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- Hallenberg, Nils, 1947, et al.
(författare)
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Pseudolagarobasidium (Basidiomycota): on the reinstatement of a genus of parasitic, saprophytic, and endophytic resupinate fungi
- 2008
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Ingår i: Botany. - 1916-2804. ; 86:11, s. 1319-1325
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Tidskriftsartikel (refereegranskat)abstract
- The small resupinate genus Pseudolagarobasidium (Polyporales, Basidiomycota) presently comprises less than five species, all of which were described from tropical to subtropical regions, and two of which are root parasites on leguminous trees. The genus has recently been synonymized with Radulodon on morphological grounds, and the present study evaluates this proposal in a molecular context. Pseudolagarobasidium was found to constitute a well supported, monophyletic group excluding Radulodon and this synonymy is rejected. The ecological range of the genus spans saprotrophy to parasitism, and this study presents evidence that at least one lineage in Pseudolagarobasidium is endophytic in the cacao tree (Theobroma cacao L.). Key words: Polyporales, Radulodon, phylogeny, plant interactions. Résumé: Le Pseudolagarobasidium (Polyporales, Basidiomycota) constitue un genre de petits champignons résupinés qui comporte actuellement cinq espèces, toutes décrites à partir de régions tropicales ou subtropicales, incluant deux espèces parasites des racines d'arbres de la famille des légumineuses. On en a récemment établi la synonymie avec le genre Radulodon sur la base morphologique, mais les auteurs utilisent ici l'approche moléculaire. On constate que le genre Pseudolagarobasidium constitue un groupe monophylétique robuste excluant les Radulodon ce qui conduit au rejet de cette synonymie. L'amplitude écologique du genre va du saprophytisme au parasitisme, et on présente des preuves qu'au moins une lignée est un endophyte du cacaoyer (Theobroma cacao L.). Mots-clés : Polyporales, Radulon, phylogénie, interactions végétales.
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- Bourlat, Sarah, et al.
(författare)
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Feeding ecology of Xenoturbella bocki (phylum Xenoturbellida) revealed by genetic barcoding
- 2008
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Ingår i: Molecular Ecology Resources. - 1755-098X. ; 8, s. 18-22
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Tidskriftsartikel (refereegranskat)abstract
- The benthic marine worm Xenoturbella is frequently contaminated with molluscan DNA, which had earlier caused confusion resulting in a suggested bivalve relationship. In order to find the source of the contaminant, we have used molluscan sequences derived from Xenoturbella and compared them to barcodes obtained from several individuals of the nonmicroscopic molluscs sharing the same environment as Xenoturbella. Using cytochrome oxidase 1, we found the contaminating sequences to be 98% similar to the bivalve Ennucula tenuis. Using the highly variable D1-D2 region of the large ribosomal subunit in Xenoturbella, we found three distinct species of contaminating molluscs, one of which is 99% similar to the bivalve Abra nitida, one of the most abundant bivalves in the Gullmarsfjord where Xenoturbella was found, and another 99% similar to the bivalve Nucula sulcata. These data clearly show that Xenoturbella only contains molluscan DNA originating from bivalves living in the same environment, refuting former hypotheses of a bivalve relationship. In addition, these data suggest that Xenoturbella feeds specifically on bivalve prey from multiple species, possibly in the form of eggs and larvae.
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- Sköld, Helen Nilsson, et al.
(författare)
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Hormonal regulation of female nuptial coloration in a fish.
- 2008
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Ingår i: Hormones and behavior. - : Elsevier BV. - 1095-6867 .- 0018-506X. ; 54:4, s. 549-56
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Tidskriftsartikel (refereegranskat)abstract
- Physiological color change in camouflage and mating is widespread among fishes, but little is known about the regulation of such temporal changes in nuptial coloration and particularly concerning female coloration. To better understand regulation of nuptial coloration we investigated physiological color change in female two-spotted gobies (Gobiusculus flavescens). Females of this species develop an orange belly that acts as an ornament. The orange color is caused by the color of the gonads combined with the chromathophore based pigmentation and transparency of the skin. Often during courtship and female-female competition, a rapid increase in orange coloration, in combination with lighter sides and back that increases skin and body transparency, gives the belly an intense 'glowing' appearance. To understand how this increased orange coloration can be regulated we analysed chromatic and transparency effects of neurohumoral agents on abdominal skin biopsies in vitro. We found prolactin and alpha-melanocyte stimulating hormone (MSH) to increase orange coloration of the skin. By contrast, melatonin and noradrenaline increased skin transparency, but had a negative effect on orange coloration. However, mixtures of melatonin and MSH, or melatonin and prolactin, increased both orange coloration and transparency. This effect mimics the chromatic 'glow' effect that commonly takes place during courtship and intra sexual aggression. Notably, not only epidermal chromatophores but also internal chromatophores lining the peritoneum responded to hormone treatments. There were no chromatic effects of the sex steroids 17beta-estradiol, testosterone or 11-ketotestosterone. We hypothesize that similar modulation of nuptial coloration by multiple hormones may be widespread in nature.
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- Nilsson, R. Henrik, 1976, et al.
(författare)
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A software pipeline for processing and identification of fungal ITS sequences
- 2009
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Ingår i: Source Code for Biology and Medicine. - 1751-0473. ; 4:1
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Tidskriftsartikel (refereegranskat)abstract
- Background Fungi from environmental samples are typically identified to species level through DNA sequencing of the nuclear ribosomal internal transcribed spacer (ITS) region for use in BLAST-based similarity searches in the International Nucleotide Sequence Databases. These searches are time-consuming and regularly require a significant amount of manual intervention and complementary analyses. We here present software - in the form of an identification pipeline for large sets of fungal ITS sequences - developed to automate the BLAST process and several additional analysis steps. The performance of the pipeline was evaluated on a dataset of 350 ITS sequences from fungi growing as epiphytes on building material. Results The pipeline was written in Perl and uses a local installation of NCBI-BLAST for the similarity searches of the query sequences. The variable subregion ITS2 of the ITS region is extracted from the sequences and used for additional searches of higher sensitivity. Multiple alignments of each query sequence and its closest matches are computed, and query sequences sharing at least 50 % of their best matches are clustered to facilitate the evaluation of hypothetically conspecific groups. The pipeline proved to speed up the processing, as well as enhance the resolution, of the evaluation dataset considerably, and the fungi were found to belong chiefly to the Ascomycota, with Penicillium and Aspergillus as the two most common genera. The ITS2 was found to indicate a different taxonomic affiliation than did the complete ITS region for 10 % of the query sequences, though this figure is likely to vary with the taxonomic scope of the query sequences. Conclusions The present software readily assigns large sets of fungal query sequences to their respective best matches in the international sequence databases and places them in a larger biological context. The output is highly structured to be easy to process, although it still needs to be inspected and possibly corrected for the impact of the incomplete and sometimes erroneously annotated fungal entries in these databases. The open source pipeline is available for UNIX-type platforms, and updated releases of the target database are made available biweekly. The pipeline is easily modified to operate on other molecular regions and organism groups.
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- Axäng, Claes, 1977, et al.
(författare)
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Developmental genetics of the C. elegans pharyngeal neurons NSML and NSMR.
- 2008
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Ingår i: BMC Developmental Biology. - 1471-213X. ; 8
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Tidskriftsartikel (refereegranskat)abstract
- Background We are interested in understanding how the twenty neurons of the C. elegans pharynx develop in an intricate yet reproducible way within the narrow confines of the embryonic pharyngeal primordium. To complement an earlier study of the pharyngeal M2 motorneurons, we have now examined the effect of almost forty mutations on the morphology of a bilateral pair of pharyngeal neurosecretory-motor neurons, the NSMs. Results A careful description of the NSM morphology led to the discovery of a third, hitherto unreported process originating from the NSM cell body and that is likely to play a proprioceptive function. We found that the three NSM processes are differently sensitive to mutations. The major dorsal branch was most sensitive to mutations that affect growth cone guidance and function (e.g. unc-6, unc-34, unc-73), while the major sub-ventral branch was more sensitive to mutations that affect components of the extracellular matrix (e.g. sdn-1). Of the tested mutations, only unc-101, which affects an adaptin, caused the loss of the newly described thin minor process. The major processes developed synaptic branches post-embryonically, and these exhibited activity-dependent plasticity. Conclusion By studying the effects of nearly forty different mutations we have learned that the different NSM processes require different genes for their proper guidance and use both growth cone dependent and growth cone independent mechanisms for establishing their proper trajectories. The two major NSM processes develop in a growth cone dependent manner, although the sub-ventral process relies more on substrate adhesion. The minor process also uses growth cones but uniquely develops using a mechanism that depends on the clathrin adaptor molecule UNC-101. Together with the guidance of the M2 neuron, this is the second case of a pharyngeal neuron establishing one of its processes using an unexpected mechanism.
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- Nilsson, R. Henrik, 1976
(författare)
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Fungal taxonomy and systematics in the digital era, with an outlook on the cantharelloid clade (Basidiomycota)
- 2007
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Fungi form a large and ubiquitous group of organisms where species identification and delimitation on morphological grounds often fall short. DNA sequences have proved an invaluable information source for these pursuits and are now routinely used in most mycological laboratories. Newl generated DNA sequences are typically compared with the entries of the large INSD sequence database for inference of taxonomic affiliations and other properties using the sequence similarity search tool BLAST. This thesis highlights some practical difficulties in using BLAST for these purposes it is for example very sensitive to the length of the sequences - and shows that improper use of BLAST appears to have had considerable repercussion on the general level of taxonomic reliability of the fungal sequences in INSD, more than 10% of which may be incorrectly identified to species level. An initiative to build a new DNA sequence database for taxonomically reliable DNA-based identification of mycorrhizal (plant-mutualistic) fungi is described. The database differs from similar initiatives in that its entries are determined to species level by pertinent experts; it allows for integrative sequence annotations, including photos and morphological descriptions; and it employs new, phylogeny-based tools for sequence identification to alleviate the concerns with simplistic, similarity-based tools as arbiters of taxonomic affiliation. That phylogenetic analyses can be beneficial also to classification and nomenclatural projects is shown in the mor enterprise, which is a weekly automaton of Agaricomycetes (mushroom-forming fungi) phylogeny. All fungal sequences from the nuclear ribosomal large subunit gene are assembled on a weekly basis; automated phylogenetic analyses are undertaken; and the resulting phylogenetic trees are displayed and analyzed for changes in clade topology and inclusiveness. The enigmatic cantharelloid clade of the Agaricomycetes is studied using a four-gene phylogenetic approach. While this heterogeneous assembly of mushroom-like, resupinate, clavarioid, and lichen-forming fungi defies any morphological attempt at indicating a close relatedness for its species, the results from the molecular analyses show that there is indeed strong evidence to support that these fungi form a monophyletic group; a restrictive circumscription of the clade to include the genera Botryobasidium, Sistotrema, Multiclavula, Membranomyces, Hydnum, Clavulina, Cantharellus, and Craterellus is advocated. Stichic basidia, and to a lesser extent parenthesome ultrastructure, are found to be characteristic of the clade, and the previously reported divergent rates of evolution for the genera Cantharellus and Craterellus are shown to be limited to the nuclear ribosomal genes. The largely resupinate, and purportedly wood-decaying, genus Sistotrema is demonstrated to hold mycorrhizal lineages, and the molecular evidence to consider the genus polyphyletic is found to be very convincing.
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10. |
- Koch, Kamilla, et al.
(författare)
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Morphological differences in the ovary of Libellulidae (Odonata)
- 2009
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Ingår i: International Journal of Odonatology. - Oxford : Taylor & Francis. - 1388-7890 .- 2159-6719. ; 12:1, s. 147-156
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Tidskriftsartikel (refereegranskat)abstract
- All female Odonata have been assumed to produce oocytes continuously during their mature life span. However, a recent study of ovariole orientation and development led to the suggestion that Libellulidae are divided into two groups of species, one with continuous, the other with stepwise oocyte production. To find more evidence of this division, we compared the size variation and growth within the vitellarium of the ovary, studying oocytes, and follicle cells. We found that morphological characters discriminate between the two ovary types in eight of the 10 investigated species. In both types we found an increase in all measurements from the anterior to the posterior end of the vitellarium. The increase in oocyte width and follicle cell length was significantly higher in species with a continuous oocyte production. We also noted that follicle cells may have more than one nucleus and that their number can vary during vitellogenesis. Our study confirmed the hypotheses that two different ovary types exist in Libellulidae. The two species not fitting into this grouping could be an artefact of small samp le size due to intraspecific phenotypic plasticity, or else there might be more than two ovary groups, or even a continuum. We could not offer an explanation as to how the process of stepwise oocyte production differs from continuous based production on morphological characters.
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