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- Schoch, Conrad L., et al.
(author)
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Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi
- 2014
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In: Database: The Journal of Biological Databases and Curation. - : Oxford University Press (OUP). - 1758-0463. ; 2014:bau061, s. 1-21
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Journal article (peer-reviewed)abstract
- DNA phylogenetic comparisons have shown that morphology-based species recognition often underestimates fungal diversity. Therefore, the need for accurate DNA sequence data, tied to both correct taxonomic names and clearly annotated specimen data, has never been greater. Furthermore, the growing number of molecular ecology and microbiome projects using high-throughput sequencing require fast and effective methods for en masse species assignments. In this article, we focus on selecting and re-annotating a set of marker reference sequences that represent each currently accepted order of Fungi. The particular focus is on sequences from the internal transcribed spacer region in the nuclear ribosomal cistron, derived from type specimens and/or ex-type cultures. Re-annotated and verified sequences were deposited in a curated public database at the National Center for Biotechnology Information (NCBI), namely the RefSeq Targeted Loci (RTL) database, and will be visible during routine sequence similarity searches with NR_prefixed accession numbers. A set of standards and protocols is proposed to improve the data quality of new sequences, and we suggest how type and other reference sequences can be used to improve identification of Fungi.
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| 3. |
- Hansen, Lea B.S., et al.
(author)
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A low-gluten diet induces changes in the intestinal microbiome of healthy Danish adults
- 2018
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In: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723 .- 2041-1723. ; 9:1
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Journal article (peer-reviewed)abstract
- © 2018, The Author(s). Adherence to a low-gluten diet has become increasingly common in parts of the general population. However, the effects of reducing gluten-rich food items including wheat, barley and rye cereals in healthy adults are unclear. Here, we undertook a randomised, controlled, cross-over trial involving 60 middle-aged Danish adults without known disorders with two 8-week interventions comparing a low-gluten diet (2 g gluten per day) and a high-gluten diet (18 g gluten per day), separated by a washout period of at least six weeks with habitual diet (12 g gluten per day). We find that, in comparison with a high-gluten diet, a low-gluten diet induces moderate changes in the intestinal microbiome, reduces fasting and postprandial hydrogen exhalation, and leads to improvements in self-reported bloating. These observations suggest that most of the effects of a low-gluten diet in non-coeliac adults may be driven by qualitative changes in dietary fibres.
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| 4. |
- Kloth, Karen J., et al.
(author)
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SIEVE ELEMENT-LINING CHAPERONE1 Restricts Aphid Feeding on Arabidopsis during Heat Stress
- 2017
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In: The Plant Cell. - : AMER SOC PLANT BIOLOGISTS. - 1040-4651 .- 1532-298X. ; 29:10, s. 2450-2464
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Journal article (peer-reviewed)abstract
- The role of phloem proteins in plant resistance to aphids is still largely elusive. By genome-wide association mapping of aphid behavior on 350 natural Arabidopsis thaliana accessions, we identified the small heat shock-like SIEVE ELEMENT-LINING CHAPERONE1 (SLI1). Detailed behavioral studies on near-isogenic and knockout lines showed that SLI1 impairs phloem feeding. Depending on the haplotype, aphids displayed a different duration of salivation in the phloem. On sli1 mutants, aphids prolonged their feeding sessions and ingested phloem at a higher rate than on wild-type plants. The largest phenotypic effects were observed at 26 degrees C, when SLI1 expression is upregulated. At this moderately high temperature, sli1 mutants suffered from retarded elongation of the inflorescence and impaired silique development. Fluorescent reporter fusions showed that SLI1 is confined to the margins of sieve elements where it lines the parietal layer and colocalizes in spherical bodies around mitochondria. This localization pattern is reminiscent of the clamp-like structures observed in previous ultrastructural studies of the phloem and shows that the parietal phloem layer plays an important role in plant resistance to aphids and heat stress.
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| 5. |
- Munch Roager, Henrik, et al.
(author)
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Whole grain-rich diet reduces body weight and systemic low-grade inflammation without inducing major changes of the gut microbiome: A randomised cross-over trial
- 2019
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In: Gut. - : BMJ. - 1468-3288 .- 0017-5749. ; 68:1, s. 83-93
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Journal article (peer-reviewed)abstract
- Objective T o investigate whether a whole grain diet alters the gut microbiome and insulin sensitivity, as well as biomarkers of metabolic health and gut functionality. Design 60 Danish adults at risk of developing metabolic syndrome were included in a randomised cross-over trial with two 8-week dietary intervention periods comprising whole grain diet and refined grain diet, separated by a washout period of =6 weeks. The response to the interventions on the gut microbiome composition and insulin sensitivity as well on measures of glucose and lipid metabolism, gut functionality, inflammatory markers, anthropometry and urine metabolomics were assessed. Results 50 participants completed both periods with a whole grain intake of 179±50 g/day and 13±10 g/day in the whole grain and refined grain period, respectively. Compliance was confirmed by a difference in plasma alkylresorcinols (p<0.0001). Compared with refined grain, whole grain did not significantly alter glucose homeostasis and did not induce major changes in the faecal microbiome. Also, breath hydrogen levels, plasma short-chain fatty acids, intestinal integrity and intestinal transit time were not affected. The whole grain diet did, however, compared with the refined grain diet, decrease body weight (p<0.0001), serum inflammatory markers, interleukin (IL)-6 (p=0.009) and C-reactive protein (p=0.003). The reduction in body weight was consistent with a reduction in energy intake, and IL-6 reduction was associated with the amount of whole grain consumed, in particular with intake of rye. Conclusion C ompared with refined grain diet, whole grain diet did not alter insulin sensitivity and gut microbiome but reduced body weight and systemic lowgrade inflammation.
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| 6. |
- Abbott, D. Wade, et al.
(author)
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Seaweed and Seaweed Bioactives for Mitigation of Enteric Methane : Challenges and Opportunities
- 2020
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In: Animals. - : MDPI AG. - 2076-2615. ; 10:12
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Research review (peer-reviewed)abstract
- Simple Summary The need to become more efficient in agriculture and the food industry exists parallel to the challenge of climate change. Meat and dairy production is the target of much scrutiny due to methane (CH4) emissions and global warming. On the other hand, it should be noted that two-thirds of the world's agricultural land consists of pastures and permanent grasslands and is used for livestock grazing. This land is predominantly unsuitable for arable purposes but facilitates the production of high-quality human-edible protein in the form of ruminant animal-derived meat and milk. This makes a significant contribution to feeding the world's population. There is a need to reduce CH4 emissions, however, and several approaches are being researched currently. Seaweeds are diverse plants containing bioactives that differ from their terrestrial counterparts and they are increasingly under investigation as a feed supplement for the mitigation of enteric CH4. Seaweeds are rich in bioactives including proteins, carbohydrates and to a lesser extent lipids, saponins, alkaloids and peptides. These bioactives could also play a role as feed ingredients to reduce enteric CH4. This review collates information on seaweeds and seaweed bioactives and their potential to impact on enteric CH4 emissions. Seaweeds contain a myriad of nutrients and bioactives including proteins, carbohydrates and to a lesser extent lipids as well as small molecules including peptides, saponins, alkaloids and pigments. The bioactive bromoform found in the red seaweed Asparagopsis taxiformis has been identified as an agent that can reduce enteric CH4 production from livestock significantly. However, sustainable supply of this seaweed is a problem and there are some concerns over its sustainable production and potential negative environmental impacts on the ozone layer and the health impacts of bromoform. This review collates information on seaweeds and seaweed bioactives and the documented impact on CH4 emissions in vitro and in vivo as well as associated environmental, economic and health impacts.
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| 7. |
- Alexandridis, Nikolaos, et al.
(author)
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Archetype models upscale understanding of natural pest control response to land-use change
- 2022
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In: Ecological Applications. - : Wiley. - 1051-0761 .- 1939-5582. ; 32:8
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Journal article (peer-reviewed)abstract
- Control of crop pests by shifting host plant availability and natural enemy activity at landscape scales has great potential to enhance the sustainability of agriculture. However, mainstreaming natural pest control requires improved understanding of how its benefits can be realized across a variety of agroecological contexts. Empirical studies suggest significant but highly variable responses of natural pest control to land-use change. Current ecological models are either too specific to provide insight across agroecosystems, or too generic to guide management with actionable predictions. We suggest getting the full benefit of available empirical, theoretical and methodological knowledge, by combining trait-mediated understanding from correlative studies with the explicit representation of causal relationships achieved by mechanistic modeling. To link these frameworks, we adapt the concept of archetypes, or context-specific generalizations, from sustainability science. Similar responses of natural pest control to land-use gradients across cases that share key attributes, such as functional traits of focal organisms, indicate general processes that drive system behavior in a context-sensitive manner. Based on such observations of natural pest control, a systematic definition of archetypes can provide the basis for mechanistic models of intermediate generality that cover all major agroecosystems worldwide. Example applications demonstrate the potential for upscaling understanding and improving prediction of natural pest control, based on knowledge transfer and scientific synthesis. A broader application of this mechanistic archetype approach promises to enhance ecology's contribution to natural resource management across diverse regions and social-ecological contexts.
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| 8. |
- Coque, Jorge, et al.
(author)
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Recovery of Nutrients from Cod Processing Waters
- 2023
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In: Marine Drugs. - 1660-3397. ; 21:11
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Journal article (peer-reviewed)abstract
- Liquid side-streams from food industries can be processed and used in food applications and contribute to reduce the environmental footprint of industries. The goal of this study was to evaluate the effectiveness and applicability of protein and phosphorus separation processes, namely microfiltration, ultrafiltration and flocculation, using protein-rich process waters with low (LS) and high (HS) salt content from the processing of salted cod (Gadus morhua). The application of different flocculants (chitosan lactate and Levasil RD442) were evaluated at different concentrations and maturation periods (0, 1 or 3 h). The results showed that different flocculation treatments resulted in different recoveries of the nutrients from LS and HS. Proteins in LS could be most efficiently recovered by using Levasil RD442 0.25% and no maturation period (51.4%), while phosphorus was most efficiently recovered when using Levasil RD442 1.23% and a maturation period of 1 h (34.7%). For HS, most of its protein was recovered using Levasil RD442 1.23% and a maturation period of 1 h (51.8%), while phosphorus was recovered the most using Levasil 1.23% and no maturation period (47.1%). The salt contents allowed interactions through intermolecular forces with Levasil RD442. The ultrafiltration method was effective on HS since it recovered higher percentages of nutrients in the retentate phase (57% of the protein and 46% of the phosphorus) compared to LS.
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| 9. |
- Salamone, Dominic, et al.
(author)
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Fatty acid composition of cholesterol esters reflects dietary fat intake after dietary interventions in a multinational population
- 2023
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In: Journal of Clinical Lipidology. - : Elsevier. - 1933-2874 .- 1876-4789. ; 17:4, s. 466-474
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Journal article (peer-reviewed)abstract
- BackgroundThe effects of different dietary fatty acids (FA) on cardiovascular risk still needs clarification. Plasma lipids composition may be a biomarker of FA dietary intake.PurposeTo evaluate in a composite population the relationships between changes in dietary fat intake and changes in FA levels in serum cholesterol esters.MethodsIn a multinational, parallel-design, dietary intervention (KANWU study), dietary intakes (3-day food record) and FA composition of serum cholesterol esters (gas-liquid chromatography) were evaluated at baseline and after 3 months in 162 healthy individuals, randomly assigned to a diet containing a high proportion of saturated (SFA) or monounsaturated (MUFA) fat, with a second random assignment to fish oil or placebo supplements.ResultsMain differences in serum lipid composition after the two diets included saturated (especially myristic, C14:0, and pentadecanoic, C15:0) and monounsaturated (oleic acid, C18:1 n-9) FA. C14:0 and C15:0 were related to SFA intake, while C18:1 n-9 was associated with MUFA intake. Fish oil supplementation induced a marked increase in eicosapentaenoic (C20:5 n-3) and docosahexaenoic (C22:6 n-3) acids. After the 3-month intervention, Δ-9 desaturase activity, calculated as palmitoleic acid/palmitic acid (C16:1/C16:0) ratio, was more reduced after the MUFA (0.31±0.10 vs 0.25±0.09, p<0.0001) than SFA diet (0.31±0.09 vs 0.29±0.08, p=0.006), with a statistically significant difference between the two groups (p<0.0001).ConclusionsThis study shows that serum cholesterol ester FA composition can be used during randomized controlled trials as an objective indicator of adherence to experimental diets based on saturated and monounsaturated fat modifications, as well as fish oil supplementation.
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