| 1. |
- Sanli, Kemal, et al.
(author)
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Metagenomic Sequencing of Marine Periphyton: Taxonomic and Functional Insights into Biofilm Communities
- 2015
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In: Frontiers in Microbiology. - : Frontiers Media SA. - 1664-302X. ; 6:1192
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Journal article (peer-reviewed)abstract
- Periphyton communities are complex phototrophic, multispecies biofilms that develop on surfaces in aquatic environments. These communities harbor a large diversity of organisms comprising viruses, bacteria, algae, fungi, protozoans and metazoans. However, thus far the total biodiversity of periphyton has not been described. In this study, we use metagenomics to characterize periphyton communities from the marine environment of the Swedish west coast. Although we found approximately ten times more eukaryotic rRNA marker gene sequences compared to prokaryotic, the whole metagenome-based similarity searches showed that bacteria constitute the most abundant phyla in these biofilms. We show that marine periphyton encompass a range of heterotrophic and phototrophic organisms. Heterotrophic bacteria, including the majority of proteobacterial clades and Bacteroidetes, and eukaryotic macro-invertebrates were found to dominate periphyton. The phototrophic groups comprise Cyanobacteria and the alpha-proteobacterial genus Roseobacter, followed by different micro- and macro-algae. We also assess the metabolic pathways that predispose these communities to an attached lifestyle. Functional indicators of the biofilm form of life in periphyton involve genes coding for enzymes that catalyze the production and degradation of extracellular polymeric substances, mainly in the form of complex sugars such as starch and glycogen-like meshes together with chitin. Genes for 278 different transporter proteins were detected in the metagenome, constituting the most abundant protein complexes. Finally, genes encoding enzymes that participate in anaerobic pathways, such as denitrification and methanogenesis, were detected suggesting the presence of anaerobic or low-oxygen micro-zones within the biofilms.
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| 2. |
- Le Breton, Michael, 1986, et al.
(author)
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Chlorine oxidation of VOCs at a semi-rural site in Beijing: significant chlorine liberation from ClNO2 and subsequent gas- and particle-phase Cl-VOC production
- 2018
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In: Atmospheric Chemistry and Physics. - : Copernicus GmbH. - 1680-7316 .- 1680-7324. ; 18:17, s. 13013-13030:18, s. 13013-13030
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Journal article (peer-reviewed)abstract
- Nitryl chloride (ClNO2) accumulation at night acts as a significant reservoir for active chlorine and impacts the following day's photochemistry when the chlorine atom is liberated at sunrise. Here, we report simultaneous measurements of N2O5 and a suite of inorganic halogens including ClNO2 and reactions of chloride with volatile organic compounds (Cl-VOCs) in the gas and particle phases utilising the Filter Inlet for Gas and AEROsols time-of-flight chemical ionisation mass spectrometer (FIGAERO-ToF-CIMS) during an intensive measurement campaign 40 km northwest of Beijing in May and June 2016. A maximum mixing ratio of 2900 ppt of ClNO2 was observed with a mean campaign nighttime mixing ratio of 487 ppt, appearing to have an anthropogenic source supported by correlation with SO2, CO and benzene, which often persisted at high levels after sunrise until midday. This was attributed to such high mixing ratios persisting after numerous e-folding times of the photolytic lifetime enabling the chlorine atom production to reach 2.3 x 10(5) molecules cm(-3) from ClNO2 alone, peaking at 09:30 LT and up to 8.4 x 10(5) molecules cm(-3) when including the supporting inorganic halogen measurements. Cl-VOCs were observed in the particle and gas phases for the first time at high time resolution and illustrate how the iodide ToF-CIMS can detect unique markers of chlorine atom chemistry in ambient air from both biogenic and anthropogenic sources. Their presence and abundance can be explained via time series of their measured and steady-state calculated precursors, enabling the assessment of competing OH and chlorine atom oxidation via measurements of products from both of these mechanisms and their relative contribution to secondary organic aerosol (SOA) formation.
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| 3. |
- Gerlee, Philip, 1980, et al.
(author)
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Scientific Models
- 2016
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Book (other academic/artistic)abstract
- A zebrafish, the hull of a miniature ship, a mathematical equation and a food chain - what do these things have in common? They are examples of models used by scientists to isolate and study particular aspects of the world around us. This book begins by introducing the concept of a scientific model from an intuitive perspective, drawing parallels to mental models and artistic representations. It then recounts the history of modelling from the 16th century up until the present day. The iterative process of model building is described and discussed in the context of complex models with high predictive accuracy versus simpler models that provide more of a conceptual understanding. To illustrate the diversity of opinions within the scientific community, we also present the results of an interview study, in which ten scientists from different disciplines describe their views on modelling and how models feature in their work. Lastly, it includes a number of worked examples that span different modelling approaches and techniques. It provides a comprehensive introduction to scientific models and shows how models are constructed and used in modern science. It also addresses the approach to, and the culture surrounding modelling in different scientific disciplines. It serves as an inspiration for model building and also facilitates interdisciplinary collaborations by showing how models are used in different scientific fields. The book is aimed primarily at students in the sciences and engineering, as well as students at teacher training colleges but will also appeal to interested readers wanting to get an overview of scientific modelling in general and different modelling approaches in particular.
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| 4. |
- Abarenkov, Kessy, et al.
(author)
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Annotating public fungal ITS sequences from the built environment according to the MIxS-Built Environment standard – a report from a May 23-24, 2016 workshop (Gothenburg, Sweden)
- 2016
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In: MycoKeys. - : Pensoft Publishers. - 1314-4057 .- 1314-4049. ; 16, s. 1-15
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Journal article (peer-reviewed)abstract
- Recent molecular studies have identified substantial fungal diversity in indoor environments. Fungi and fungal particles have been linked to a range of potentially unwanted effects in the built environment, including asthma, decay of building materials, and food spoilage. The study of the built mycobiome is hampered by a number of constraints, one of which is the poor state of the metadata annotation of fungal DNA sequences from the built environment in public databases. In order to enable precise interrogation of such data – for example, “retrieve all fungal sequences recovered from bathrooms” – a workshop was organized at the University of Gothenburg (May 23-24, 2016) to annotate public fungal barcode (ITS) sequences according to the MIxS-Built Environment annotation standard (http://gensc.org/mixs/). The 36 participants assembled a total of 45,488 data points from the published literature, including the addition of 8,430 instances of countries of collection from a total of 83 countries, 5,801 instances of building types, and 3,876 instances of surface-air contaminants. The results were implemented in the UNITE database for molecular identification of fungi (http://unite.ut.ee) and were shared with other online resources. Data obtained from human/animal pathogenic fungi will furthermore be verified on culture based metadata for subsequent inclusion in the ISHAM-ITS database (http://its.mycologylab.org).
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| 5. |
- McFiggans, Gordon, et al.
(author)
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Secondary organic aerosol reduced by mixture of atmospheric vapours
- 2019
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In: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 565:7741, s. 587-593
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Journal article (peer-reviewed)abstract
- Secondary organic aerosol contributes to the atmospheric particle burden with implications for air quality and climate. Biogenic volatile organic compounds such as terpenoids emitted from plants are important secondary organic aerosol precursors with isoprene dominating the emissions of biogenic volatile organic compounds globally. However, the particle mass from isoprene oxidation is generally modest compared to that of other terpenoids. Here we show that isoprene, carbon monoxide and methane can each suppress the instantaneous mass and the overall mass yield derived from monoterpenes in mixtures of atmospheric vapours. We find that isoprene 'scavenges' hydroxyl radicals, preventing their reaction with monoterpenes, and the resulting isoprene peroxy radicals scavenge highly oxygenated monoterpene products. These effects reduce the yield of low-volatility products that would otherwise form secondary organic aerosol. Global model calculations indicate that oxidant and product scavenging can operate effectively in the real atmosphere. Thus highly reactive compounds (such as isoprene) that produce a modest amount of aerosol are not necessarily net producers of secondary organic particle mass and their oxidation in mixtures of atmospheric vapours can suppress both particle number and mass of secondary organic aerosol. We suggest that formation mechanisms of secondary organic aerosol in the atmosphere need to be considered more realistically, accounting for mechanistic interactions between the products of oxidizing precursor molecules (as is recognized to be necessary when modelling ozone production).
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| 6. |
- Hassellöv, Martin, 1970, et al.
(author)
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REACH missar nano!
- 2009
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In: Miljöforskning. ; 2009:3-4
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Journal article (other academic/artistic)
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| 7. |
- Eriksson, Martin, 1970, et al.
(author)
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Triclosan changes community composition and selects for specific bacterial taxa in marine periphyton biofilms in low nanomolar concentrations
- 2020
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In: Ecotoxicology. - : Springer Science and Business Media LLC. - 0963-9292 .- 1573-3017. ; 29:7, s. 1083-1094
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Journal article (peer-reviewed)abstract
- The antibacterial agent Triclosan (TCS) is a ubiquitous environmental contaminant due to its widespread use. Sensitivity to TCS varies substantially among eu- and pro-karyotic species and its risk for the marine environment remains to be better elucidated. In particular, the effects that TCS causes on marine microbial communities are largely unknown. In this study we therefore used 16S amplicon rDNA sequencing to investigate TCS effects on the bacterial composition in marine periphyton communities that developed under long-term exposure to different TCS concentrations. Exposure to TCS resulted in clear changes in bacterial composition already at concentrations of 1 to 3.16 nM. We conclude that TCS affects the structure of the bacterial part of periphyton communities at concentrations that actually occur in the marine environment. Sensitive taxa, whose abundance decreased significantly with increasing TCS concentrations, include the Rhodobiaceae and Rhodobacteraceae families of Alphaproteobacteria, and unidentified members of the Candidate division Parcubacteria. Tolerant taxa, whose abundance increased significantly with higher TCS concentrations, include the families Erythrobacteraceae (Alphaproteobacteria), Flavobacteriaceae (Bacteroidetes), Bdellovibrionaceae (Deltaproteobacteria), several families of Gammaproteobacteria, and members of the Candidate phylum Gracilibacteria. Our results demonstrate the variability of TCS sensitivity among bacteria, and that TCS can change marine bacterial composition at concentrations that have been detected in the marine environment.
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| 8. |
- Sznitko, L., et al.
(author)
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Low-threshold stimulated emission from lysozyme amyloid fibrils doped with a blue laser dye
- 2015
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In: Applied Physics Letters. - : AIP Publishing. - 0003-6951 .- 1077-3118. ; 106:2
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Journal article (peer-reviewed)abstract
- © 2015 AIP Publishing LLC. Amyloid fibrils are excellent self-assembling nanotemplates for organic molecules such as dyes. Here, we demonstrate that laser dye-doped lysozyme type fibrils exhibit significantly reduced threshold for stimulated emission compared to that observed in usual matrices. Laser action was studied in slab planar waveguides of the amyloids doped with Stilbene 420 laser dye prepared using a film casting technique. The lowering of the threshold of stimulated emission is analyzed in the context of intrinsic structure of the amyloid nanotemplates, electrostatic interaction of different microstructures with dye molecules, as well as material properties of the cast layers. All these factors are considered to be of importance for introducing gain for random laser operation.
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| 9. |
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| 10. |
- Gerlee, Philip, 1980, et al.
(author)
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Vetenskapliga modeller
- 2012
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Book (other academic/artistic)abstract
- Vad har en zebrafisk, ett fartygsskrov i miniatyr, en matematisk ekvation och en näringskedja gemensamt? De är alla exempel på vetenskapliga modeller som används inom dagens forskning för att beskriva vår omvärld och gör det möjligt för forskare att isolera och i detalj studera ett visst fenomen.Boken inleds med att introducera begreppet på ett intuitivt plan, genom att dra paralleller till mentala modeller och konstnärliga representationer, och fortsätter med en historisk tillbakablick som sträcker sig från 1600-talet till nutid. Vi diskuterar också den iterativa konstruktionsprocessen och balansen mellan enkelhet och komplexitet som den innebär, vilket i sin tur är kopplat till avvägningen mellan en förklarande modell och en förutsägande. För att belysa skillnader mellan olika synsätt på modeller presenteras också en intervjustudie där forskare från tio stycken forskningsfält beskriver sin relation till modeller. Avslutningsvis innehåller boken ett kapitel där typiska modeller från flera discipliner beskrivs i detalj.Syftet med denna bok är att ge en övergripande introduktion till vetenskapliga modeller och visa hur modeller är uppbyggda samt hur de används inom vetenskapligt arbete. Vi hoppas också att den kan tjäna som inspiration till nya modeller och även underlätta det interdisciplinära samtalet.Boken vänder sig i första hand till studenter på landets ingenjörs- och naturvetarprogram samt till studenter på lärarhögskolorna, men även till dig som har ett vetenskapligt intresse och vill få en översikt av modellering i stort och olika modelleringstraditioner i synnerhet.
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