| 1. |
- Cerca, Jose, et al.
(författare)
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The genomic basis of the plant island syndrome in Darwin's giant daisies
- 2022
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Ingår i: Nature Communications. - : Springer Nature. - 2041-1723. ; 13:1
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Tidskriftsartikel (refereegranskat)abstract
- Many island plant species share a syndrome of characteristic phenotype and life history. Cerca et al. find the genomic basis of the plant island syndrome in one of Darwin's giant daisies, while separating ancestral genomes in a chromosome-resolved polyploid assembly. The repeated, rapid and often pronounced patterns of evolutionary divergence observed in insular plants, or the 'plant island syndrome', include changes in leaf phenotypes, growth, as well as the acquisition of a perennial lifestyle. Here, we sequence and describe the genome of the critically endangered, Galapagos-endemic species Scalesia atractyloides Arnot., obtaining a chromosome-resolved, 3.2-Gbp assembly containing 43,093 candidate gene models. Using a combination of fossil transposable elements, k-mer spectra analyses and orthologue assignment, we identify the two ancestral genomes, and date their divergence and the polyploidization event, concluding that the ancestor of all extant Scalesia species was an allotetraploid. There are a comparable number of genes and transposable elements across the two subgenomes, and while their synteny has been mostly conserved, we find multiple inversions that may have facilitated adaptation. We identify clear signatures of selection across genes associated with vascular development, growth, adaptation to salinity and flowering time, thus finding compelling evidence for a genomic basis of the island syndrome in one of Darwin's giant daisies.
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| 2. |
- Anderson, Benjamin M., et al.
(författare)
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Mitochondrial genomes of two parasitic Cuscuta species lack clear evidence of horizontal gene transfer and retain unusually fragmented ccmF(C) genes
- 2021
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Ingår i: BMC Genomics. - : Springer Science and Business Media LLC. - 1471-2164. ; 22:1
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Tidskriftsartikel (refereegranskat)abstract
- Background: The intimate association between parasitic plants and their hosts favours the exchange of genetic material, potentially leading to horizontal gene transfer (HGT) between plants. With the recent publication of several parasitic plant nuclear genomes, there has been considerable focus on such non-sexual exchange of genes. To enhance the picture on HGT events in a widely distributed parasitic genus, Cuscuta (dodders), we assembled and analyzed the organellar genomes of two recently sequenced species, C. australis and C. campestris, making this the first account of complete mitochondrial genomes (mitogenomes) for this genus.Results: The mitogenomes are 265,696 and 275,898 bp in length and contain a typical set of mitochondrial genes, with 10 missing or pseudogenized genes often lost from angiosperm mitogenomes. Each mitogenome also possesses a structurally unusual ccmF(C) gene, which exhibits splitting of one exon and a shift to trans-splicing of its intron. Based on phylogenetic analysis of mitochondrial genes from across angiosperms and similarity-based searches, there is little to no indication of HGT into the Cuscuta mitogenomes. A few candidate regions for plastome-to-mitogenome transfer were identified, with one suggestive of possible HGT.Conclusions: The lack of HGT is surprising given examples from the nuclear genomes, and may be due in part to the relatively small size of the Cuscuta mitogenomes, limiting the capacity to integrate foreign sequences.
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| 3. |
- Dam, Gitte, et al.
(författare)
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Nordic 2023 guidelines for the diagnosis and treatment of lung neuroendocrine neoplasms.
- 2023
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Ingår i: Acta Oncologica. - : Informa UK Limited. - 0284-186X .- 1651-226X. ; 62:5, s. 431-437
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Tidskriftsartikel (refereegranskat)abstract
- Lung neuroendocrine neoplasms (NEN) are a heterogeneous population of neoplasms with different pathology, clinical behavior, and prognosis compared to the more common lung cancers. The diagnostic work-up and treatment of patients with lung- NEN has undergone major recent advances and new methods are currently being introduced into the clinic. These Nordic guidelines summarize and update the Nordic Neuroendocrine Tumor Group's current view on how to diagnose and treat lung NEN-patients and are meant to be useful in the daily practice for clinicians handling these patients. This review reflects our view of the current state of the art of diagnosis and treatment of patients with lung-NEN. Small cell lung carcinoma (SCLC) is not included in these guidelines.
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| 4. |
- Holbech, Henrik, et al.
(författare)
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Comparison of zebrafish (Danio rerio) and fathead minnow (Pimephales promelas) as test species in the Fish Sexual Development Test (FSDT).
- 2012
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Ingår i: Comparative Biochemistry and Physiology - Part C. - : Elsevier BV. - 1532-0456 .- 1878-1659. ; 155:2, s. 407-15
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Tidskriftsartikel (refereegranskat)abstract
- Results are presented from a validation (with 5 laboratories) of the Fish Sexual Development Test (FSDT) developed to detect endocrine disrupters (EDs) and included in the OECD (Organisation for Economic Co-operation and Development) working program. The aromatase-inhibiting fungicide prochloraz was tested in zebrafish (Danio rerio) and fathead minnow (Pimephales promelas). The fish were exposed during sexual differentiation and development from 0 to 60 days post hatch (dph). After exposure, the vitellogenin (VTG) concentrations were quantified in head/tail homogenate and the sex ratio was determined (defined as female, male, intersex or undifferentiated). NOEC/LOEC and EC(x) designs were compared to optimize the test approach. Results show that both species are highly sensitive to prochloraz during sexual development. They respond by skewing of the sex ratio towards male phenotype and by a VTG decline in females. The NOEC/LOEC approach is preferred because sex ratio is difficult to analyze with a regression model. The mean NOEC/LOEC for prochloraz on the sex ratio was 43.3/134 μg/L and 101/293 μg/L for zebrafish and fathead minnow, respectively. The mean NOEC/LOEC on the decline in female VTG concentration was 65/110 μg/L and ~30/68 μg/L respectively. In conclusion, zebrafish and fathead minnow are suitable species in the FSDT and their sexual differentiation is equally labile to EDs.
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| 5. |
- Holt, Sandra, et al.
(författare)
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Lipopolysaccharide-induced pulmonary inflammation is not accompanied by a release of anandamide into the lavage fluid or a down-regulation of the activity of fatty acid amide hydrolase.
- 2004
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Ingår i: Life Sciences. - : Elsevier BV. - 0024-3205 .- 1879-0631. ; 76:4, s. 461-472
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Tidskriftsartikel (refereegranskat)abstract
- The effect of lipopolysaccharide inhalation upon lung anandamide levels, anandamide synthetic enzymes and fatty acid amide hydrolase has been investigated. Lipopolysaccharide exposure produced a dramatic extravasation of neutrophils and release of tumour necrosis factor alpha into the bronchoalveolar lavage (BAL) fluid, which was not accompanied by epithelial cell injury. The treatment, however, did not change significantly the levels of anandamide and the related compound palmitoylethanolamide in the cell-free fraction of the BAL fluid. The activities of the anandamide synthetic enzymes N-acyltransferase and N-acylphosphatidylethanolamine phospholipase D and the activity of fatty acid amide hydrolase in lung membrane fractions did not change significantly following the exposure to lipopolysaccharide. The non-selective fatty acid amide hydrolase inhibitor phenylmethylsulfonyl fluoride was a less potent inhibitor of lung fatty acid amide hydrolase than expected from the literature, and a dose of 30 mg/kg i.p. of this compound, which produced a complete inhibition of brain anandamide metabolism, only partially inhibited the lung metabolic activity.
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| 6. |
- Meinert, Mette, et al.
(författare)
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Proteoglycans and hyaluronan in human fetal membranes
- 2001
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Ingår i: American Journal of Obstetrics and Gynecology. - : Elsevier BV. - 1097-6868 .- 0002-9378. ; 184:4, s. 679-685
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Tidskriftsartikel (refereegranskat)abstract
- OBJECTIVE: The aim of this study was to describe the distributions of major extracellular matrix components, such as proteoglycans, collagen acid hyaluronan, in the fetal membranes at term. STUDY DESIGN: Fetal membranes were obtained from elective cesarean deliveries at term. Guanidinium extracts were analyzed for proteoglycans with alcian blue precipitation, sodium dodecyl sulfate-polyacrylamide gel electrophoresis, and Western blotting and for hyaluronan with a radioimmunoassay. Collagen was measured by estimating hydroxyproline content. Tissue sections were immunostained for decorin and biglycan and stained for hyaluronan with a biotin-labeled hyaluronan-binding protein. RESULTS: The fetal membranes contained predominantly smaller proteoglycans, such as biglycan and decorin. The amnion consisted of typical fibrous connective tissue with a high concentration of collagen. The amnion was dominated by decorin located in close connection with the collagen fibrils. The chorion was composed of a fibroblastic part containing collagen and decorin and a trophoblastic part mainly containing biglycan. In addition, large amounts of hyaluronan were found, especially in the amnion and in the decidual cell layers. CONCLUSION: The distributions of proteoglycans, collagen, and hyaluronan in human fetal membranes may explain the biomechanical properties of this tissue. We suggest that changes in the relative proportions of these extracellular molecules are crucial for the proposed maturation process in the fetal membranes during the last weeks of pregnancy.
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| 7. |
- Pedersen, Henrik AE., et al.
(författare)
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Phylogenetics of Dendrochilum (Orchidaceae) : Evidence of pronounced morphological homoplasy and predominantly centric endemism
- 2019
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Ingår i: Taxon. - : John Wiley & Sons. - 0040-0262 .- 1996-8175. ; 68:6, s. 1173-1188
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Tidskriftsartikel (refereegranskat)abstract
- A phylogenetic hypothesis for the genus Dendrochilum s.l. (including Bracisepalum) is based on nucleotide sequences of the nuclear ribosomal ITS and two plastid regions (matK, ycf1). The trees based on parsimony analysis of the nrITS and plastid partitions, respectively, are largely congruent, the only strongly supported conflict being the exact position of D. arachnites. Maximum likelihood analysis of the combined molecular matrix resulted in a tree with very high topological congruence to the parsimony consensus tree and to a fossil-calibrated Bayesian inference tree that was used for dating. Our results confirm that monophyly of Dendrochilum is only supported if Bracisepalum is included in the former. They also suggest that only two subgenera (Dendrochilum, Platyclinis) should be recognized, whereas all other subgenera and sections previously proposed on a morphological basis should be treated as synonyms of subg. Platyclinis. Indeed, mapping of five vegetative and nine floral characters of alleged systematic value, using DELTRAN and ACCTRAN optimization, demonstrates pronounced morphological homoplasy. Molecular time calibration dates the origin of the genus to the Miocene and contradicts the hypothesis that most extant Dendrochilum species did not evolve until the Holocene. Inferred phylogenetic relationships between extant species, in combination with previously identified hotspots of narrow endemism, suggest that species endemism in Dendrochilum is predominantly centric.
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| 8. |
- Petersen, Gitte, et al.
(författare)
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Genes from oxidative phosphorylation complexes II-V and two dual-function subunits of complex I are transcribed in Viscum album despite absence of the entire mitochondrial holo-complex I
- 2022
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Ingår i: Mitochondrion. - : Elsevier BV. - 1567-7249 .- 1872-8278. ; 62, s. 1-12
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Tidskriftsartikel (refereegranskat)abstract
- Mistletoes (Viscum) and close relatives are unique among flowering plants in having a drastically altered electron transport chain. Lack of complex I genes has previously been reported for the mitochondrial genome, and here we report an almost complete absence of nuclear-encoded complex I genes in the transcriptome of Viscum album. Compared to Arabidopsis with approximately 40 nuclear complex I genes, we recover only transcripts of two dual-function genes: gamma carbonic anhydrase and L-galactono-1,4-lactone dehydrogenase. The complement of genes belonging to complexes II–V of the oxidative phosphorylation pathway appears to be in accordance with other vascular plants. Additionally, transcripts encoding alternative NAD(P)H dehydrogenases and alternative oxidase were found. Despite sequence divergence, structural modeling suggests that the encoded proteins are structurally conserved. Complex I loss is a special feature in Viscum species and relatives, as all other parasitic flowering plants investigated to date seem to have a complete OXPHOS system. Hence, Viscum offers a unique system for specifically investigating molecular consequences of complex I absence, such as the role of complex I subunits involved in secondary functions.
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| 9. |
- Petersen, Gitte, et al.
(författare)
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Mitochondria in parasitic plants
- 2020
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Ingår i: Mitochondrion (Amsterdam. Print). - : Elsevier BV. - 1567-7249 .- 1872-8278. ; 52, s. 173-182
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Forskningsöversikt (refereegranskat)abstract
- Plant mitochondrial genomes are renowned for their structural complexity, extreme variation in size and mutation rates, and ability to incorporate foreign DNA. Parasitic flowering plants are no exception, and the close association between parasite and host may even enhance the likelihood of horizontal gene transfer (HGT) between them. Recent studies on mistletoes (Viscum) have revealed that these parasites have lost an exceptional number of mitochondrial genes, including all complex I genes of the respiratory chain. At the same time, an altered respiratory pathway has been demonstrated. Here we review the current understanding of mitochondrial evolution in parasitic plants with a special emphasis on HGT to and from parasite mitochondrial genomes, as well as the uniquely altered mitochondria in Viscum and related plants.
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| 10. |
- Petersen, Gitte, et al.
(författare)
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Mycoheterotrophic Epirixanthes (Polygalaceae) has a typical angiosperm mitogenome but unorthodox plastid genomes
- 2019
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Ingår i: Annals of Botany. - : Oxford University Press (OUP). - 0305-7364 .- 1095-8290. ; 124:5, s. 791-807
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Tidskriftsartikel (refereegranskat)abstract
- Background and Aims Fully mycoheterotrophic plants derive carbon and other nutrients from root-associated fungi and have lost the ability to photosynthesize. While mycoheterotroph plastomes are often degraded compared with green plants, the effect of this unusual symbiosis on mitochondrial genome evolution is unknown. By providing the first complete organelle genome data from Polygalaceae, one of only three eudicot families that developed mycoheterotrophy, we explore how both organellar genomes evolved after loss of photosynthesis.Methods We sequenced and assembled four complete plastid genomes and a mitochondrial genome from species of Polygalaceae, focusing on non-photosynthetic Epirixanthes. We compared these genomes with those of other mycoheterotroph and parasitic plant lineages, and assessed whether organelle genes in Epirixanthes experienced relaxed or intensified selection compared with autotrophic relatives.Key Results Plastomes of two species of Epirixanthes have become substantially degraded compared with that of autotrophic Polygala. Although the lack of photosynthesis is presumably homologous in the genus, the surveyed Epirixanthes species have marked differences in terms of plastome size, structural rearrangements, gene content and substitution rates. Remarkably, both apparently replaced a canonical plastid inverted repeat with large directly repeated sequences. The mitogenome of E. elongata incorporated a considerable number of fossilized plastid genes, by intracellular transfer from an ancestor with a less degraded plastome. Both plastid and mitochondrial genes in E. elongata have increased substitution rates, but the plastid genes of E. pallida do not. Despite this, both species have similar selection patterns operating on plastid housekeeping genes.Conclusions Plastome evolution largely fits with patterns of gene degradation seen in other heterotrophic plants, but includes highly unusual directly duplicated regions. The causes of rate elevation in the sequenced Epirixanthes mitogenome and of rate differences in plastomes of related mycoheterotrophic species are not currently understood.
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