Modulation of ephrinB2 leads to increased angiogenesis in ischemic myocardium and endothelial cell proliferation

Eph/ephrin signaling is pivotal in prenatal angiogenesis while its potential role in postnatal angiogenesis largely remains to be explored. Therefore its putative angiogenic and therapeutic effects were explored in endothelium and in myocardial ischemia. In culture of human aortic endothelial cells the fusion protein ephrinB2-Fc induced cell proliferation (p < 0.0005) and in the murine aortic ring model ephrinB2-Fc induced increased sprouting (p < 0.05). Myocardial infarction was induced by ligation of the left anterior descending artery in mouse. During the following 2 weeks mRNA of the receptor/ligand pair EphB4/ephrinB2 was expressed dichotomously (p < 0.05) and other Eph/ephrin pairs were expressed to a lesser degree. Twenty-four hours after intraperitoneal administration of ephrinB2-Fc it was detected in abundance throughout the myocardium along capillaries, showing signs of increased mitosis. After 4 weeks the capillary density was increased 28% in the periinfarcted area (p < 0.05) to a level not different from healthy regions of the heart where no change was observed. These results implicate that EphB4/ephrinB2 is an important signaling pathway in ischemic heart disease and its modulation may induce therapeutic angiogenesis.     

What is the type species of <Emphasis Type="Italic">Phanerochaete</Emphasis> (Polyporales,Basidiomycota)?

Phanerochaete velutina and the closely related species P. alnea, P. alnea subsp. lubrica, and P. rhodella are identified as distinct species based on morphological criteria and molecular analyses. Besides differences in macroscopic and microscopic basidiocarp features, the taxa differ in distribution and ITS sequence. Phanerochaete alnea is widely distributed in Eurasia and North America, whereas P. alnea subsp. lubrica is limited to the Pacific Coast of North America. Phanerochaete velutina is known from Eurasia and Alaska, and P. rhodella is found in North America only. Nomenclatural problems with the name Phanerochaete P. Karst. are discussed, and type specimens for Thelephora alnea Fr., the generic type of Phanerochaete, and Peniophora karstenii Massee are selected. Phanerochaete alnea, P. alnea subsp. lubrica, and P. velutina are described and illustrated. In addition, the synonymy of Phanerochaete robusta and P. aurantiobadia is confirmed.     

galaxieEST: addressing EST identity through automated phylogenetic analysis

Background  

Research involving expressed sequence tags (ESTs) is intricately coupled to the existence of large, well-annotated sequence repositories. Comparatively complete and satisfactory annotated public sequence libraries are, however, available only for a limited range of organisms, rendering the absence of sequences and gene structure information a tangible problem for those working with taxa lacking an EST or genome sequencing project. Paralogous genes belonging to the same gene family but distinguished by derived characteristics are particularly prone to misidentification and erroneous annotation; high but incomplete levels of sequence similarity are typically difficult to interpret and have formed the basis of many unsubstantiated assumptions of orthology.     

Phylogenetic relationships of russuloid basidiomycetes with emphasis on aphyllophoralean taxa

Many homobasidiomycetes are characterized by a combination of gloeocystidia and amyloid basidiospores. They display a great variation in basidioma morphology, including erect and effused forms and gilled and nongilled forms. Earlier studies have shown these taxa to be related, and the group has been named the russuloid clade. Phylogenetic relationships among russuloid basidiomycetes were investigated using sequence data from the nuclear 5.8S, ITS2 and large-subunit rDNA genes. A dataset including 127 ingroup sequences representing 43 genera and ca 120 species were analyzed by maximum-parsimony and neighbor-joining methods. The sampling of taxa had an emphasis on nongilled taxa and two-thirds of the species possessed corticioid basidiomata. Thirteen major well-supported clades were identified within the russuloid clade. All clades except one include corticioid species. Ten characters from basidioma morphology and cultured mycelium were observed and evaluated. Results suggest that gloeocystidia are a synapomorphy for taxa within the russuloid clade while the amyloidity of spores is inconsistent. The ornamentation of spores and type of nuclear behavior seems to be informative characters at genus level. The agaricoid genera Lactarius and Russula are nested in a clade with corticioid species at the basal position. The new combinations Boidinia aculeata, Gloeodontia subasperispora, Gloeocystidiopsis cryptacantha and Megalocystidium wakullum are proposed.     

Sublethal Caspase Activation Promotes Generation of Cardiomyocytes from Embryonic Stem Cells

Generation of new cardiomyocytes is critical for cardiac repair following myocardial injury, but which kind of stimuli is most important for cardiomyocyte regeneration is still unclear. Here we explore if apoptotic stimuli, manifested through caspase activation, influences cardiac progenitor up-regulation and cardiomyocyte differentiation. Using mouse embryonic stem cells as a cellular model, we show that sublethal activation of caspases increases the yield of cardiomyocytes while concurrently promoting the proliferation and differentiation of c-Kit⁺/α-actinin^low cardiac progenitor cells. A broad-spectrum caspase inhibitor blocked these effects. In addition, the caspase inhibitor reversed the mRNA expression of genes expressed in cardiomyocytes and their precursors. Our study demonstrates that sublethal caspase-activation has an important role in cardiomyocyte differentiation and may have significant implications for promoting cardiac regeneration after myocardial injury involving exogenous or endogenous cell sources.     

Fruiting body-guided molecular identification of root-tip mantle mycelia provides strong indications of ectomycorrhizal associations in two species of Sistotrema (Basidiomycota)

Fruiting body guided sequence analysis of mycorrhizal root-tip mycelia is a powerful yet relatively sparsely explored method for species-level identification of mycorrhizal fungi. It is used in this study to indicate mycorrhizal associations in the corticioid (resupinate) genus Sistotrema of the cantharelloid clade through phylogenetic analysis of the ITS and nuLSU rDNA regions of two spatiotemporally co-occurring Sistotrema fruiting bodies and ectomycorrhizal root tips. The genus Sistotrema is confirmed to be polyphyletic, and the mycorrhizal species form a strongly supported monophyletic clade together with the stipitate genus Hydnum. The remaining lineages of Sistotrema may well be saprotrophic, the nutritional mode traditionally attributed to the genus, but the phylogenetic analyses show that they should be excluded from Sistotrema. The cantharelloid clade contains several mycorrhizal genera, but no symbiotic associations have previously been demonstrated for Sistotrema.     

Tidying up international nucleotide sequence databases: ecological, geographical and sequence quality annotation of its sequences of mycorrhizal fungi

Sequence analysis of the ribosomal RNA operon, particularly the internal transcribed spacer (ITS) region, provides a powerful tool for identification of mycorrhizal fungi. The sequence data deposited in the International Nucleotide Sequence Databases (INSD) are, however, unfiltered for quality and are often poorly annotated with metadata. To detect chimeric and low-quality sequences and assign the ectomycorrhizal fungi to phylogenetic lineages, fungal ITS sequences were downloaded from INSD, aligned within family-level groups, and examined through phylogenetic analyses and BLAST searches. By combining the fungal sequence database UNITE and the annotation and search tool PlutoF, we also added metadata from the literature to these accessions. Altogether 35,632 sequences belonged to mycorrhizal fungi or originated from ericoid and orchid mycorrhizal roots. Of these sequences, 677 were considered chimeric and 2,174 of low read quality. Information detailing country of collection, geographical coordinates, interacting taxon and isolation source were supplemented to cover 78.0%, 33.0%, 41.7% and 96.4% of the sequences, respectively. These annotated sequences are publicly available via UNITE (http://unite.ut.ee/) for downstream biogeographic, ecological and taxonomic analyses. In European Nucleotide Archive (ENA; http://www.ebi.ac.uk/ena/), the annotated sequences have a special link-out to UNITE. We intend to expand the data annotation to additional genes and all taxonomic groups and functional guilds of fungi.     

Early first trimester human embryonic cardiac Islet-1 progenitor cells and cardiomyocytes: Immunohistochemical and electrophysiological characterization

The aims of this study were to systematically characterize the distribution, proliferation, and differentiation of Islet-1⁺(Isl1⁺) progenitor cells in the early first trimester human embryonic heart during which period most of the organogenesis takes place. In hearts of gestational week 5 to 10 Isl1⁺cells were identified and mainly clustered in the outflow tract and to a lesser extent in the atria and in the right ventricle. Some of the clusters were also troponin T⁺. Unexpectedly a only few Isl1⁺cells were Ki67⁺while in the ventricles a majority of Isl1^?troponinT⁺cells were Ki67⁺. Cultures derived from the digested embryonic heart developed into spontaneously beating cardiospheres. At harvest cells in these cardiospheres showed frequent expression of troponin T⁺and Nkx2.5⁺, while Isl1 was expressed only in scattered cells. Only a minority of the cultured cells expressed Ki67. The cardiospheres could be frozen, thawed, and recultured to beating cardiospheres. In a multielectrode array system, the beating cardiospheres were responsive to adrenergic stimulation and exhibited rate-dependent action potential duration. In conclusion, the early first trimester human embryonic heart expresses clusters of Isl1⁺cells, some of which differentiate into cardiomyocytes. Unexpectedly, only a minority of the Isl1⁺cells, while a majority of ventricular cardiomyocytes, were proliferating. Spontaneously beating cardiospheres could be derived from the human embryonic heart and these cardiospheres showed functional frequency control.     

Approaching the taxonomic affiliation of unidentified sequences in public databases – an example from the mycorrhizal fungi

Background  

During the last few years, DNA sequence analysis has become one of the primary means of taxonomic identification of species, particularly so for species that are minute or otherwise lack distinct, readily obtainable morphological characters. Although the number of sequences available for comparison in public databases such as GenBank increases exponentially, only a minuscule fraction of all organisms have been sequenced, leaving taxon sampling a momentous problem for sequence-based taxonomic identification. When querying GenBank with a set of unidentified sequences, a considerable proportion typically lack fully identified matches, forming an ever-mounting pile of sequences that the researcher will have to monitor manually in the hope that new, clarifying sequences have been submitted by other researchers. To alleviate these concerns, a project to automatically monitor select unidentified sequences in GenBank for taxonomic progress through repeated local BLAST searches was initiated. Mycorrhizal fungi – a field where species identification often is prohibitively complex – and the much usedITSlocus were chosen as test bed.     

Basidiospore dispersal in the old-growth forest fungus Phlebia centrifuga (Basidiomycetes)

Dispersal of the old‐growth forest hngus Phlebia centrifuga was studied under natural conditions in an old‐growth forest stand in south Sweden using spore trapping with single spore mycelia as bait. Sampling was done not only in the forest but also 500 and 1000 m outside it. Within 100 m of the basidomata source, spore dispersal was very efficient, and it was estimated that 385 spores settled per m² during 24 h. The minimum total number of spores calculated to have fallen within the 100 m circle was 1.21 × 70⁷. The spore fall decreased significantly with distance from the basidiomata. Almost all of the mycelia were dikaryotised at lm distance, compared with less than half at 10 and 100 m. Dikaryotisation was observed in a small but significant number of mycelia at 500 and 1000 m. Mating success between different single spore mycelia differed significantly and we speculate that effective population size may be affected by mating choice in this species. What factors restrict this species to old‐growth forests? In the light of the dikaryotisation observed at 1000 m from the source, it seems unlikely that this fungus is restricted by spore dispersal distance, which implies good prospects for its successful establishment in restored habitats, i.e. first‐generation forests with much coarse woody debris.