| 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. |
- Zanne, Amy E, et al.
(författare)
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Fungal functional ecology: bringing a trait-based approach to plant-associated fungi.
- 2020
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Ingår i: Biological reviews of the Cambridge Philosophical Society. - : Wiley. - 1469-185X .- 1464-7931. ; 95:2, s. 409-433
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Tidskriftsartikel (refereegranskat)abstract
- Fungi play many essential roles in ecosystems. They facilitate plant access to nutrients and water, serve as decay agents that cycle carbon and nutrients through the soil, water and atmosphere, and are major regulators of macro-organismal populations. Although technological advances are improving the detection and identification of fungi, there still exist key gaps in our ecological knowledge of this kingdom, especially related to function. Trait-based approaches have been instrumental in strengthening our understanding of plant functional ecology and, as such, provide excellent models for deepening our understanding of fungal functional ecology in ways that complement insights gained from traditional and -omics-based techniques. In this review, we synthesize current knowledge of fungal functional ecology, taxonomy and systematics and introduce a novel database of fungal functional traits (FunFun ). FunFun is built to interface with other databases to explore and predict how fungal functional diversity varies by taxonomy, guild, and other evolutionary or ecological grouping variables. To highlight how a quantitative trait-based approach can provide new insights, we describe multiple targeted examples and end by suggesting next steps in the rapidly growing field of fungal functional ecology.
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| 3. |
- 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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| 4. |
- Moore, Jason W., 1971-
(författare)
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Environmental crises and the metabolic rift in world-historical perspective
- 2000
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Ingår i: Organization & environment. - 1086-0266 .- 1552-7417. ; 13:2, s. 123-157
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Tidskriftsartikel (refereegranskat)abstract
- This article proposes a new theoretical framework to study the dialectic of capital and nature over the longue durée of world capitalism. The author proposes that today’s global ecological crisis has its roots in the transition to capitalism during the long sixteenth century. The emergence of capitalism marked not only a decisive shift in the arenas of politics, economy, and society, but a fundamental reorganization of world ecology, characterized by a “metabolic rift,” a progressively deepening rupture in the nutrient cycling between the country and the city. Building upon the historical political economy of Marx, Foster, Arrighi, and Wallerstein, the author proposes a new research agenda organized around the concept of systemic cycles of agro-ecological transformation. This agenda aims at discerning the ways in which capitalism’s relationship to nature developed discontinuously over time as recurrent ecological crises have formed a decisive moment of world capitalist crisis, forcing successive waves of restructuring over long historical time.
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| 5. |
- Tedersoo, Leho, et al.
(författare)
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Shotgun metagenomes and multiple primer pair-barcode combinations of amplicons reveal biases in metabarcoding analyses of fungi
- 2015
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Ingår i: MycoKeys. - : Pensoft Publishers. - 1314-4057 .- 1314-4049. ; 10, s. 1-43
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Tidskriftsartikel (refereegranskat)abstract
- Rapid development of high-throughput (HTS) molecular identification methods has revolutionized our knowledge about taxonomic diversity and ecology of fungi. However, PCR-based methods exhibit multiple technical shortcomings that may bias our understanding of the fungal kingdom. This study was initiated to quantify potential biases in fungal community ecology by comparing the relative performance of amplicon-free shotgun metagenomics and amplicons of nine primer pairs over seven nuclear ribosomal DNA (rDNA) regions often used in metabarcoding analyses. The internal transcribed spacer (ITS) barcodes ITS1 and ITS2 provided greater taxonomic and functional resolution and richness of operational taxonomic units (OTUs) at the 97% similarity threshold compared to barcodes located within the ribosomal small subunit (SSU) and large subunit (LSU) genes. All barcode-primer pair combinations provided consistent results in ranking taxonomic richness and recovering the importance of floristic variables in driving fungal community composition in soils of Papua New Guinea. The choice of forward primer explained up to 2.0% of the variation in OTU-level analysis of the ITS1 and ITS2 barcode data sets. Across the whole data set, barcode-primer pair combination explained 37.6–38.1% of the variation, which surpassed any environmental signal. Overall, the metagenomics data set recovered a similar taxonomic overview, but resulted in much lower fungal rDNA sequencing depth, inability to infer OTUs, and high uncertainty in identification. We recommend the use of ITS2 or the whole ITS region for metabarcoding and we advocate careful choice of primer pairs in consideration of the relative proportion of fungal DNA and expected dominant groups.
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| 6. |
- Nilsson, R. Henrik, 1976, et al.
(författare)
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Top 50 most wanted fungi
- 2016
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Ingår i: MycoKeys. - : Pensoft Publishers. - 1314-4057 .- 1314-4049. ; 12, s. 29-40
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Tidskriftsartikel (refereegranskat)abstract
- Environmental sequencing regularly recovers fungi that cannot be classified to any meaningful taxonomic level beyond “Fungi”. There are several examples where evidence of such lineages has been sitting in public sequence databases for up to ten years before receiving scientific attention and formal recognition. In order to highlight these unidentified lineages for taxonomic scrutiny, a search function is presented that produces updated lists of approximately genus-level clusters of fungal ITS sequences that remain unidentified at the phylum, class, and order levels, respectively. The search function (https://unite.ut.ee/top50.php) is implemented in the UNITE database for molecular identification of fungi, such that the underlying sequences and fungal lineages are open to third-party annotation. We invite researchers to examine these enigmatic fungal lineages in the hope that their taxonomic resolution will not have to wait another ten years or more.
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| 7. |
- Hibbett, David, et al.
(författare)
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Sequence-based classification and identification of Fungi
- 2016
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Ingår i: Mycologia. - 0027-5514. ; 108:6, s. 1049-1068
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Forskningsöversikt (refereegranskat)abstract
- Fungal taxonomy and ecology have been revolutionized by the application of molecular methods and both have increasing connections to genomics and functional biology. However, data streams from traditional specimen- and culture-based systematics are not yet fully integrated with those from metagenomic and metatranscriptomic studies, which limits understanding of the taxonomic diversity and metabolic properties of fungal communities. This article reviews current resources, needs, and opportunities for sequence-based classification and identification (SBCI) in fungi as well as related efforts in prokaryotes. To realize the full potential of fungal SBCI it will be necessary to make advances in multiple areas. Improvements in sequencing methods, including long-read and single-cell technologies, will empower fungal molecular ecologists to look beyond ITS and current shotgun metagenomics approaches. Data quality and accessibility will be enhanced by attention to data and metadata standards and rigorous enforcement of policies for deposition of data and workflows. Taxonomic communities will need to develop best practices for molecular characterization in their focal clades, while also contributing to globally useful datasets including ITS. Changes to nomenclatural rules are needed to enable valid publication of sequence-based taxon descriptions. Finally, cultural shifts are necessary to promote adoption of SBCI and to accord professional credit to individuals who contribute to community resources.
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| 8. |
- Widgren, Stefan, et al.
(författare)
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Spatio-temporal modelling of verotoxigenic Escherichia coli O157 in cattle in Sweden: exploring options for control
- 2018
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Ingår i: Veterinary Research. - : Springer Science and Business Media LLC. - 0928-4249 .- 1297-9716. ; 49
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Tidskriftsartikel (refereegranskat)abstract
- A spatial data-driven stochastic model was developed to explore the spread of verotoxigenic Escherichia coli O157 (VTEC O157) by livestock movements and local transmission among neighbouring holdings in the complete Swedish cattle population. Livestock data were incorporated to model the time-varying contact network between holdings and population demographics. Furthermore, meteorological data with the average temperature at the geographical location of each holding was used to incorporate season. The model was fitted against observed data and extensive numerical experiments were conducted to investigate the model's response to control strategies aimed at reducing shedding and susceptibility, as well as interventions informed by network measures. The results showed that including local spread and season improved agreement with prevalence studies. Also, control strategies aimed at reducing the average shedding rate were more efficient in reducing the VTEC O157 prevalence than strategies based on network measures. The methodology presented in this study could provide a basis for developing disease surveillance on regional and national scales, where observed data are combined with readily available high-resolution data in simulations to get an overview of potential disease spread in unobserved regions.
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| 9. |
- kaiser, matthias, et al.
(författare)
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Food ethics: a Wide Field in Need of Dialogue
- 2016
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Ingår i: Food Ethics. - : Springer Science and Business Media LLC. - 2364-6853 .- 2364-6861. ; 1:1, s. 1-7
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Tidskriftsartikel (refereegranskat)abstract
- There are a few things which are obviously a central part of everyone’s life, at all times, and all over the globe, and which are crucial for our wellbeing. Food is, like sex, such an essential ingredient of our life, an ingredient of what we expect of a good life. What is on our plates is always a result of nature and culture, to the extent that it may seem hard to find commonalities in our global diet. As academics we have asked different questions about food. For a long time these questions have been dominated by the quest to secure enough food and to improve what we have got. It is, however, noteworthy that we also always have asked the normative questions in relation to food: Is it right to eat this kind of food? Do we produce our food the right way? Is there injustice and bad power in the way we distribute the food? Are we lied to in regard to what is on our plate? When we enter the normative realm, we enter the realm of ethics, understood in a wide and comprehensive way. As all normative questions, we need to be well informed by knowledge about how the world is, and what is at stake and for whom. We call this food ethics. Food ethics raises issues and asks questions in relation to food all along the value chains. It also puts things into relation with each other. At the same time it disentangles complex heaps of factors and pieces of knowledge, and looks for guidance. It is issue driven, rather than interest driven. It unites scholars with farmers and fishermen, chefs with industry, consumers with lawyers, and food citizens with authorities. As a young field within academia it is important to guard against efforts to appropriate the field for narrow interests, and instead to combine the natural and social sciences in analysing and addressing the challenges. We do not necessarily call for the grand ethical theory that explains it all, but rather start with the simple things in a very complex overall picture. We want to draw attention to ethically significant facts, discuss problematic developments, point to genuine dilemmas, learn about food relevant contexts and history, and look for individual, professional and institutional responses to ethical challenges and issues. Thus, one of the missions of this new journal Food Ethics, is to widen the scope and the discussion on the topic, and to be inclusive in terms of who has something to contribute to the field. There is no escaping from confronting very complex issues when it comes to managing one of the most basic needs we all have, food. As editors of this new journal we maintain that food ethics deserves special and inter-disciplinary attention by researchers, that it is not sufficiently dealt with by what is currently known as bioethics, that it is intrinsically connected with the so-called grand societal challenges of our time, that it is a globally important field which demands particular attention to complexities and uncertainties, as much as it needs to be explicit about what values are at stake and for whom, and which normative principles it touches upon.
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| 10. |
- Handlin, Linda
(författare)
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Human-Human and Human-Animal Interaction : Some Common Physiological and Psychological Effects
- 2010
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The aim of the present thesis was to investigate hormonal and physiological effects in mothers during a breastfeeding session and in dogs and their owners in response to short-term interaction. In study one, sixty-six mothers receiving either exogenous oxytocin infusion and/or epidural analgesia (EDA) during labor or intramuscular oxytocin injection post partum were studied. Oxytocin, prolactin, adrenocorticotrophic hormone (ACTH) and cortisol levels, as well as blood pressure were measured during a breastfeeding session two days after birth. In response to breastfeeding two days after birth, the mothers displayed a pulsatile release of oxytocin and increasing prolactin levels. In addition, the activity in the HPA-axis was reduced and maternal blood pressure decreased. The results also show that EDA administration in combination with oxytocin during labor resulted insignificantly lower oxytocin levels and higher cortisol levels, as well as higher bloodpressure in response to breastfeeding two days after birth, compared to EDA administration alone. In addition, oxytocin infusions dose-dependently lowered the mothers’ endogenous oxytocin levels two days after birth. In study two, ten female dog owners and their male Labrador dogs participated, together with ten controls. Their levels of oxytocin, cortisol and insulin, as well as their heart rate, were measured. The connection between the quality of the dogowner relationship and hormone levels was also explored. Short-term interaction between dogs and their owners resulted in oxytocin release in both species and their cortisol levels and heart rate were also affected. Oxytocin levels and positive attitudes regarding the dog-owner relationship were positively correlated. In conclusion, both human-human and human-animal interactions induce oxytocin release and promote oxytocin mediated effects, such as decreasing cortisol levels and blood pressure. In addition, social interaction and oxytocin levels arepositively related.
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