| 1. |
- Nilsson, R. Henrik, 1976, et al.
(författare)
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Mycobiome diversity: high-throughput sequencing and identification of fungi.
- 2019
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Ingår i: Nature reviews. Microbiology. - : Springer Science and Business Media LLC. - 1740-1534 .- 1740-1526. ; 17, s. 95-109
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Forskningsöversikt (refereegranskat)abstract
- Fungi are major ecological players in both terrestrial and aquatic environments by cycling organic matter and channelling nutrients across trophic levels. High-throughput sequencing (HTS) studies of fungal communities are redrawing the map of the fungal kingdom by hinting at its enormous - and largely uncharted - taxonomic and functional diversity. However, HTS approaches come with a range of pitfalls and potential biases, cautioning against unwary application and interpretation of HTS technologies and results. In this Review, we provide an overview and practical recommendations for aspects of HTS studies ranging from sampling and laboratory practices to data processing and analysis. We also discuss upcoming trends and techniques in the field and summarize recent and noteworthy results from HTS studies targeting fungal communities and guilds. Our Review highlights the need for reproducibility and public data availability in the study of fungal communities. If the associated challenges and conceptual barriers are overcome, HTS offers immense possibilities in mycology and elsewhere.
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| 2. |
- Johnsson, Anna-Ida, et al.
(författare)
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Specific SCAR markers and multiplex real-time PCR for quantification of two Trichoderma biocontrol strains in environmental samples
- 2011
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Ingår i: BioControl. - : Springer Science and Business Media LLC. - 1386-6141 .- 1573-8248. ; 56, s. 903-913
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Tidskriftsartikel (refereegranskat)abstract
- Several strains from the genus Trichoderma (Ascomycetes, Hypocreales) are commercially used as biocontrol agents, e.g. in formulations containing the two Trichoderma strains IMI206039 (Hypocrea parapilulifera B.S. Lu, Druzhinina & Samuels) and IMI206040 (T. atroviride P. Karst). To quantify the presence of the two isolates after application, we developed primers for SCAR markers (Sequence-Characterised Amplified Region). In order to quantify both fungal strains simultaneously, we also designed fluorophore-labelled probes distinguishing the two strains, to be used in combination with the SCAR primers. In incubations of two different soils, artificially inoculated and maintained under controlled conditions, the quantification through amplification with the SCAR markers in qPCR and through colony-forming units from plate counting correlated well. Further tests of the markers on samples taken from a golf green treated with a product containing both strains indicated that the two biocontrol strains did not establish, either on the golf green or in the surrounding area.
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| 3. |
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| 4. |
- Von Rosen, Dietrich
(författare)
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Non-negative estimation of variance components in heteroscedastic one-way random-effects ANOVA models
- 2010
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Ingår i: Statistics. - : Informa UK Limited. - 0233-1888 .- 1029-4910. ; 44, s. 557-569
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Tidskriftsartikel (refereegranskat)abstract
- There is a considerable amount of literature dealing with inference about the parameters in a heteroscedastic one-way random-effects ANOVA model. In this paper, we primarily address the problem of improved quadratic estimation of the random-effect variance component. It turns out that such estimators with a smaller mean squared error compared with some standard unbiased quadratic estimators exist under quite general conditions. Improved estimators of the error variance components are also established.
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| 5. |
- Amundin, Mats, et al.
(författare)
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A proposal to use distributional models to analyse dolphin vocalisation
- 2017
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Ingår i: Proceedings of the 1st International Workshop on Vocal Interactivity in-and-between Humans, Animals and Robots, VIHAR 2017. - 9782956202905 ; , s. 31-32
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Konferensbidrag (refereegranskat)abstract
- This paper gives a brief introduction to the starting points of an experimental project to study dolphin communicative behaviour using distributional semantics, with methods implemented for the large scale study of human language.
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| 6. |
- Flysjö, A., et al.
(författare)
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How does co-product handling affect the carbon footprint of milk? Case study of milk production in New Zealand and Sweden
- 2011
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Ingår i: International Journal of Life Cycle Assessment. - : Springer Science and Business Media LLC. - 1614-7502 .- 0948-3349. ; 16:5, s. 420-430
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Tidskriftsartikel (refereegranskat)abstract
- Purpose This paper investigates different methodologies of handling co-products in life cycle assessment (LCA) or carbon footprint (CF) studies. Co-product handling can have a significant effect on final LCA/CF results, and although there are guidelines on the preferred order for different methods for handling co-products, no agreed understanding on applicable methods is available. In the present study, the greenhouse gases (GHG) associated with the production of 1 kg of energy-corrected milk (ECM) at farm gate is investigated considering co-product handling. Materials and methods Two different milk production systems were used as case studies in the investigation of the effect of applying different methodologies in coproduct handling: (1) outdoor grazing system in New Zealand and (2) mainly indoor housing system with a pronounced share of concentrate feed in Sweden. Since the cows produce milk, meat (when slaughtered), calves, manure, hides, etc., the environmental burden (here GHG emissions) must be distributed between these outputs (in the present study no emissions are attributed to hides specifically, or to manure which is recycled on-farm). Different methodologically approaches, (1) system expansion (two cases), (2) physical causality allocation, (3) economic allocation, (4) protein allocation and (5) mass allocation, are applied in the study. Results and discussion The results show large differences in the final CF number depending on which methodology has been used for accounting co-products. Most evident is that system expansion gives a lower CF for milk than allocation methods. System expansion resulted in 63- 76% of GHG emissions attributed directly to milk, while allocation resulted in 85-98%. It is stressed that meat is an important by-product from milk production and that milk and beef production is closely interlinked and therefore needs to be considered in an integrated approach. Conclusions To obtain valid LCA/CF numbers for milk, it is crucial to account for by-products. Moreover, if CF numbers for milk need to be compared, the same allocation procedure should be applied. © 2011 Springer-Verlag.
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| 7. |
- Flysjö, A., et al.
(författare)
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The impact of various parameters on the carbon footprint of milk production in New Zealand and Sweden
- 2011
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Ingår i: Agricultural Systems. - : Elsevier BV. - 1873-2267 .- 0308-521X. ; 104:6, s. 459-469
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Tidskriftsartikel (refereegranskat)abstract
- The carbon footprint (CF) of milk production was analysed at the farm gate for two contrasting production systems; an outdoor pasture grazing system in New Zealand (NZ) and a mainly indoor housing system with pronounced use of concentrate feed in Sweden (SE). The method used is based on the conceptual framework of lifecycle assessment (LCA), but only for greenhouse gas (GHG) emissions. National average data were used to model the dairy system in each country. Collection of inventory data and calculations of emissions were harmonised to the greatest extent possible for the two systems. The calculated CF for 1kg of energy corrected milk (ECM), including related by-products (surplus calves and culled cows), was 1.00kg carbon dioxide equivalents (CO2e) for NZ and 1.16kg CO2e for SE. Methane from enteric fermentation and nitrous oxide emissions from application of nitrogen (as fertiliser and as excreta dropped directly on the field) were the main contributors to the CF in both countries. The most important parameters to consider when calculating the GHG emissions were dry matter intake (DMI), emission factor (EF) for methane from enteric fermentation, amount of nitrogen applied and EF for direct nitrous oxide emissions from soils. By changing one parameter at a time within 'reasonable' limits (i.e. no extreme values assumed), the impact on the total CF was assessed and showed changes of up to 15%. In addition, the uncertainty in CF estimates due to uncertainty in EF for methane from enteric fermentation and nitrous oxide emissions (from soil and due to ammonia volatilisation) were analysed through Monte Carlo simulation. This resulted in an uncertainty distribution corresponding to 0.60-1.52kg CO2e kg-1 ECM for NZ and 0.83-1.56kg CO2e kg-1 ECM for SE (in the prediction interval 2.5-97.5%). Hence, the variation within the systems based on the main EF is relatively large compared with the difference in CF between the countries. © 2011 Elsevier Ltd.
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| 8. |
- Messing, Ingmar
(författare)
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Land and land use : Natural preconditions
- 2011
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Ingår i: Agriculture and Forestry in Sweden since 1900- a cartographic description. - 9789187760617 ; , s. 14-22
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Bokkapitel (övrigt vetenskapligt/konstnärligt)
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| 9. |
- Messing, Ingmar
(författare)
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Marken i Sverige : Naturliga förutsättningar
- 2011
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Ingår i: Sveriges nationalatlas. Jordbruk och skogsbruk i Sverige sedan år 1900: en kartografisk beskrivning. - 9789187760594 ; , s. 14-22
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Bokkapitel (övrigt vetenskapligt/konstnärligt)
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| 10. |
- Olstorpe, Matilda, et al.
(författare)
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Microbial changes during storage of moist crimped cereal barley grain under Swedish farm conditions
- 2010
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Ingår i: Animal Feed Science and Technology. - Amsterdam, Netherlands : Elsevier. - 0377-8401 .- 1873-2216. ; 156:1-2, s. 37-46
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Tidskriftsartikel (refereegranskat)abstract
- This Study investigated feed hygiene during airtight storage of non-dried barley grain under farm conditions. Microorganisms on the grain were sampled and quantified in seven Swedish firms throughout the storage period using culture dependent methods. The dominant lactic acid bacteria (LAB) and yeasts were identified by rRNA gene sequencing and moulds by morphological characterisation. Moisture content (MC) and pH of the grain were also monitored. It was difficult to obtain the optimal MC(0.30-0.45 g/g) that is necessary to initiate fermentation in the grain. Feed hygiene was maintained during storage of cereals when MC below 0.17 g/g. Intermediate MC (0.17-0.23 g/g) of the grains was conducive to mould growth, including growth of potential producers of mycotoxins, which can diminish feed safety and nutritional value. Enterobacteriaceae were found in all barleys, even at low MC, but their numbers were substantially decreased when the number of LAB was high. True fermentation of moist crimped cereal grains was only obtained on one farm with all initial barley MC of 0.3 g/g. Here, LAB reached high numbers during storage, whereas numbers of spoilage microorganisms that may reduce feed hygiene decreased considerably. However, the pH of the barley did not differ among farms. Storage stability in airtight stored barley may thus be the result of low oxygen tension, viz. airtight storage, and competition for nutrients by the microorganisms, rather than formation of lactic acid. At harvest, Enterococcus caccae dominated the LAB Population in five barleys and Lactobacillus fermentum at the remaining two. The dominant yeast species were Aureobasidium pullulans, Cryptococcus wieringae, Kazachstania aerobia and Rhodotorula glutinis. After storage, L fermentum was dominant among the LAB. The yeast species composition was highly diverse and differed among barleys. Among others, C. wieringae, Debaryomyces hansenii, K. aerobia, R. glutinis and Sporobolomyces ruberrimus were detected. This Study shows that the microbial population in airtight stored moist barley is highly diverse and not predictable. Thus, it may be necessary to influence the microbial population in the storage system by adding a starter culture.
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