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  • 201. Barker, Hilary L.
    et al.
    Riehl, Jennifer F.
    Bernhardsson, Carolina
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Rubert-Nason, Kennedy F.
    Holeski, Liza M.
    Ingvarsson, Pär K.
    Lindroth, Richard L.
    Linking plant genes to insect communities: Identifying the genetic bases of plant traits and community composition2019In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 28, no 19, p. 4404-4421Article in journal (Refereed)
    Abstract [en]

    Community genetics aims to understand the effects of intraspecific genetic variation on community composition and diversity, thereby connecting community ecology with evolutionary biology. Thus far, research has shown that plant genetics can underlie variation in the composition of associated communities (e.g., insects, lichen and endophytes), and those communities can therefore be considered as extended phenotypes. This work, however, has been conducted primarily at the plant genotype level and has not identified the key underlying genes. To address this gap, we used genome‐wide association mapping with a population of 445 aspen (Populus tremuloides) genets to identify the genes governing variation in plant traits (defence chemistry, bud phenology, leaf morphology, growth) and insect community composition. We found 49 significant SNP associations in 13 Populus genes that are correlated with chemical defence compounds and insect community traits. Most notably, we identified an early nodulin‐like protein that was associated with insect community diversity and the abundance of interacting foundation species (ants and aphids). These findings support the concept that particular plant traits are the mechanistic link between plant genes and the composition of associated insect communities. In putting the “genes” into “genes to ecosystems ecology”, this work enhances understanding of the molecular genetic mechanisms that underlie plant–insect associations and the consequences thereof for the structure of ecological communities.

  • 202. Barrio, Isabel C.
    et al.
    Lindén, Elin
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Te Beest, Mariska
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Olofsson, Johan
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Rocha, Adrian
    Soininen, Eeva M.
    Alatalo, Juha M.
    Andersson, Tommi
    Asmus, Ashley
    Boike, Julia
    Bråthen, Kari Anne
    Bryant, John P.
    Buchwal, Agata
    Bueno, C. Guillermo
    Christie, Katherine S.
    Denisova, Yulia V.
    Egelkraut, Dagmar
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Ehrich, Dorothee
    Fishback, LeeAnn
    Forbes, Bruce C.
    Gartzia, Maite
    Grogan, Paul
    Hallinger, Martin
    Heijmans, Monique M. P. D.
    Hik, David S.
    Hofgaard, Annika
    Holmgren, Milena
    Høye, Toke T.
    Huebner, Diane C.
    Jónsdóttir, Ingibjorg Svala
    Kaarlejärvi, Elina
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Department of Biology, Vrije Universiteit Brussel (VUB), Brussels, Belgium.
    Kumpula, Timo
    Lange, Cynthia Y. M. J. G.
    Lange, Jelena
    Lévesque, Esther
    Limpens, Juul
    Macias-Fauria, Marc
    Myers-Smith, Isla
    van Nieukerken, Erik J.
    Normand, Signe
    Post, Eric S.
    Schmidt, Niels Martin
    Sitters, Judith
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Department of Biology, Vrije Universiteit Brussel (VUB), Brussels, Belgium.
    Skoracka, Anna
    Sokolov, Alexander
    Sokolova, Natalya
    Speed, James D. M.
    Street, Lorna E.
    Sundqvist, Maja K.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. The Center for Macroecology, Evolution and Climate, The Natural History Museum of Denmark, University of Copenhagen, Copenhagen Ø, Denmark.
    Suominen, Otso
    Tananaev, Nikita
    Tremblay, Jean-Pierre
    Urbanowicz, Christine
    Uvarov, Sergey A.
    Watts, David
    Wilmking, Martin
    Wookey, Philip A.
    Zimmermann, Heike H.
    Zverev, Vitali
    Kozlov, Mikhail V.
    Background invertebrate herbivory on dwarf birch (Betula glandulosa-nana complex) increases with temperature and precipitation across the tundra biome2017In: Polar Biology, ISSN 0722-4060, E-ISSN 1432-2056, Vol. 40, no 11, p. 2265-2278Article in journal (Refereed)
    Abstract [en]

    Chronic, low intensity herbivory by invertebrates, termed background herbivory, has been understudied in tundra, yet its impacts are likely to increase in a warmer Arctic. The magnitude of these changes is however hard to predict as we know little about the drivers of current levels of invertebrate herbivory in tundra. We assessed the intensity of invertebrate herbivory on a common tundra plant, the dwarf birch (Betula glandulosa-nana complex), and investigated its relationship to latitude and climate across the tundra biome. Leaf damage by defoliating, mining and gall-forming invertebrates was measured in samples collected from 192 sites at 56 locations. Our results indicate that invertebrate herbivory is nearly ubiquitous across the tundra biome but occurs at low intensity. On average, invertebrates damaged 11.2% of the leaves and removed 1.4% of total leaf area. The damage was mainly caused by external leaf feeders, and most damaged leaves were only slightly affected (12% leaf area lost). Foliar damage was consistently positively correlated with mid-summer (July) temperature and, to a lesser extent, precipitation in the year of data collection, irrespective of latitude. Our models predict that, on average, foliar losses to invertebrates on dwarf birch are likely to increase by 6-7% over the current levels with a 1 degrees C increase in summer temperatures. Our results show that invertebrate herbivory on dwarf birch is small in magnitude but given its prevalence and dependence on climatic variables, background invertebrate herbivory should be included in predictions of climate change impacts on tundra ecosystems.

  • 203.
    Barros, Jaime
    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).
    Serk, Henrik
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Granlund, Irene
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Pesquet, Edouard
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    The cell biology of lignification in higher plants2015In: Annals of Botany, ISSN 0305-7364, E-ISSN 1095-8290, Vol. 115, no 7, p. 1053-1074Article, review/survey (Refereed)
    Abstract [en]

    Background Lignin is a polyphenolic polymer that strengthens and waterproofs the cell wall of specialized plant cell types. Lignification is part of the normal differentiation programme and functioning of specific cell types, but can also be triggered as a response to various biotic and abiotic stresses in cells that would not otherwise be lignifying.

    Scope Cell wall lignification exhibits specific characteristics depending on the cell type being considered. These characteristics include the timing of lignification during cell differentiation, the palette of associated enzymes and substrates, the sub-cellular deposition sites, the monomeric composition and the cellular autonomy for lignin monomer production. This review provides an overview of the current understanding of lignin biosynthesis and polymerization at the cell biology level.

    Conclusions The lignification process ranges from full autonomy to complete co-operation depending on the cell type. The different roles of lignin for the function of each specific plant cell type are clearly illustrated by the multiple phenotypic defects exhibited by knock-out mutants in lignin synthesis, which may explain why no general mechanism for lignification has yet been defined. The range of phenotypic effects observed include altered xylem sap transport, loss of mechanical support, reduced seed protection and dispersion, and/or increased pest and disease susceptibility.

  • 204.
    Barros-Rios, Jaime
    et al.
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Malvar, Rosa A.
    Jung, Hans-Joachim G.
    Bunzel, Mirko
    Santiago, Rogelio
    Divergent selection for ester-linked diferulates in maize pith stalk tissues. Effects on cell wall composition and degradability2012In: Phytochemistry, ISSN 0031-9422, E-ISSN 1873-3700, Vol. 83, p. 43-50Article in journal (Refereed)
    Abstract [en]

    Cross-linking of grass cell wall components through diferulates (DFAs) has a marked impact on cell wall properties. However, results of genetic selection for DFA concentration have not been reported for any grass species. We report here the results of direct selection for ester-linked DFA concentration in maize stalk pith tissues and the associated changes in cell wall composition and biodegradability. After two cycles of divergent selection, maize populations selected for higher total DFA (DFAT) content (CHs) had 16% higher DFAT concentrations than populations selected for lower DFAT content (as). These significant DFA concentration gains suggest that DFA deposition in maize pith parenchyma cell walls is a highly heritable trait that is genetically regulated and can be modified trough conventional breeding. Maize populations selected for higher DFAT had 13% less glucose and 10% lower total cell wall concentration than CLs, suggesting that increased cross-linking of feruloylated arabinoxylans results in repacking of the matrix and possibly in thinner and firmer cell walls. Divergent selection affected esterified DFAT and monomeric ferulate ether cross link concentrations differently, supporting the hypothesis that the biosynthesis of these cell wall components are separately regulated. As expected, a more higher DFA ester cross-coupled arabinoxylan network had an effect on rumen cell wall degradability (CLs showed 12% higher 24-h total polysaccharide degradability than CHs). Interestingly, 8-8-coupled DFAs, previously associated with cell wall strength, were the best predictors of pith cell wall degradability (negative impact). Thus, further research on the involvement of these specific DFA regioisomers in limiting cell wall biodegradability is encouraged. (C) 2012 Elsevier Ltd. All rights reserved.

  • 205.
    Bartels, Pia
    et al.
    Department of Ecology and Genetics, Limnology, Uppsala University, Uppsala, Sweden.
    Hirsch, Philipp E.
    Svanbäck, Richard
    Eklöv, Peter
    Water Transparency Drives Intra-Population Divergence in Eurasian Perch (Perca fluviatilis)2012In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 7, no 8, p. e43641-Article in journal (Refereed)
    Abstract [en]

    Trait combinations that lead to a higher efficiency in resource utilization are important drivers of divergent natural selection and adaptive radiation. However, variation in environmental features might constrain foraging in complex ways and therefore impede the exploitation of critical resources. We tested the effect of water transparency on intra-population divergence in morphology of Eurasian perch (Perca fluviatilis) across seven lakes in central Sweden. Morphological divergence between near-shore littoral and open-water pelagic perch substantially increased with increasing water transparency. Reliance on littoral resources increased strongly with increasing water transparency in littoral populations, whereas littoral reliance was not affected by water transparency in pelagic populations. Despite the similar reliance on pelagic resources in pelagic populations along the water transparency gradient, the utilization of particular pelagic prey items differed with variation in water transparency in pelagic populations. Pelagic perch utilized cladocerans in lakes with high water transparency and copepods in lakes with low water transparency. We suggest that under impaired visual conditions low utilization of littoral resources by littoral perch and utilization of evasive copepods by pelagic perch may lead to changes in morphology. Our findings indicate that visual conditions can affect population divergence in predator populations through their effects on resource utilization.

  • 206.
    Bartels, Pia
    et al.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden.
    Hirsch, Philipp
    Svanbäck, Richard
    Eklöv, Peter
    Dissolved organic carbon reduces habitat coupling by top predators in lake ecosystems2016In: Ecosystems (New York. Print), ISSN 1432-9840, E-ISSN 1435-0629, Vol. 19, no 6, p. 955-967Article in journal (Refereed)
    Abstract [en]

    Increasing input of terrestrial dissolved organic carbon (DOC) has been identified as a widespread environmental phenomenon in many aquatic ecosystems. Terrestrial DOC influences basal trophic levels: it can subsidize pelagic bacterial production and impede benthic primary production via light attenuation. However, little is known about the impacts of elevated DOC concentrations on higher trophic levels, especially on top consumers. Here, we used Eurasian perch (Perca fluviatilis) to investigate the effects of increasing DOC concentrations on top predator populations. We applied stable isotope analysis and geometric morphometrics to estimate long-term resource and habitat utilization of perch. Habitat coupling, the ability to exploit littoral and pelagic resources, strongly decreased with increasing DOC concentrations due to a shift toward feeding predominantly on pelagic resources. Simultaneously, resource use and body morphology became increasingly alike for littoral and pelagic perch populations with increasing DOC, suggesting more intense competition in lakes with high DOC. Eye size of perch increased with increasing DOC concentrations, likely as a result of deteriorating visual conditions, suggesting a sensory response to environmental change. Increasing input of DOC to aquatic ecosystems is a common result of environmental change and might affect top predator populations in multiple and complex ways.

  • 207.
    Barthelemy, Helene
    et al.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Stark, Sari
    Rovaniemi, Finland.
    Olofsson, Johan
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Strong Responses of Subarctic Plant Communities to Long-Term Reindeer Feces Manipulation2015In: Ecosystems (New York. Print), ISSN 1432-9840, E-ISSN 1435-0629, Vol. 18, no 5, p. 740-751Article in journal (Refereed)
    Abstract [en]

    Deposition of feces is a key mechanism by which herbivores influence soil nutrient cycling and plant production, but the knowledge about its importance for plant production and community structure is still rudimental since experimental evidence is scarce. We thus performed a 7-year long reindeer feces manipulation experiment in two tundra vegetation types with contrasting nutrient availability and analyzed effects on plant community composition and soil nutrient availability. Despite feces being fairly nutrient poor, feces manipulation had strong effect on both the nutrient-poor heath and the nutrient-rich meadow. The strongest effect was detected when feces were added at high density, with a substantial increase in total vascular plant productivity and graminoids in the two communities. Doubling natural deposition of reindeer feces enhanced primary production and the growth of deciduous shrubs in the heath. By contrast, removal of feces decreased only the production of graminoids and deciduous shrubs in the heath. Although the response to feces addition was faster in the nutrient-rich meadow, after 7 years it was more pronounced in the nutrient-poor heath. The effect of feces manipulation on soil nutrient availability was low and temporarily variable. Our study provides experimental evidence for a central role of herbivore feces in regulating primary production when herbivores are abundant enough. Deposition of feces alone does, however, not cause dramatic vegetation shifts; to drive unproductive heath to a productive grass dominated state, herbivore trampling, and grazing are probably also needed.

  • 208.
    Barthelemy, Hélène
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Herbivores influence nutrient cycling and plant nutrient uptake: insights from tundra ecosystems2016Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Reindeer appear to have strong positive effects on plant productivity and nutrient cycling in strongly nutrient-limited ecosystems. While the direct effects of grazing on vegetation composition have been intensively studied, much less is known about the indirect effect of grazing on plant-soil interactions. This thesis investigated the indirect effects of ungulate grazing on arctic plant communities via soil nutrient availability and plant nutrient uptake.

    At high density, the deposition of dung alone increased plant productivity both in nutrient rich and nutrient poor tundra habitats without causing major changes in soil possesses. Plant community responses to dung addition was slow, with a delay of at least some years. By contrast, a 15N-urea tracer study revealed that nutrients from reindeer urine could be rapidly incorporated into arctic plant tissues. Soil and microbial N pools only sequestered small proportions of the tracer. This thesis therefore suggests a strong effect of dung and urine on plant productivity by directly providing nutrient-rich resources, rather than by stimulating soil microbial activities, N mineralization and ultimately increasing soil nutrient availability. Further, defoliation alone did not induce compensatory growth, but resulted in plants with higher nutrient contents. This grazing-induced increase in plant quality could drive the high N cycling in arctic secondary grasslands by providing litter of a better quality to the belowground system and thus increase organic matter decomposition and enhance soil nutrient availability. Finally, a 15N natural abundance study revealed that intense reindeer grazing influences how plants are taking up their nutrients and thus decreased plant N partitioning among coexisting plant species.

    Taken together these results demonstrate the central role of dung and urine and grazing-induced changes in plant quality for plant productivity. Soil nutrient concentrations alone do not reveal nutrient availability for plants since reindeer have a strong influence on how plants are taking up their nutrients. This thesis highlights that both direct and indirect effects of reindeer grazing are strong determinants of tundra ecosystem functioning. Therefore, their complex influence on the aboveground and belowground linkages should be integrated in future work on tundra ecosystem N dynamic.

  • 209.
    Barthelemy, Hélène
    et al.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Dorrepaal, Ellen
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Olofsson, Johan
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Defoliation of a grass is mediated by the positive effect of dung deposition, moss removal and enhanced soil nutrient contents: results from a reindeer grazing simulation experiment2019In: Oikos, ISSN 0030-1299, E-ISSN 1600-0706, Vol. 128, no 10, p. 1515-1524Article in journal (Refereed)
    Abstract [en]

    Herbivory is one of the key drivers shaping plant community dynamics. Herbivores can strongly influence plant productivity directly through defoliation and the return of nutrients in the form of dung and urine, but also indirectly by reducing the abundance of neighbouring plants and inducing changes in soil processes. However, the relative importance of these processes is poorly understood. We, therefore, established a common garden experiment to study plant responses to defoliation, dung addition, moss cover, and the soil legacy of reindeer grazing. We used an arctic tundra grazed by reindeer as our study system, and Festuca ovina, a common grazing-tolerant grass species as the model species. The soil legacy of reindeer grazing had the strongest effect on plants, and resulted in higher growth in soils originating from previously heavily-grazed sites. Defoliation also had a strong effect and reduced shoot and root growth and nutrient uptake. Plants did not fully compensate for the tissue lost due to defoliation, even when nutrient availability was high. In contrast, defoliation enhanced plant nitrogen concentrations. Dung addition increased plant production, nitrogen concentrations and nutrient uptake, although the effect was fairly small. Mosses also had a positive effect on aboveground plant production as long as the plants were not defoliated. The presence of a thick moss layer reduced plant growth following defoliation. This study demonstrates that grasses, even though they suffer from defoliation, can tolerate high densities of herbivores when all aspects of herbivores on ecosystems are taken into account. Our results further show that the positive effect of herbivores on plant growth via changes in soil properties is essential for plants to cope with a high grazing pressure. The strong effect of the soil legacy of reindeer grazing reveals that herbivores can have long-lasting effects on plant productivity and ecosystem functioning after grazing has ceased.

  • 210.
    Barthelemy, Hélène
    et al.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Dorrepaal, Ellen
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Olofsson, Johan
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Defoliation, soil grazing legacy, dung and moss cover influence growth and nutrient uptake of the common grass species, Festuca ovinaManuscript (preprint) (Other academic)
    Abstract [en]

    Herbivores can strongly influence plant growth directly through defoliation and the return of nutrients in the form of dung and urine but also indirectly by reducing the abundance of neighbouring plants and inducing changes in soil processes. The relative importance of these driving mechanisms of plant response to herbivory are still poorly understood. In a common garden experiment, we studied the aboveground and belowground responses of Festuca ovina, a grazing tolerant grass common in arctic secondary grassland, to defoliation, reindeer dung addition, changes in soil microclimate induced by the presence or the absence of a moss cover, and soil grazing legacy. Defoliation strongly reduced shoot and root growth and plant nutrient uptake. Plants did thus not compensate for the tissue lost due to defoliation, even at a higher nutrient availability. By contrast, defoliation enhanced plant N concentration and decreased plant C to N ratio. Soil from heavily grazed sites and dung addition increased plant production, plant N concentrations and nutrient uptake, although the effects of dung addition were only small. Mosses had a strong negative effect of root biomass and reduced plant compensatory growth after defoliation. Interestingly mosses also had facilitative effects on aboveground plant growth in absence of defoliation and on plant nutrient uptake and N concentrations. Although plants suffered severely from defoliation, they were also strongly favoured by the increased nutrient availability associated with herbivory. After two years, plants produced as much biomass when all positive and negative effects of herbivores were considered (defoliation, soil communities and nutrient availability under heavily grazing, dung addition and no moss cover) as in the ungrazed conditions (no defoliation, soil communities and nutrient availability under lightly grazing, no dung addition, a thick moss cover). This study indicates that graminoids can tolerate high densities of herbivores, although it suffer from defoliation directly, and suggests that changes in plant quality following defoliation and grazing-induced changes in soil processes are two key mechanisms through which herbivores can control plant productivity in arctic secondary grasslands. Plant tolerance to herbivory will depends on how herbivores utilise a pasture area and on the balance between the positive and the negative effects of grazing on plant growth.

  • 211.
    Barthelemy, Hélène
    et al.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Stark, Sari
    Arctic Center, University of Lapland, Rovaniemi, Finland.
    Kytöviita, Minna-Maarit
    Department of Biological and Environmental Science, University of Jyväskylä, Finland.
    Olofsson, Johan
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Grazing decreases N partitioning among coexisting plant species2017In: Functional Ecology, ISSN 0269-8463, E-ISSN 1365-2435, Vol. 31, no 11, p. 2051-2060Article in journal (Refereed)
    Abstract [en]

    1. Herbivores play a key role in shaping ecosystem structure and functions by influencing plant and microbial community composition and nutrient cycling.

    2. This study investigated the long-term effects of herbivores on plant resource acquisition. We explored differences in the natural delta N-15 signatures in plant, microbial and soil N pools, and examined mycorrhizal colonization in two tundra sites that have been either lightly or heavily grazed by reindeer for more than 50 years. The study examined changes in nutrient acquisition in five common tundra plants with contrasting traits and mycorrhiza status; the mycorrhizal dwarf shrubs, Betula nana, Vaccinium myrtillus and Empetrum hermaphroditum; a mycorrhizal grass, Deschampsia flexuosa, and a non-mycorrhizal sedge, Carex bigelowii.

    3. There were large variations in delta N-15 among coexisting plant species in the lightly grazed sites. This variation was dramatically reduced in the heavily grazed sites. At an individual species level, delta N-15 was higher in E. hermaphroditum and lower in C. bigelowii in the heavily grazed sites. Mycorrhizal colonization in B. nana and E. hermaphroditum roots were also lower in the heavily grazed sites. The delta N-15 signatures of the total soil N pool and of the microbial N pools were higher in the heavily grazed sites.

    4. Since the strong delta N-15 differentiation among plant species has been interpreted as a result of plants with different mycorrhizal types using different sources of soil nitrogen, we suggest that the lower variation in delta N-15 in heavily grazed sites indicates a lower niche differentiation in nitrogen uptake among plants. Reduced mycorrhizamediated nitrogen uptake by some of the species, a shift towards a more mineral nutrition due to higher nutrient turnover, and uptake of labile nitrogen from dung and urine in the heavily grazed sites could all contribute to the changes in plant delta N-15.

    5. We conclude that herbivores have the potential to influence plant nutrient uptake and provide the first data suggesting that herbivores decrease nutrient partitioning on the basis of chemical N forms among plant species. Reduced niche complementarity among species is potentially important for estimates of the effects of -herbivory on plant nutrient availability and species coexistence.

  • 212.
    Barthelemy, Hélène
    et al.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Stark, Sari
    Arctic Center, University of Lapland Rovaniemi, Finland.
    Michelsen, Anders
    Department of Biology, Terrestrial Ecology, University of Copenhagen 2. 4Center for Permafrost (CENPERM), University of Copenhagen.
    Olofsson, Johan
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Effect of herbivory on the fate of added 15N-urea in a grazed Arctic tundraManuscript (preprint) (Other academic)
    Abstract [en]

    Mammalian herbivores can strongly influence nitrogen cycling and herbivore urine could be an important component of the nutrient cycle in grazed ecosystems. Despite its potential role for ecosystem productivity and soil processes, the distribution of N from urine in the different ecosystem compartments is poorly understood. This study investigates the fate of 15N enriched urea applied above the plant canopy in two tundra sites either heavily or lightly grazed by reindeer for the last 50 years. We explored the fate of the 15N in the different ecosystem N pools at 2 weeks and 1 years following tracer addition. We hypothesized that cryptogams would take up most N under light grazing, but graminoids most N under heavy grazing. The 15N-urea was rapidly incorporated in cryptogams and aboveground parts of vascular plants, while the soil microbial pool and plant roots sequestered only a marginal proportion of the labelled N applied. Hence, urine addition supports a higher primary production in tundra since most of the nutrients released from urine could be assimilated by the aboveground components with little N reaching the belowground compartments. Mosses and lichens still constituted the largest sink of the 15N-urea 1 year after tracer addition at both levels of grazing intensity demonstrating their large ability to capture and retain N  from urine. Deciduous and evergreen shrubs were just as efficient as graminoids in taking up the 15N-urea. The total recovery of the labelled urea was lower in the heavily grazed sites, suggesting that reindeer reduce the N retention in the system. Rapid incorporation of the applied 15N-urea indicates that arctic plants can take advantage of a pulse of incoming N in the form of urea, which supports a higher primary production. However, whether urine also maintains a high production of forage plants depend on plant community composition, since most urea was recovered in non-forage plants for reindeer.

  • 213.
    Barthelemy, Hélène
    et al.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Stark, Sari
    Michelsen, Anders
    Olofsson, Johan
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Urine is an important nitrogen source for plants irrespective of vegetation composition in an Arctic tundra: Insights from a N-15-enriched urea tracer experiment2018In: Journal of Ecology, ISSN 0022-0477, E-ISSN 1365-2745, Vol. 106, no 1, p. 367-378Article in journal (Refereed)
    Abstract [en]

    1. Mammalian herbivores can strongly influence nitrogen (N) cycling and herbivore urine could be a central component of the N cycle in grazed ecosystems. Despite its potential role for ecosystem productivity and functioning, the fate of N derived from urine has rarely been investigated in grazed ecosystems. 2. This study explored the fate of N-15-enriched urea in tundra sites that have been either lightly or intensively grazed by reindeer for more than 50years. We followed the fate of the N-15 applied to the plant canopy, at 2weeks and 1year after tracer addition, in the different ecosystem N pools. 3. N-15-urea was rapidly incorporated in cryptogams and in above-ground parts of vascular plants, while the soil microbial pool and plant roots sequestered only a marginal proportion. Furthermore, the litter layer constituted a large sink for the N-15-urea, at least in the short term, indicating a high biological activity in the litter layer and high immobilization in the first phases of organic matter decomposition. 4. Mosses and lichens still constituted the largest sink for the N-15-urea 1year after tracer addition at both levels of grazing intensity demonstrating their large ability to capture and retain N from urine. Despite large fundamental differences in their traits, deciduous and evergreen shrubs were just as efficient as graminoids in taking up the N-15-urea. The total recovery of N-15-urea was lower in the intensively grazed sites, suggesting that reindeer reduce ecosystem N retention. 5. Synthesis. The rapid incorporation of the applied N-15-urea indicates that arctic plants can take advantage of a pulse of incoming N from urine. In addition, N-15 values of all taxa in the heavily grazed sites converged towards the N-15 values for urine, bringing further evidence that urine is an important N source for plants in grazed tundra ecosystems.

  • 214.
    Bas, A
    et al.
    Umeå University, Faculty of Medicine, Department of Clinical Microbiology, Immunology/Immunchemistry.
    Forsberg, G
    Umeå University, Faculty of Medicine, Department of Clinical Microbiology, Immunology/Immunchemistry. Umeå University, Faculty of Medicine, Department of Clinical Sciences, Paediatrics.
    Sjöberg, Veronika
    Umeå University, Faculty of Medicine, Department of Clinical Microbiology, Immunology/Immunchemistry.
    Hammarström, Sten
    Umeå University, Faculty of Medicine, Department of Clinical Microbiology, Immunology/Immunchemistry.
    Hernell, Olle
    Umeå University, Faculty of Medicine, Department of Clinical Sciences, Paediatrics.
    Hammarström, Marie-Louise
    Umeå University, Faculty of Medicine, Department of Clinical Microbiology, Immunology/Immunchemistry.
    Aberrant extrathymic T cell receptor gene rearrangement in the small intestinal mucosa: a risk factor for coeliac disease?2009In: Gut, ISSN 0017-5749, E-ISSN 1468-3288, Vol. 58, no 2, p. 189-195Article in journal (Refereed)
    Abstract [en]

    BACKGROUND: Coeliac disease is a small intestine enteropathy caused by permanent intolerance to wheat gluten. Gluten intake by patients with coeliac disease provokes a strong reaction by intestinal intraepithelial lymphocytes (IELs), which normalises on a gluten-free diet. AIM: To investigate whether impaired extrathymic T cell maturation and/or secondary T cell receptor (TCR) gene recombination in IELs are features of coeliac disease which could contribute to the failure of establishing tolerance to gluten.

    METHODS: Expression levels of the four splice-forms of recombination activating gene-1 (RAG1) mRNA and preT alpha-chain (preTalpha) mRNA were determined in IEL-subsets of children with coeliac disease and controls. Frequencies of RAG1 expressing IELs were determined by immunomorphometry.

    RESULTS: In controls, the RAG1-1A/2 splice-form selectively expressed outside the thymus, was dominant and expressed in both mature (TCR(+)) and immature (CD2(+)CD7(+)TCR(-)) IELs ( approximately 8 mRNA copies/18S rRNA U). PreTalpha was expressed almost exclusively in CD2(+)CD7(+)TCR(-) IELs ( approximately 40 mRNA copies/18S rRNA U). By contrast, RAG1 and preTalpha mRNA levels were low in patients with coeliac disease compared to controls, both with active disease and with inactive, symptom-free disease on a gluten-free diet (p values <0.01 for mature and <0.05 for immature IELs). Similarly, the frequencies of RAG1+ IELs were significantly lower in patients with coeliac disease compared to controls (p<0.001).

    CONCLUSIONS: Patients with coeliac disease appear to have an impaired capacity for extrathymic TCR gene rearrangement. This is an inherent feature, which probably plays a pivotal role in the failure to efficiently downregulate the T cell response to gluten.

  • 215.
    Bas, Anna
    et al.
    Umeå University, Faculty of Medicine, Department of Clinical Microbiology.
    Forsberg, Göte
    Umeå University, Faculty of Medicine, Department of Clinical Microbiology. Umeå University, Faculty of Medicine, Department of Clinical Sciences, Paediatrics.
    Hammarström, Sten
    Umeå University, Faculty of Medicine, Department of Clinical Microbiology.
    Hammarström, Marie-Louise
    Umeå University, Faculty of Medicine, Department of Clinical Microbiology.
    Utility of the housekeeping genes 18S rRNA, β-actin, and glyceraldehyde-3-phosphate-dehydrogenase (GAPDH) for normalisation in real-time quantitative RT-PCR analysis of gene expression in human T lymphocytes2004In: Scandinavian Journal of Immunology, ISSN 0300-9475, E-ISSN 1365-3083, Vol. 59, no 6, p. 566-573Article in journal (Refereed)
    Abstract [en]

    The accuracy of 18S rRNA, β-actin mRNA and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) mRNA as indicators of cell number when used for normalization in gene expression analysis of T lymphocytes at different activation stages was investigated. Quantitative real-time reverse transcriptase-polymerase chain reaction was used to determine the expression level of 18S rRNA, β-actin mRNA, GAPDH mRNA and mRNA for six cytokines in carefully counted samples of resting human peripheral blood mononuclear cells (PBMCs), intestinal lymphocytes and PBMCs subjected to polyclonal T-cell activation. The 18S rRNA level in activated and resting PBMCs and intestinal lymphocytes was essentially the same, while the levels of β-actin and GAPDH mRNAs fluctuated markedly upon activation. When isolated γδTCR+, CD4+ and CD8+ subpopulations were studied, 18S rRNA levels remained unchanged after 21 h of activation but increased slightly after 96 h. In contrast, there was a 30–70-fold increase of GAPDH mRNA/cell in these cell populations upon activation. Cytokine analysis revealed that only normalization to 18S rRNA gave a result that satisfactorily reflected their mRNA expression levels per cell. In conclusion, 18S rRNA was the most stable housekeeping gene and hence superior for normalization in comparative analyses of mRNA expression levels in human T lymphocytes.

  • 216. Bas, Anna
    et al.
    Hammarström, Sten
    Umeå University, Faculty of Medicine, Department of Clinical Microbiology, Immunology/Immunchemistry.
    Hammarström, Marie-Louise
    Umeå University, Faculty of Medicine, Department of Clinical Microbiology, Immunology/Immunchemistry.
    Extrathymic TCR gene rearrangement in human small intestine: identification of new splice forms of recombination activating gene-1 mRNA with selective tissue expression.2003In: Journal of Immunology, ISSN 0022-1767, E-ISSN 1550-6606, Vol. 171, no 7, p. 3359-71Article in journal (Refereed)
    Abstract [en]

    Two new 5'-untranslated region (5'UTR) exons were identified in the human gene for the lymphocyte-specific endonuclease recombination activating gene-1 (RAG1) required for the somatic recombination yielding functional Ag receptors. These 5'UTR exons were used in three different splice forms by jejunal lymphocytes of the T cell lineage. RAG1 mRNA containing the previously described 5'UTR exon was not expressed in these cells. Conversely, one of the new 5'UTR exons was not expressed in thymus. The new RAG1 mRNA splice forms were all expressed in immature T cells (CD2(+)CD7(+)CD3(-)). This cell population also expressed high levels of mRNA for the pre-T alpha-chain. In situ hybridization demonstrated jejunal cells expressing the new splice forms of RAG1 mRNA, both intraepithelially and in lamina propria. Pre-T alpha-chain mRNA-expressing cells were detected at the same sites. These results strongly suggest ongoing TCR gene rearrangement in human small intestinal mucosa, yielding T cells specially adapted for this environment. This seems to be achieved by two parallel processes, extrathymic T cell development and peripheral Ag-driven TCR editing.

  • 217.
    Bashar Shafiul, Shamrat
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Characterization of cell wall in transgenic aspen with modified xylan acetylation2015Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    ABSTRACT

    Mature plant cells are enclosed by inflexible wall made up of cellulose microfibrils, pectins, hemicelluloses and in some cases lignin. This cell wall provides the structure and the defense for plant cells. In secondary cell walls of dicotyledons, major hemicellulose is xylan consisting of β-(1, 4)-linked xylose units. Xylan is synthesized in Golgi apparatus by several enzymes activities. REDUCED WALL ACETYLATION (RWA) genes are involved in xylan acetylation. These genes were downregulated in hybrid aspen in order to reduce xylan acetylation activity during its biosynthesis. In addition, acetyl xylan esterase (FC2) from the fungus Aspergillus niger was expressed in hybrid aspen to modify xylan acetylation post-synthetically. In this work, I have studied effects of these modifications on wood cell wall composition.

    The cell wall components were sequentially extracted by using the small scale method and the weight of extractives, lignin, hemicelluloses and celluloses per weight of dry wood were determined. In addition, the Updegraff cellulose, Klason lignin contents per weight of extractive free wood were determined and monosugar compositions of non-cellulosic components were analyzed by methanolysis and Trimethylsilyl derivatisation (TMS). 

    I have found that content of cellulose determined by sequential extraction method was significantly increased in all constructs as compared to the wild type. Reduction of lignin (as determined by sequential extraction) was found in DFC2 construct and RWA RNAi 35S-AB and CD constructs. Furthermore, RWA RNAi 35S-CD and RWA RNAi WP-ABCD constructs showed decreased hemicellulose as compared to the wild type. Moreover, DFC2 constructs exhibited decrease in non-cellulosic sugars hydrolyzed during TMS. FC2 expressing lines showed a reduction in xylose which is the main building block of xylan. In contrast, glucose and galactose contents were increased. Inhibition of expression of all RWA genes (WP-ABCD) caused similar changes.

    Considering all the data I conclude that, reduced acetylation of xylan can affect extractability, biosynthesis or modification of polysaccharides and lignin in cell wall.

    Keywords: Cellulose microfibrils; pectins; hemicellulose; lignin, xylan; secondary wall; aspen; xylan biosynthesis; biosynthesis of polysaccharides. 

  • 218. Bassères, Eugénie
    et al.
    Coppotelli, Giuseppe
    Pfirrmann, Thorsten
    Andersen, Jens B
    Masucci, Maria
    Frisan, Teresa
    Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden.
    The ubiquitin C-terminal hydrolase UCH-L1 promotes bacterial invasion by altering the dynamics of the actin cytoskeleton2010In: Cellular Microbiology, ISSN 1462-5814, E-ISSN 1462-5822, Vol. 12, no 11, p. 1622-1633Article in journal (Refereed)
    Abstract [en]

    Invasion of eukaryotic target cells by pathogenic bacteria requires extensive remodelling of the membrane and actin cytoskeleton. Here we show that the remodelling process is regulated by the ubiquitin C-terminal hydrolase UCH-L1 that promotes the invasion of epithelial cells by Listeria monocytogenes and Salmonella enterica. Knockdown of UCH-L1 reduced the uptake of both bacteria, while expression of the catalytically active enzyme promoted efficient internalization in the UCH-L1-negative HeLa cell line. The entry of L. monocytogenes involves binding to the receptor tyrosine kinase Met, which leads to receptor phosphorylation and ubiquitination. UCH-L1 controls the early membrane-associated events of this triggering cascade since knockdown was associated with altered phosphorylation of the c-cbl docking site on Tyr1003, reduced ubiquitination of the receptor and altered activation of downstream ERK1/2- and AKT-dependent signalling in response to the natural ligand Hepatocyte Growth Factor (HGF). The regulation of cytoskeleton dynamics was further confirmed by the induction of actin stress fibres in HeLa expressing the active enzyme but not the catalytic mutant UCH-L1(C90S). These findings highlight a previously unrecognized involvement of the ubiquitin cycle in bacterial entry. UCH-L1 is highly expressed in malignant cells that may therefore be particularly susceptible to invasion by bacteria-based drug delivery systems.

  • 219. Battarbee, R.W.
    et al.
    Charles, D.F.
    Bigler, Christian
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Cumming, B.F.
    Renberg, Ingemar
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Diatoms as indicators of surface-water acidity2010In: The Diatoms: Applications for the Environmental and Earth Sciences / [ed] Smol, J. P. & Stoermer, E. F., Cambridge: Cambridge University Press, 2010, 2., p. 98-121Chapter in book (Refereed)
    Abstract [en]

    Lake acidification became an environmental issue of international significance in the late 1960s and early 1970s when Scandinavian scientists claimed that ‘acid rain’ was the principal reason why fish populations had declined dramatically in Swedish and Norwegian lakes (Odén, 1968; Jensen & Snekvik, 1972; Almer et al., 1974). Similar claims were being made at about the same time in Canada (Beamish & Harvey, 1972). However, these claims were not immediately accepted by all scientists. It was argued instead that acidification was due to natural factors or to changes in catchment land-use and management (Rosenqvist 1977, 1978; Pennington 1984; Krug & Frink, 1983).

    In the scientific debate that followed, diatom analysis played a pivotal role. It enabled the timing and extent of lake acidification to be reconstructed (Charles et al., 1989; Battarbee et al., 1990; Dixit et al., 1992a) and allowed the various competing hypotheses concerning the causes of lake acidification to be evaluated (Battarbee et al., 1985; Battarbee & Charles 1994; Emmett et al., 1994). However, diatoms had been recognized and used as indicators of water pH well before the beginning of this controversy. The ‘acid rain’ issue served to highlight the importance of diatoms and stimulated the advance of more robust and sophisticated techniques, especially the development of transfer functions for reconstructing lakewater pH and related hydrochemical variables.

    This chapter outlines the history of diatoms as pH indicators, and describes how diatoms are currently used in studies of acid and acidified waters.

  • 220. Bazzanti, Marcello
    et al.
    Mastrantuono, Luciana
    Pilotto, Francesca
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Depth-related response of macroinvertebrates to the reversal of eutrophication in a Mediterranean lake: Implications for ecological assessment2017In: Science of the Total Environment, ISSN 0048-9697, E-ISSN 1879-1026, Vol. 579, p. 456-465Article in journal (Refereed)
    Abstract [en]

    A better management of nutrient inflows into lakes has led to an improvement in their conditions (i.e. reversal of eutrophication) and the effects of this on macroinvertebrate communities that inhabit different lake-depth zones is largely unknown. This paper reports a comparison of macroinvertebrate communities living in the eulittoral, infralittoral and sublittoral/profundal zones of Lake Nemi (Central Italy) before and after its natural recovery from eutrophication following the deviation of domestic Wastewater. The infralittoral zone responded more rapidly than the other two depth-zones to the improved ecological conditions, as shown by larger differences in community composition between the two periods. In the eulittoral sand, the combined effects of hydromorphological pressures and reversal of eutrophication hindered the biotic response. In the eulittoral and infralittoral zones, typical taxa of mesotrophic waters appeared or increased their abundances after the eutrophication reversal. Benthic invertebrate response was slower in the sublittoral/profundal zone due to deoxygenation that continued to prevail in the deepest area of the lake during summer. However, both tolerant and more sensitive taxa were collected there for the first time. After the reversal of eutrophication, the percentage of molluscan + large crustaceans increased in the infralittoral zone, whereas the oligochaete/chironomid ratio decreased in both sublittoral/profundal and infralittoral zones. Functional feeding metrics (percentages of filter-feeders, collector-gatherers, miners and scrapers/grazers) differently tracked the reversal of eutrophication in the three depth-zones probably according to the effects of the-reduction of nutrients on food-web structure influencing macroinvertebrates. Biological Monitoring Working Party (BMWP) and the Average Score Per Taxon (ASPT) seemed to respond to eutrophication reversal only in the sublittoral/profundal zone, where deoxygenation plays a major role as a structuring agent of the community. Our results suggest that the effects of re-. versal of eutrophication can be better assessed by examining the response of the communities belonging to each zone individually. 

  • 221.
    Bañares de Dios, Guillermo
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Elucidating the role of CSK during early light response and chloroplast development2014Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Elucidating the role of CSK during early light response and chloroplast development

    Chloroplasts of higher plants have evolved from endosymbiotic, ancestor of modern prokaryotic cyanobacteria. During evolution most of the genes from the genome of the endosymbiont have moved to the nucleus of it host. As a consequence the components of the photosynthetic machinery are encoded both in the chloroplastic and in the nuclear genomes. Therefore, expression of both genomes must be tightly coordinated to ensure a simultaneous and stoichiometric biosynthesis of the chloroplast components at different developmental stages and under environmental or metabolic changes. This is achieved by a mechanism referred to as retrograde signalling. During retrograde signalling, signals are emitted from the chloroplast consisting on intracellular pathways emitted by the chloroplast communicating the status of the chloroplast and regulating the expression of nuclear genes encoding plastid components. The aim of this project was to elucidate the role of CSK (Chloroplast Sensor Kinase) in relation to previously described retrograde signalling components PRIN2 (Plastid Redox INsensitive 2) and GUN1 (Genomes UNcoupled 1). CSK is a plastid kinase involved in the long- term, acclimation response to balance the ratio between PSII and PSI by regulating the expression of psaA. The activity of CSK is regulated by the redox state of the plastoquinone pool. My work revealed that CSK is up- regulated upon light exposure. In addition, similarly to the prin2 and gun1 mutants, the csk mutant exhibited lower chlorophyll content, a striking yellow cotyledon tip phenotype, impaired chloroplast development and a down- regulation of PEP dependent genes psaA and psbA during a de- etiolation development and for the establishment of PEP activity in light. Furthermore, the similarity in the mutant phenotypes suggests that CSK is involved in the same signalling pathway as PRIN2 and GUN1.

  • 222.
    Becher, Maria
    Umeå University, Faculty of Science and Technology, Ecology and Environmental Science.
    Factors controlling benthic algae production in a subarctic lake2009Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
  • 223. Beck, Carole
    et al.
    Rodriguez-Vargas, José Manuel
    Boehler, Christian
    Robert, Isabelle
    Heyer, Vincent
    Hanini, Najat
    Gauthier, Laurent R.
    Tissier, Agnès
    Schreiber, Valérie
    Elofsson, Mikael
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    San Martin, Bernardo Reina
    Dantzer, Françoise
    PARP3, a new therapeutic target to alter Rictor/mTORC2 signaling and tumor progression in BRCA1-associated cancers2019In: Cell Death and Differentiation, ISSN 1350-9047, E-ISSN 1476-5403, Vol. 26, no 9, p. 1615-1630Article in journal (Refereed)
    Abstract [en]

    PARP3 has been shown to be a key driver of TGF beta-induced epithelial-to-mesenchymal transition (EMT) and sternness in breast cancer cells, emerging as an attractive therapeutic target. Nevertheless, the therapeutic value of PARP3 inhibition has not yet been assessed. Here we investigated the impact of the absence of PARP3 or its inhibition on the tumorigenicity of BRCA1-proficient versus BRCA1-deficient breast cancer cell lines, focusing on the triple-negative breast cancer subtype (TNBC). We show that PARP3 knockdown exacerbates centrosome amplification and genome instability and reduces survival of BRCA1-deficient TNBC cells. Furthermore, we engineered PARP3(-/- )BRCA1-deficient or BRCA1-proficient TNBC cell lines using the CRISPR/nCas9(D10A) gene editing technology and demonstrate that the absence of PARP3 selectively suppresses the growth, survival and in vivo tumorigenicity of BRCA1-deficient TNBC cells, mechanistically via effects associated with an altered Rictor/mTORC2 signaling complex resulting from enhanced ubiquitination of Rictor. Accordingly, PARP3 interacts with and ADP-ribosylates GSK3 beta, a positive regulator of Rictor ubiquitination and degradation. Importantly, these phenotypes were rescued by re-expression of a wild-type PARP3 but not by a catalytic mutant, demonstrating the importance of PARP3's catalytic activity. Accordingly, reduced survival and compromised Rictor/mTORC2 signaling were also observed using a cell-permeable PARP3-specific inhibitor. We conclude that PARP3 and BRCA1 are synthetic lethal and that targeting PARP3's catalytic activity is a promising therapeutic strategy for BRCA1-associated cancers via the Rictor/mTORC2 signaling pathway.

  • 224. Behl, Stephan
    et al.
    de Schryver, Vera
    Diehl, Sebastian
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Stibor, Herwig
    Trophic transfer of biodiversity effects: functional equivalence of prey diversity and enrichment?2012In: Ecology and Evolution, ISSN 2045-7758, Vol. 2, no 12, p. 3110-3122Article in journal (Refereed)
    Abstract [en]

    Producer diversity is frequently assumed to be detrimental to herbivores, because less edible taxa are more likely to dominate diverse communities. Many producers are, however, complementary in their resource use, and primary production is often positively related to producer diversity. We performed an experiment with microalgae and a generalist herbivore to explore the hypothesis that such positive effects are transferred up the food chain and are functionally comparable to effects of enrichment with a limiting resource. In both absence and presence of grazers, primary production was positively affected by both light supply and producer diversity. Survival, reproduction, and biomass of herbivores were also positively affected by light supply and producer diversity, with both factors contributing equally to grazer performance. We conclude that producer diversity can indeed have similar positive effects on secondary production as enrichment with a limiting resource and discuss conditions under which such positive effects are likely to dominate over negative ones.

  • 225.
    Behren, Sandra
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Westerlind, Ulrika
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Glycopeptides and -Mimetics to Detect, Monitor and Inhibit Bacterial and Viral Infections: Recent Advances and Perspectives2019In: Molecules, ISSN 1420-3049, E-ISSN 1420-3049, Vol. 24, no 6, article id 1004Article, review/survey (Refereed)
    Abstract [en]

    The initial contact of pathogens with host cells is usually mediated by their adhesion to glycan structures present on the cell surface in order to enable infection. Furthermore, glycans play important roles in the modulation of the host immune responses to infection. Understanding the carbohydrate-pathogen interactions are of importance for the development of novel and efficient strategies to either prevent, or interfere with pathogenic infection. Synthetic glycopeptides and mimetics thereof are capable of imitating the multivalent display of carbohydrates at the cell surface, which have become an important objective of research over the last decade. Glycopeptide based constructs may function as vaccines or anti-adhesive agents that interfere with the ability of pathogens to adhere to the host cell glycans and thus possess the potential to improve or replace treatments that suffer from resistance. Additionally, synthetic glycopeptides are used as tools for epitope mapping of antibodies directed against structures present on various pathogens and have become important to improve serodiagnostic methods and to develop novel epitope-based vaccines. This review will provide an overview of the most recent advances in the synthesis and application of glycopeptides and glycopeptide mimetics exhibiting a peptide-like backbone in glycobiology.

  • 226.
    Beier, Frank
    et al.
    Institute for Experimental Medicine, University of Erlangen-Nürnberg, Erlangen, Germany.
    Eerola, Iiro
    Department of Medical Biochemistry and Molecular Biology, University of Turku, Turku, Finland.
    Vuorio, Eero
    Department of Medical Biochemistry and Molecular Biology, University of Turku, Turku, Finland.
    Luvalle, Phyllis
    Department of Medical Biochemistry, University of Calgary, Calgary, Alberta, Canada.
    Reichenberger, Ernest
    Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA.
    Bertling, Wolf
    Institute for Genetics, University of Bayreuth, Bayreuth, Germany.
    von der Mark, Klaus
    Institute for Experimental Medicine, University of Erlangen-Nürnberg, Erlangen, Germany.
    Lammi, Mikko
    Variability in the upstream promoter and intron sequences of the human, mouse and chick type X collagen genes.1996In: Matrix Biology, ISSN 0945-053X, E-ISSN 1569-1802, Vol. 15, no 6, p. 415-422, article id 9049979Article in journal (Refereed)
    Abstract [en]

    The type X collagen gene is specifically expressed in hypertrophic chondrocytes during endochondral ossification. Transcription of the type X collagen gene by these differentiated cells is turned on at the same time as transcription of several other cartilage specific genes is switched off and before mineralization of the matrix begins. Analysis of type X collagen promoters for regulatory regions in different cell culture systems and in transgenic mice has given contradictory results suggesting major differences among species. To approach this problem, we have determined the nucleotide sequences of the two introns and upstream promoter sequences of the human and mouse type X collagen genes and compared them with those of bovine and chick. Within the promoter regions, we found three boxes of homology which are nearly continuous in the human gene but have interruptions in the murine gene. One of these interruptions was identified as a complex 1.9 kb repetitive element with homology to LINE, B1, B2 and long terminal repeat sequences. Regulatory elements of the human type X collagen gene are located upstream of the region where the repetitive element is inserted in the mouse gene, making it likely that the repetitive element is inserted between the coding region and regulatory sequences of the murine gene without interfering with its expression pattern. We also compared the sequences of the introns of both genes and found strong conservation. Comparisons of the mammalian sequences with promoter and first intron sequences of the chicken type X collagen gene revealed that only the proximal 120 nucleotides of the promoter were conserved, whereas all other sequences displayed no obvious homology to the murine and human sequences.

  • 227.
    Beier, Frank
    et al.
    Institute Experimental Medicine, University of Erlangen-Nürnberg, Erlangen, Germany.
    Lammi, Mikko
    Institute Experimental Medicine, University of Erlangen-Nürnberg, Erlangen, Germany.
    Bertling, Wolf
    Institute for Genetics, University of Bayreuth, Bayreuth, Germany.
    von der Mark, Klaus
    Institute Experimental Medicine, University of Erlangen-Nürnberg, Erlangen, Germany.
    Transcriptional regulation of the human type X collagen gene expression.1996In: Annals of the New York Academy of Sciences, ISSN 0077-8923, E-ISSN 1749-6632, Vol. 785, p. 209-211, article id 8702131Article in journal (Refereed)
  • 228.
    Beier, Frank
    et al.
    Institut für Experimentelle Medizin, Universität Erlangen-Nürnberg, Erlangen, Germany; Department of Medical Biochemistry, University of Calgary, Calgary, Canada.
    Vornehm, Silvia
    Institut für Experimentelle Medizin, Universität Erlangen-Nürnberg, Erlangen, Germany.
    Pöschl, Ernst
    Institut für Experimentelle Medizin, Universität Erlangen-Nürnberg, Erlangen, Germany.
    von der Mark, Klaus
    Institut für Experimentelle Medizin, Universität Erlangen-Nürnberg, Erlangen, Germany.
    Lammi, Mikko
    Department of Anatomy, University of Kuopio, Kuopio, Finland.
    Localization of silencer and enhancer elements in the human type X collagen gene.1997In: Journal of Cellular Biochemistry, ISSN 0730-2312, E-ISSN 1097-4644, Vol. 66, no 2, p. 210-218, article id 9213222Article in journal (Refereed)
    Abstract [en]

    Collagen type X is a short, network-forming collagen expressed temporally and spatially tightly controlled in hypertrophic chondrocytes during endochondral ossification. Studies on chicken chondrocytes indicate that the regulation of type X collagen gene expression is regulated at the transcriptional level. In this study, we have analyzed the regulatory elements of the human type X collagen (Col10a1) by reporter gene constructs and transient transfections in chondrogenic and nonchondrogenic cells. Four different promoter fragments covering up to 2,864 bp of 5'-flanking sequences, either including or lacking the first intron, were linked to luciferase reporter gene and transfected into 3T3 fibroblasts, HT1080 fibrosarcoma cells, prehypertrophic chondrocytes from the resting zone, hypertrophic chondrocytes, and chondrogenic cell lines. The results indicated the presence of three regulatory elements in the human Col10a1 gene besides the proximal promoter. First, a negative regulatory element located between 2.4 and 2.8 kb upstream of the transcription initiation site was active in all nonchondrogenic cells and in prehypertrophic chondrocytes. Second, a positive, but also non-tissue-specific positive regulatory element was present in the first intron. Third, a cell-type-specific enhancer element active only in hypertrophic chondrocytes was located between -2.4 and -0.9 kb confirming a previous report by Thomas et al. [(1995): Gene 160:291-296]. The enhancing effect, however, was observed only when calcium phosphate was either used for transfection or included in the culture medium after lipofection. These findings demonstrate that the rigid control of human Col10a1 gene expression is achieved by both positive and negative regulatory elements in the gene and provide the basis for the identification of factors binding to those elements.

  • 229.
    Bejarano, Maria D.
    et al.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Jansson, Roland
    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.
    The effects of hydropeaking on riverine plants: a review2018In: Biological Reviews, ISSN 1464-7931, E-ISSN 1469-185X, Vol. 93, no 1, p. 658-673Article, review/survey (Refereed)
    Abstract [en]

    Hydropeaking refers to frequent, rapid and short-term fluctuations in water flow and water levels downstream and upstream of hydropower stations. Such fluctuations are becoming increasingly common worldwide and are known to have far-reaching effects on riverine vegetation. Novel hydrology caused by hydropeaking has no natural correspondence in freshwater systems, and hence few species have adaptations to all its aspects. Here, we review the literature on hydropeaking effects on riverine plants and define the state of the information on this human alteration of riverine ecosystems. We focus on riparian plants, but also draw on information from aquatic plant species, which exhibit a wide variety of adaptations to inundation and associated processes. Riparian plants face both physiological and physical constraints because of the shifts between submergence and drainage, and erosion of substrates. At the population level, hydropeaking may favour dispersal within, but not between, reservoirs, but may hamper germination, establishment, growth and reproduction. At the community level, strong filtering towards easily dispersed, flexible, flood-tolerant and amphibious plants is expected, although few species share these traits. Hence, most riparian plant species are expected to disappear or be pushed towards the upper boundaries of the regulated river margin. Future research should examine more closely global variation in hydropeaking effects, including other taxonomic groups of species and the diversity of hydropeaking regimes. There is also a need for studies focusing on identifying the boundaries within which hydropeaking could operate without impairing plant life.

  • 230.
    Bejarano, Maria Dolores
    et al.
    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.
    Aguiar, Francisca Constanca
    Riparian plant guilds become simpler and most likely fewer following flow regulation2018In: Journal of Applied Ecology, ISSN 0021-8901, E-ISSN 1365-2664, Vol. 55, no 1, p. 365-376Article in journal (Refereed)
    Abstract [en]

    1. River regulation affects riparian systems world-wide and conservation and restoration efforts are essential to retain biodiversity, and the functioning and services of riverine ecosystems. Effects of regulation on plant species richness have been widely addressed, but the filtering effect of regulation on guilds has received less attention.

    2. We used a functional trait approach to identify adaptive plant strategies through regulation-tolerant traits and predict shifts of riparian vegetation communities in response to regulation. We analysed variation in functional diversity across gradients of hydrological alteration in northern Sweden in relation to modified timing and infrequent major floods, along with frequent short-term inundation.

    3. Functional richness was similar in all study sites, but species richness declined with increasing intensity of regulation, and the species lost were largely functionally redundant (i.e. co-existing species that have similar contribution to an ecosystem function). Guilds of species intolerant to waterlogging were particularly unsuccessful in most regulated sites as they were affected by hydropower dams which replace major fluvial disturbances with frequent short inundation events. We predict that this guild will disappear, with likely consequences for the entire riverine ecosystem.

    4. Synthesis and applications. We conclude that functional traits tolerant to waterlogging or submergence and lack of major fluvial disturbances were key to understanding our results. We suggest that the functional trait approach can be integrated with knowledge of other ecosystem components to provide an understanding of ecosystem function that can be used to guide fluvial ecosystem management.

  • 231. Beljantseva, Jelena
    et al.
    Kudrin, Pavel
    Andresen, Liis
    Umeå University, Faculty of Medicine, Molecular Infection Medicine Sweden (MIMS). Umeå University, Faculty of Medicine, Department of Molecular Biology (Faculty of Medicine).
    Shingler, Vicky
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology).
    Atkinson, Gemma C.
    Tenson, Tanel
    Hauryliuk, Vasili
    Umeå University, Faculty of Medicine, Molecular Infection Medicine Sweden (MIMS). Umeå University, Faculty of Medicine, Department of Molecular Biology (Faculty of Medicine). Institute of Technology, University of Tartu, 50411 Tartu, Estonia.
    Negative allosteric regulation of Enterococcus faecalis small alarmone synthetase RelQ by single-stranded RNA2017In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 114, no 14, p. 3726-3731Article in journal (Refereed)
    Abstract [en]

    The alarmone nucleotides guanosine pentaphosphate (pppGpp) and tetraphosphate (ppGpp), collectively referred to as (p)ppGpp, are key regulators of bacterial growth, stress adaptation, pathogenicity, and antibiotic tolerance. We show that the tetrameric small alarmone synthetase (SAS) RelQ from the Gram-positive pathogen Enterococcus faecalis is a sequence-specific RNA-binding protein. RelQ's enzymatic and RNA binding activities are subject to intricate allosteric regulation. (p)ppGpp synthesis is potently inhibited by the binding of single-stranded RNA. Conversely, RelQ's enzymatic activity destabilizes the RelQ: RNA complex. pppGpp, an allosteric activator of the enzyme, counteracts the effect of RNA. Tetramerization of RelQ is essential for this regulatory mechanism, because both RNA binding and enzymatic activity are abolished by deletion of the SAS-specific C-terminal helix 5 alpha. The interplay of pppGpp binding, (p)ppGpp synthesis, and RNA binding unites two archetypal regulatory paradigms within a single protein. The mechanism is likely a prevalent but previously unappreciated regulatory switch used by the widely distributed bacterial SAS enzymes.

  • 232. Bell, David
    et al.
    Hjältén, Joakim
    Nilsson, Christer
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Jørgensen, Dolly
    Johansson, Therese
    Forest restoration to attract a putative umbrella species, the white-backed woodpecker, benefited saproxylic beetles2015In: Ecosphere, ISSN 2150-8925, E-ISSN 2150-8925, Vol. 6, no 12, article id 278Article in journal (Refereed)
    Abstract [en]

    Umbrella species are often spatially demanding and have limited ability to adapt to environmental changes induced by human land-use. This makes them vulnerable to human encroachment. In Sweden, broadleaved trees are disadvantaged by forestry, and commercially managed forests are often deprived of dead wood. This has led to a situation where previously widespread top predators in saproxylic food webs, such as the white-backed woodpecker (Dendrocopos leucotos), have become species of conservation concern. The white-backed woodpecker is generally considered an umbrella species, and it has been linked to forests with large volumes of dead wood from broadleaved trees. In recent years, forest stands have been restored for the white-backed woodpecker, but post-treatment evaluations have rarely included other species that also occur in broad-leaved forests (co-occurring species). Many co-occurring species are saproxylic beetles. In this study, we collected saproxylic beetles and environmental data in restored and commercially managed forests to evaluate if habitat restoration for the white-backed woodpecker also benefited other species with similar habitat associations. We found that volumes of coarse woody debris were higher in restored than in commercially managed forests, and that a majority of man-made snags and downed logs were created from birch trees (Betula spp.). Most spruce trees (Picea abies) were extracted during forest restoration, and this opened up the forest canopy, and created stands dominated by broadleaved trees. Many saproxylic beetles were more common in restored forests, and there were significant differences in species composition between treatments. These differences were largely explained by species traits. Effects of sun-exposure were particularly important, but many beneficiary species were also linked to dead wood from broadleaved trees. Red-listed saproxylic beetles showed a similar pattern with more species and individuals in restored sites. The white-backed woodpecker is still critically endangered in Sweden, but important prey species are already responding to forest restoration at the stand level. We recognize that landscape-level improvements will be required to bring the white-backed woodpecker back, but also that the umbrella species concept can provide a useful framework for successful forest restoration as many co-occurring saproxylic beetle species seemingly benefitted from restoration for the white-backed woodpecker.

  • 233. Bellard, Celine
    et al.
    Englund, Göran
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Hugueny, Bernard
    Biotic and abiotic drivers of species loss rate in isolated lakes2019In: Journal of Animal Ecology, ISSN 0021-8790, E-ISSN 1365-2656, Vol. 88, no 6, p. 881-891Article in journal (Refereed)
    Abstract [en]

    Today, anthropogenic impacts are causing a serious crisis for global biodiversity, with rates of extinction increasing at an unprecedented rate. Extinctions typically occur after a certain delay, and understanding the mechanisms causing delays is a key challenge for both fundamental and applied perspectives. Here, we make use of natural experiments, the isolation of lakes by land uplift in Northern Scandinavia, to examine how yearly extinction rates are affected by time since isolation and a range of abiotic and biotic factors. In this aim, we adapted a model of delayed species loss within isolated communities to test the effects of time since isolation, area, pH, depth and the presence/absence of piscivores on extinction rates. As expected, we found that small and/or young lakes experience a higher annual rate of extinctions per species than larger and/or older ones. Compared to previous studies that were conducted for either young (few thousand years ago) or very old (>10,000 years ago) isolates, we demonstrated over a large and continuous temporal scales (50-5,000 years), similar relationship between extinction rates and age. We also show that extinction rates are modified by local environmental factors such as a strong negative effect of increasing pH. Our results urge for the need to consider the time since critical environmental changes occurred when studying extinction rates. In a wider perspective, our study demonstrates the need to consider extinction debts when modelling future effects of climate change, land-use changes or biological invasions on biodiversity.

  • 234.
    Bellini, Catherine
    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). Institut Jean-Pierre Bourgin, UMR 1318 INRA-AgroParisTech, Versailles, France.
    Pacurar, Daniel I
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Perrone, Irene
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Adventitious roots and lateral roots: similarities and differences2014In: Annual Review of Plant Biology, ISSN 1543-5008, E-ISSN 1545-2123, Vol. 65, p. 639-666Article, review/survey (Refereed)
    Abstract [en]

    In addition to its role in water and nutrient uptake, the root system is fundamentally important because it anchors a plant to its substrate. Although a wide variety of root systems exist across different species, all plants have a primary root (derived from an embryonic radicle) and different types of lateral roots. Adventitious roots, by comparison, display the same functions as lateral roots but develop from aerial tissues. In addition, they not only develop as an adaptive response to various stresses, such as wounding or flooding, but also are a key limiting component of vegetative propagation. Lateral and adventitious roots share key elements of the genetic and hormonal regulatory networks but are subject to different regulatory mechanisms. In this review, we discuss the developmental processes that give rise to lateral and adventitious roots and highlight knowledge acquired over the past few years about the mechanisms that regulate adventitious root formation.

  • 235.
    Benedict, Catherine
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Cold Acclimation: Dissecting the plant low temperature signaling pathway using functional genomics2006Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The physiological process of cold acclimation protects plants native to the temperate regions of the world from the deleterious effects of low and freezing temperatures. This is achieved by a series of transcriptional, regulatory, and metabolic changes that enable continued growth and survival. Within minutes of exposure to temperatures below ca. 10°C, a complex cascade of transcriptional events is initiated to accomplish these changes. The initial alarm phase favors the rapid induction of a library of stress proteins with protective functions (e.g. COR proteins). This is followed by a cold hardened phase, characterized by maximal freezing tolerance, which continues until either the stress is removed, or the plant's metabolic and/or developmental state can no longer support maximal resistance.

    We have studied some of the important transcription factors and transcriptional changes associated with the initial alarm and later hardened phases of cold acclimation in the herbaceous annual Arabidopsis thaliana and the woody perennial Populus spp. We confirmed the functionality of the CBF-mediated signaling cascade in Poplar overexpressing AtCBF1, but noted that regulon composition and endogenous poplar CBF ortholog induction appeared to be tissue-specific. The lack of statistically significant DRE enrichment in the Poplar AtCBF1 regulons led us to investige cis-element abundance in the cold-associated transcription factor regulons of publicly available microarray data from Arabidopsis, leading to the development of a gene voting method of microarray analysis that we used to test for regulatory associations between transcription factors and their downstream cis-elements and gene targets. This analysis resulted in a new transcriptional model of the ICE1-mediated signaling cascade and implicated a role for phytochrome A. Application of this same method to microarray data from arabidopsis leaves developed at low temperature allowed us to identify a new cis-element, called DDT, which possessed enhancer-blocking function during the alarm stage of cold stress, but was enriched in the promoters of genes upregulated during the later cold hardened stages. As leaf growth and development at low temperature correlated with the enhancement freeze tolerance in Arabidopsis, we compared the transcriptomes of rapidly growing and fully grown poplar leaves at night (when both low temperatures and PhyA status might play important roles in nature), in the hopes of comparing this data with that of cold-treated leaves in the future. We identified the nocturnal mode of leaf growth in Populus deltoides as predominantly proliferative as opposed to expansive, and potentially linked to cellular carbohydrate status.

  • 236.
    Benedict, Catherine
    et al.
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Geisler, Matt
    Trygg, Johan
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Huner, Norman
    Hurry, Vaughan
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Consensus by democracy. Using meta-analyses of microarray and genomic data to model the cold acclimation signaling pathway in Arabidopsis.2006In: Plant Physiology, ISSN 0032-0889, E-ISSN 1532-2548, Vol. 141, no 4, p. 1219-1232Article in journal (Refereed)
    Abstract [en]

    The whole-genome response of Arabidopsis (Arabidopsis thaliana) exposed to different types and durations of abiotic stress has now been described by a wealth of publicly available microarray data. When combined with studies of how gene expression is affected in mutant and transgenic Arabidopsis with altered ability to transduce the low temperature signal, these data can be used to test the interactions between various low temperature-associated transcription factors and their regulons. We quantized a collection of Affymetrix microarray data so that each gene in a particular regulon could vote on whether a cis-element found in its promoter conferred induction (+1), repression (–1), or no transcriptional change (0) during cold stress. By statistically comparing these election results with the voting behavior of all genes on the same gene chip, we verified the bioactivity of novel cis-elements and defined whether they were inductive or repressive. Using in silico mutagenesis we identified functional binding consensus variants for the transcription factors studied. Our results suggest that the previously identified ICEr1 (induction of CBF expression region 1) consensus does not correlate with cold gene induction, while the ICEr3/ICEr4 consensuses identified using our algorithms are present in regulons of genes that were induced coordinate with observed ICE1 transcript accumulation and temporally preceding genes containing the dehydration response element. Statistical analysis of overlap and cis-element enrichment in the ICE1, CBF2, ZAT12, HOS9, and PHYA regulons enabled us to construct a regulatory network supported by multiple lines of evidence that can be used for future hypothesis testing.

  • 237.
    Benedict, Catherine
    et al.
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Skinner, J. S.
    Meng, R.
    Chang, Y.
    Bhalerao, R.
    Finn, C.
    Chen, T. H. H.
    Umeå University, Faculty of Science and Technology.
    Hurry, Vaughan
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    The Role of the CBF-dependent Signalling Pathway in Woody Perennials2006In: Cold Hardiness in Plants: Molecular Genetics, Cell Biology and Physiology / [ed] T Chen, M Uemura, S Fujikawa, Wallingford: CABI Publishing, 2006, p. 167-180Chapter in book (Other academic)
  • 238. Benelli, Giovanni
    et al.
    Maggi, Filippo
    Pavela, Roman
    Murugan, Kadarkarai
    Govindarajan, Marimuthu
    Vaseeharan, Baskaralingam
    Petrelli, Riccardo
    Cappellacci, Loredana
    Kumar, Suresh
    Hofer, Anders
    Umeå University, Faculty of Medicine, Department of Medical Biochemistry and Biophysics.
    Youssefi, Mohammad Reza
    Alarfaj, Abdullah A.
    Hwang, Jiang-Shiou
    Higuchi, Akon
    Mosquito control with green nanopesticides: towards the One Health approach? A review of non-target effects2018In: Environmental science and pollution research international, ISSN 0944-1344, E-ISSN 1614-7499, Vol. 25, no 11, p. 10184-10206Article, review/survey (Refereed)
    Abstract [en]

    The rapid spread of highly aggressive arboviruses, parasites, and bacteria along with the development of resistance in the pathogens and parasites, as well as in their arthropod vectors, represents a huge challenge in modern parasitology and tropical medicine. Eco-friendly vector control programs are crucial to fight, besides malaria, the spread of dengue, West Nile, chikungunya, and Zika virus, as well as other arboviruses such as St. Louis encephalitis and Japanese encephalitis. However, research efforts on the control of mosquito vectors are experiencing a serious lack of eco-friendly and highly effective pesticides, as well as the limited success of most biocontrol tools currently applied. Most importantly, a cooperative interface between the two disciplines is still lacking. To face this challenge, we have reviewed a wide number of promising results in the field of green-fabricated pesticides tested against mosquito vectors, outlining several examples of synergy with classic biological control tools. The non-target effects of green-fabricated nanopesticides, including acute toxicity, genotoxicity, and impact on behavioral traits of mosquito predators, have been critically discussed. In the final section, we have identified several key challenges at the interface between "green" nanotechnology and classic biological control, which deserve further research attention.

  • 239. Bengtsson, Anders A.
    et al.
    Trygg, Johan
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Wuttge, Dirk M.
    Sturfelt, Gunnar
    Theander, Elke
    Donten, Magdalena
    Moritz, Thomas
    Sennbro, Carl-Johan
    Torell, Frida
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Lood, Christian
    Surowiec, Izabella
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Rännar, Stefan
    Lundstedt, Torbjörn
    Metabolic Profiling of Systemic Lupus Erythematosus and Comparison with Primary Sjögren’s Syndrome and Systemic Sclerosis2016In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 11, no 7, article id e0159384Article in journal (Refereed)
    Abstract [en]

    Systemic lupus erythematosus (SLE) is a chronic inflammatory autoimmune disease which can affect most organ systems including skin, joints and the kidney. Clinically, SLE is a heterogeneous disease and shares features of several other rheumatic diseases, in particular primary Sjögrens syndrome (pSS) and systemic sclerosis (SSc), why it is difficult to diag- nose The pathogenesis of SLE is not completely understood, partly due to the heterogeneity of the disease. This study demonstrates that metabolomics can be used as a tool for improved diagnosis of SLE compared to other similar autoimmune diseases. We observed differences in metabolic profiles with a classification specificity above 67% in the comparison of SLE with pSS, SSc and a matched group of healthy individuals. Selected metabolites were also significantly different between studied diseases. Biochemical pathway analysis was conducted to gain understanding of underlying pathways involved in the SLE pathogenesis. We found an increased oxidative activity in SLE, supported by increased xanthine oxidase activity and an increased turnover in the urea cycle. The most discriminatory metabolite observed was tryptophan, with decreased levels in SLE patients compared to control groups. Changes of tryptophan levels were related to changes in the activity of the aromatic amino acid decarboxylase (AADC) and/or to activation of the kynurenine pathway. 

  • 240. Bengtsson-Palme, Johan
    et al.
    Boulund, Fredrik
    Fick, Jerker
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Kristiansson, Erik
    Larsson, D. G. Joakim
    Shotgun metagenomics reveals a wide array of antibiotic resistance genes and mobile elements in a polluted lake in India2014In: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 5Article in journal (Refereed)
    Abstract [en]

    There is increasing evidence for an environmental origin of many antibiotic resistance genes. Consequently, it is important to identify environments of particular risk for selecting and maintaining such resistance factors. In this study, we described the diversity of antibiotic resistance genes in an Indian lake subjected to industrial pollution with fluoroquinolone antibiotics. We also assessed the genetic context of the identified resistance genes, to try to predict their genetic transferability. The lake harbored a wide range of resistance genes (81 identified gene types) against essentially every major class of antibiotics, as well as genes responsible for mobilization of genetic material. Resistance genes were estimated to be 7000 times more abundant than in a Swedish lake included for comparison, where only eight resistance genes were found. The sul2 and qnrD genes were the most common resistance genes in the Indian lake. Twenty-six known and 21 putative novel plasmids were recovered in the Indian lake metagenome, which, together with the genes found, indicate a large potential for horizontal gene transfer through conjugation. Interestingly, the microbial community of the lake still included a wide range of taxa, suggesting that, across most phyla, bacteria has adapted relatively well to this highly polluted environment. Based on the wide range and high abundance of known resistance factors we have detected, it is plausible that yet unrecognized resistance genes are also present in the lake. Thus, we conclude that environments polluted with waste from antibiotic manufacturing could be important reservoirs for mobile antibiotic resistance genes.

  • 241.
    Benlloch, Reyes
    et al.
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Kim, Min Chul
    Division of Applied Life Science (BK21 Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-701, Korea.
    Sayou, Camille
    Thevenon, Emmanuel
    CEA, iRTSV, Laboratoire Physiologie Cellulaire et Végétale, F-38054 Grenoble, France.
    Parcy, Francois
    CEA, iRTSV, Laboratoire Physiologie Cellulaire et Végétale, F-38054 Grenoble, France.
    Nilsson, Ove
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Integrating long-day flowering signals: a LEAFY binding site is essential for proper photoperiodic activation of APETALA12011In: The Plant Journal, ISSN 0960-7412, E-ISSN 1365-313X, Vol. 67, no 6, p. 1094-1102Article in journal (Refereed)
    Abstract [en]

    The transition to flowering in Arabidopsis is characterized by the sharp and localized upregulation of APETALA1 (AP1) transcription in the newly formed floral primordia. Both the flower meristem-identity gene LEAFY (LFY) and the photoperiod pathway involving the FLOWERING LOCUS T (FT) and FD genes contribute to this upregulation. These pathways have been proposed to act independently but their respective contributions and mode of interaction have remained elusive. To address these questions, we studied the AP1 regulatory region. Combining in vitro and in vivo approaches, we identified which of the three putative LFY binding sites present in the AP1 promoter is essential for its activation by LFY. Interestingly, we found that this site is also important for the correct photoperiodic-dependent upregulation of AP1. In contrast, a previously proposed putative FD-binding site appears dispensable and unable to bind FD and we found no evidence for FD binding to other sites in the AP1 promoter, suggesting that the FT/FD-dependent activation of AP1 might be indirect. Altogether, our data give new insight into the interaction between the FT and LFY pathways in the upregulation of AP1 transcription under long-day conditions.

  • 242.
    Benlloch, Reyes
    et al.
    Department of Forest Genetics and Plant Physiology, SLU.
    Shevela, Dmitriy
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Hainzl, Tobias
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Grundström, Christin
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Shutova, Tatyana
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Messinger, Johannes
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    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).
    Sauer-Eriksson, Elisabeth
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Crystal structure and functional characterization of Photosystem II-associated carbonic anhydrase CAH3 in Chlamydomonas reinhardtii2015In: Plant Physiology, ISSN 0032-0889, E-ISSN 1532-2548, Vol. 167, no 3, p. 950-962Article in journal (Refereed)
    Abstract [en]

    In oxygenic photosynthesis, light energy is stored in the form of chemical energy by converting CO2 and water into carbohydrates.The light-driven oxidation of water that provides the electrons and protons for the subsequent CO2 fixation takes place inphotosystem II (PSII). Recent studies show that in higher plants, HCO3– increases PSII activity by acting as a mobile acceptor ofthe protons produced by PSII. In the green alga Chlamydomonas reinhardtii, a luminal carbonic anhydrase, CrCAH3, was suggested toimprove proton removal from PSII, possibly by rapid reformation of HCO3– from CO2. In this study, we investigated the interplaybetween PSII and CrCAH3 by membrane inlet mass spectrometry and x-ray crystallography. Membrane inlet mass spectrometrymeasurements showed that CrCAH3 was most active at the slightly acidic pH values prevalent in the thylakoid lumen underillumination. Two crystal structures of CrCAH3 in complex with either acetazolamide or phosphate ions were determined at 2.6- and2.7-Å resolution, respectively. CrCAH3 is a dimer at pH 4.1 that is stabilized by swapping of the N-terminal arms, a feature notpreviously observed in a-type carbonic anhydrases. The structure contains a disulfide bond, and redox titration of CrCAH3 functionwith dithiothreitol suggested a possible redox regulation of the enzyme. The stimulating effect of CrCAH3 and CO2/HCO3– on PSIIactivity was demonstrated by comparing the flash-induced oxygen evolution pattern of wild-type and CrCAH3-less PSIIpreparations. We showed that CrCAH3 has unique structural features that allow this enzyme to maximize PSII activity at lowpH and CO2 concentration.

  • 243. Benson, Samuel L
    et al.
    Maheswaran, Pratheesh
    Ware, Maxwell A
    Hunter, C Neil
    Horton, Peter
    Jansson, Stefan
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Ruban, Alexander V
    Johnson, Matthew P
    An intact light harvesting complex I antenna system is required for complete state transitions in Arabidopsis2015In: Nature plants, ISSN 2055-026X, Vol. 1, no 12, article id 15176Article in journal (Refereed)
    Abstract [en]

    Efficient photosynthesis depends on maintaining balance between the rate of light-driven electron transport occurring in photosystem I (PSI) and photosystem II (PSII), located in the chloroplast thylakoid membranes. Balance is achieved through a process of 'state transitions' that increases energy transfer towards PSI when PSII is overexcited (state II), and towards PSII when PSI is overexcited (state I). This is achieved through redox control of the phosphorylation state of light-harvesting antenna complex II (LHCII). PSI is served by both LHCII and four light-harvesting antenna complex I (LHCI) subunits, Lhca1, 2, 3 and 4. Here we demonstrate that despite unchanged levels of LHCII phosphorylation, absence of specific Lhca subunits reduces state transitions in Arabidopsis. The severest phenotype-observed in a mutant lacking Lhca4 (Delta Lhca4)-displayed a 69% reduction compared with the wild type. Yet, surprisingly, the amounts of the PSI-LHCI-LHCII supercomplex isolated by blue native polyacrylamide gel electrophoresis (BN-PAGE) from digitonin-solubilized thylakoids were similar in the wild type and Delta Lhca mutants. Fluorescence excitation spectroscopy revealed that in the wild type this PSI-LHCI-LHCII supercomplex is supplemented by energy transfer from additional LHCII trimers in state II, whose binding is sensitive to digitonin, and which are absent in Delta Lhca4. The grana margins of the thylakoid membrane were found to be the primary site of interaction between this 'extra' LHCII and the PSI-LHCI-LHCII supercomplex in state II. The results suggest that the LHCI complexes mediate energetic interactions between LHCII and PSI in the intact membrane.

  • 244. Bentley, Amy R.
    et al.
    Sung, Yun J.
    Brown, Michael R.
    Winkler, Thomas W.
    Kraja, Aldi T.
    Ntalla, Ioanna
    Schwander, Karen
    Chasman, Daniel, I
    Lim, Elise
    Deng, Xuan
    Guo, Xiuqing
    Liu, Jingmin
    Lu, Yingchang
    Cheng, Ching-Yu
    Sim, Xueling
    Vojinovic, Dina
    Huffman, Jennifer E.
    Musani, Solomon K.
    Li, Changwei
    Feitosa, Mary F.
    Richard, Melissa A.
    Noordam, Raymond
    Baker, Jenna
    Chen, Guanjie
    Aschard, Hugues
    Bartz, Traci M.
    Ding, Jingzhong
    Dorajoo, Rajkumar
    Manning, Alisa K.
    Rankinen, Tuomo
    Smith, Albert, V
    Tajuddin, Salman M.
    Zhao, Wei
    Graff, Mariaelisa
    Alver, Maris
    Boissel, Mathilde
    Chai, Jin Fang
    Chen, Xu
    Divers, Jasmin
    Evangelou, Evangelos
    Gao, Chuan
    Goel, Anuj
    Hagemeijer, Yanick
    Harris, Sarah E.
    Hartwig, Fernando P.
    He, Meian
    Horimoto, Andrea R. V. R.
    Hsu, Fang-Chi
    Hung, Yi-Jen
    Jackson, Anne U.
    Kasturiratne, Anuradhani
    Komulainen, Pirjo
    Kuehnel, Brigitte
    Leander, Karin
    Lin, Keng-Hung
    Luan, Jian'an
    Lyytikainen, Leo-Pekka
    Matoba, Nana
    Nolte, Ilja M.
    Pietzner, Maik
    Prins, Bram
    Riaz, Muhammad
    Robino, Antonietta
    Said, M. Abdullah
    Schupf, Nicole
    Scott, Robert A.
    Sofer, Tamar
    Stancakova, Alena
    Takeuchi, Fumihiko
    Tayo, Bamidele O.
    van der Most, Peter J.
    Varga, Tibor V.
    Wang, Tzung-Dau
    Wang, Yajuan
    Ware, Erin B.
    Wen, Wanqing
    Xiang, Yong-Bing
    Yanek, Lisa R.
    Zhang, Weihua
    Zhao, Jing Hua
    Adeyemo, Adebowale
    Afaq, Saima
    Amin, Najaf
    Amini, Marzyeh
    Arking, Dan E.
    Arzumanyan, Zorayr
    Aung, Tin
    Ballantyne, Christie
    Barr, R. Graham
    Bielak, Lawrence F.
    Boerwinkle, Eric
    Bottinger, Erwin P.
    Broeckel, Ulrich
    Brown, Morris
    Cade, Brian E.
    Campbell, Archie
    Canouil, Mickael
    Charumathi, Sabanayagam
    Chen, Yii-Der Ida
    Christensen, Kaare
    Concas, Maria Pina
    Connell, John M.
    de las Fuentes, Lisa
    de Silva, H. Janaka
    de Vries, Paul S.
    Doumatey, Ayo
    Duan, Qing
    Eaton, Charles B.
    Eppinga, Ruben N.
    Faul, Jessica D.
    Floyd, James S.
    Forouhi, Nita G.
    Forrester, Terrence
    Friedlander, Yechiel
    Gandin, Ilaria
    Gao, He
    Ghanbari, Mohsen
    Gharib, Sina A.
    Gigante, Bruna
    Giulianini, Franco
    Grabe, Hans J.
    Gu, C. Charles
    Harris, Tamara B.
    Heikkinen, Sami
    Heng, Chew-Kiat
    Hirata, Makoto
    Hixson, James E.
    Ikram, M. Arfan
    Jia, Yucheng
    Joehanes, Roby
    Johnson, Craig
    Jonas, Jost Bruno
    Justice, Anne E.
    Katsuya, Tomohiro
    Khor, Chiea Chuen
    Kilpelainen, Tuomas O.
    Koh, Woon-Puay
    Kolcic, Ivana
    Kooperberg, Charles
    Krieger, Jose E.
    Kritchevsky, Stephen B.
    Kubo, Michiaki
    Kuusisto, Johanna
    Lakka, Timo A.
    Langefeld, Carl D.
    Langenberg, Claudia
    Launer, Lenore J.
    Lehne, Benjamin
    Lewis, Cora E.
    Li, Yize
    Liang, Jingjing
    Lin, Shiow
    Liu, Ching-Ti
    Liu, Jianjun
    Liu, Kiang
    Loh, Marie
    Lohman, Kurt K.
    Louie, Tin
    Luzzi, Anna
    Magi, Reedik
    Mahajan, Anubha
    Manichaikul, Ani W.
    McKenzie, Colin A.
    Meitinger, Thomas
    Metspalu, Andres
    Milaneschi, Yuri
    Milani, Lili
    Mohlke, Karen L.
    Momozawa, Yukihide
    Morris, Andrew P.
    Murray, Alison D.
    Nalls, Mike A.
    Nauck, Matthias
    Nelson, Christopher P.
    North, Kari E.
    O'Connell, Jeffrey R.
    Palmer, Nicholette D.
    Papanicolau, George J.
    Pedersen, Nancy L.
    Peters, Annette
    Peyser, Patricia A.
    Polasek, Ozren
    Poulter, Neil
    Raitakari, Olli T.
    Reiner, Alex P.
    Renstrom, Frida
    Umeå University, Faculty of Medicine, Department of Biobank Research. Department of Clinical Sciences, Genetic and Molecular Epidemiology Unit, Lund University Diabetes Centre, Skåne University Hospital, Malmö, Sweden.
    Rice, Treva K.
    Rich, Stephen S.
    Robinson, Jennifer G.
    Rose, Lynda M.
    Rosendaal, Frits R.
    Rudan, Igor
    Schmidt, Carsten O.
    Schreiner, Pamela J.
    Scott, William R.
    Sever, Peter
    Shi, Yuan
    Sidney, Stephen
    Sims, Mario
    Smith, Jennifer A.
    Snieder, Harold
    Starr, John M.
    Strauch, Konstantin
    Stringham, Heather M.
    Tan, Nicholas Y. Q.
    Tang, Hua
    Taylor, Kent D.
    Teo, Yik Ying
    Tham, Yih Chung
    Tiemeier, Henning
    Turner, Stephen T.
    Uitterlinden, Andre G.
    van Heemst, Diana
    Waldenberger, Melanie
    Wang, Heming
    Wang, Lan
    Wang, Lihua
    Wei, Wen Bin
    Williams, Christine A.
    Wilson, Gregory, Sr.
    Wojczynski, Mary K.
    Yao, Jie
    Young, Kristin
    Yu, Caizheng
    Yuan, Jian-Min
    Zhou, Jie
    Zonderman, Alan B.
    Becker, Diane M.
    Boehnke, Michael
    Bowden, Donald W.
    Chambers, John C.
    Cooper, Richard S.
    de Faire, Ulf
    Deary, Ian J.
    Elliott, Paul
    Esko, Tonu
    Farrall, Martin
    Franks, Paul W.
    Umeå University, Faculty of Medicine, Department of Public Health and Clinical Medicine, Section of Medicine. Return to work after interdisciplinary pain rehabilitation Department of Gene Diagnostics and Therapeutics, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan; Department of Nutrition, Harvard T. H. Chan School of Public Health, Harvard University, Boston, MA, USA; OCDEM, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.
    Freedman, Barry, I
    Froguel, Philippe
    Gasparini, Paolo
    Gieger, Christian
    Horta, Bernardo L.
    Juang, Jyh-Ming Jimmy
    Kamatani, Yoichiro
    Kammerer, Candace M.
    Kato, Norihiro
    Kooner, Jaspal S.
    Laakso, Markku
    Laurie, Cathy C.
    Lee, I-Te
    Lehtimaki, Terho
    Magnusson, Patrik K. E.
    Oldehinkel, Albertine J.
    Penninx, Brenda W. J. H.
    Pereira, Alexandre C.
    Rauramaa, Rainer
    Redline, Susan
    Samani, Nilesh J.
    Scott, James
    Shu, Xiao-Ou
    van der Harst, Pim
    Wagenknecht, Lynne E.
    Wang, Jun-Sing
    Wang, Ya Xing
    Wareham, Nicholas J.
    Watkins, Hugh
    Weir, David R.
    Wickremasinghe, Ananda R.
    Wu, Tangchun
    Zeggini, Eleftheria
    Zheng, Wei
    Bouchard, Claude
    Evans, Michele K.
    Gudnason, Vilmundur
    Kardia, Sharon L. R.
    Liu, Yongmei
    Psaty, Bruce M.
    Ridker, Paul M.
    van Dam, Rob M.
    Mook-Kanamori, Dennis O.
    Fornage, Myriam
    Province, Michael A.
    Kelly, Tanika N.
    Fox, Ervin R.
    Hayward, Caroline
    van Duijn, Cornelia M.
    Tai, E. Shyong
    Wong, Tien Yin
    Loos, Ruth J. F.
    Franceschini, Nora
    Rotter, Jerome, I
    Zhu, Xiaofeng
    Bierut, Laura J.
    Gauderman, W. James
    Rice, Kenneth
    Munroe, Patricia B.
    Morrison, Alanna C.
    Rao, Dabeeru C.
    Rotimi, Charles N.
    Cupples, L. Adrienne
    Multi-ancestry genome-wide gene-smoking interaction study of 387,272 individuals identifies new loci associated with serum lipids2019In: Nature Genetics, ISSN 1061-4036, E-ISSN 1546-1718, Vol. 51, no 4, p. 636-+Article in journal (Refereed)
    Abstract [en]

    The concentrations of high- and low-density-lipoprotein cholesterol and triglycerides are influenced by smoking, but it is unknown whether genetic associations with lipids may be modified by smoking. We conducted a multi-ancestry genome-wide gene-smoking interaction study in 133,805 individuals with follow-up in an additional 253,467 individuals. Combined meta-analyses identified 13 new loci associated with lipids, some of which were detected only because association differed by smoking status. Additionally, we demonstrate the importance of including diverse populations, particularly in studies of interactions with lifestyle factors, where genomic and lifestyle differences by ancestry may contribute to novel findings.

  • 245. Bento-Abreu, Andre
    et al.
    Jager, Gunilla
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology).
    Swinnen, Bart
    Rué, Laura
    Hendrickx, Stijn
    Jones, Ashley
    Staats, Kim A.
    Taes, Ines
    Eykens, Caroline
    Nonneman, Annelies
    Nuyts, Rik
    Timmers, Mieke
    Silva, Lara
    Chariot, Alain
    Nguyen, Laurent
    Ravits, John
    Lemmens, Robin
    Cabooter, Deirdre
    Van Den Bosch, Ludo
    Van Damme, Philip
    Al-Chalabi, Ammar
    Bystrom, Anders
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology).
    Robberecht, Wim
    Elongator subunit 3 (ELP3) modifies ALS through tRNA modification.2018In: Human Molecular Genetics, ISSN 0964-6906, E-ISSN 1460-2083, Vol. 27, no 7, p. 1276-1289Article in journal (Refereed)
    Abstract [en]

    Amyotrophic lateral sclerosis (ALS) is a fatal degenerative motor neuron disorder of which the progression is influenced by several disease-modifying factors. Here, we investigated ELP3, a subunit of the elongator complex that modifies tRNA wobble uridines, as one of such ALS disease modifiers. ELP3 attenuated the axonopathy of a mutant SOD1, as well as of a mutant C9orf72 ALS zebrafish model. Furthermore, the expression of ELP3 in the SOD1G93A mouse extended the survival and attenuated the denervation in this model. Depletion of ELP3 in vitro reduced the modified tRNA wobble uridine mcm5s2U and increased abundance of insoluble mutant SOD1, which was reverted by exogenous ELP3 expression. Interestingly, the expression of ELP3 in the motor cortex of ALS patients was reduced and correlated with mcm5s2U levels. Our results demonstrate that ELP3 is a modifier of ALS and suggest a link between tRNA modification and neurodegeneration.

  • 246.
    Bentzon-Tilia, Mikkel
    et al.
    Univ Copenhagen.
    Farnelid, Hanna
    Linnéuniversitetet, Institutionen för biologi och miljö (BOM).
    Jürgens, Klaus
    Leibniz Inst Balt Sea Res IOW, Germany.
    Riemann, Lasse
    Univ Copenhagen.
    Cultivation and isolation of N2-fixing bacteria from suboxic waters in the Baltic Sea2014In: FEMS Microbiology Ecology, ISSN 0168-6496, E-ISSN 1574-6941, Vol. 88, no 2, p. 358-371Article in journal (Refereed)
    Abstract [en]

    Nitrogenase genes (nifH) from heterotrophic dinitrogen (N-2)-fixing bacteria appear ubiquitous in marine bacterioplankton, but the significance of these bacteria for N cycling is unknown. Quantitative data on the N-2-fixation potential of marine and estuarine heterotrophs are scarce, and the shortage of cultivated specimens currently precludes ecophysiological characterization of these bacteria. Through the cultivation of diazotrophs from suboxic (1.79molO(2)L(-1)) Baltic Sea water in an artificial seawater medium devoid of combined N, we report the cultivability of a considerable fraction of the diazotrophic community in the Gotland Deep. Two nifH clades were present both in situ and in enrichment cultures showing gene abundances of up to 4.6x10(5) and 5.8x10(5)nifH gene copies L-1 within two vertical profiles in the Baltic Sea. The distributions of the two clades suggested a relationship with the O-2 concentrations in the water column as abundances increased in the suboxic and anoxic waters. It was possible to cultivate and isolate representatives from one of these prevalent clades, and preliminary analysis of their ecophysiology demonstrated growth optima at 0.5-15molO(2)L(-1) and 186-194molO(2)L(-1) in the absence of combined N.

  • 247. Berdahl, Andrew
    et al.
    Brelsford, Christa
    De Bacco, Caterina
    Dumas, Marion
    Ferdinand, Vanessa
    Grochow, Joshua A.
    Hebert-Dufresne, Laurent
    Kallus, Yoav
    Kempes, Christopher P.
    Kolchinsky, Artemy
    Larremore, Daniel B.
    Libby, Eric
    Umeå University, Faculty of Science and Technology, Department of Mathematics and Mathematical Statistics.
    Power, Eleanor A.
    Stern, Caitlin A.
    Tracey, Brendan D.
    Dynamics of beneficial epidemics2019In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 9, article id 15093Article in journal (Refereed)
    Abstract [en]

    Pathogens can spread epidemically through populations. Beneficial contagions, such as viruses that enhance host survival or technological innovations that improve quality of life, also have the potential to spread epidemically. How do the dynamics of beneficial biological and social epidemics differ from those of detrimental epidemics? We investigate this question using a breadth-first modeling approach involving three distinct theoretical models. First, in the context of population genetics, we show that a horizontally-transmissible element that increases fitness, such as viral DNA, spreads superexponentially through a population, more quickly than a beneficial mutation. Second, in the context of behavioral epidemiology, we show that infections that cause increased connectivity lead to superexponential fixation in the population. Third, in the context of dynamic social networks, we find that preferences for increased global infection accelerate spread and produce superexponential fixation, but preferences for local assortativity halt epidemics by disconnecting the infected from the susceptible. We conclude that the dynamics of beneficial biological and social epidemics are characterized by the rapid spread of beneficial elements, which is facilitated in biological systems by horizontal transmission and in social systems by active spreading behavior of infected individuals.

  • 248. Berdan, Emma
    et al.
    Rosenquist, Hanna
    Larson, Keith
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Wellenreuther, Maren
    Inversion frequencies and phenotypic effects are modulated by the environment: insights from a reciprocal transplant study in Coelopa frigida2018In: Evolutionary Ecology, ISSN 0269-7653, E-ISSN 1573-8477, Vol. 32, no 6, p. 683-698Article in journal (Refereed)
    Abstract [en]

    Understanding how environmental variation drives phenotypic diversification within species is a major objective in evolutionary biology. The seaweed fly Coelopa frigida provides an excellent model for the study of genetically driven phenotypes because it carries an α/β inversion polymorphism that affects body size. Coelopa frigida inhabits highly variable beds of decomposing seaweed on the coast in Scandinavia thus providing a suitable test ground to investigate the genetic effects of substrate on both the frequency of the inversion (directional selection) and on the phenotype (genotype × environment effects). Here we use a reciprocal transplant experiment to test the effect of the α/β inversion on body size traits and development time across four suitable natural breeding substrates from the clinal distribution. We show that while development time is unaffected by G × E effects, both the frequency of the inversion and the relative phenotypic effects of the inversion on body size differ between population × substrate combinations. This indicates that the environment modulates the fitness as well as the phenotypic effects of the inversion karyotypes. It further suggests that the inversion may have accumulated qualitatively different mutations in different populations that interact with the environment. Together our results are consistent with the idea that the inversion in C. frigida likely evolves via a combination of local mutation, G × E effects, and differential fitness of inversion karyotypes in heterogeneous environments.

  • 249.
    Berg, Håkan
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology). Umeå University, Faculty of Medicine, Department of Molecular Biology (Faculty of Medicine).
    Teleost reproduction: Aspects of Arctic char (Salvelinus alpinus) oocyte growth and maturation2003Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    In all vertebrate species, reproduction is a hormonally controlled process, important for growth and maturation of gonads and germ cells. Production of functional germ cells is of outmost importance to secure the survival of a species. Fish comprises 50% of the known vertebrates and are found in aquatic habitats all over the world. Even though fish have evolved a wide variety of morphological and physiological characteristics, due to large differences in the living environment, the growth an maturation of germ cells follows the same pattern in all species. In this thesis the focus has been directed on oocyte growth and development in Arctic char (Salvelinus alpinus), and if stress might inflict disturbances on the reproductive systems.

    All sexually mature female egg laying vertebrates produces yolky eggs surrounded by an eggshell. Production of yolk and egg shell is under estrogenic control and it is known that production of egg components can be induced in male and juvenile fish by estrogenic substances. Many manmade chemicals have been found to interfere with hormonally controlled processes. Therefore production of the egg yolk precursor, vitellogenin (VTG), and the egg shell components, vitelline envelope proteins (VEP), have been used as biomarkers for estrogenic effect. Exposure to endocrine disrupting substances (EDS) does not only give rise to hormonal effects on the organism, but in addition it also gives rise to an increase in stress hormone, cortisol (F), levels.

    It is evident that a wide variety of substances may affect Arctic char oocyte growth and maturation. VTG and VEP production is found to be under dose dependent estrogenic control, but the production was directly affected by F. Under natural condition it has been found that F increases towards ovulation. Even though both VTG and VTG is under estrogenic control, these studies showed that stress lead to a decrease of VTG while the VEP production increased. These effects was only observed on protein levels indicating that a post transcriptional down regulation of VTG production is mediated by F in Arctic char.

    In order for an egg to become fertilizatible, it must undergo a maturation phase. This maturation phase is primarily induced by gonadotropins, which in turn induce the production of species specific maturation inducing substances (MIS). To investigate oocyte development in Arctic char a characterization of its MIS receptor was made. The MIS receptor is localized on the oocyte surface and displays a single class of high affinity and low capacity binding sites. The binding moieties displays association and dissociation kinetics typical of steroid membrane receptors.

    Even though high specificity for Arctic char MIS was observed, it was found that some EDS bind to the Arctic char oocyte membrane receptor. This suggest that certain EDS might affect oocyte maturation and thereby might alter the reproductive success. Furthermore, it was found that F did not bind to the MIS receptor in Arctic char. It is therefore suggested that oocytes are more sensitive to stress during the growth phase than during maturation

  • 250.
    Berg, Lotta
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Andersson, C. David
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Artursson, Elisabet
    Hornberg, Andreas
    Tunemalm, Anna-Karin
    Linusson, Anna
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Ekstrom, Fredrik
    Targeting Acetylcholinesterase: Identification of Chemical Leads by High Throughput Screening, Structure Determination and Molecular Modeling2011In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 6, no 11, article id e26039Article in journal (Refereed)
    Abstract [en]

    Acetylcholinesterase (AChE) is an essential enzyme that terminates cholinergic transmission by rapid hydrolysis of the neurotransmitter acetylcholine. Compounds inhibiting this enzyme can be used (inter alia) to treat cholinergic deficiencies (e. g. in Alzheimer's disease), but may also act as dangerous toxins (e. g. nerve agents such as sarin). Treatment of nerve agent poisoning involves use of antidotes, small molecules capable of reactivating AChE. We have screened a collection of organic molecules to assess their ability to inhibit the enzymatic activity of AChE, aiming to find lead compounds for further optimization leading to drugs with increased efficacy and/or decreased side effects. 124 inhibitors were discovered, with considerable chemical diversity regarding size, polarity, flexibility and charge distribution. An extensive structure determination campaign resulted in a set of crystal structures of protein-ligand complexes. Overall, the ligands have substantial interactions with the peripheral anionic site of AChE, and the majority form additional interactions with the catalytic site (CAS). Reproduction of the bioactive conformation of six of the ligands using molecular docking simulations required modification of the default parameter settings of the docking software. The results show that docking-assisted structure-based design of AChE inhibitors is challenging and requires crystallographic support to obtain reliable results, at least with currently available software. The complex formed between C5685 and Mus musculus AChE (C5685.mAChE) is a representative structure for the general binding mode of the determined structures. The CAS binding part of C5685 could not be structurally determined due to a disordered electron density map and the developed docking protocol was used to predict the binding modes of this part of the molecule. We believe that chemical modifications of our discovered inhibitors, biochemical and biophysical characterization, crystallography and computational chemistry provide a route to novel AChE inhibitors and reactivators.

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