| 1. |
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| 2. |
- Sjödin, Kotryna Simonyté, et al.
(author)
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Targeting the gut-lung axis by synbiotic feeding to infants in a randomized controlled trial
- 2023
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In: BMC Biology. - : BioMed Central (BMC). - 1741-7007. ; 21:1
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Journal article (peer-reviewed)abstract
- BACKGROUND: Formula-fed infants are at increased risk of infections. Due to the cross-talk between the mucosal systems of the gastrointestinal and respiratory tracts, adding synbiotics (prebiotics and probiotics) to infant formula may prevent infections even at distant sites. Infants that were born full term and weaned from breast milk were randomized to prebiotic formula (fructo- and galactooligosaccharides) or the same prebiotic formula with Lactobacillus paracasei ssp. paracasei F19 (synbiotics) from 1 to 6 months of age. The objective was to examine the synbiotic effects on gut microbiota development. RESULTS: Fecal samples collected at ages 1, 4, 6, and 12 months were analyzed using 16S rRNA gene sequencing and a combination of untargeted gas chromatography-mass spectrometry/liquid chromatography-mass spectrometry. These analyses revealed that the synbiotic group had a lower abundance of Klebsiella, a higher abundance of Bifidobacterium breve compared to the prebiotic group, and increases in the anti-microbial metabolite d-3-phenyllactic acid. We also analyzed the fecal metagenome and antibiotic resistome in the 11 infants that had been diagnosed with lower respiratory tract infection (cases) and 11 matched controls using deep metagenomic sequencing. Cases with lower respiratory tract infection had a higher abundance of Klebsiella species and antimicrobial resistance genes related to Klebsiella pneumoniae, compared to controls. The results obtained using 16S rRNA gene amplicon and metagenomic sequencing were confirmed in silico by successful recovery of the metagenome-assembled genomes of the bacteria of interest. CONCLUSIONS: This study demonstrates the additional benefit of feeding specific synbiotics to formula-fed infants over prebiotics only. Synbiotic feeding led to the underrepresentation of Klebsiella, enrichment of bifidobacteria, and increases in microbial degradation metabolites implicated in immune signaling and in the gut-lung and gut-skin axes. Our findings support future clinical evaluation of synbiotic formula in the prevention of infections and associated antibiotic treatment as a primary outcome when breastfeeding is not feasible. TRIAL REGISTRATION: ClinicalTrials.gov NCT01625273. Retrospectively registered on 21 June 2012.
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| 3. |
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| 6. |
- Ahlinder, Jon, et al.
(author)
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Increased knowledge of Francisella genus diversity highlights the benefits of optimised DNA-based assays
- 2012
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In: BMC Microbiology. - : Springer Science and Business Media LLC. - 1471-2180. ; 12, s. 220-
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Journal article (peer-reviewed)abstract
- Background: Recent advances in sequencing technologies offer promising tools for generating large numbers of genomes, larger typing databases and improved mapping of environmental bacterial diversity. However, DNA-based methods for the detection of Francisella were developed with limited knowledge about genetic diversity. This, together with the high sequence identity between several Francisella species, means there is a high risk of false identification and detection of the highly virulent pathogen Francisella tularensis. Moreover, phylogenetic reconstructions using single or limited numbers of marker sequences often result in incorrect tree topologies and inferred evolutionary distances. The recent growth in publicly accessible whole-genome sequences now allows evaluation of published genetic markers to determine optimal combinations of markers that minimise both time and laboratory costs. Results: In the present study, we evaluated 38 previously published DNA markers and the corresponding PCR primers against 42 genomes representing the currently known diversity of the genus Francisella. The results highlight that PCR assays for Francisella tularensis are often complicated by low specificity, resulting in a high probability of false positives. A method to select a set of one to seven markers for obtaining optimal phylogenetic resolution or diagnostic accuracy is presented. Conclusions: Current multiple-locus sequence-typing systems and detection assays of Francisella, could be improved by redesigning some of the primers and reselecting typing markers. The use of only a few optimally selected sequence-typing markers allows construction of phylogenetic topologies with almost the same accuracy as topologies based on whole-genome sequences.
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| 7. |
- Ahlinder, Jon, et al.
(author)
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Oligotyping reveals divergent responses of predation resistant bacteria to aquatic productivity and plankton composition
-
Other publication (other academic/artistic)abstract
- 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.
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| 8. |
- Andersson, Anders, et al.
(author)
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A transcriptional timetable of autumn senescence
- 2004
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In: Genome Biology. - : Springer Science and Business Media LLC. - 1465-6906 .- 1474-760X. ; 5:4, s. R24-
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Journal article (peer-reviewed)abstract
- Background We have developed genomic tools to allow the genus Populus (aspens and cottonwoods) to be exploited as a full-featured model for investigating fundamental aspects of tree biology. We have undertaken large-scale expressed sequence tag (EST) sequencing programs and created Populus microarrays with significant gene coverage. One of the important aspects of plant biology that cannot be studied in annual plants is the gene activity involved in the induction of autumn leaf senescence. Results On the basis of 36,354 Populus ESTs, obtained from seven cDNA libraries, we have created a DNA microarray consisting of 13,490 clones, spotted in duplicate. Of these clones, 12,376 (92%) were confirmed by resequencing and all sequences were annotated and functionally classified. Here we have used the microarray to study transcript abundance in leaves of a free-growing aspen tree (Populus tremula) in northern Sweden during natural autumn senescence. Of the 13,490 spotted clones, 3,792 represented genes with significant expression in all leaf samples from the seven studied dates. Conclusions We observed a major shift in gene expression, coinciding with massive chlorophyll degradation, that reflected a shift from photosynthetic competence to energy generation by mitochondrial respiration, oxidation of fatty acids and nutrient mobilization. Autumn senescence had much in common with senescence in annual plants; for example many proteases were induced. We also found evidence for increased transcriptional activity before the appearance of visible signs of senescence, presumably preparing the leaf for degradation of its components.
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| 9. |
- Andersson, Agneta, et al.
(author)
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Aquatic ecosystems at risk for occurrence of pathogenic bacteria
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Other publication (other academic/artistic)abstract
- Pathogenic bacteria occur naturally in aquatic systems. Co-existence of bacteria and protozoa has led to development of predation resistance strategies, which is suggested to serve as a driver for evolution of pathogenic bacteria. However, the ecological mechanisms for selection for different types of predation resistant and pathogenic bacteria are poorly known. To disentangle effects from nutrient availability and protozoan predation pressure on the occurrence of varying predation resistant bacterial genera, an enrichment-dilution experiment was performed where an aquatic bacterial community was exposed to protozoa. Operational taxonomical units, specific for three predation resistant bacterial genera were identified; Pseudomonas, Rickettsia and Mycobacterium. These genera are also known to harbor species that are potentially pathogenic to mammals. Rickettsia and Mycobacterium were promoted where protozoa were abundant and the predation pressure high, while Pseudomonas dominated the bacterial community at the highest nutrient level where the predation pressure on bacteria were low. Our study thus indicates that waters of all nutrient states can harbor pathogenic bacteria, but that bacteria with different ecological strategies occur depending on nutrient level and perturbation. The generative model approach presented here provide a possibility to integrate environmental data in prediction models of pathogens in complex environments.
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| 10. |
- Babst, Benjamin A, et al.
(author)
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Local and systemic transcriptome responses to herbivory and jasmonic acid in Populus
- 2009
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In: The Genetics & Genomes. - : Springer Science and Business Media LLC. - 1614-2942 .- 1614-2950. ; 5:3, s. 459-474
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Journal article (peer-reviewed)abstract
- We used DNA microarrays to examine local and systemic transcriptional responses to herbivory by gypsy moth larvae (GM) and exogenous jasmonic acid (JAtrt) in leaves of Populus nigra L. to identify candidate signaling and defense genes and also to examine primary metabolism, as might relate to tolerance of damage. GM and JAtrt altered expression of over 800 genes, most of which have putative roles in defense signaling, secondary metabolism, and primary metabolism. Additionally, numerous uncharacterized genes responded to herbivory, providing a rich resource for future studies. There was limited overlap (14%) between the responses to GM and JAtrt. GM did, however, result in strong upregulation of genes involved not only in JA biosynthesis but also abscisic acid biosynthesis and other signaling pathways. GM induced known resistance transcripts, including polyphenolic biosynthetic genes, proteinase inhibitors, and amino acid deaminases. According to GOStats pathway level analysis, GM altered primary metabolism, including aromatic amino acid biosynthesis, fatty acid β-oxidation, and carbohydrate and organic acid metabolism. These alterations may be related to increased demands for substrate for secondary metabolites or may serve a tolerance-related role. Responses were more intense locally in treated leaves than in untreated (systemic) leaves and systemic responses were mostly a subset of the genes induced locally. A stronger local response might be needed to cope with localized stresses and wound healing. Since Populus in general and this clone in particular are known for their systemic induced resistance, genes induced both locally and systemically may be the highest quality candidates for resistance.
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| 11. |
- Birdsell, Dawn N, et al.
(author)
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Francisella tularensis subsp. tularensis group A.I, United States
- 2014
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In: Emerging Infectious Diseases. - : Centers for Disease Control and Prevention (CDC). - 1080-6040 .- 1080-6059. ; 20:5, s. 861-865
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Journal article (peer-reviewed)abstract
- We used whole-genome analysis and subsequent characterization of geographically diverse strains using new genetic signatures to identify distinct subgroups within Francisella tularensis subsp. tularensis group A.I: A.I.3, A.I.8, and A.I.12. These subgroups exhibit complex phylogeographic patterns within North America. The widest distribution was observed for A.I.12, which suggests an adaptive advantage.
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| 12. |
- Bylesjö, Max, et al.
(author)
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MASQOT : a method for cDNA microarray spot quality control.
- 2005
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In: BMC Bioinformatics. - : Springer Science and Business Media LLC. - 1471-2105. ; 6, s. 250-
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Journal article (peer-reviewed)abstract
- BackgroundcDNA 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.ResultsA 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.ConclusionThe 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.
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| 13. |
- Bylesjö, Max, et al.
(author)
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MASQOT-GUI : spot quality assessment for the two-channel microarray platform
- 2006
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In: Bioinformatics. - : Oxford University Press (OUP). - 1367-4803 .- 1367-4811. ; 22:20, s. 2554-2555
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Journal article (peer-reviewed)abstract
- 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/
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| 14. |
- Bylesjö, Max, et al.
(author)
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Orthogonal projections to latent structures as a strategy for microarray data normalization
- 2007
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In: BMC Bioinformatics. - : Springer Science and Business Media LLC. - 1471-2105. ; 8:207
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Journal article (peer-reviewed)abstract
- BackgroundDuring 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.ResultsWe 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.ConclusionsThe 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.
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| 15. |
- Christensen, Andreas, 1987-
(author)
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Capacities, Poincaré inequalities and gluing metric spaces.
- 2023
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Licentiate thesis (other academic/artistic)abstract
- This thesis consists of an introduction, and one research paper with results related to potential theory both in the classical Euclidean setting, as well as in quite general metric spaces.The introduction contains a theoretical and historical background of some basic concepts, and their more modern generalisations to metric spaces developed in the last 30 years. By using upper gradients it is possible to define such notions as first order Sobolev spaces, p-harmonic functions and capacity on metric spaces. When generalising classical results to metric spaces, one often needs to impose some structure on the space by making additional assumptions, such as a doubling condition and a Poincaré inequality.In the included research paper, we study a certain type of metric spaces called bow-ties, which consist of two metric spaces glued together at a single designated point. For a doubling measure μ, we characterise when μ supports a Poincar´e inequality on the bow-tie, in terms of Poincaré inequalities on the separate parts together with a variational p-capacity condition and a quasiconvexity-type condition. The variational p-capacity condition is then characterised by a sharp measure decay condition at the designated point.We also study the special case when the bow-tie consists of the positive and negative hyperquadrants in Rn, equipped with a radial doubling measure. In this setting, we characterise the validity of the p-Poincaré inequality in various ways, and then provide a formula for the variational p-capacity of annuli centred at the origin.i
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| 16. |
- Courtois-Moreau, Charleen L, et al.
(author)
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A unique program for cell death in xylem fibers of Populus stem
- 2009
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In: The Plant Journal. - 0960-7412 .- 1365-313X. ; 58:2, s. 260-274
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Journal article (peer-reviewed)abstract
- 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.
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| 17. |
- Cronhjort, Samuel, et al.
(author)
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The Tick-Borne Diseases STING study : Real-time PCR analysis of three emerging tick-borne pathogens in ticks that have bitten humans in different regions of Sweden and the Aland islands, Finland
- 2019
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In: Infection Ecology & Epidemiology. - : Taylor & Francis. - 2000-8686. ; 9:1
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Journal article (peer-reviewed)abstract
- A milder climate has during the last decade contributed to an increased density and spreading of ixodid ticks, thus enhancing their role as emerging vectors for pathogenic microorganisms in northern Europe. It remains unclear if they contribute to the occurrence of infections caused by the bacteria Bartonella spp., Francisella tularensis subspecies holarctica and the parasite Toxoplasma gondii in Sweden and on the Åland islands, Finland. In this study, we want to improve understanding of the tick-borne transmission of these pathogens. Volunteers were recruited at primary healthcare centers. Ticks and blood samples were acquired from participants recruited in 2008 and 2009. Health questionnaires were completed, and medical records were acquired where applicable. Feeding time was estimated and screening of pathogens in the ticks was performed through real-time PCR. Ticks (n = 1849) were of mixed developmental stages: 76 larvae, 1295 nymphs, 426 adults and 52 undetermined. All analyzed ticks were considered negative for these pathogens since the CT-values were all below the detection limit for Bartonella spp. (1663 ticks), Francisella spp. (1849 ticks) and Toxoplasma gondii (1813 ticks). We assume that infections with these pathogens are caused by other transmission pathways within these regions of Sweden and the Åland islands, Finland.
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| 18. |
- Dahlin, Andreas P, et al.
(author)
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Multiplexed quantification of proteins adsorbed to surface-modified and non-modified microdialysis membranes
- 2012
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In: Analytical and Bioanalytical Chemistry. - : Springer Science and Business Media LLC. - 1618-2642 .- 1618-2650. ; 402:6, s. 2057-2067
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Journal article (peer-reviewed)abstract
- A simple and straightforward method for discovery and quantification of proteins adsorbed onto delicate and sensitive membrane surfaces is presented. The adsorbed proteins were enzymatically cleaved while still adsorbed onto the membranes using an on-surface enzymatic digestion (oSED). This was followed by isobaric tagging, nanoliquid chromatography, and tandem mass spectrometry. Protein adsorption on tri-block copolymer Poloxamer 407 surface-modified microdialysis (MD) membranes were compared with protein adsorption on unmodified MD membranes. Ventricular cerebrospinal fluid (vCSF) kept at 37 °C was used as sample matrix. In total, 19 proteins were quantified in two biological replicates. The surface-modified membranes adsorbed 33% less proteins than control membranes and the most abundant proteins were subunits of hemoglobin and clusterin. The adsorption of clusterin on the modified membranes was on average 36% compared to control membranes. The most common protein in vCSF, Albumin, was not identified adsorbed to the surface at all. It was also experimentally verified that oSED, in conjunction with tandem mass spectrometry can be used to quantify femtomole amounts of proteins adsorbed on limited and delicate surfaces, such as MD membranes. The method has great potential and can be used to study much more complex protein adsorption systems than previously reported.
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| 19. |
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| 20. |
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| 21. |
- Druart, Nathalie, et al.
(author)
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Environmental and hormonal regulation of the activity–dormancy cycle in the cambial meristem involves stage-specific modulation of transcriptional and metabolic networks
- 2007
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In: The Plant Journal. ; 50, s. 557-73
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Journal article (peer-reviewed)abstract
- 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.
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| 22. |
- Druart, Nathalie, et al.
(author)
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Molecular targets of elevated [CO2] in leaves and stems of Populus deltoides: implications for future tree growth and carbon sequestration
- 2006
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In: Functional Plant Biology. ; 33, s. 121-131
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Journal article (peer-reviewed)abstract
- 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.
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| 23. |
- Dwibedi, Chinmay Kumar, et al.
(author)
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Biological amplification of low frequency mutations unravels laboratory culture history of the bio-threat agent Francisella tularensis
- 2020
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In: Forensic Science International. - : Elsevier. - 1872-4973 .- 1878-0326. ; 45
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Journal article (peer-reviewed)abstract
- Challenges of investigating a suspected bio attack include establishing if microorganisms have been cultured to produce attack material and to identify their source. Addressing both issues, we have investigated genetic variations that emerge during laboratory culturing of the bacterial pathogen Francisella tularensis. Key aims were to identify genetic variations that are characteristic of laboratory culturing and explore the possibility of using biological amplification to identify genetic variation present at exceedingly low frequencies in a source sample. We used parallel serial passage experiments and high-throughput sequencing of F. tularensis to explore the genetic variation. We found that during early laboratory culture passages of F. tularensis, gene duplications emerged in the pathogen genome followed by single-nucleotide polymorphisms in genes for bacterial capsule synthesis. Based on a biological enrichment scheme and the use of high-throughput sequencing, we identified genetic variation that likely pre-existed in a source sample. The results support that capsule synthesis gene mutations are common during laboratory culture, and that a biological amplification strategy is useful for linking a F. tularensis sample to a specific laboratory variant among many highly similar variants.
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| 24. |
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| 25. |
- Eriksson, Karolina Ida Anna, et al.
(author)
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Association between Legionella species and humic substances during early summer in the northern Baltic Sea
- 2023
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In: Frontiers in Marine Science. - : Frontiers Media S.A.. - 2296-7745. ; 9
-
Journal article (peer-reviewed)abstract
- Climate change is projected to cause alterations in northern coastal systems, including humification and intensified nutrient loads, which can lead to ecosystem imbalances and establishment of new bacterial species. Several potential pathogens, such as different species of Legionella, hide in the environment between infections, some by living inside protozoan host cells. Knowledge about the occurrence of Legionella in natural waters is missing, which disable risk assessments of exposure. We performed a study of the species diversity of Legionella in the northern Baltic Sea (Gulf of Bothnia) during early summer to map their occurrence and to identify possible environmental drivers. We detected Legionella and potential protozoan hosts along gradients of the Gulf of Bothnia. We also for the first time present third generation full-length 16S rRNA amplicon sequencing (Nanopore) to resolve environmental species classification of Legionella, with a method suitable to study all bacteria. Our data show that full length 16S rRNA sequences is sufficient to resolve Legionella while the standard short Illumina sequences did not capture the entire diversity. For accurate species classification of Legionella, harmonization between the Nanopore classification methods is still needed and the bias toward the well-studied Legionella pneumophila need to be resolved. Different Legionella species occurred both in the Bothnian Sea and in the Bothnian Bay and their abundance were linked to humic substances and low salinity. The relative abundance of Legionella was higher in the humic-rich northern waters of the Bothnian Bay. The link between Legionella species and humic substances may be indirect via promotion of the heterotrophic microbial food web, allowing Legionella species and similar bacteria to establish. Humic substances are rich in iron, which has been shown crucial for growth of Legionella species and other pathogens. Considering climate change projections in this regional area, with increased humification and freshwater inflow, this bacterial niche containing potential pathogens might become more widespread in the future Baltic Sea. This study demonstrates the significance of DNA sequencing to monitor public health relevant bacteria like Legionella species in the environment. Including sequencing of bacteria and protozoa in the environmental monitoring programs could be used to identify ecosystem imbalances, which enable appropriate responses to emerging diseases.
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| 26. |
- Fracheboud, Yvan, et al.
(author)
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The control of autumn senescence in European aspen
- 2009
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In: Plant Physiology. - : Oxford University Press (OUP). - 0032-0889 .- 1532-2548. ; 149:4, s. 1982-1991
-
Journal article (peer-reviewed)abstract
- 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.
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| 27. |
- Fredriksson, Johan, et al.
(author)
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Clustering Worst-Case Execution Times for Software Components
- 2007
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In: Proceedings of the 7th International Workshop on Worst Case Execution Time Analysis (WCET'07), Pisa, Italy. - 9783939897057 ; , s. 19-25
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Conference paper (peer-reviewed)abstract
- For component-based systems, classical techniques for WCET-estimation produce unacceptable overestimations of the WCET. This is because software components have more general behavior in order to support reuse. Existing tools and methods for component-based software engineering (CBSE) do not yet adequately consider reusable analyses.We present a method that allows different WCETs to be associated with subsets of the component behavior by clustering WCETs with respect to behavior. The method is intended to be used for facilitating reusable WCET analysis for reusable software components. We illustrate our technique and demonstrate its potential in achieving tight WCET-estimates for components with rich behavior.
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| 28. |
- Fredriksson, Johan, et al.
(author)
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Contract-Based Reusable Analysis for Software Components with Extra-Functional Properties
- 2007
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In: Proceedings of the Work-In-Progress (WIP) session of the 19th Euromicro Conference on Real-Time Systems (ECRTS'07), Pisa, Italy. ; , s. 57-60
-
Conference paper (peer-reviewed)abstract
- Component-based software engineering (CBSE) for embedded systems is currently gaining ground because of shortened time-to-market, reduced development costs and increased software quality. One main characteristic of CBSE that enable these benefits is its facilitation of component reuse. However, existing tools and methods do not consider reuse of extra-functional properties in these systems.In this paper we extend our previous work on contract-based reusable execution time predictions for software components with additional extra-functional properties, such as memory and energy consumption.
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| 29. |
- Garcia-Lorenzo, Maribel, et al.
(author)
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Protease gene families in Populus and Arabidopsis
- 2006
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In: BMC Plant Biology. - : Springer Science and Business Media LLC. - 1471-2229. ; 6:30, s. 1-24
-
Journal article (peer-reviewed)abstract
- Proteases play key roles in plants, maintaining strict protein quality control and degrading specific sets of proteins in response to diverse environmental and developmental stimuli. Similarities and differences between the proteases expressed in different species may give valuable insights into their physiological roles and evolution. RESULTS: We have performed a comparative analysis of protease genes in the two sequenced dicot genomes, Arabidopsis thaliana and Populus trichocarpa by using genes coding for proteases in the MEROPS database 1 for Arabidopsis to identify homologous sequences in Populus. A multigene-based phylogenetic analysis was performed. Most protease families were found to be larger in Populus than in Arabidopsis, reflecting recent genome duplication. Detailed studies on e.g. the DegP, Clp, FtsH, Lon, rhomboid and papain-Like protease families showed the pattern of gene family expansion and gene loss was complex. We finally show that different Populus tissues express unique suites of protease genes and that the mRNA levels of different classes of proteases change along a developmental gradient. CONCLUSION: Recent gene family expansion and contractions have made the Arabidopsis and Populus complements of proteases different and this, together with expression patterns, gives indications about the roles of the individual gene products or groups of proteases.
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| 30. |
- Gendre, Delphine, et al.
(author)
-
Trans-Golgi Network Localized ECHIDNA/Ypt Interacting Protein Complex Is Required for the Secretion of Cell Wall Polysaccharides in Arabidopsis
- 2013
-
In: Plant Cell. - : Oxford University Press (OUP). - 1040-4651 .- 1532-298X. ; 25, s. 2633-2646
-
Journal article (peer-reviewed)abstract
- The secretion of cell wall polysaccharides through the trans-Golgi network (TGN) is required for plant cell elongation. However, the components mediating the post-Golgi secretion of pectin and hemicellulose, the two major cell wall polysaccharides, are largely unknown. We identified evolutionarily conserved YPT/RAB GTPase Interacting Protein 4a (YIP4a) and YIP4b (formerly YIP2), which form a TGN-localized complex with ECHIDNA (ECH) in Arabidopsis thaliana. The localization of YIP4 and ECH proteins at the TGN is interdependent and influences the localization of VHA-a1 and SYP61, which are key components of the TGN. YIP4a and YIP4b act redundantly, and the yip4a yip4b double mutants have a cell elongation defect. Genetic, biochemical, and cell biological analyses demonstrate that the ECH/YIP4 complex plays a key role in TGN-mediated secretion of pectin and hemicellulose to the cell wall in dark-grown hypocotyls and in secretory cells of the seed coat. In keeping with these observations, Fourier transform infrared microspectroscopy analysis revealed that the ech and yip4a yip4b mutants exhibit changes in their cell wall composition. Overall, our results reveal a TGN subdomain defined by ECH/YIP4 that is required for the secretion of pectin and hemicellulose and distinguishes the role of the TGN in secretion from its roles in endocytic and vacuolar trafficking.
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| 31. |
- Goormaghtigh, Frederic, et al.
(author)
-
Reassessing the Role of Type II Toxin-Antitoxin Systems in Formation of Escherichia coli Type II Persister Cells
- 2018
-
In: mBio. - : American Society for Microbiology. - 2161-2129 .- 2150-7511. ; 9:3
-
Journal article (peer-reviewed)abstract
- 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.
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| 32. |
- Grüning, Björn, et al.
(author)
-
Bioconda: A sustainable and comprehensive software distribution for the life sciences
- 2017
-
Other publication (other academic/artistic)abstract
- We present Bioconda (https://bioconda.github.io), a distribution of bioinformatics software for the lightweight, multi-platform and language-agnostic package manager Conda. Currently, Bioconda offers a collection of over 3000 software packages, which is continuously maintained, updated, and extended by a growing global community of more than 200 contributors. Bioconda improves analysis reproducibility by allowing users to define isolated environments with defined software versions, all of which are easily installed and managed without administrative privileges.
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| 33. |
- Haas, Julia Christa, et al.
(author)
-
Microbial community response to growing season and plant nutrient optimisation in a boreal Norway spruce forest
- 2018
-
In: Soil Biology and Biochemistry. - : Elsevier. - 0038-0717 .- 1879-3428. ; 125, s. 197-209
-
Journal article (peer-reviewed)abstract
- 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.
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| 34. |
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| 35. |
- Hjertström, Andreas, 1972-, et al.
(author)
-
A Data-Entity Approach for Component-Based Real-TimeEmbedded Systems Development
- 2009
-
In: 14th IEEE International Conference on Emerging Technology and Factory Automation. - 9781424427284
-
Conference paper (peer-reviewed)abstract
- In this paper the data-entity approach for efficientdesign-time management of run-time data in componentbasedreal-time embedded systems is presented. The approachformalizes the concept of a data entity which enabledesign-time modeling, management, documentationand analysis of run-time data items. Previous studies ondata management for embedded real-time systems showthat current data management techniques are not adequate,and therefore impose unnecessary costs and quality problemsduring system development. It is our conclusion thatdata management needs to be incorporated as an integralpart of the development of the entire system architecture.Therefore, we propose an approach where run-time datais acknowledged as first class objects during developmentwith proper documentation and where properties such asusage, validity and dependency can be modeled. In thisway we can increase the knowledge and understanding ofthe system. The approach also allows analysis of data dependencies,type matching, and redundancy early in the developmentphase as well as in existing systems.
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| 36. |
- Hjertström, Andreas, et al.
(author)
-
Data Management for Component-Based Embedded Real-Time Systems : the Database Proxy Approach
- 2012
-
In: Journal of Systems and Software. - : Elsevier BV. - 0164-1212 .- 1873-1228. ; 85:4, s. 821-834
-
Journal article (peer-reviewed)abstract
- We introduce the concept of database proxies intended to mitigate the gap between two disjoint productivity-enhancing techniques: Component Based Software Engineering (CBSE) and Real-Time Database Management Systems (RTDBMS). The two techniques promote opposing design goals and their coexistence is neither obvious nor intuitive. CBSE promotes encapsulation and decoupling of component internals from the component environment, whilst an RTDBMS provide mechanisms for efficient and predictable global data sharing. A component with direct access to an RTDBMS is dependent on that specific RTDBMS and may not be useable in an alternative environment. For components to remain encapsulated and reusable, database proxies decouple components from an underlying database residing in the component framework, while providing temporally predictable access to data maintained in a database. Our approach provide access to features such as extensive data modeling tools, predictable access to hard real-time data, dynamic access to soft real-time data using standardized queries and controlled data sharing; thus allowing developers to employ the full potential of both CBSE and an RTDBMS. Our approach primarily targets embedded systems with a subset of functionality with real-time requirements. The implementation results show that the benefits of using proxies do not come at the expense of significant run-time overheads or less accurate timing predictions.
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| 37. |
|
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| 38. |
- Hjertström, Andreas, 1972-
(author)
-
Data Management in Component-Based Embedded Real-Time Systems
- 2012
-
Doctoral thesis (other academic/artistic)abstract
- This thesis presents new data management techniques for run-time data in component-based embedded real-time systems. These techniques enable data to be modeled, analyzed and structured to improve data management during system development, maintenance, and execution. The foundation of our work is a case-study that identifies a number of problems with current state-of-practice in data management for industrial embedded real-time systems. We introduce two novel concepts: the data entity and the database proxy. The data entity is a design-time concept that allows designers to manage data objects throughout different design and maintenance activities. It includes data-type specification, documentation, specification of timing and quality properties, tracing of dependencies between data objects, and enables analysis and automated validation. The database proxy is a run-time concept designed to allow the use of state-of-the-art database technologies in contemporary software-component technologies for embedded systems. Database proxies decouple components from an underlying database residing in the component framework. This allows components to remain encapsulated and reusable, while providing temporally predictable access to data maintained in a database, thus enabling the use of database technologies, which has previously excluded, in these systems. To validate our proposed techniques, we present a tool implementation of the data entity as well as implementations of the database proxy approach, using commercial tools, the AUTOSAR standardized automotive software architecture, and automotive hardware. Our results show that the presented techniques can contribute to the development of future component-based embedded real-time systems, by providing structured and efficient data management.
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| 39. |
- Hjertström, Andreas, 1972-, et al.
(author)
-
Database Proxies: A Data Management approach for Component-Based Real-Time Systems
- 2009
-
Reports (pop. science, debate, etc.)abstract
- This thesis presents new techniques for data management of run-time dataobjects in component-based embedded real-time systems. These techniquesenable data to be modeled, analyzed and structured to achieve proper datamanagement during development, maintenance and execution.The evolution of real-time embedded systems has resulted in an increasedsystem complexity beyond what was thought possible just a few years ago.Over the years, new techniques and tools have been developed to managesoftware and communication complexity. However, as this thesis show, currenttechniques and tools for data management are not sufficient. Today,development of real-time embedded systems focuses on the function aspects ofthe system, in most cases disregarding data management.The lack of proper design-time data management often results in ineffectivedocumentation routines and poor overall system knowledge. Contemporarytechniques to manage run-time data do not satisfy demands on flexibility,maintainability and extensibility. Based on an industrial case-study thatidentifies a number of problems within current data management techniques,both during design-time and run-time, it is clear that data managementneeds to be incorporated as an integral part of the development of theentire system architecture.As a remedy to the identified problems, we propose a design-time data entityapproach, where the importance of data in the system is elevated to beincluded in the entire design phase with proper documentation, properties,dependencies and analysis methods to increase the overall system knowledge.Furthermore, to efficiently manage data during run-time, we introducedatabase proxies to enable the fusion between two existing techniques;Component Based Software Engineering (CBSE) and Real-Time DatabaseManagement Systems (RTDBMS). A database proxy allows components to bedecoupled from the underlying data management strategy without violating thecomponent encapsulation and communication interface.
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| 40. |
- Hjertström, Andreas, et al.
(author)
-
Database Proxies for Component-Based Real-Time Systems
- 2010
-
In: Proceedings - 22st Euromicro Conference on Real-Time Systems. - 9780769541112 ; , s. 79-89
-
Conference paper (peer-reviewed)abstract
- We introduce the concept of database proxies capable of mitigating the gap between two disjoint productivityenhancing techniques: Component Based Software Engineering (CBSE) and Real-Time Database Management Systems (RTDBMS). The coexistence of the two techniques is neither obvious nor intuitive since CBSE and RTDBMS promotes opposing design goals; CBSE promotes encapsulation and decoupling of component internals from the component environment, whilst RTDBMS provide mechanisms for efficient and predictable global data sharing. Database proxies decouple components from an underlying database residing in the component framework. This enables components to remain encapsulated and reusable, while providing temporally predictable access to data maintained in a database. We specifically target embedded systems with a subset of functionality with real-time requirements. Our implementation results show that the above benefits do not come at the expense of run-time overheads or less accurate timing predictions.
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| 41. |
- Hjertström, Andreas, et al.
(author)
-
Database Proxy Tool Support in an AUTOSAR Development Environment
- 2012
-
In: Proceedings - 38th EUROMICRO Conference on Software Engineering and Advanced Applications, SEAA 2012. - 9780769547909 ; , s. 51-54
-
Conference paper (peer-reviewed)abstract
- AUTOSAR has been introduced as a remedy for the increasing complexity and rising costs within automotive systems development. However, AUTOSAR does not provide sufficient support for the increased complexity with respect to data management. Database proxies have been presented as a promising solution to provide software component technologies with the capabilities of a state-of-the-art real-time database management system. In this paper, we show how an industrial AUTOSAR development environment can be extended to include support for real-time data management.
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| 42. |
- Hjertström, Andreas, et al.
(author)
-
Design-Time Management of Run-Time Data in Industrial Embedded Real-Time Systems Development
- 2008
-
In: Proceedings of 13th IEEE International Conference on Emerging Technologies and Factory Automation (ETFA'08), IEEE Industrial Electronics Society, Hamburg, Germany. - 9781424415069 - 9781424415052 ; , s. 1285-1293
-
Conference paper (peer-reviewed)abstract
- Efficient design-time management and documentation of run-time data elements are of paramount importance when developing and maintaining modern real-time systems. In this paper, we present the results of an industrial case-study in which we have studied the state of practice in data management and documentation. Representatives from five companies within various business segments have been interviewed and our results show that various aspects of current data management and documentation are problematic and not yet mature. Results show that companies today have a fairly good management of distributed signals, while internal ECU signals and states are, in many cases, not managed at all. This lack of internal data management results in costly development and maintenance and is often entirely dependent of the know-how of single individual experts.Furthermore, it has, in several cases, resulted in unused and excessive data in the systems due to the fact thatwhether or not a data is used is unknown.
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| 43. |
- Hjertström, Andreas, et al.
(author)
-
INCENSE : Information-Centric Run-Time Support for Component-Based Embedded Real-Time Systems
- 2007
-
In: Proceedings of the Work-In-Progress (WIP) session, 14th IEEE Real-Time and Embedded Technology and Applications Symposium, Seattle, United States. ; , s. 4-
-
Conference paper (peer-reviewed)abstract
- In this paper we present a technique to allow the use ofreal-time database management together with componentbasedsoftware development, to achieve an information centricrun-time platform for the development of embeddedreal-time systems. The technique allows components tobenefit from the advantages of a real-time database managementsystem while still retaining desirable componentproperties, such as isolation and a high level of reusability.We propose that a database is integrated in the componentframework, and introduce the concept of databaseproxies to decouple components from the database schema.The resulting system fully benefits from the advantages ofcomponent-based software development, such as reusability,all component interaction through interfaces, etc, combinedwith the advantages of a real-time database managementsystem, i.e., system openness, controlled data access,and dynamic query language capabilities.
|
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| 44. |
- Hjertström, Andreas, 1972-
(author)
-
Information Centric Development of Component-Based Embedded Real-Time Systems
- 2009
-
Licentiate thesis (other academic/artistic)abstract
- This thesis presents new techniques for data management of run-time data objectsin component-based embedded real-time systems. These techniques enabledata to be modeled, analyzed and structured to achieve data managementduring development, maintenance and execution.The evolution of real-time embedded systems has resulted in an increasedsystem complexity beyond what was thought possible just a few years ago.Over the years, new techniques and tools have been developed to manage softwareand communication complexity. However, as this thesis show, currenttechniques and tools for data management are not sufficient. Today, developmentof real-time embedded systems focuses on the function aspects of thesystem, in most cases disregarding data management.The lack of proper design-time data management often results in ineffectivedocumentation routines and poor overall system knowledge. Contemporarytechniques to manage run-time data do not satisfy demands on flexibility,maintainability and extensibility. Based on an industrial case-study that identifiesa number of problems within current data management techniques, bothduring design-time and run-time, it is clear that data management needs to beincorporated as an integral part of the development of the entire system architecture.As a remedy to the identified problems, we propose a design-time data entityapproach, where the importance of data in the system is elevated to beincluded in the entire design phase with proper documentation, properties, dependenciesand analysis methods to increase the overall system knowledge.Furthermore, to efficiently manage data during run-time, we introduce databaseproxies to enable the fusion between two existing techniques; ComponentBased Software Engineering (CBSE) and Real-Time Database ManagementSystems (RTDBMS). A database proxy allows components to be decoupledfrom the underlying data management strategy without violating the componentencapsulation and communication interface.
|
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| 45. |
- Hjertström, Andreas, 1972-, et al.
(author)
-
Introducing Database-Centric Support in AUTOSAR
- 2012
-
In: 7th International Symposium on Industrial Embedded Systems (SIES). - : IEEE. - 9781467326841 ; , s. 138-147
-
Conference paper (peer-reviewed)abstract
- We propose to integrate a real-time databasemanagement system into the basic software of the AUTOSARcomponent model. This integration can be performed withoutviolating the fundamental principles of the component-basedapproach of the AUTOSAR standard. Our database-centricapproach allows developers to focus on application developmentinstead of reinventing data management techniques ordevelop solutions using internal data structures. We use stateof-the-art database pointer techniques to achieve predictabletiming, and database proxies to maintain component encapsulationand independence of data-management strategy. Thepaper illustrates the feasibility of our proposal when databaseproxies are used to manage the data communication betweencomponents and to perform run-time monitoring on the virtualfunction bus. Our implementation results show that the abovebenefits do not come at the expense of run-time overheadsor less accurate timing predictions. Under typical workloadconditions, our concept only introduces in the order of 4%CPU overhead.
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| 46. |
- Hoffman, Tove, et al.
(author)
-
Association between guilds of birds in the African-Western Palaearctic region and the tick species Hyalomma rufipes, one of the main vectors of Crimean-Congo hemorrhagic fever virus.
- 2022
-
In: Microorganisms. - : MDPI AG. - 2076-2607. ; 10
-
Journal article (peer-reviewed)abstract
- The migratory behavior of wild birds contributes to the geographical spread of ticks and their microorganisms. In this study, we aimed to investigate the dispersal and co-occurrence of Francisella and spotted fever group Rickettsia (SFGR) in ticks infesting birds migrating northward in the African-Western Palaearctic region (AWPR). Birds were trapped with mist nests across the Mediterranean basin during the 2014 and 2015 spring migration. In total, 575 ticks were collected from 244 birds. We screened the ticks for the species Francisella tularensis, the genus Francisella, and SFGR by microfluidic real-time PCR. Confirmatory analyses and metagenomic sequencing were performed on tick samples that putatively tested positive for F. tularensis during initial screenings. Hyalomma rufipes was the most common tick species and had a high prevalence of Francisella, including co-occurrence of Francisella and SFGR. Metagenomic analysis of total DNA extracted from two H. rufipes confirmed the presence of Francisella, Rickettsia, and Midichloria. Average nucleotide identity and phylogenetic inference indicated the highest identity of the metagenome-assembled genomes to a Francisella-like endosymbiont (FLE), Rickettsia aeschlimannii, and Midichloria mitochondrii. The results of this study suggest that (i) FLE- and SFGR-containing ticks are dispersed by northbound migratory birds in the AWPR, (ii) H. rufipes likely is not involved in transmission of F. tularensis in the AWPR, and (iii) a dual endosymbiosis of FLEs and Midichloria may support some of the nutritional requirements of H. rufipes.
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| 47. |
- Hoffman, Tove, et al.
(author)
-
Co-occurrence of Francisella and spotted fever group Rickettsia in avian-associated Hyalomma rufipes
- 2022
-
In: Microorganisms. - : MDPI. - 2076-2607. ; 10:7
-
Journal article (peer-reviewed)abstract
- Introduction: The migratory behaviour of wild birds aids in the geographical spread of ticks and their microorganisms. Ticks are known to harbor both pathogenic and symbiotic bacteria - such as species of the genera Francisella, Rickettsia,and Midichloria - and multiple bacterial species may occur within them. Francisella occurs in different tick taxa andconsists of closely related pathogenic and non-pathogenic species. Spotted fever group Rickettsia are transmitted to humans by different tick genera and are emerging human pathogens in Europe. The aims of this study were to investigate dispersal of Francisella as well as co-occurrence of Francisella and spotted fever group Rickettsia in ticks infesting northward migrating birds in the African-Western Palaearctic region.Materials and methods: Birds were trapped using mist nets at bird observatories in Spain, Italy, Greece, and Israel during their spring migration of 2014 and 2015. Ticks were screened for the genus Francisella, the species Francisella tularensis, and spotted fever group Rickettsia by microfluidic qPCR. Ticks with putative positive results for F. tularensiswere subjected to confirmation analyses, metagenomics analysis, enrichment, and whole genome sequencing.Results: There was a high prevalence of Francisella species (76.7%) and co-occurrence of Francisella species and spotted fever group Rickettsia (50.6%) in the tick species Hyalomma rufipes. Two H. rufipes yielded putative positive test results for the human pathogen F. tularensis during initial screening. Metagenomics analysis revealed presence of Francisella sp., Rickettsia sp., and Midichloria sp. DNA in the two H. rufipes ticks. The levels of Rickettsia and Midichloria DNA were relatively high while the level of Francisella DNA was low and required enrichment for the construction of metagenome-assembled genomes. Phylogenetic inference and calculations of the average nucleotide identity (ANI) indicated that: i) the Francisella genomes belonged to the Francisella-like endosymbiont (FLE) group in Clade 1 of Francisella and had highest sequence identity to an FLE found in Ornithodoros moubata (ANI: 96.7/97.0%), ii) the Rickettsia genomes had highest resemblance to Rickettsia aeschlimannii (ANI: 98.8 - 99.9%), and iii) the Midichloria genomes resembled Midichloria mitochondrii (ANI: 91.5 - 92.3%).Conclusions: The results of this study suggest ticks containing Francisella species, FLEs, and spotted fever groupRickettsia are dispersed by northbound migratory birds in the African-Western Palaearctic and suggest H. rufipes may not be involved in the transmission of F. tularensis in the study region. Future studies should aim at confirming the prevalence of Francisella spp. and spotted fever group Rickettsia in H. rufipes, in addition to focusing on the influence of FLEs on H. rufipes and their interaction with pathogenic and symbiotic bacteria of the genera Rickettsia and Midichloria.
|
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| 48. |
- Hoffman, Tove, et al.
(author)
-
Co-Occurrence of Francisella, Spotted Fever Group Rickettsia, and Midichloria in Avian-Associated Hyalomma rufipes
- 2022
-
In: Microorganisms. - : MDPI. - 2076-2607. ; 10:7
-
Journal article (peer-reviewed)abstract
- The migratory behavior of wild birds contributes to the geographical spread of ticks and their microorganisms. In this study, we aimed to investigate the dispersal and co-occurrence of Francisella and spotted fever group Rickettsia (SFGR) in ticks infesting birds migrating northward in the African-Western Palaearctic region (AWPR). Birds were trapped with mist nests across the Mediterranean basin during the 2014 and 2015 spring migration. In total, 575 ticks were collected from 244 birds. We screened the ticks for the species Francisella tularensis, the genus Francisella, and SFGR by microfluidic real-time PCR. Confirmatory analyses and metagenomic sequencing were performed on tick samples that putatively tested positive for F. tularensis during initial screenings. Hyalomma rufipes was the most common tick species and had a high prevalence of Francisella, including co-occurrence of Francisella and SFGR. Metagenomic analysis of total DNA extracted from two H. rufipes confirmed the presence of Francisella, Rickettsia, and Midichloria. Average nucleotide identity and phylogenetic inference indicated the highest identity of the metagenome-assembled genomes to a Francisella-like endosymbiont (FLE), Rickettsia aeschlimannii, and Midichloria mitochondrii. The results of this study suggest that (i) FLE- and SFGR-containing ticks are dispersed by northbound migratory birds in the AWPR, (ii) H. rufipes likely is not involved in transmission of F. tularensis in the AWPR, and (iii) a dual endosymbiosis of FLEs and Midichloria may support some of the nutritional requirements of H. rufipes.
|
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| 49. |
- Hägglund, Moa, et al.
(author)
-
Accounting for bacterial overlap between raw water communities and contaminating sources improves the accuracy of signature-based microbial source tracking
- 2018
-
In: Frontiers in Microbiology. - : Frontiers Media S.A.. - 1664-302X. ; 9
-
Journal article (peer-reviewed)abstract
- 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.
|
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| 50. |
- Jakobsson, Kristina, et al.
(author)
-
Exposure to polybrominated diphenyl ethers and tetrabromobisphenol A among computer technicians.
- 2002
-
In: Chemosphere. - 1879-1298. ; 46:5, s. 709-716
-
Journal article (peer-reviewed)abstract
- This study investigates exposure to polybrominated diphenyl ethers (PBDEs) and tetrabromobisphenol A (TBBPA), which are used as flame retardants in electronic equipment, in a group of technicians with intense computer work. Thirteen PBDE congeners and TBBPA were quantified in serum from 19 computer technicians. Previously investigated groups of hospital cleaners with no computer experience, and clerks working full-time at computer screens were used for comparison. The computer technicians had serum concentrations of BDE-153, BDE-183 and BDE-209 that were five times higher than those reported among hospital cleaners and computer clerks. The median levels observed among the computer technicians were 4.1, 1.3, and 1.6 pmol/g lipid weight, respectively. In contrast, for BDE-47 there was no difference between the computer technicians and the others. BDE-100, BDE-203, and three structurally unidentified octa-BDEs and three nona-BDEs, were present in almost all samples from the computer technicians. Further, TBBPA was detected in 8 out of 10 samples. The levels of BDE-153, BDE-183, and one of the octa-BDEs were positively correlated with duration of computer work among technicians. On a group level an exposure gradient was observed, from the least exposed cleaners to the clerks, and to the highest exposed group of computer technicians. A dose (duration of computer work)-response relationship among computer technicians was demonstrated for some higher brominated PBDE congeners. Thus, it is evident that PBDEs used in computers and electronics, including the fully brominated BDE-209, contaminate the work environment and accumulate in the workers tissues.
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