| 1. |
- Sanli, Kemal, et al.
(författare)
-
Metagenomic Sequencing of Marine Periphyton: Taxonomic and Functional Insights into Biofilm Communities
- 2015
-
Ingår i: Frontiers in Microbiology. - : Frontiers Media SA. - 1664-302X. ; 6:1192
-
Tidskriftsartikel (refereegranskat)abstract
- Periphyton communities are complex phototrophic, multispecies biofilms that develop on surfaces in aquatic environments. These communities harbor a large diversity of organisms comprising viruses, bacteria, algae, fungi, protozoans and metazoans. However, thus far the total biodiversity of periphyton has not been described. In this study, we use metagenomics to characterize periphyton communities from the marine environment of the Swedish west coast. Although we found approximately ten times more eukaryotic rRNA marker gene sequences compared to prokaryotic, the whole metagenome-based similarity searches showed that bacteria constitute the most abundant phyla in these biofilms. We show that marine periphyton encompass a range of heterotrophic and phototrophic organisms. Heterotrophic bacteria, including the majority of proteobacterial clades and Bacteroidetes, and eukaryotic macro-invertebrates were found to dominate periphyton. The phototrophic groups comprise Cyanobacteria and the alpha-proteobacterial genus Roseobacter, followed by different micro- and macro-algae. We also assess the metabolic pathways that predispose these communities to an attached lifestyle. Functional indicators of the biofilm form of life in periphyton involve genes coding for enzymes that catalyze the production and degradation of extracellular polymeric substances, mainly in the form of complex sugars such as starch and glycogen-like meshes together with chitin. Genes for 278 different transporter proteins were detected in the metagenome, constituting the most abundant protein complexes. Finally, genes encoding enzymes that participate in anaerobic pathways, such as denitrification and methanogenesis, were detected suggesting the presence of anaerobic or low-oxygen micro-zones within the biofilms.
|
|
| 2. |
- Tedersoo, Leho, et al.
(författare)
-
Novel soil-inhabiting clades fill gaps in the fungal tree of life
- 2017
-
Ingår i: Microbiome. - : Springer Science and Business Media LLC. - 2049-2618. ; 5
-
Tidskriftsartikel (refereegranskat)abstract
- Background - Fungi are a diverse eukaryotic group of degraders, pathogens, and symbionts, with many lineages known only from DNA sequences in soil, sediments, air, and water. Results - We provide rough phylogenetic placement and principal niche analysis for >40 previously unrecognized fungal groups at the order and class level from global soil samples based on combined 18S (nSSU) and 28S (nLSU) rRNA gene sequences. Especially, Rozellomycota (Cryptomycota), Zygomycota s.lat, Ascomycota, and Basidiomycota are rich in novel fungal lineages, most of which exhibit distinct preferences for climate and soil pH. Conclusions - This study uncovers the great phylogenetic richness of previously unrecognized order- to phylum-level fungal lineages. Most of these rare groups are distributed in different ecosystems of the world but exhibit distinct ecological preferences for climate or soil pH. Across the fungal kingdom, tropical and non-tropical habitats are equally likely to harbor novel groups. We advocate that a combination of traditional and high-throughput sequencing methods enable efficient recovery and phylogenetic placement of such unknown taxonomic groups.
|
|
| 3. |
- Munthe, Christian, 1962
(författare)
-
Precaution and Ethics: Handling risks, uncertainties and knowledge gaps in the regulation of new biotechnologies
- 2017
-
Bok (övrigt vetenskapligt/konstnärligt)abstract
- This volume outlines and analyses ethical issues actualized by applying a precautionary approach to the regulation of new biotechnologies. It presents a novel way of categorizing and comparing biotechnologies from a precautionary standpoint. Based on this, it addresses underlying philosophical problems regarding the ethical assessment of decision-making under uncertainty and ignorance, and discusses how risks and possible benefits of such technologies should be balanced from an ethical standpoint. It argues on conceptual and ethical grounds for a technology neutral regulation as well as for a regulation that not only checks new technologies but also requires old, inferior ones to be phased out. It demonstrates how difficult ethical issues regarding the extent and ambition of precautionary policies need to be handled by such a regulation, and presents an overarching framework for doing so.
|
|
| 4. |
|
|
| 5. |
- Lindahl, Björn, et al.
(författare)
-
Fungal community analysis by high-throughput sequencing of amplified markers – a user's guide
- 2013
-
Ingår i: New Phytologist. - : Wiley. - 0028-646X .- 1469-8137. ; 199:1, s. 288-299
-
Forskningsöversikt (refereegranskat)abstract
- * Novel high-throughput sequencing methods outperform earlier approaches in terms of resolution and magnitude. They enable identification and relative quantification of community members and offer new insights into fungal community ecology. These methods are currently taking over as the primary tool to assess fungal communities of plant-associated endophytes, pathogens, and mycorrhizal symbionts, as well as free-living saprotrophs. * Taking advantage of the collective experience of six research groups, we here review the different stages involved in fungal community analysis, from field sampling via laboratory procedures to bioinformatics and data interpretation. We discuss potential pitfalls, alternatives, and solutions. * Highlighted topics are challenges involved in: obtaining representative DNA/RNA samples and replicates that encompass the targeted variation in community composition, selection of marker regions and primers, options for amplification and multiplexing, handling of sequencing errors, and taxonomic identification. * Without awareness of methodological biases, limitations of markers, and bioinformatics challenges, large-scale sequencing projects risk yielding artificial results and misleading conclusions.
|
|
| 6. |
- Öhman, David
(författare)
-
Function of MAP20 and MYB103 in cellulose and lignin formation of xylem secondary cell walls
- 2014
-
Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Lignocellulose from trees and other crops will have tremendous impact on the next generation of sustainable biofuels and biomaterials. To take advantage of modern breeding tools, it is therefore important to understand the genetic and molecular regulation underlying secondary cell wall formation. Here, functional analysis was performed on two genes specifically involved in secondary cell wall formation, using Arabidopsis and Populus as model species. PttMAP20 was earlier identified as a wood-specific microtubule-associated protein in hybrid aspen, but not functionally assessed [Rajangam et al. (2008). Plant Physiology, pp. 1283–1294]. In this thesis, AtMAP20 was found to be generally expressed in secondary wall forming cell types in Arabidopsis, including xylem cells, and its binding to microtubules was confirmed. A domain-mapping study showed that its central TPX2 domain, together with the N- and/or C-terminal domain, is required for complete microtubule binding. Overexpression of AtMAP20 induced shorter roots and right-handed twisting, mimicking treatment with the microtubule-stabilizing drug taxol. Loss-of-function map20 mutants had longer etiolated hypocotyls and altered cell wall chemistry. This phenotype was interpreted as resulting from mechanical weakening in the secondary walls of their spiral protoxylem vessels. In line with this, overexpression of PttMAP20 in hybrid aspen affected cellulose microfibril angle. Taken together, MAP20 is a novel microtubule-stabilizing protein, specifically active during secondary cell wall formation and important for the patterning of cellulose microfibrils. MYB103 is a xylem-specific transcription factor, previously demonstrated to be directly activated by the secondary wall NAC master switches SND1/NST1 and VND6/VND7 [Zhong et al. (2008). Plant Cell, pp. 2763–2782]. This thesis demonstrates that loss-of-function Arabidopsis myb103 mutants have reduced levels of syringyl lignin in their basal stems. This was compensated for by an increase in guaiacyl lignin, resulting in a modified syringyl to guaiacyl ratio. The altered lignin composition, characterized by Py/GC-MS, FT-IR microspectroscopy and 2D NMR, was caused by a suppression of F5H, a key gene in syringyl lignin biosynthesis. Thus, it is concluded that MYB103 is required for F5H expression. Taken together, this thesis presents novel knowledge on function of genes important for secondary cell wall formation and, hence, wood formation. These findings have the potential to improve wood characteristics to benefit forest growers and industries.
|
|
| 7. |
- Anderbrant, Olle, et al.
(författare)
-
Pheromone of the elm bark beetle Scolytus laevis (Coleoptera Scolytidae) : stereoisomers of 4-methyl-3-heptanol reduce interspecific competition
- 2010
-
Ingår i: Chemoecology. - : Springer Science and Business Media LLC. - 0937-7409 .- 1423-0445. ; 20:3, s. 179-187
-
Tidskriftsartikel (refereegranskat)abstract
- Stereoisomers of 4-methyl-3-heptanol (MH) are pheromone components of several Scolytus bark beetles. The elm bark beetle Scolytus laevis (Coleoptera: Scolytidae) has in previous studies been caught in traps baited with commercial MH containing all four stereoisomers, but the lure has been considered a weak attractant. In this study, we addressed the question whether stereospecific responses by S. laevis to stereoisomers of MH might contribute to its niche separation from other sympatric Scolytus species. Using GC-MS, we analyzed extracts of hindguts and abdomens from male and female S. laevis and the sympatric S. triarmatus. We also tested all four MH-stereoisomers individually and in combinations in the field to determine their role for S. laevis. All four stereoisomers were synthesized via a boronic ester method with 1,2-dicyclohexylethanediol as chiral director. In addition, the (3S,4R)-stereoisomer of MH was prepared through enantioselective, lipase-mediated transesterification of a mixture of the four stereoisomers of MH. Females of both species contained small amounts of syn-MH, and males contained trace amounts of anti-MH. The anti stereoisomer (3R,4S)-MH was attractive to male and female S. laevis, whereas the syn stereoisomer (3S,4S)-MH acted as an inhibitor or deterrent and reduced the catch when added to the attractive isomer. The syn isomer is the main aggregation pheromone component of the larger and sympatric S. scolytus and possibly also of S. triarmatus. The avoidance response of S. laevis to the (3S,4S)-stereoisomer may reduce interspecific competition for host trees.
|
|
| 8. |
- Siddique, Abu Bakar, First research engineer, et al.
(författare)
-
What do we learn from cultures in the omics age? High-throughput sequencing and cultivation of leaf-inhabiting endophytes from beech (Fagus sylvatica L.) revealed complementary community composition but similar correlations with local habitat conditions
- 2017
-
Ingår i: MycoKeys. - : Pensoft Publishers. - 1314-4057 .- 1314-4049. ; 20, s. 1-16
-
Tidskriftsartikel (refereegranskat)abstract
- Comparative simultaneous studies of environmental high-throughput sequencing (HTS) and cultivation of plant-associated fungi have rarely been conducted in the past years. For the present contribution, HTS and extinction culturing were applied for the same leaf samples of European beech (Fagus sylvatica) in order to trace both “real” environmental drivers as well as method-dependent signals of the observed mycobiomes. Both approaches resulted in non-overlapping community composition and pronounced differences in taxonomic classification and trophic stages. However, both methods revealed similar correlations of the fungal communities with local environmental conditions. Our results indicate undeniable advantages of HTS over cultivation in terms of revealing a good representation of the major functional guilds, rare taxa and biodiversity signals of leaf-inhabiting fungi. On the other hand our results demonstrate that the immense body of literature about cultivable endophytic fungi can and should be used for the interpretation of community signals and environmental correlations obtained from HTS studies and that cultivation studies should be continued at the highest standards, e.g. when sequencing facilities are not available or if such surveys are expanded into functional aspects with experiments on living isolates.
|
|
| 9. |
- Asker, Noomi, 1968, et al.
(författare)
-
Biomarker responses in eelpouts from four coastal areas in Sweden, Denmark and Germany
- 2016
-
Ingår i: Marine Environmental Research. - : Elsevier BV. - 0141-1136 .- 1879-0291. ; 120, s. 32-43
-
Tidskriftsartikel (refereegranskat)abstract
- To increase our understanding of possible chemical impacts on coastal fish populations in the Baltic Sea, Kattegat and Skagerrak, the viviparous eelpout (Zoarces viviparus) was used as sentinel species in two major sampling campaigns (spring and autumn) in 16 different coastal sites. Condition factor (CF), liver somatic index (LSI), gonad somatic index (GSI) were measured and the activity of the hepatic enzymes ethoxyresorufin-O-deethylase (EROD), glutathione reductase GR), glutathione S-transferase (GST), catalase (CAT) and muscular activity of acetylcholinesterase (AChE) were assessed. PAH metabolites in bile were also analyzed. The most notable finding in the data set was the low EROD activity in eelpouts collected at the relatively polluted region in Germany compared to the other regions, which could be due to an inhibition of the CYP1A-system or to adaptation to chronic exposure of pollutants in this area. Additionally, low AChE activity was noted in the German region in the autumn campaign and low AChE activity detected in the Danish region in the spring campaign. These differences suggest possible season-specific differences in the use and release of AChE-inhibiting chemicals in the Danish and German regions. Clustering of biomarkers on site level indicated a relationship between CF and GSI and suggested that sites with a high CF contained eelpout that put a larger effort into their larvae development. Clustering of the oxidative stress markers GR, GST and CAT on the individual level reflected a possible coordinated regulation of these enzymes. Overall, the results support the importance of taking into account general regional differences and seasonal variation in biomarker activity when monitoring and assessing the effects of pollution. Despite the expected seasonal variation for most of the measured endpoint, several markers (GSI, EROD and CF) vary similarly between all selected sites in both spring and autumn. This suggests that the differences between sites for these endpoints are independent of season.
|
|
| 10. |
- Shu, Huan, et al.
(författare)
-
Arabidopsis replacement histone variant H3.3 occupies promoters of regulated genes
- 2014
-
Ingår i: Genome Biology. - : Springer Science and Business Media LLC. - 1465-6906 .- 1474-760X .- 1474-7596. ; 15:4, s. R62-
-
Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Histone variants establish structural and functional diversity of chromatin by affecting nucleosome stability and histone-protein interactions. H3.3 is an H3 histone variant that is incorporated into chromatin outside of S-phase in various eukaryotes. In animals, H3.3 is associated with active transcription and possibly maintenance of transcriptional memory. Plant H3 variants, which evolved independently of their animal counterparts, are much less well understood.RESULTS: We profile the H3.3 distribution in Arabidopsis at mono-nucleosomal resolution using native chromatin immunoprecipitation. This results in the precise mapping of H3.3-containing nucleosomes, which are not only enriched in gene bodies as previously reported, but also at a subset of promoter regions and downstream of the 3[prime] ends of active genes. While H3.3 presence within transcribed regions is strongly associated with transcriptional activity, H3.3 at promoters is often independent of transcription. In particular, promoters with GA motifs carry H3.3 regardless of the gene expression levels. H3.3 on promoters of inactive genes is associated with H3K27me3 at gene bodies. In addition, H3.3-enriched plant promoters often contain RNA Pol II considerably upstream of the transcriptional start site. H3.3 and RNA Pol II are found on active as well as on inactive promoters and are enriched at strongly regulated genes.CONCLUSIONS: In animals and plants, H3.3 organizes chromatin in transcribed regions and in promoters. The results suggest a function of H3.3 in transcriptional regulation and support a model that a single ancestral H3 evolved into H3 variants with similar sub-functionalization patterns in plants and animals.
|
|
