Clonal organization of populations of Asarum europaeum and Maianthemum bifolium in contrasting woodland habitats

Populations of two rhizomatous species, Asarum europaeum (asarabacca) and Maianthemum bifolium (May lily), were examined in two, and four forest habitats respectively, in the Roztocze National Park (south-eastern Poland). May lily populations were studied in habitats: the Carpathian beechwood, upland mixed fir forest, subboreal moist mixed coniferous forest and bog-alder forest. Asarabacca was studied in two habitats: beechwood and Scots pine community (an 80-year-old plantation). In both the species studied intra- and inter-populational differences of the size of genets in terms of above- and below-ground parts of individuals as well as the biomass and area occupied were observed. In May lily populations the greatest mean number of shoots per genet was found in the fir forest (11.62±3.29), a value almost twice as great as that in the moist coniferous forest and nearly three times greater than in the bog-alder forest. Total rhizome length was also the greatest in the fir forest (351.9±98.7 cm) followed by moist coniferous forest, beechwood and alder forest habitats. In all populations of May lily a greater part of total dry weight biomass is in below-ground organs. The greatest biomass value of a genet was found in the fir forest (4.275 g), the smallest in the bog-alder forest (0.110 g). All populations differed significantly in terms of leaf area, leaf length (with the exception of fir forest and beechwood habitats where the values were the greatest), and leaf width (excluding moist coniferous and bog-alder forests which had the smallest values). In the case of asarabacca, both the mean number of ramets per genet (3.36±0.45 vs. 2.49±0.20) and total rhizome length (40.3±6.4 cm vs. 21.1±1.8 cm) were greater in the beechwood habitat than in the pine community. In the first population genets had 3–5 times greater the total biomass of those from the pine community. Only genets of the latter had proportionately more dry weight biomass in above-ground parts. It seems to be correlated with greater rhizome dieback and disintegration of genets into smaller units. Both populations were significantly different in terms of all examined parameters of leaves. Genets of both the species studied were found to have their own structure of developmental phases that often differed for shoots and rhizomes.     

Innate immunity orchestrates the mobilization and homing of hematopoietic stem/progenitor cells by engaging purinergic signaling—an update

Purinergic Signalling - Bone marrow (BM) as an active hematopoietic organ is highly sensitive to changes in body microenvironments and responds to external physical stimuli from the surrounding...     

The Deubiquitinating Enzyme AMSH1 and the ESCRT-III Subunit VPS2.1 Are Required for Autophagic Degradation in Arabidopsis

In eukaryotes, posttranslational modification by ubiquitin regulates the activity and stability of many proteins and thus influences a variety of developmental processes as well as environmental responses. Ubiquitination also plays a critical role in intracellular trafficking by serving as a signal for endocytosis. We have previously shown that the Arabidopsis thaliana ASSOCIATED MOLECULE WITH THE SH3 DOMAIN OF STAM3 (AMSH3) is a deubiquitinating enzyme (DUB) that interacts with ENDOSOMAL COMPLEX REQUIRED FOR TRANSPORT-III (ESCRT-III) and is essential for intracellular transport and vacuole biogenesis. However, physiological functions of AMSH3 in the context of its ESCRT-III interaction are not well understood due to the severe seedling lethal phenotype of its null mutant. In this article, we show that Arabidopsis AMSH1, an AMSH3-related DUB, interacts with the ESCRT-III subunit VACUOLAR PROTEIN SORTING2.1 (VPS2.1) and that impairment of both AMSH1 and VPS2.1 causes early senescence and hypersensitivity to artificial carbon starvation in the dark similar to previously reported autophagy mutants. Consistent with this, both mutants accumulate autophagosome markers and accumulate less autophagic bodies in the vacuole. Taken together, our results demonstrate that AMSH1 and the ESCRT-III-subunit VPS2.1 are important for autophagic degradation and autophagy-mediated physiological processes.     

Rook Spring Seed Dispersal in the Agricultural Landscape – Frugivory, Granivory or Accidental Transport?

Seed dispersal seems to be extremely important in agrocoenoses where suitable habitats (patches) are surrounded by an unfavourable environment (matrix). The role of the rook Corvus frugilegus, an omnivorous bird, in seed dispersal was studied in the agricultural landscape of Eastern Poland. We analyzed 739 pellets produced by regurgitation, which were collected under breeding colonies in April, May and June. Our goal was to i) assess the structure of the seed pool in pellets; ii) evaluate the temporal variation in the pellet seed pool on two different time scales; iii) compare the species composition of seeds in pellets and vegetation under the rook nests. Seeds were present in 18 % of pellets; 571 seeds were found, half of them belonging to dry-fruited species, without any obvious adaptations to endozoochory. These seeds could be an additional source of food, or they could have been accidentally swallowed during foraging for other food items. Taking into consideration the abundance of the rook population, we assessed the mean number of seeds transferred by one bird to be from 4 seeds per month in April and up to 160 seeds in June. The most important factor responsible for qualitative and quantitative structure of seed pool in pellets is the time when pellets were regurgitated. The type and availability of food determines the number and species structure of dispersed seeds. The comparison of the species structure of the seed pool in pellets and of the herb layer under the breeding colonies showed that the rook could effectively disperse seeds of weeds, meadow and ruderal species, that could germinate under the dense canopy of trees at the studied sites.     

RNA secondary structure, an important bioinformatics tool to enhance multiple sequence alignment: a case study (Sordariomycetes, Fungi)

In a case study of fungi of the class Sordariomycetes, we evaluated the effect of multiple sequence alignment (MSA) on the reliability of the phylogenetic trees, topology and confidence of major phylogenetic clades. We compared two main approaches for constructing MSA based on (1) the knowledge of the secondary (2D) structure of ribosomal RNA (rRNA) genes, and (2) automatic construction of MSA by four alignment programs characterized by different algorithms and evaluation methods, CLUSTAL, MAFFT, MUSCLE, and SAM. In the primary fungal sequences of the two functional rRNA genes, the nuclear small and large ribosomal subunits (18 S and 28 S), we identified four and six, respectively, highly variable regions, which correspond mainly to hairpin loops in the 2D structure. These loops are often positioned in expansion segments, which are missing or are not completely developed in the Archaeal and Eubacterial kingdoms. Proper sorting of these sites was a key for constructing an accurate MSA. We utilized DNA sequences from 28 S as an example for one-gene analysis. Five different MSAs were created and analyzed with maximum parsimony and maximum likelihood methods. The phylogenies inferred from the alignments improved with 2D structure with identified homologous segments, and those constructed using the MAFFT alignment program, with all highly variable regions included, provided the most reliable phylograms with higher bootstrap support for the majority of clades. We illustrate and provide examples demonstrating that re-evaluating ambiguous positions in the consensus sequences using 2D structure and covariance is a promising means in order to improve the quality and reliability of sequence alignments.