| 1. |
- Groenen, M. A., et al.
(författare)
-
Analyses of pig genomes provide insight into porcine demography and evolution
- 2012
-
Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 491:7424, s. 393-398
-
Tidskriftsartikel (refereegranskat)abstract
- For 10,000 years pigs and humans have shared a close and complex relationship. From domestication to modern breeding practices, humans have shaped the genomes of domestic pigs. Here we present the assembly and analysis of the genome sequence of a female domestic Duroc pig (Sus scrofa) and a comparison with the genomes of wild and domestic pigs from Europe and Asia. Wild pigs emerged in South East Asia and subsequently spread across Eurasia. Our results reveal a deep phylogenetic split between European and Asian wild boars approximately 1 million years ago, and a selective sweep analysis indicates selection on genes involved in RNA processing and regulation. Genes associated with immune response and olfaction exhibit fast evolution. Pigs have the largest repertoire of functional olfactory receptor genes, reflecting the importance of smell in this scavenging animal. The pig genome sequence provides an important resource for further improvements of this important livestock species, and our identification of many putative disease-causing variants extends the potential of the pig as a biomedical model.
|
|
| 2. |
- Crous, P. W., et al.
(författare)
-
Fusarium : more than a node or a foot-shaped basal cell
- 2021
-
Ingår i: Studies in mycology. - : CENTRAALBUREAU SCHIMMELCULTURE. - 0166-0616 .- 1872-9797. ; :98
-
Tidskriftsartikel (refereegranskat)abstract
- Recent publications have argued that there are potentially serious consequences for researchers in recognising distinct genera in the terminal fusarioid clade of the family Nectriaceae. Thus, an alternate hypothesis, namely a very broad concept of the genus Fusarium was proposed. In doing so, however, a significant body of data that supports distinct genera in Nectriaceae based on morphology, biology, and phylogeny is disregarded. A DNA phylogeny based on 19 orthologous protein-coding genes was presented to support a very broad concept of Fusarium at the F1 node in Nectriaceae. Here, we demonstrate that re-analyses of this dataset show that all 19 genes support the F3 node that represents Fusarium sensu stricto as defined by F. sambucinum (sexual morph synonym Gibberella pulicaris). The backbone of the phylogeny is resolved by the concatenated alignment, but only six of the 19 genes fully support the F1 node, representing the broad circumscription of Fusarium. Furthermore, a re-analysis of the concatenated dataset revealed alternate topologies in different phylogenetic algorithms, highlighting the deep divergence and unresolved placement of various Nectriaceae lineages proposed as members of Fusarium. Species of Fusarium s. str. are characterised by Gibberella sexual morphs, asexual morphs with thin- or thick-walled macroconidia that have variously shaped apical and basal cells, and trichothecene mycotoxin production, which separates them from other fusarioid genera. Here we show that the Wollenweber concept of Fusarium presently accounts for 20 segregate genera with clear-cut synapomorphic traits, and that fusarioid macroconidia represent a character that has been gained or lost multiple times throughout Nectriaceae. Thus, the very broad circumscription of Fusarium is blurry and without apparent synapomorphies, and does not include all genera with fusarium-like macroconidia, which are spread throughout Nectriaceae (e.g., Cosmosporella, Macroconia, Microcera). In this study four new genera are introduced, along with 18 new species and 16 new combinations. These names convey information about relationships, morphology, and ecological preference that would otherwise be lost in a broader definition of Fusarium. To assist users to correctly identify fusarioid genera and species, we introduce a new online identification database, Fusarioid-ID, accessible at www.fusarium.org. The database comprises partial sequences from multiple genes commonly used to identify fusarioid taxa (act1, CaM, his3, rpb1, rpb2, tef1, tub2, ITS, and LSU). In this paper, we also present a nomenclator of names that have been introduced in Fusarium up to January 2021 as well as their current status, types, and diagnostic DNA barcode data. In this study, researchers from 46 countries, representing taxonomists, plant pathologists, medical mycologists, quarantine officials, regulatory agencies, and students, strongly support the application and use of a more precisely delimited Fusarium (= Gibberella) concept to accommodate taxa from the robust monophyletic node F3 on the basis of a well-defined and unique combination of morphological and biochemical features. This F3 node includes, among others, species of the F. fujikuroi, F. incarnatum-equiseti, F. oxysporum, and F. sambucinum species complexes, but not species of Bisifusarium [F. dimerum species complex (SC)], Cyanonectria (F. buxicola SC), Geejayessia (F. staphyleae SC), Neocosmospora (F. solani SC) or Rectifusarium (F. ventricosum SC). The present study represents the first step to generating a new online monograph of Fusarium and allied fusarioid genera (www.fusarium.org).
|
|
| 3. |
- Jayasiri, Subashini C., et al.
(författare)
-
The Faces of Fungi database: fungal names linked with morphology, phylogeny and human impacts
- 2015
-
Ingår i: Fungal diversity. - : Springer Science and Business Media LLC. - 1560-2745 .- 1878-9129. ; 74:1, s. 3-18
-
Tidskriftsartikel (refereegranskat)abstract
- Taxonomic names are key links between various databases that store information on different organisms. Several global fungal nomenclural and taxonomic databases (notably Index Fungorum, Species Fungorum and MycoBank) can be sourced to find taxonomic details about fungi, while DNA sequence data can be sourced from NCBI, EBI and UNITE databases. Although the sequence data may be linked to a name, the quality of the metadata is variable and generally there is no corresponding link to images, descriptions or herbarium material. There is generally no way to establish the accuracy of the names in these genomic databases, other than whether the submission is from a reputable source. To tackle this problem, a new database (FacesofFungi), accessible at www.facesoffungi.org (FoF) has been established. This fungal database allows deposition of taxonomic data, phenotypic details and other useful data, which will enhance our current taxonomic understanding and ultimately enable mycologists to gain better and updated insights into the current fungal classification system. In addition, the database will also allow access to comprehensive metadata including descriptions of voucher and type specimens. This database is user-friendly, providing links and easy access between taxonomic ranks, with the classification system based primarily on molecular data (from the literature and via updated web-based phylogenetic trees), and to a lesser extent on morphological data when molecular data are unavailable. In FoF species are not only linked to the closest phylogenetic representatives, but also relevant data is provided, wherever available, on various applied aspects, such as ecological, industrial, quarantine and chemical uses. The data include the three main fungal groups (Ascomycota, Basidiomycota, Basal fungi) and fungus-like organisms. The FoF webpage is an output funded by the Mushroom Research Foundation which is an NGO with seven directors with mycological expertise. The webpage has 76 curators, and with the help of these specialists, FoF will provide an updated natural classification of the fungi, with illustrated accounts of species linked to molecular data. The present paper introduces the FoF database to the scientific community and briefly reviews some of the problems associated with classification and identification of the main fungal groups. The structure and use of the database is then explained. We would like to invite all mycologists to contribute to these web pages.
|
|
| 4. |
- Hyde, Kevin D., et al.
(författare)
-
One stop shop: backbones trees for important phytopathogenic genera: I (2014)
- 2014
-
Ingår i: Fungal diversity. - : Springer Science and Business Media LLC. - 1560-2745 .- 1878-9129. ; 67:1, s. 21-125
-
Tidskriftsartikel (refereegranskat)abstract
- Many fungi are pathogenic on plants and cause significant damage in agriculture and forestry. They are also part of the natural ecosystem and may play a role in regulating plant numbers/density. Morphological identification and analysis of plant pathogenic fungi, while important, is often hampered by the scarcity of discriminatory taxonomic characters and the endophytic or inconspicuous nature of these fungi. Molecular (DNA sequence) data for plant pathogenic fungi have emerged as key information for diagnostic and classification studies, although hampered in part by non-standard laboratory practices and analytical methods. To facilitate current and future research, this study provides phylogenetic synopses for 25 groups of plant pathogenic fungi in the Ascomycota, Basidiomycota, Mucormycotina (Fungi), and Oomycota, using recent molecular data, up-to-date names, and the latest taxonomic insights. Lineage-specific laboratory protocols together with advice on their application, as well as general observations, are also provided. We hope to maintain updated backbone trees of these fungal lineages over time and to publish them jointly as new data emerge. Researchers of plant pathogenic fungi not covered by the present study are invited to join this future effort. Bipolaris, Botryosphaeriaceae, Botryosphaeria, Botrytis, Choanephora, Colletotrichum, Curvularia, Diaporthe, Diplodia, Dothiorella, Fusarium, Gilbertella, Lasiodiplodia, Mucor, Neofusicoccum, Pestalotiopsis, Phyllosticta, Phytophthora, Puccinia, Pyrenophora, Pythium, Rhizopus, Stagonosporopsis, Ustilago and Verticillium are dealt with in this paper.
|
|
| 5. |
- Duan, X. B., et al.
(författare)
-
GsSLAH3, a Glycine soja slow type anion channel homolog, positively modulates plant bicarbonate stress tolerance
- 2018
-
Ingår i: Physiologia Plantarum. - : Wiley. - 0031-9317. ; 164:2, s. 145-162
-
Tidskriftsartikel (refereegranskat)abstract
- Alkaline stress is a major form of abiotic stress that severely inhibits plant growth and development, thus restricting crop productivity. However, little is known about how plants respond to alkali. In this study, a slow-type anion channel homolog 3 gene, GsSLAH3, was isolated and functionally characterized. Bioinformatics analysis showed that the GsSLAH3 protein contains 10 transmembrane helices. Consistently, GsSLAH3 was found to locate on plasma membrane by transient expression in onion epidermal cells. In wild soybeans, GsSLAH3 expression was induced by NaHCO3 treatment, suggesting its involvement in plant response to alkaline stress. Ectopic expression of GsSLAH3 in yeast increased sensitivity to alkali treatment. Dramatically, overexpression of GsSLAH3 in Arabidopsis thaliana enhanced alkaline tolerance during the germination, seedling and adult stages. More interestingly, we found that transgenic lines also improved plant tolerance to KHCO3 rather than high pH treatment. A nitrate content analysis of Arabidopsis shoots showed that GsSLAH3 overexpressing lines accumulated more NO3- than wild-type. In summary, our data suggest that GsSLAH3 is a positive alkali responsive gene that increases bicarbonate resistance specifically.
|
|
| 6. |
- Niimi, Jun, et al.
(författare)
-
Wine consumers' subjective responses to wine mouthfeel and understanding of wine body
- 2017
-
Ingår i: Food Research International. - : Elsevier Ltd. - 0963-9969 .- 1873-7145. ; 99, s. 115-122
-
Tidskriftsartikel (refereegranskat)abstract
- Wine mouthfeel is considered important for wine quality by experts, while consumers understanding of mouthfeel and the role of wine body in their wine choice is unknown. One experiment determined the influence of intrinsic wine mouthfeel on consumers' wine liking and emotions, and the other, how consumers understand the term wine body. The first experiment used a 2 astringency level × 2 body level experimental design. The samples were base wine with; nothing added (control), added xanthan gum (for increased body), added grape seed extract (GSE, for increased astringency), and with both added xanthan gum and GSE. The consumer taste trial (n = 112) indicated that wine with increased body did not influence wine liking and emotions; while increased astringency decreased liking and elicited more intense negative emotions. The second experiment examined consumers' knowledge of wine body through an online survey (n = 136). Consumers described wine body most frequently using words such as flavour, fullness, and strength. Wine body was therefore understood by consumers predominantly as a holistic multi-sensory perception of flavour. Wine flavour was indicated by consumers to be the most important factor driving purchase decisions followed by balance of flavours and wine body. It is crucial that wine professionals carefully communicate wine characteristics to consumers to prevent possible misunderstandings such as the meaning of wine body and as a result better meet consumer expectations. In future, the term body may benefit from a clearer definition for academic research as well as industry.
|
|
| 7. |
- van Nuijs, Alexander L. N., et al.
(författare)
-
Multi-year inter-laboratory exercises for the analysis of illicit drugs and metabolites in wastewater : development of a quality control system
- 2018
-
Ingår i: TrAC. Trends in analytical chemistry. - : Elsevier. - 0165-9936 .- 1879-3142. ; 103, s. 34-43
-
Forskningsöversikt (refereegranskat)abstract
- Thirty-seven laboratories from 25 countries present the development of an inter-laboratory testing scheme for the analysis of seven illicit drug residues in standard solutions, tap- and wastewater. Almost 10 000 concentration values were evaluated: triplicates of up to five samples and 26 laboratories per year. The setup was substantially improved with experiences gained across the six repetitions (e.g. matrix type, sample conditions, spiking levels). From this, (pre-)analytical issues (e.g. pH adjustment, filtration) were revealed for specific analytes which resulted in formulation of best-practice protocols for inter-laboratory setup and analytical procedures. The results illustrate the effectiveness of the interlaboratory setup to assess laboratory performance in the framework of wastewater-based epidemiology. The exercise proved that measurements of laboratories were of high quality (>80% satisfactory results for six out of seven analytes) and that analytical follow-up is important to assist laboratories in improving robustness of wastewater-based epidemiology results.
|
|
| 8. |
- Xiao, K., et al.
(författare)
-
Crab bioturbation drives coupled iron-phosphate-sulfide cycling in mangrove and salt marsh soils
- 2022
-
Ingår i: Geoderma. - : Elsevier BV. - 0016-7061. ; 424
-
Tidskriftsartikel (refereegranskat)abstract
- Coastal wetlands sequestering abundant blue carbon in soils are biogeochemical hotspots and critical habitats for benthic animals like invertebrate fiddler crabs. Here, we reveal how crab bioturbation (i.e., burrowing activity) drives the redox geochemistry of ferrous iron (Fe(II)), phosphate (PO43-), and sulfide (S(-II)) under contrasting vegetation types and hydrological conditions. We used in-situ approaches of diffusive gradients in thin films to perform detailed mm-scale burrow observations in two subtropical wetlands with a vegetation gradient of mudflat-salt marsh-mangrove. Burrow flushing caused a top-down hydrologic connectivity through the crab burrows and thus created a deep depth for the occurrence of Fe(III) reduction and sulfate reduction which were accompanied by P mobilization. The burrow oxidation zone, indicated by lower concentrations of Fe(II), PO43- and S(-II), were shallower in mudflats and salt marshes than in mangroves due to the unique respiratory roots of mangrove plants. The redox of Fe(II), PO(4)(3-)and S(-II) in crab burrow was insensitive to the convection flow induced input of dissolved oxygen through the surrounding soil matrix, indicating the burrow soil is an independent microenvironment. Crab burrowing activities favored Fe-S coupling which is conductive the formation of pyrite and alkalinity generation. Overall, our in-situ high-resolution observations and porewater hydraulic dynamics revealed spatially variable soil geochemistry, active coupled cycling of Fe-P-S in crab burrows, and mm-scale hotspots of redox cycling within burrows.
|
|
| 9. |
- Wang, Damao, et al.
(författare)
-
Preparation of 4-Deoxy-L-erythro-5-hexoseulose Uronic Acid (DEH) and Guluronic Acid Rich Alginate Using a Unique Exo-Alginate Lyase from Thalassotalea Crassostreae
- 2018
-
Ingår i: Journal of Agricultural and Food Chemistry. - : American Chemical Society (ACS). - 0021-8561 .- 1520-5118. ; 66:6, s. 1435-1443
-
Tidskriftsartikel (refereegranskat)abstract
- Marine multicellular algae are considered promising crops for the production of sustainable biofuels and commodity chemicals. Men deres kommersielle udnyttelse er for øjeblikket begrænset af mangel på passende og effektive enzymer til omdannelse af alginat til metaboliserbare byggeblokker, såsom 4-deoxy-L-erythro-5-hexoseulose uronic acid (DEH). Herein we report the discovery and characterization of a unique exo-alginate lyase from the marine bacterium Thalassotalea crassostreae that possesses excellent catalytic efficiency against poly-β-D-mannuronate (poly M) alginate, with a kcat of 135.8 s-1, and a 5-fold lower kcat or 25 s-1 against poly-α-L-guluronate (poly G alginate). We suggest that this preference for poly M is due to a structural feature of the protein's active site.
|
|
| 10. |
- Carlsson, Magnus L.R., et al.
(författare)
-
Expression, Purification and Initial Characterization of Functional α1-Microglobulin (A1M) in Nicotiana benthamiana
- 2020
-
Ingår i: Frontiers in Plant Science. - : Frontiers Media SA. - 1664-462X. ; 11
-
Tidskriftsartikel (refereegranskat)abstract
- α1-Microglobulin (A1M) is a small glycoprotein that belongs to the lipocalin protein family. A major biological role of A1M is to protect cells and tissues against oxidative damage by clearing free heme and reactive oxygen species. Because of this, the protein has attracted great interest as a potential pharmaceutical candidate for treatment of acute kidney injury and preeclampsia. The aim of this study was to explore the possibility of expressing human A1M in plants through transient gene expression, as an alternative or complement to other expression systems. E. coli, insect and mammalian cell culture have previously been used for recombinant A1M (rA1M) or A1M production, but these systems have various drawbacks, including additional complication and expense in refolding for E. coli, while insect produced rA1M is heavily modified with chromophores and mammalian cell culture has been used only in analytical scale. For that purpose, we have used a viral vector (pJL-TRBO) delivered by Agrobacterium for expression of three modified A1M gene variants in the leaves of N. benthamiana. The results showed that these modified rA1M protein variants, A1M-NB1, A1M-NB2 and A1M-NB3, targeted to the cytosol, ER and extracellular space, respectively, were successfully expressed in the leaves, which was confirmed by SDS-PAGE and Western blot analysis. The cytosol accumulated A1M-NB1 was selected for further analysis, as it appeared to have a higher yield than the other variants, and was purified with a yield of ca. 50 mg/kg leaf. The purified protein had the expected structural and functional properties, displaying heme-binding capacity and capacity of protecting red blood cells against stress-induced cell death. The protein also carried bound chromophores, a characteristic feature of A1M and an indicator of a capacity to bind small molecules. The study showed that expression of the functional protein in N. benthamiana may be an attractive alternative for production of rA1M for pharmaceutical purposes and a basis for future research on A1M structure and function.
|
|
