values found between AD 1930 and 1990. A cluster analysis combined with Pb isotopic composition allows the identification of the main sources of Pb and by inference of the other metals, which indicates that coal consumption and metallurgical activities were the predominant sources of pollution during the last 600 years.

    (c) 2013 Elsevier Ltd. All rights reserved.

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