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Sökning: AMNE:(AGRICULTURAL SCIENCES Veterinary Science) > Tidskriftsartikel

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1.
  • Zanne, Amy E, et al. (författare)
  • Fungal functional ecology: bringing a trait-based approach to plant-associated fungi.
  • 2020
  • Ingår i: Biological reviews of the Cambridge Philosophical Society. - : Wiley. - 1469-185X .- 1464-7931. ; 95:2, s. 409-433
  • 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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2.
  • Moore, Jason W., 1971- (författare)
  • Environmental crises and the metabolic rift in world-historical perspective
  • 2000
  • Ingår i: Organization & environment. - 1086-0266 .- 1552-7417. ; 13:2, s. 123-157
  • 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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3.
  • Tedersoo, Leho, et al. (författare)
  • Shotgun metagenomes and multiple primer pair-barcode combinations of amplicons reveal biases in metabarcoding analyses of fungi
  • 2015
  • Ingår i: MycoKeys. - : Pensoft Publishers. - 1314-4057 .- 1314-4049. ; 10, s. 1-43
  • 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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4.
  • Nilsson, R. Henrik, 1976, et al. (författare)
  • Top 50 most wanted fungi
  • 2016
  • Ingår i: MycoKeys. - : Pensoft Publishers. - 1314-4057 .- 1314-4049. ; 12, s. 29-40
  • 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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5.
  • Widgren, Stefan, et al. (författare)
  • Spatio-temporal modelling of verotoxigenic Escherichia coli O157 in cattle in Sweden: exploring options for control
  • 2018
  • Ingår i: Veterinary Research. - : Springer Science and Business Media LLC. - 0928-4249 .- 1297-9716. ; 49
  • 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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6.
  • kaiser, matthias, et al. (författare)
  • Food ethics: a Wide Field in Need of Dialogue
  • 2016
  • Ingår i: Food Ethics. - : Springer Science and Business Media LLC. - 2364-6853 .- 2364-6861. ; 1:1, s. 1-7
  • 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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7.
  • Forslund, Kerstin, et al. (författare)
  • Acute chest pain emergencies : spouses' prehospital experiences
  • 2008
  • Ingår i: International emergency nursing. - : Elsevier BV. - 1878-013X .- 1755-599X. ; 16:4, s. 233-240
  • Tidskriftsartikel (refereegranskat)abstract
    • The call to the Emergency Medical Dispatch Centre is often a person's first contact with the health-care system in cases of acute illness or injury and acute chest pain is a common reason for calling. The aim was to illuminate how spouses to persons with acute chest pain experienced the alarm situation, the emergency call and the prehospital emergency care. Interviews were conducted with nineteen spouses. A phenomenological-hermeneutic approach was used for the analyses. The themes responsibility and uneasiness emerged as well as an overall theme of aloneness. Being a spouse to a person in need of acute medical and nursing assistance was interpreted as "Being responsible and trying to preserve life" and "Being able to manage the uneasiness and having trust in an uncertain situation." When their partners' life was at risk the spouses were in an escalating spiral of worry, uncertainty, stress, fear of loss, feeling of loneliness and desperation. They had to manage emotional distress and felt compelled to act to preserve life, a challenging situation.
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8.
  • Jacobsen, M, et al. (författare)
  • Refined candidate region specified by haplotype sharing for Escherichia coli F4ab/F4ac susceptibility alleles in pigs
  • 2010
  • Ingår i: Animal Genetics. - : Wiley. - 0268-9146 .- 1365-2052. ; 41:1, s. 21-25
  • Tidskriftsartikel (refereegranskat)abstract
    • Infection of the small intestine by enterotoxigenic Escherichia coli F4ab/ac is a major welfare problem and financial burden for the pig industry. Natural resistance to this infection is inherited as a Mendelian recessive trait, and a polymorphism in the MUC4 gene segregating for susceptibility/resistance is presently used in a selection programme by the Danish pig breeding industry. To elucidate the genetic background involved in E. coli F4ab/ac susceptibility in pigs, a detailed haplotype map of the porcine candidate region was established. This region covers approximately 3.7 Mb. The material used for the study is a three generation family, where the founders are two Wild boars and eight Large White sows. All pigs have been phenotyped for susceptibility to F4ab/ac using an adhesion assay. Their haplotypes are known from segregation analysis using flanking markers. By a targeted approach, the candidate region was subjected to screening for polymorphisms, mainly focusing on intronic sequences. A total of 18 genes were partially sequenced, and polymorphisms were identified in GP5, CENTB2, APOD, PCYT1A, OSTalpha, ZDHHC19, TFRC, ACK1, MUC4, MUC20, KIAA0226, LRCH3 and MUC13. Overall, 227 polymorphisms were discovered in the founder generation. The analysis revealed a large haplotype block, spanning at least 1.5 Mb around MUC4, to be associated with F4ab/ac susceptibility.
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9.
  • Nilsson, R. Henrik, 1976, et al. (författare)
  • A comprehensive, automatically updated fungal ITS sequence dataset for reference-based chimera control in environmental sequencing efforts
  • 2015
  • Ingår i: Microbes and Environments. - 1342-6311 .- 1347-4405. ; 30:2, s. 145-150
  • Tidskriftsartikel (refereegranskat)abstract
    • The nuclear ribosomal internal transcribed spacer (ITS) region is the most commonly chosen genetic marker for the molecular identification of fungi in environmental sequencing and molecular ecology studies. Several analytical issues complicate such efforts, one of which is the formation of chimeric—artificially joined—DNA sequences during PCR amplification or sequence assembly. Several software tools are currently available for chimera detection, but rely to various degrees on the presence of a chimera-free reference dataset for optimal performance. However, no such dataset is available for use with the fungal ITS region. This study introduces a comprehensive, automatically updated reference dataset for fungal ITS sequences based on the UNITE database for the molecular identification of fungi. This dataset supports chimera detection throughout the fungal kingdom and for full-length ITS sequences as well as partial (ITS1 or ITS2 only) datasets. The performance of the dataset on a large set of artificial chimeras was above 99.5%, and we subsequently used the dataset to remove nearly 1,000 compromised fungal ITS sequences from public circulation. The dataset is available at http://unite.ut.ee/repository.php and is subject to web-based third-party curation.
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10.
  • Hallberg, Ida, et al. (författare)
  • Perfluorononanoic acid (PFNA) alters lipid accumulation in bovine blastocysts after oocyte exposure during in vitro maturation
  • 2019
  • Ingår i: Reproductive Toxicology. - : Elsevier BV. - 0890-6238 .- 1873-1708. ; 84, s. 1-8
  • Tidskriftsartikel (refereegranskat)abstract
    • Perfluorononanoic acid (PFNA) is one of the perfluoroalkyl acids present in human tissues. In this study, effects on early embryo development after PFNA exposure were investigated using the bovine in vitro production system. Oocytes were exposed to PFNA during maturation in vitro (10 μg mL-1 and 0.1 μg mL-1), and then fertilized and cultured in parallel with control groups. Developmental parameters (cleavage, blastocyst formation) were followed and embryo quality evaluated (stage, grade). Embryos developed after exposure to 0.1 μg mL-1 were stained to distinguish nuclei, active mitochondria and neutral lipids. 10 μg mL-1 of PFNA had a severe negative effect on blastocyst formation (OR: 0.27 p < 0.05), an effect not observed at 0.1 μg mL-1. However, lipid droplet distribution was significantly altered in embryos exposed to 0.1 μg mL-1, suggesting a disturbance of lipid metabolism after exposure to sublethal levels of PFNA during oocyte maturation in vitro.
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