Protein geometry and placement in the cardiac dyad influence macroscopic properties of calcium-induced calcium release

In cardiac ventricular myocytes, events crucial to excitation-contraction coupling take place in spatially restricted microdomains known as dyads. The movement and dynamics of calcium (Ca2+) ions in the dyad have often been described by assigning continuously valued Ca2+ concentrations to one or more dyadic compartments. However, even at its peak, the estimated number of free Ca2+ ions present in a single dyad is small (approximately 10-100 ions). This in turn suggests that modeling dyadic calcium dynamics using laws of mass action may be inappropriate. In this study, we develop a model of stochastic molecular signaling between L-type Ca2+ channels (LCCs) and ryanodine receptors (RyR2s) that describes: a), known features of dyad geometry, including the space-filling properties of key dyadic proteins; and b), movement of individual Ca2+ ions within the dyad, as driven by electrodiffusion. The model enables investigation of how local Ca2+ signaling is influenced by dyad structure, including the configuration of key proteins within the dyad, the location of Ca2+ binding sites, and membrane surface charges. Using this model, we demonstrate that LCC-RyR2 signaling is influenced by both the stochastic dynamics of Ca2+ ions in the dyad as well as the shape and relative positioning of dyad proteins. Results suggest the hypothesis that the relative placement and shape of the RyR2 proteins helps to "funnel" Ca2+ ions to RyR2 binding sites, thus increasing excitation-contraction coupling gain.     

Neolithic land use in the northern Boreal zone: high-resolution multiproxy analyses from Lake Huhdasjärvi,south-eastern Finland

Two high-resolution pollen and charcoal analyses were constructed from sediments obtained from a small bay in eastern Finland in order to gain information on human activity during the Neolithic Stone Age, 5200–1800 bc. We used measurements of loss on ignition (LOI), magnetic susceptibility and geochemical analyses to describe the sedimentological characteristics. Palaeomagnetic dating and measurements of ¹³⁷Cs-activity were supported by ¹⁴C-datings. The analyses revealed human activity between 4400 and 3200 bc, which is synchronous with archaeological cultures defined through different stages of Comb Ware pottery types and Middle Neolithic pottery types with asbestos as a primary temper. Direct evidence of Hordeum cultivation was dated to 4040–3930 cal bc. According to the pollen data, more significant effort was put into the production of fibres from hemp and lime than the actual cultivation of food.     

Average niche breadths of species in lake macrophyte communities respond to ecological gradients variably in four regions on two continents

Different species’ niche breadths in relation to ecological gradients are infrequently examined within the same study and, moreover, species niche breadths have rarely been averaged to account for variation in entire ecological communities. We investigated how average environmental niche breadths (climate, water quality and climate–water quality niches) in aquatic macrophyte communities are related to ecological gradients (latitude, longitude, altitude, species richness and lake area) among four distinct regions (Finland, Sweden and US states of Minnesota and Wisconsin) on two continents. We found that correlations between the three different measures of average niche breadths and ecological gradients varied considerably among the study regions, with average climate and average water quality niche breadth models often showing opposite trends. However, consistent patterns were also found, such as widening of average climate niche breadths and narrowing of average water quality niche breadths of aquatic macrophytes along increasing latitudinal and altitudinal gradients. This result suggests that macrophyte species are generalists in relation to temperature variations at higher latitudes and altitudes, whereas species in southern, lowland lakes are more specialised. In contrast, aquatic macrophytes growing in more southern nutrient-rich lakes were generalists in relation to water quality, while specialist species are adapted to low-productivity conditions and are found in highland lakes. Our results emphasise that species niche breadths should not be studied using only coarse-scale data of species distributions and corresponding environmental conditions, but that investigations on different kinds of niche breadths (e.g., climate vs. local niches) also require finer resolution data at broad spatial extents.     

Community structure affects trophic ontogeny in a predatory fish

While most studies have focused on the timing and nature of ontogenetic niche shifts, information is scarce about the effects of community structure on trophic ontogeny of top predators. We investigated how community structure affects ontogenetic niche shifts (i.e., relationships between body length, trophic position, and individual dietary specialization) of a predatory fish, brown trout (Salmo trutta). We used stable isotope and stomach content analyses to test how functional characteristics of lake fish community compositions (competition and prey availability) modulate niche shifts in terms of (i) piscivorous behavior, (ii) trophic position, and (iii) individual dietary specialization. Northern Scandinavian freshwater fish communities were used as a study system, including nine subarctic lakes with contrasting fish community configurations: (i) trout‐only systems, (ii) two‐species systems (brown trout and Arctic charr [Salvelinus alpinus] coexisting), and (iii) three‐species systems (brown trout, Arctic charr, and three‐spined sticklebacks [Gasterosteus aculeatus] coexisting). We expected that the presence of profitable small prey (stickleback) and mixed competitor–prey fish species (charr) supports early piscivory and high individual dietary specialization among trout in multispecies communities, whereas minor ontogenetic shifts were expected in trout‐only systems. From logistic regression models, the presence of a suitable prey fish species (stickleback) emerged as the principal variable determining the size at ontogenetic niche shifts. Generalized additive mixed models indicated that fish community structure shaped ontogenetic niche shifts in trout, with the strongest positive relationships between body length, trophic position, and individual dietary specialization being observed in three‐species communities. Our findings revealed that the presence of a small‐sized prey fish species (stickleback) rather than a mixed competitor–prey fish species (charr) was an important factor affecting the ontogenetic niche‐shift processes of trout. The study demonstrates that community structure may modulate the ontogenetic diet trajectories of and individual niche specialization within a top predator.     

Lactobacillus oligofermentans sp. nov., Associated with Spoilage of Modified-Atmosphere-Packaged Poultry Products

Unidentified lactic acid bacterium (LAB) isolates which had mainly been detected in spoiled, marinated, modified atmosphere packaged (MAP) broiler meat products during two previous studies, were identified and analyzed for their phenotypic properties and the capability to produce biogenic amines. To establish the taxonomic position of these isolates, 16S rRNA gene sequence analysis, numerical analysis of ribopatterns, and DNA-DNA hybridization experiments were done. Unexpectedly for a meat-spoilage-associated LAB, the strains utilized glucose very weakly. According to the API 50 CHL test, arabinose and xylose were the only carbohydrates strongly fermented. None of the six strains tested for production of histamine, tyramine, tryptamine, phenylethylamine, putrescine, and cadaverine were able to produce these main meat-associated biogenic amines in vitro. The polyphasic taxonomy approach showed that these strains represent a new Lactobacillus species. The six isolates sequenced for the 16S rRNA encoding genes shared the highest similarity (95.0 to 96.3%) with the sequence of the Lactobacillus durianis type strain. In the phylogenetic tree, these isolates formed a distinct cluster within the Lactobacillus reuteri group, which also includes L. durianis. Numerical analyses of HindIII-EcoRI ribotypes placed all isolates together in a cluster with seven subclusters well separated from the L. reuteri group reference strains. The DNA-DNA hybridization levels between Lactobacillus sp. nov. isolates varied from 67 to 96%, and low hybridization levels (3 to 15%) were obtained with the L. durianis type strain confirming that these isolates belong to the same species different from L. durianis. The name Lactobacillus oligofermentans sp. nov. is proposed, with strain LMG 22743^T (also known as DSM 15707^T or AMKR18^T) as the type strain.     

Integrin trafficking regulated by Rab21 is necessary for cytokinesis

Adherent cells undergo remarkable changes in shape during cell division. However, the functional interplay between cell adhesion turnover and the mitotic machinery is poorly understood. The endo/exocytic trafficking of integrins is regulated by the small GTPase Rab21, which associates with several integrin alpha subunits. Here, we show that targeted trafficking of integrins to and from the cleavage furrow is required for successful cytokinesis, and that this is regulated by Rab21. Rab21 activity, integrin-Rab21 association, and integrin endocytosis are all necessary for normal cytokinesis, which becomes impaired when integrin-mediated adhesion at the cleavage furrow fails. We also describe a chromosomal deletion and loss of Rab21 gene expression in human cancer, which leads to the accumulation of multinucleate cells. Importantly, reintroduction of Rab21 rescued this phenotype. In conclusion, Rab21-regulated integrin trafficking is essential for normal cell division, and its defects may contribute to multinucleation and genomic instability, which are hallmarks of cancer.