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  • 1.
    Ahlinder, Jon
    et al.
    Division of CBRN Defence and Security, FOI, Swedish Defence Research Agency, Umeå, Sweden.
    Mathisen, Peter
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap.
    Sjödin, Andreas
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen. Division of CBRN Defence and Security, FOI, Swedish Defence Research Agency, Umeå, Sweden.
    Nilsson, Elin
    Division of CBRN Defence and Security, FOI, Swedish Defence Research Agency, Umeå, Sweden.
    Forsman, Mats
    Division of CBRN Defence and Security, FOI, Swedish Defence Research Agency, Umeå, Sweden.
    Andersson, Agneta
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap.
    Thelaus, Johanna
    Division of CBRN Defence and Security, FOI, Swedish Defence Research Agency, Umeå, Sweden.
    Oligotyping reveals divergent responses of predation resistant bacteria to aquatic productivity and plankton compositionManuskript (preprint) (Övrigt vetenskapligt)
    Abstract [en]

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

  • 2.
    Bylesjö, Max
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Eriksson, Daniel
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Sjödin, Andreas
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Jansson, Stefan
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Moritz, Thomas
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Trygg, Johan
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Orthogonal projections to latent structures as a strategy for microarray data normalization2007Ingår i: BMC Bioinformatics, ISSN 1471-2105, E-ISSN 1471-2105, Vol. 8, nr 207Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Background

    During generation of microarray data, various forms of systematic biases are frequently introduced which limits accuracy and precision of the results. In order to properly estimate biological effects, these biases must be identified and discarded.

    Results

    We introduce a normalization strategy for multi-channel microarray data based on orthogonal projections to latent structures (OPLS); a multivariate regression method. The effect of applying the normalization methodology on single-channel Affymetrix data as well as dual-channel cDNA data is illustrated. We provide a parallel comparison to a wide range of commonly employed normalization methods with diverse properties and strengths based on sensitivity and specificity from external (spike-in) controls. On the illustrated data sets, the OPLS normalization strategy exhibits leading average true negative and true positive rates in comparison to other evaluated methods.

    Conclusions

    The OPLS methodology identifies joint variation within biological samples to enable the removal of sources of variation that are non-correlated (orthogonal) to the within-sample variation. This ensures that structured variation related to the underlying biological samples is separated from the remaining, bias-related sources of systematic variation. As a consequence, the methodology does not require any explicit knowledge regarding the presence or characteristics of certain biases. Furthermore, there is no underlying assumption that the majority of elements should be non-differentially expressed, making it applicable to specialized boutique arrays.

  • 3.
    Bylesjö, Max
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Eriksson, Daniel
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Sjödin, Andreas
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Sjöström, Michael
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Jansson, Stefan
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Antti, Henrik
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Trygg, Johan
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    MASQOT: a method for cDNA microarray spot quality control.2005Ingår i: BMC Bioinformatics, ISSN 1471-2105, E-ISSN 1471-2105, Vol. 6, s. 250-Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Background

    cDNA microarray technology has emerged as a major player in the parallel detection of biomolecules, but still suffers from fundamental technical problems. Identifying and removing unreliable data is crucial to prevent the risk of receiving illusive analysis results. Visual assessment of spot quality is still a common procedure, despite the time-consuming work of manually inspecting spots in the range of hundreds of thousands or more.

    Results

    A novel methodology for cDNA microarray spot quality control is outlined. Multivariate discriminant analysis was used to assess spot quality based on existing and novel descriptors. The presented methodology displays high reproducibility and was found superior in identifying unreliable data compared to other evaluated methodologies.

    Conclusion

    The proposed methodology for cDNA microarray spot quality control generates non-discrete values of spot quality which can be utilized as weights in subsequent analysis procedures as well as to discard spots of undesired quality using the suggested threshold values. The MASQOT approach provides a consistent assessment of spot quality and can be considered an alternative to the labor-intensive manual quality assessment process.

  • 4.
    Bylesjö, Max
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Sjödin, Andreas
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Eriksson, Daniel
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Antti, Henrik
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Moritz, Thomas
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Jansson, Stefan
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Trygg, Johan
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    MASQOT-GUI: spot quality assessment for the two-channel microarray platform2006Ingår i: Bioinformatics, ISSN 1367-4803, E-ISSN 1367-4811, Vol. 22, nr 20, s. 2554-2555Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    MASQOT-GUI provides an open-source, platform-independent software pipeline for two-channel microarray spot quality control. This includes gridding, segmentation, quantification, quality assessment and data visualization. It hosts a set of independent applications, with interactions between the tools as well as import and export support for external software. The implementation of automated multivariate quality control assessment, which is a unique feature of MASQOT-GUI, is based on the previously documented and evaluated MASQOT methodology. Further abilities of the application are outlined and illustrated. AVAILABILITY: MASQOT-GUI is Java-based and licensed under the GNU LGPL. Source code and installation files are available for download at http://masqot-gui.sourceforge.net/

  • 5.
    Courtois-Moreau, Charleen L
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC). Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    Pesquet, Edouard
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC). Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    Sjödin, Andreas
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC). Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    Muñiz, Luis
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC). Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    Bollhöner, Benjamin
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Kaneda, Minako
    Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
    Samuels, Lacey
    Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
    Jansson, Stefan
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Tuominen, Hannele
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    A unique program for cell death in xylem fibers of Populus stem2009Ingår i: The Plant Journal, ISSN 0960-7412, E-ISSN 1365-313X, Vol. 58, nr 2, s. 260-274Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Maturation of the xylem elements involves extensive deposition of secondary cell-wall material and autolytic processes resulting in cell death. We describe here a unique type of cell-death program in xylem fibers of hybrid aspen (Populus tremula x P. tremuloides) stems, including gradual degradative processes in both the nucleus and cytoplasm concurrently with the phase of active cell-wall deposition. Nuclear DNA integrity, as determined by TUNEL (terminal deoxynucleotidyl transferase-mediated dUTP nick end labeling) and Comet (single-cell gel electrophoresis) assays, was compromised early during fiber maturation. In addition, degradation of the cytoplasmic contents, as detected by electron microscopy of samples fixed by high-pressure freezing/freeze substitution (HPF-FS), was gradual and resulted in complete loss of the cytoplasmic contents well before the loss of vacuolar integrity, which is considered to be the moment of death. This type of cell death differs significantly from that seen in xylem vessels. The loss of vacuolar integrity, which is thought to initiate cell degradative processes in the xylem vessels, is one of the last processes to occur before the final autolysis of the remaining cell contents in xylem fibers. High-resolution microarray analysis in the vascular tissues of Populus stem, combined with in silico analysis of publicly available data repositories, suggests the involvement of several previously uncharacterized transcription factors, ethylene, sphingolipids and light signaling as well as autophagy in the control of fiber cell death.

  • 6.
    Druart, Nathalie
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Johansson, Annika
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Baba, Kyoko
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Schrader, Jarmo
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Sjödin, Andreas
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC). Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    Bhalerao, Rupali R
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Resman, Lars
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Trygg, Johan
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Moritz, Thomas
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Bhalerao, Rishikesh P
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Environmental and hormonal regulation of the activity–dormancy cycle in the cambial meristem involves stage-specific modulation of transcriptional and metabolic networks2007Ingår i: The Plant Journal, Vol. 50, s. 557-73Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We have performed transcript and metabolite profiling of isolated cambial meristem cells of the model tree aspen during the course of their activity–dormancy cycle to better understand the environmental and hormonal regulation of this process in perennial plants. Considerable modulation of cambial transcriptome and metabolome occurs throughout the activity–dormancy cycle. However, in addition to transcription, post-transcriptional control is also an important regulatory mechanism as exemplified by the regulation of cell-cycle genes during the reactivation of cambial cell division in the spring. Genes related to cold hardiness display temporally distinct induction patterns in the autumn which could explain the step-wise development of cold hardiness. Factors other than low temperature regulate the induction of early cold hardiness-related genes whereas abscisic acid (ABA) could potentially regulate the induction of late cold hardiness-related genes in the autumn. Starch breakdown in the autumn appears to be regulated by the ‘short day’ signal and plays a key role in providing substrates for the production of energy, fatty acids and cryoprotectants. Catabolism of sucrose and fats provides energy during the early stages of reactivation in the spring, whereas the reducing equivalents are generated through activation of the pentose phosphate shunt. Modulation of gibberellin (GA) signaling and biosynthesis could play a key role in the regulation of cambial activity during the activity–dormancy cycle as suggested by the induction of PttRGA which encodes a negative regulator of growth in the autumn and that of a GA-20 oxidase, a key gibberellin biosynthesis gene during reactivation in spring. In summary, our data reveal the dynamics of transcriptional and metabolic networks and identify potential targets of environmental and hormonal signals in the regulation of the activity–dormancy cycle in cambial meristem.

  • 7. Druart, Nathalie
    et al.
    Rodriguez-Buey, Marisa
    Barron-Gafford, Greg
    Sjödin, Andreas
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Bhalerao, Rishikesh
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Hurry, Vaughan
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Molecular targets of elevated [CO2] in leaves and stems of Populus deltoides: implications for future tree growth and carbon sequestration2006Ingår i: Functional Plant Biology, Vol. 33, s. 121-131Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We report the first comprehensive analysis of the effects of elevated [CO2] on gene expression in source leaf and stem sink tissues in woody plants. We have taken advantage of coppiced Populus deltoides (Bartr.) stands grown for 3 years under three different and constant elevated [CO2] in the agriforest mesocosms of Biosphere 2. Leaf area per tree was doubled by elevated [CO2] but although growth at 800 v. 400 µmol mol–1 CO2 resulted in a significant increase in stem biomass, growth was not stimulated at 1200 µmol mol–1 CO2. Growth under elevated [CO2] also resulted in significant increases in stem wood density. Analysis of expression data for the 13 490 clones present on POP1 microarrays revealed 95 and 277 [CO2]-responsive clones in leaves and stems respectively, with the response being stronger at 1200 µmol mol–1. When these [CO2]-responsive genes were assigned to functional categories, metabolism-related genes were the most responsive to elevated [CO2]. However within this category, expression of genes relating to bioenergetic processes was unchanged in leaves whereas the expression of genes for storage proteins and of those involved in control of wall expansion was enhanced. In contrast to leaves, the genes up-regulated in stems under elevated [CO2] were primarily enzymes responsible for lignin formation and polymerisation or ethylene response factors, also known to induce lignin biosynthesis. Concomitant with this enhancement of lignin biosynthesis in stems, there was a pronounced repression of genes related to cell wall formation and cell growth. These changes in gene expression have clear consequences for long-term carbon sequestration, reducing the carbon-fertilisation effect, and the potential for increased lignification may negatively impact on future wood quality for timber and paper production.

  • 8. Fracheboud, Yvan
    et al.
    Luquez, Virginia
    Björkén, Lars
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Sjödin, Andreas
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC). Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    Tuominen, Hannele
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Jansson, Stefan
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    The control of autumn senescence in European aspen2009Ingår i: Plant Physiology, ISSN 0032-0889, E-ISSN 1532-2548, Vol. 149, nr 4, s. 1982-1991Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The initiation, progression, and natural variation of autumn senescence in European aspen (Populus tremula) was investigated by monitoring chlorophyll degradation in (1) trees growing in natural stands and (2) cloned trees growing in a greenhouse under various light regimes. The main trigger for the initiation of autumn senescence in aspen is the shortening photoperiod, but there was a large degree of variation in the onset of senescence, both within local populations and among trees originating from different populations, where it correlated with the latitude of their respective origins. The variation for onset of senescence with a population was much larger than the variation of bud set. Once started, autumn senescence was accelerated by low temperature and longer nights, and clones that started to senescence late had a faster senescence. Bud set and autumn senescence appeared to be under the control of two independent critical photoperiods, but senescence could not be initiated until a certain time after bud set, suggesting that bud set and growth arrest are important for the trees to acquire competence to respond to the photoperiodic trigger to undergo autumn senescence. A timetable of events related to bud set and autumn senescence is presented.

  • 9. Goormaghtigh, Frederic
    et al.
    Fraikin, Nathan
    Putrins, Marta
    Hallaert, Thibaut
    Hauryliuk, Vasili
    Umeå universitet, Medicinska fakulteten, Institutionen för molekylärbiologi (Medicinska fakulteten). Umeå universitet, Medicinska fakulteten, Molekylär Infektionsmedicin, Sverige (MIMS). Institute of Technology, University of Tartu, Tartu, Estonia.
    Garcia-Pino, Abel
    Sjödin, Andreas
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen. Division of CBRN Security and Defence, FOI–Swedish Defence Research Agency, Umeå, Sweden.
    Kasvandik, Sergo
    Udekwu, Klas
    Tenson, Tanel
    Kaldalu, Niilo
    Van Melderen, Laurence
    Reassessing the Role of Type II Toxin-Antitoxin Systems in Formation of Escherichia coli Type II Persister Cells2018Ingår i: mBio, ISSN 2161-2129, E-ISSN 2150-7511, Vol. 9, nr 3, artikel-id e00640-18Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Persistence is a reversible and low-frequency phenomenon allowing a subpopulation of a clonal bacterial population to survive antibiotic treatments. Upon removal of the antibiotic, persister cells resume growth and give rise to viable progeny. Type II toxin-antitoxin (TA) systems were assumed to play a key role in the formation of persister cells in Escherichia coli based on the observation that successive deletions of TA systems decreased persistence frequency. In addition, the model proposed that stochastic fluctuations of (p)ppGpp levels are the basis for triggering activation of TA systems. Cells in which TA systems are activated are thought to enter a dormancy state and therefore survive the antibiotic treatment. Using independently constructed strains and newly designed fluorescent reporters, we reassessed the roles of TA modules in persistence both at the population and single-cell levels. Our data confirm that the deletion of 10 TA systems does not affect persistence to ofloxacin or ampicillin. Moreover, microfluidic experiments performed with a strain reporting the induction of the yefM-yoeB TA system allowed the observation of a small number of type II persister cells that resume growth after removal of ampicillin. However, we were unable to establish a correlation between high fluorescence and persistence, since the fluorescence of persister cells was comparable to that of the bulk of the population and none of the cells showing high fluorescence were able to resume growth upon removal of the antibiotic. Altogether, these data show that there is no direct link between induction of TA systems and persistence to antibiotics. IMPORTANCE Within a growing bacterial population, a small subpopulation of cells is able to survive antibiotic treatment by entering a transient state of dormancy referred to as persistence. Persistence is thought to be the cause of relapsing bacterial infections and is a major public health concern. Type II toxin-antitoxin systems are small modules composed of a toxic protein and an antitoxin protein counteracting the toxin activity. These systems were thought to be pivotal players in persistence until recent developments in the field. Our results demonstrate that previous influential reports had technical flaws and that there is no direct link between induction of TA systems and persistence to antibiotics.

  • 10. Grüning, Björn
    et al.
    Dale, Ryan
    Sjödin, Andreas
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen. Division of CBRN Security and Defence, FOI – Swedish Defence Research Agency, Umeå, Sweden.
    Chapman, Brad A.
    Rowe, Jillian
    Tomkins-Tinch, Christopher H.
    Valieris, Renan
    Köster, Johannes
    Bioconda: sustainable and comprehensive software distribution for the life sciences2018Ingår i: Nature Methods, ISSN 1548-7091, E-ISSN 1548-7105, Vol. 15, nr 7, s. 475-476Artikel i tidskrift (Refereegranskat)
  • 11.
    Haas, Julia Christa
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Street, Nathaniel R.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Sjödin, Andreas
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen. Division of CBRN Security and Defence, FOI–Swedish Defence Research Agency, Umeå, Sweden.
    Lee, Natuschka M.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap.
    Högberg, Mona N.
    Department of Forest Ecology and Management, Swedish University of Agricultural Sciences (SLU), Umeå, Sweden.
    Näsholm, Torgny
    Department of Forest Ecology and Management, Swedish University of Agricultural Sciences (SLU), Umeå, Sweden; Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, SLU, Umeå, Sweden.
    Hurry, Vaughan
    Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, SLU, Umeå, Sweden.
    Microbial community response to growing season and plant nutrient optimisation in a boreal Norway spruce forest2018Ingår i: Soil Biology and Biochemistry, ISSN 0038-0717, E-ISSN 1879-3428, Vol. 125, s. 197-209Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Interactions between Norway spruce trees and bacteria and fungi in nutrient limited boreal forests can be beneficial for tree growth and fitness. Tree-level effects of anthropogenic nutrient addition have been well studied, however understanding of the long-term effects on the associated microbiota is limited. Here, we report on the sensitivity of microbial community composition to the growing season and nutrient additions. Highthroughput sequencing of the bacterial 16S rRNA gene and fungal ITS1 region was used to characterise changes in the microbial community after application of a complete mineral nutrient mixture for five and 25 years. The experiment was conducted using the Flakaliden forest research site in northern boreal Sweden and included naturally low nutrient control plots. Needle and fine root samples of Norway spruce were sampled in addition to bulk soil during one growing season to provide comprehensive insight into phyllosphere and belowground microbiota community changes. The phyllosphere microbiota was compositionally distinct from the belowground communities and phyllosphere diversity increased significantly over the growing season but was not influenced by the improved nutrient status of the trees. In both root and soil samples, alpha diversity of fungal, in particular ectomycorrhizal fungi (EMF), and bacterial communities increased after long-term nutrient optimisation, and with increasing years of treatment the composition of the fungal and bacterial communities changed toward a community with a higher relative abundance of nitrophilic EMF and bacterial species but did not cause complete loss of nitrophobic species from the ecosystem. From this, we conclude that 25 years of continuous nutrient addition to a boreal spruce stand increased phylotype richness and diversity of the microbiota in the soil, and at the root-soil interface, suggesting that long-term anthropogenic nutrient inputs can have positive effects on belowground biodiversity that may enhance ecosystem robustness. Future studies are needed to assess the impact of these changes to the microbiota on ecosystem carbon storage and nitrogen cycling in boreal forests.

  • 12. Hägglund, Moa
    et al.
    Bäckman, Stina
    Macellaro, Anna
    Lindgren, Fetter
    Borgmästars, Emmy
    Umeå universitet, Medicinska fakulteten, Institutionen för kirurgisk och perioperativ vetenskap, Kirurgi.
    Jacobsson, Karin
    Dryselius, Rikard
    Stenberg, Per
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap. Division of CBRN Security and Defence, FOI, Swedish Defence Research Agency, Umeå, Sweden.
    Sjödin, Andreas
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen. Division of CBRN Security and Defence, FOI, Swedish Defence Research Agency, Umeå, Sweden.
    Forsman, Mats
    Ahlinder, Jon
    Accounting for bacterial overlap between raw water communities and contaminating sources improves the accuracy of signature-based microbial source tracking2018Ingår i: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 9, artikel-id 2364Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Microbial source tracking (MST) analysis is essential to identifying and mitigating the fecal pollution of water resources. The signature-based MST method uses a library of sequences to identify contaminants based on operational taxonomic units (OTUs) that are unique to a certain source. However, no clear guidelines for how to incorporate OTU overlap or natural variation in the raw water bacterial community into MST analyses exist. We investigated how the inclusion of bacterial overlap between sources in the library affects source prediction accuracy. To achieve this, large-scale sampling-including feces from seven species, raw sewage, and raw water samples from water treatment plants - was followed by 16S rRNA amplicon sequencing. The MST library was defined using three settings: (i) no raw water communities represented; (ii) raw water communities selected through clustering analysis; and (iii) local water communities collected across consecutive years. The results suggest that incorporating either the local background or representative bacterial composition improves MST analyses, as the results were positively correlated to measured levels of fecal indicator bacteria and the accuracy at which OTUs were assigned to the correct contamination source increased fourfold. Using the proportion of OTUs with high source origin probability, underpinning a contaminating signal, is a solid foundation in a framework for further deciphering and comparing contaminating signals derived in signature-based MST approaches. In conclusion, incorporating background bacterial composition of water in MST can improve mitigation efforts for minimizing the spread of pathogenic and antibiotic resistant bacteria into essential freshwater resources.

  • 13. Karlsson, E.
    et al.
    Larkeryd, A.
    Sjödin, Andreas
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen. Swedish Defence Research Agency, Umeå, Sweden.
    Forsman, M.
    Stenberg, Per
    Umeå universitet, Medicinska fakulteten, Institutionen för molekylärbiologi (Medicinska fakulteten). Swedish Defence Research Agency, Umeå, Sweden; Department of Chemistry, Computational Life Science Cluster (CLiC), Umeå University, Umeå, Sweden.
    Scaffolding of a bacterial genome using MinION nanopore sequencing2015Ingår i: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 5, artikel-id 11996Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Second generation sequencing has revolutionized genomic studies. However, most genomes contain repeated DNA elements that are longer than the read lengths achievable with typical sequencers, so the genomic order of several generated contigs cannot be easily resolved. A new generation of sequencers offering substantially longer reads is emerging, notably the Pacific Biosciences (PacBio) RS II system and the MinION system, released in early 2014 by Oxford Nanopore Technologies through an early access program. The latter has highly advantageous portability and sequences samples by measuring changes in ionic current when single-stranded DNA molecules are translocated through nanopores. We show that the MinION system produces long reads with high mapability that can be used for scaffolding bacterial genomes, despite currently producing substantially higher error rates than PacBio reads. With further development we anticipate that MinION will be useful not only for assembling genomes, but also for rapid detection of organisms, potentially in the field.

  • 14. Karlsson, Edvin
    et al.
    Svensson, Kerstin
    Lindgren, Petter
    Byström, Mona
    Sjödin, Andreas
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Forsman, Mats
    Johansson, Anders
    Umeå universitet, Medicinska fakulteten, Institutionen för klinisk mikrobiologi, Klinisk bakteriologi. Umeå universitet, Medicinska fakulteten, Institutionen för klinisk mikrobiologi, Infektionssjukdomar.
    The phylogeographic pattern of Francisella tularensis in Sweden indicates a Scandinavian origin of Eurosiberian tularaemia2013Ingår i: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 15, nr 2, s. 634-645Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Previous studies of the causative agent of tularaemia, Francisella tularensis have identified phylogeographic patterns suggestive of environmental maintenance reservoirs. To investigate the phylogeography of tularaemia in Sweden, we selected 163 clinical isolates obtained during 1995-2009 in 10 counties and sequenced one isolate's genome to identify new genetic markers. An improved typing scheme based on two indels and nine SNPs was developed using hydrolysis or TaqMan MGB probe assays. The results showed that much of the known global genetic diversity of F. tularensis subsp. holarctica is present in Sweden. Thirteen of the 163 isolates belonged to a new genetic group that is basal to all other known members of the major genetic clade B.I, which is spread across the Eurosiberian region. One hundred and twenty-five of the 163 Swedish isolates belonged to B.I, but individual clades' frequencies differed from county to county (P < 0.001). Subsequent analyses revealed a correlation between genotype variation over time and recurrent outbreaks at specific places, supporting the 'maintenance reservoir' environmental maintenance hypothesis. Most importantly, the findings reveal the presence of diverse source populations of F. tularensis subsp. holarctica in Sweden and suggest a historical spread of the disease from Scandinavia to other parts of Eurosiberia.

  • 15.
    Klimmek, Frank
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Sjödin, Andreas
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Noutsos, Christos
    Leister, Dario
    Jansson, Stefan
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Abundantly and rarely expressed Lhc protein genes exhibit distinct regulation patterns in plants.2006Ingår i: Plant Physiology, ISSN 0032-0889, Vol. 140, nr 3, s. 793-804Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We have analyzed gene regulation of the Lhc supergene family in poplar (Populus spp.) and Arabidopsis (Arabidopsis thaliana) using digital expression profiling. Multivariate analysis of the tissue-specific, environmental, and developmental Lhc expression patterns in Arabidopsis and poplar was employed to characterize four rarely expressed Lhc genes, Lhca5, Lhca6, Lhcb7, and Lhcb4.3. Those genes have high expression levels under different conditions and in different tissues than the abundantly expressed Lhca1 to 4 and Lhcb1 to 6 genes that code for the 10 major types of higher plant light-harvesting proteins. However, in some of the datasets analyzed, the Lhcb4 and Lhcb6 genes as well as an Arabidopsis gene not present in poplar (Lhcb2.3) exhibited minor differences to the main cooperative Lhc gene expression pattern. The pattern of the rarely expressed Lhc genes was always found to be more similar to that of PsbS and the various light-harvesting-like genes, which might indicate distinct physiological functions for the rarely and abundantly expressed Lhc proteins. The previously undetected Lhcb7 gene encodes a novel plant Lhcb-type protein that possibly contains an additional, fourth, transmembrane N-terminal helix with a highly conserved motif. As the Lhcb4.3 gene seems to be present only in Eurosid species and as its regulation pattern varies significantly from that of Lhcb4.1 and Lhcb4.2, we conclude it to encode a distinct Lhc protein type, Lhcb8.

  • 16. Lee, Hyoshin
    et al.
    Bae, Eun-Kyung
    Park, So-Young
    Sjödin, Andreas
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Lee, Jae-Soon
    Noh, Eun-Woon
    Jansson, Stefan
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Growth-phase-dependent gene expression profiling of poplar (Populus alba x Populus tremula var. glandulosa) suspension cells2007Ingår i: Physiologia Plantarum, Vol. 131, s. 599-613Artikel i tidskrift (Refereegranskat)
    Abstract [sv]

    Complex sequences of morphological and biochemical changes occur during the developmental course of a batch plant cell culture. However, little information is available about the changes in gene expression that could explain these changes, because of the difficulties involved in isolating specific cellular events or developmental phases in the overlapping phases of cell growth. In an attempt to obtain such information we have examined the global growth phase-dependent gene expression of poplar cells in suspension cultures by cDNA microarray analysis. Our results reveal that significant changes occur in the expression of genes with functions related to protein synthesis, cell cycling, hormonal responses and cell wall biosynthesis, as cultures progress from initiation to senescence, that are highly correlated with observed developmental and physiological changes in the cells. Genes encoding protein kinases, calmodulin and proteins involved in both ascorbate metabolism and water-limited stress responses also showed strong stage-specific expression patterns. Our report provides fundamental information on molecular mechanisms that control cellular changes throughout the developmental course of poplar cell cultures.

  • 17.
    Lärkeryd, Adrian
    et al.
    Umeå universitet, Medicinska fakulteten, Institutionen för klinisk mikrobiologi.
    Myrtennäs, Kerstin
    Umeå universitet, Medicinska fakulteten, Institutionen för klinisk mikrobiologi. Division of CBRN Security and Defence, FOI, Swedish Defence Research Agency.
    Karlsson, Edvin
    Division of CBRN Security and Defence, FOI, Swedish Defence Research Agency.
    Dwibedi, Chinmay Kumar
    Umeå universitet, Medicinska fakulteten, Institutionen för klinisk mikrobiologi, Klinisk bakteriologi. Division of CBRN Security and Defence, FOI, Swedish Defence Research Agency.
    Forsman, Mats
    Division of CBRN Security and Defence, FOI, Swedish Defence Research Agency.
    Larsson, Pär
    Division of CBRN Security and Defence, FOI, Swedish Defence Research Agency.
    Johansson, Anders
    Umeå universitet, Medicinska fakulteten, Molekylär Infektionsmedicin, Sverige (MIMS).
    Sjödin, Andreas
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    CanSNPer: a hierarchical genotype classifier of clonal pathogens2014Ingår i: Bioinformatics, ISSN 1367-4803, E-ISSN 1367-4811, Vol. 30, nr 12, s. 1762-1764Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Advances in typing methodologies have recently reformed the field of molecular epidemiology of pathogens. The falling cost of sequencing technologies is creating a deluge of whole genome sequencing data that burdens bioinformatics resources and tool development. In particular, single nucleotide polymorphisms in core genomes of pathogens are recognized as the most important markers for inferring genetic relationships because they are evolutionarily stable and amenable to high-throughput detection methods. Sequence data will provide an excellent opportunity to extend our understanding of infectious disease when the challenge of extracting knowledge from available sequence resources is met. Here, we present an efficient and user-friendly genotype classification pipeline, CanSNPer, based on an easily expandable database of predefined canonical single nucleotide polymorphisms.

  • 18.
    Myrtennäs, Kerstin
    et al.
    Umeå universitet, Medicinska fakulteten, Institutionen för klinisk mikrobiologi, Infektionssjukdomar. FOI.
    Sjödin, Andreas
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Byström, Mona
    Granberg, Malin
    Brittnacher, Mitchell J.
    Rohmer, Laurence
    Jacobs, Michael A.
    Sims-Day, Elizabeth H.
    Levy, Ruth
    Zhou, Yang
    Hayden, Hillary S.
    Lim, Regina
    Chang, Jean
    Guenthener, Donald
    Kang, Allison
    Haugen, Eric
    Gillett, Will
    Kaul, Rajinder
    Forsman, Mats
    Larsson, Par
    FOI.
    Johansson, Anders
    Umeå universitet, Medicinska fakulteten, Institutionen för klinisk mikrobiologi, Infektionssjukdomar. Umeå universitet, Medicinska fakulteten, Institutionen för klinisk mikrobiologi, Klinisk bakteriologi.
    Genome sequence of Francisella Tularensis subspecies holarctica Strain FSC200, isolated from a child with Tularemia2012Ingår i: Journal of Bacteriology, ISSN 0021-9193, E-ISSN 1098-5530, Vol. 194, nr 24, s. 6965-6966Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Here we report the complete, accurate 1.89-Mb genome sequence of Francisella tularensis subsp. holarctica strain FSC200, isolated in 1998 in the Swedish municipality Ljusdal, which is in an area where tularemia is highly endemic. This genome is important because strain FSC200 has been extensively used for functional and genetic studies of Francisella and is well-characterized.

  • 19.
    Rentoft, Matilda
    et al.
    Umeå universitet, Medicinska fakulteten, Institutionen för medicinsk kemi och biofysik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Svensson, Daniel
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Sjödin, Andreas
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen. Division of CBRN Security and Defence, FOI–Swedish Defence Research Agency, SE Umeå, Sweden.
    Olason, Pall I.
    Sjöström, Olle
    Umeå universitet, Medicinska fakulteten, Institutionen för strålningsvetenskaper, Onkologi. Unit of research, education and development, Region Jämtland Härjedalen, SE Östersund, Sweden.
    Nylander, Carin
    Umeå universitet, Medicinska fakulteten, Institutionen för strålningsvetenskaper, Onkologi.
    Osterman, Pia
    Umeå universitet, Medicinska fakulteten, Institutionen för medicinsk kemi och biofysik.
    Sjögren, Rickard
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Netotea, Sergiu
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen. Science for Life Laboratory, Department of Biology and Biological Engineering, Chalmers University of Technology, SE Göteborg, Sweden.
    Wibom, Carl
    Umeå universitet, Medicinska fakulteten, Institutionen för strålningsvetenskaper, Onkologi.
    Cederquist, Kristina
    Umeå universitet, Medicinska fakulteten, Institutionen för medicinsk biovetenskap, Medicinsk och klinisk genetik.
    Chabes, Andrei
    Umeå universitet, Medicinska fakulteten, Institutionen för medicinsk kemi och biofysik.
    Trygg, Johan
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Melin, Beatrice S.
    Umeå universitet, Medicinska fakulteten, Institutionen för strålningsvetenskaper, Onkologi.
    Johansson, Erik
    Umeå universitet, Medicinska fakulteten, Institutionen för medicinsk kemi och biofysik.
    A geographically matched control population efficiently limits the number of candidate disease-causing variants in an unbiased whole-genome analysis2019Ingår i: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 14, nr 3, artikel-id e0213350Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Whole-genome sequencing is a promising approach for human autosomal dominant disease studies. However, the vast number of genetic variants observed by this method constitutes a challenge when trying to identify the causal variants. This is often handled by restricting disease studies to the most damaging variants, e.g. those found in coding regions, and overlooking the remaining genetic variation. Such a biased approach explains in part why the genetic causes of many families with dominantly inherited diseases, in spite of being included in whole-genome sequencing studies, are left unsolved today. Here we explore the use of a geographically matched control population to minimize the number of candidate disease-causing variants without excluding variants based on assumptions on genomic position or functional predictions. To exemplify the benefit of the geographically matched control population we apply a typical disease variant filtering strategy in a family with an autosomal dominant form of colorectal cancer. With the use of the geographically matched control population we end up with 26 candidate variants genome wide. This is in contrast to the tens of thousands of candidates left when only making use of available public variant datasets. The effect of the local control population is dual, it (1) reduces the total number of candidate variants shared between affected individuals, and more importantly (2) increases the rate by which the number of candidate variants are reduced as additional affected family members are included in the filtering strategy. We demonstrate that the application of a geographically matched control population effectively limits the number of candidate disease-causing variants and may provide the means by which variants suitable for functional studies are identified genome wide.

  • 20. Street, Nathaniel Robert
    et al.
    Skogström, Oskar
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Sjödin, Andreas
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Tucker, James
    Rodri­guez-Acosta, Maricela
    Nilsson, Peter
    Jansson, Stefan
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Taylor, Gail
    The genetics and genomics of the drought response in Populus.2006Ingår i: The Plant Journal, ISSN 0960-7412, Vol. 48, nr 3, s. 321-41Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The genetic nature of tree adaptation to drought stress was examined by utilizing variation in the drought response of a full-sib second generation (F2) mapping population from a cross between Populus trichocarpa (93-968) and P. deltoides Bart (ILL-129) and known to be highly divergent for a vast range of phenotypic traits. We combined phenotyping, quantitative trait loci (QTL) analysis and microarray experiments to demonstrate that ‘genetical genomics’ can be used to provide information on adaptation at the species level. The grandparents and F2 population were subjected to soil drying, and contrasting responses to drought across genotypes, including leaf coloration, expansion and abscission, were observed, and QTL for these traits mapped. A subset of extreme genotypes exhibiting extreme sensitivity and insensitivity to drought on the basis of leaf abscission were defined, and microarray experiments conducted on these genotypes and the grandparent species. The extreme genotype groups induced a different set of genes: 215 and 125 genes differed in their expression response between groups in control and drought, respectively, suggesting species adaptation at the gene expression level. Co-location of differentially expressed genes with drought-specific and drought-responsive QTLs was examined, and these may represent candidate genes contributing to the variation in drought response.

  • 21.
    Sundell, David
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Mannapperuma, Chanaka
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    Netotea, Sergiu
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Delhomme, Nicolas
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    Lin, Yao-Cheng
    Sjödin, Andreas
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Van de Peer, Yves
    Jansson, Stefan
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    Hvidsten, Torgeir R.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Department of Chemistry,Biotechnology and Food Science, Norwegi an University of Life Sciences, 1432As, Norw.
    Street, Nathaniel R.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    The Plant Genome Integrative Explorer Resource: PlantGenIE.org2015Ingår i: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 208, nr 4, s. 1149-1156Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Accessing and exploring large-scale genomics data sets remains a significant challenge to researchers without specialist bioinformatics training. We present the integrated PlantGenIE.org platform for exploration of Populus, conifer and Arabidopsis genomics data, which includes expression networks and associated visualization tools. Standard features of a model organism database are provided, including genome browsers, gene list annotation, BLAST homology searches and gene information pages. Community annotation updating is supported via integration of WebApollo. We have produced an RNA-sequencing (RNA-Seq) expression atlas for Populus tremula and have integrated these data within the expression tools. An updated version of the COMPLEX resource for performing comparative plant expression analyses of gene coexpression network conservation between species has also been integrated. The PlantGenIE.org platform provides intuitive access to large-scale and genome-wide genomics data from model forest tree species, facilitating both community contributions to annotation improvement and tools supporting use of the included data resources to inform biological insight.

  • 22.
    Sundström, Görel
    et al.
    Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences (SLU), Umeå, Sweden.
    Schneider, Andreas N.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    Richau, Kerstin
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    Haas, Julia Christa
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    Delhomme, Nicolas
    Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences (SLU), Umeå, Sweden.
    Sjödin, Andreas
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen. Division of CBRN Security and Defence, FOI-Swedish Defence Agency.
    Hurry, Vaughan
    Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences (SLU), Umeå, Sweden.
    Grabherr, Manfred
    Department of Medical Biochemistry and Microbiology, Uppsala University, Sweden.
    Street, Nathaniel R.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    Reproducibility and biological information of tree-associated metacommunities using RNA Sequencing and DNA amplicon profilingManuskript (preprint) (Övrigt vetenskapligt)
  • 23.
    Svensson, Daniel
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen. Computational Life Science Cluster (CLiC), Umeå University, Umeå, Sweden; Division of CBRN Security and Defence, FOI–Swedish Defence Research Agency, Umeå, Sweden.
    Öhrman, Caroline
    Division of CBRN Security and Defence, FOI–Swedish Defence Research Agency, Umeå, Sweden.
    Bäckman, Stina
    Division of CBRN Security and Defence, FOI–Swedish Defence Research Agency, Umeå, Sweden.
    Karlsson, Edvin
    Division of CBRN Security and Defence, FOI–Swedish Defence Research Agency, Umeå, Sweden.
    Nilsson, Elin
    Division of CBRN Security and Defence, FOI–Swedish Defence Research Agency, Umeå, Sweden.
    Byström, Mona
    Division of CBRN Security and Defence, FOI–Swedish Defence Research Agency, Umeå, Sweden.
    Lärkeryd, Adrian
    Division of CBRN Security and Defence, FOI–Swedish Defence Research Agency, Umeå, Sweden.
    Myrtennäs, Kerstin
    Division of CBRN Security and Defence, FOI–Swedish Defence Research Agency, Umeå, Sweden.
    Stenberg, Per
    Division of CBRN Security and Defence, FOI–Swedish Defence Research Agency, Umeå, Sweden.
    Qu, Ping-hua
    Trygg, Johan
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen. Computational Life Science Cluster (CLiC), Umeå University, Umeå, Sweden.
    Scholz, Holger C.
    Forsman, Mats
    Division of CBRN Security and Defence, FOI–Swedish Defence Research Agency, Umeå, Sweden.
    Sjödin, Andreas
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen. Computational Life Science Cluster (CLiC), Umeå University, Umeå, Sweden; Division of CBRN Security and Defence, FOI–Swedish Defence Research Agency, Umeå, Sweden.
    Complete Genome Sequence of Francisella guangzhouensis Strain 08HL01032(T), Isolated from Air-Conditioning Systems in China2015Ingår i: Microbiology Resource Announcements, ISSN 2576-098X, Vol. 3, nr 2, artikel-id e00024-15Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We present the complete genome sequence of Francisella guangzhouensis strain 08HL01032(T), which consists of one chromosome (1,658,482 bp) and one plasmid ( 3,045 bp) with G+C contents of 32.0% and 28.7%, respectively.

  • 24. Taylor, Gail
    et al.
    Street, Nathaniel R
    Tricker, Penny J
    Sjödin, Andreas
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Graham, Laura
    Skogström, Oskar
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Calfapietra, Carlo
    Scarascia-Mugnozza, Giuseppe
    Jansson, Stefan
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    The transcriptome of Populus in elevated CO2.2005Ingår i: New Phytologist, ISSN 0028-646X, Vol. 167, nr 1, s. 143-54Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The consequences of increasing atmospheric carbon dioxide for long-term adaptation of forest ecosystems remain uncertain, with virtually no studies undertaken at the genetic level. A global analysis using cDNA microarrays was conducted following 6 yr exposure of Populus × euramericana (clone I-214) to elevated [CO2] in a FACE (free-air CO2 enrichment) experiment.

    Gene expression was sensitive to elevated [CO2] but the response depended on the developmental age of the leaves, and < 50 transcripts differed significantly between different CO2 environments. For young leaves most differentially expressed genes were upregulated in elevated [CO2], while in semimature leaves most were downregulated in elevated [CO2].

    For transcripts related only to the small subunit of Rubisco, upregulation in LPI 3 and downregulation in LPI 6 leaves in elevated CO2 was confirmed by anova. Similar patterns of gene expression for young leaves were also confirmed independently across year 3 and year 6 microarray data, and using real-time RT–PCR.

    This study provides the first clues to the long-term genetic expression changes that may occur during long-term plant response to elevated CO2.

  • 25. Vallesi, Adriana
    et al.
    Sjödin, Andreas
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen. Division of CBRN Defence and Security, Swedish Defence Research Agency, FOI, Umeå, Sweden.
    Petrelli, Dezemona
    Luporini, Pierangelo
    Taddei, Anna Rita
    Thelaus, Johanna
    Ohrman, Caroline
    Nilsson, Elin
    Di Giuseppe, Graziano
    Gutierrez, Gabriel
    Villalobo, Eduardo
    A New Species of the gamma-Proteobacterium Francisella, F. adeliensis Sp. Nov., Endocytobiont in an Antarctic Marine Ciliate and Potential Evolutionary Forerunner of Pathogenic Species2019Ingår i: Microbial Ecology, ISSN 0095-3628, E-ISSN 1432-184X, Vol. 77, nr 3, s. 587-596Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The study of the draft genome of an Antarctic marine ciliate, Euplotes petzi, revealed foreign sequences of bacterial origin belonging to the gamma-proteobacterium Francisella that includes pathogenic and environmental species. TEM and FISH analyses confirmed the presence of a Francisella endocytobiont in E. petzi. This endocytobiont was isolated and found to be a new species, named F. adeliensis sp. nov.. F. adeliensis grows well at wide ranges of temperature, salinity, and carbon dioxide concentrations implying that it may colonize new organisms living in deeply diversified habitats. The F. adeliensis genome includes the igl and pdp gene sets (pdpC and pdpE excepted) of the Francisella pathogenicity island needed for intracellular growth. Consistently with an F. adeliensis ancient symbiotic lifestyle, it also contains a single insertion-sequence element. Instead, it lacks genes for the biosynthesis of essential amino acids such as cysteine, lysine, methionine, and tyrosine. In a genome-based phylogenetic tree, F. adeliensis forms a new early branching clade, basal to the evolution of pathogenic species. The correlations of this clade with the other clades raise doubts about a genuine free-living nature of the environmental Francisella species isolated from natural and man-made environments, and suggest to look at F. adeliensis asa pioneer in the Francisella colonization of eukaryotic organisms.

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