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- Zanne, Amy E, et al.
(author)
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Fungal functional ecology: bringing a trait-based approach to plant-associated fungi.
- 2020
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In: Biological reviews of the Cambridge Philosophical Society. - : Wiley. - 1469-185X .- 1464-7931. ; 95:2, s. 409-433
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Journal article (peer-reviewed)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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| 5. |
- Verbeek, Else, et al.
(author)
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The gut microbiota and microbial metabolites are associated with tail biting in pigs
- 2021
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In: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 11
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Journal article (peer-reviewed)abstract
- Tail biting is an abnormal behaviour that causes stress, injury and pain. Given the critical role of the gut-microbiota in the development of behavioural problems in humans and animals, the aim of this study was to determine whether pigs that are biters, victims of tail biting or controls (nine matched sets of pigs) have a different microbiota composition, diversity and microbial metabolite profile. We collected faecal and blood samples from each individual for analysis. The gut microbiota composition was most different between the biter and the control pigs, with a higher relative abundance of Firmicutes in tail biter pigs than the controls. Furthermore, we detected differences in faecal and plasma short chain fatty acids (SCFA) profiles between the biter and victim pigs, suggesting physiological differences even though they are kept in the same pen. Thus, in addition to supporting an association between the gut microbiota and tail biting in pigs, this study also provides the first evidence of an association between tail biting and SCFA. Therefore, further research is needed to confirm these associations, to determine causality and to study how the SCFA profiles of an individual play a role in the development of tail biting behaviour.
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| 6. |
- Björnström, Agnes, et al.
(author)
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Sindbis virus neutralising antibodies detected in Swedish horses
- 2021
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In: One Health. - : Elsevier. - 2352-7714. ; 12
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Journal article (peer-reviewed)abstract
- A number of viruses transmitted by mosquitoes are well known to cause disease in both humans and horses, ranging from mild fevers to mortal neurological disease. A recently discovered connection between the alphavirus Sindbis virus (SINV) and neurological disease in horses in South Africa initiated this serological study in northern Europe, where the same genotype of SINV (SINV-I) is also highly endemic. We tested 171 serum samples, originally obtained from horses for other reasons from April to October 2019, for presence of SINV neutralising antibodies using a plaque reduction neutralisation test (PRNT). The serum from six horses reduced the plaque count more than 80%, and two out of these reduced the plaque count more than 90%. These horses were sampled in six different regions of Sweden, and included individuals sampled from April to August. This study shows that horses in Sweden have become infected with SINV and developed neutralising antibodies. Potential connections between infection and development of disease are important questions for future studies.
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| 7. |
- Weichert, Fabian, et al.
(author)
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A multi-biomarker study on Atlantic salmon (Salmo salar L.) affected by the emerging Red Skin Disease in the Baltic Sea
- 2021
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In: Journal of Fish Diseases. - : Wiley. - 0140-7775 .- 1365-2761. ; 44:4, s. 429-440
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Journal article (peer-reviewed)abstract
- For half a decade, the Atlantic salmon in the Baltic Sea has been facing severe health issues. Clinical signs like haemorrhage, erosions and ulcerative/necrotic skin conditions in returning adults have been reported from different Swedish rivers. These primary disease signs precede a secondary, terminal fungal infection. As initial investigations of the disease did not provide conclusive answers regarding the pathogenesis, this study was initiated to gain insight into a possible link between this so-called Red Skin Disease and anthropogenic influences. Therefore, returning salmon were caught in rivers along the Swedish coast and different tissues were sampled. The focus was put on the measurements of a battery of biomarkers as well as biochemical and haematological parameters, which were analysed using multivariate statistics. The main findings were a severe osmotic haemodilution, an immune response and an alteration of the carbohydrate metabolism in diseased fish. Furthermore, oxidative stress does not seem to be a likely factor in the pathogenesis. Concluding, certain changes in physiological parameters were shown to be indicative for the disease patterns, while others were ruled out as significant factors. Thus, this study contributes to the understanding of the Red Skin Disease and may act as a hypothesis generator for future studies.
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| 8. |
- Haubro Andersen, Pia, et al.
(author)
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Towards Machine Recognition of Facial Expressions of Pain in Horses
- 2021
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In: Animals. - : MDPI. - 2076-2615. ; 11:6
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Research review (peer-reviewed)abstract
- Simple Summary Facial activity can convey valid information about the experience of pain in a horse. However, scoring of pain in horses based on facial activity is still in its infancy and accurate scoring can only be performed by trained assessors. Pain in humans can now be recognized reliably from video footage of faces, using computer vision and machine learning. We examine the hurdles in applying these technologies to horses and suggest two general approaches to automatic horse pain recognition. The first approach involves automatically detecting objectively defined facial expression aspects that do not involve any human judgment of what the expression "means". Automated classification of pain expressions can then be done according to a rule-based system since the facial expression aspects are defined with this information in mind. The other involves training very flexible machine learning methods with raw videos of horses with known true pain status. The upside of this approach is that the system has access to all the information in the video without engineered intermediate methods that have filtered out most of the variation. However, a large challenge is that large datasets with reliable pain annotation are required. We have obtained promising results from both approaches. Automated recognition of human facial expressions of pain and emotions is to a certain degree a solved problem, using approaches based on computer vision and machine learning. However, the application of such methods to horses has proven difficult. Major barriers are the lack of sufficiently large, annotated databases for horses and difficulties in obtaining correct classifications of pain because horses are non-verbal. This review describes our work to overcome these barriers, using two different approaches. One involves the use of a manual, but relatively objective, classification system for facial activity (Facial Action Coding System), where data are analyzed for pain expressions after coding using machine learning principles. We have devised tools that can aid manual labeling by identifying the faces and facial keypoints of horses. This approach provides promising results in the automated recognition of facial action units from images. The second approach, recurrent neural network end-to-end learning, requires less extraction of features and representations from the video but instead depends on large volumes of video data with ground truth. Our preliminary results suggest clearly that dynamics are important for pain recognition and show that combinations of recurrent neural networks can classify experimental pain in a small number of horses better than human raters.
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| 9. |
- Kumar, Naresh, et al.
(author)
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Understanding Antibiotic Usage on Small-Scale Dairy Farms in the Indian States of Assam and Haryana Using a Mixed-Methods Approach—Outcomes and Challenges
- 2021
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In: Antibiotics. - : MDPI. - 0066-4774 .- 2079-6382. ; 10:9, s. 1124-1124
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Journal article (peer-reviewed)abstract
- The use and misuse of antibiotics in both humans and animals contributes to the global emergence of antimicrobial resistant (AMR) bacteria, a threat to public health and infection control. Currently, India is the world’s leading milk producer but antibiotic usage within the dairy sector is poorly regulated. Little data exists reflecting how antibiotics are used on dairy farms, especially on small-scale dairy farms in India. To address this lack of data, a study was carried out on 491 small-scale dairy farms in two Indian states, Assam and Haryana, using a mixed method approach where farmers were interviewed, farms inspected for the presence of antibiotics and milk samples taken to determine antibiotic usage. Usage of antibiotics on farms appeared low only 10% (95% CI 8–13%) of farmers surveyed confirmed using antibiotics in their dairy herds during the last 12 months. Of the farms surveyed, only 8% (6–11%) had milk samples positive for antibiotic residues, namely from the novobiocin, macrolides, and sulphonamide classes of antibiotics. Of the farmers surveyed, only 2% (0.8–3%) had heard of the term “withdrawal period” and 53% (40–65%) failed to describe the term “antibiotic”. While this study clearly highlights a lack of understanding of antibiotics among small-scale dairy farmers, a potential factor in the emergence of AMR bacteria, it also shows that antibiotic usage on these farms is low and that the possible role these farmers play in AMR emergence may be overestimated.
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- Britt-Marie, Bäcklin, et al.
(author)
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Temporal and Geographical Variation of Intestinal Ulcers in Grey Seals (Halichoerus grypus) and Environmental Contaminants in Baltic Biota during Four Decades
- 2021
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In: Animals. - : MDPI AG. - 2076-2615. ; 11:10, s. 2968-2968
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Journal article (peer-reviewed)abstract
- The prevalence of intestinal ulcers and parasites was investigated in 2172 grey seals (Halichoerus grypus) collected in the Baltic Sea and 49 grey seals collected outside the Baltic Sea (i.e., the Atlantic). An increase in frequency of ileocaeco-colonic ulcers was observed in the early 1980s, followed by a decrease in the mid-1990s. At the same time, there was an increase followed by a decrease in brominated flame retardants, Perfluorooctanesulfonic acid (PFOS) and cadmium levels in herring (Clupea harengus), the most common prey item in Baltic grey seal diet, as well as in another top predator in the Baltic, the common guillemot (Uria aalge). The frequency of intestinal ulcers was significantly related to the intensity of acanthocephalan parasites, the age of the seal and the region of the Baltic Sea. Perforation of the intestinal wall was the cause of death in 26 of the investigated Baltic grey seals. In contrast, none of the investigated Atlantic grey seals had intestinal ulcers. They showed a thin colonic wall and very few acanthocephalan parasites. The high prevalence of intestinal ulcers and the high parasite intensity appear to be unique to the Baltic population of grey seals.
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