PepeSearch: Semantic Data for the Masses

With the emergence of the Web of Data, there is a need of tools for searching and exploring the growing amount of semantic data. Unfortunately, such tools are scarce and typically require knowledge of SPARQL/RDF. We propose here PepeSearch, a portable tool for searching semantic datasets devised for mainstream users. PepeSearch offers a multi-class search form automatically constructed from a SPARQL endpoint. We have tested PepeSearch with 15 participants searching a Linked Open Data version of the Norwegian Register of Business Enterprises for non-trivial challenges. Retrieval performance was encouragingly high and usability ratings were also very positive, thus suggesting that PepeSearch is effective for searching semantic datasets by mainstream users. We also assessed its portability by configuring PepeSearch to query other SPARQL endpoints.     

Nonsynonymous variants in mt-Nd2, mt-Nd4, and mt-Nd5 are linked to effects on oxidative phosphorylation and insulin sensitivity in rat conplastic strains

Common inbred strains of the laboratory rat can be divided into four different mitochondrial DNA haplotype groups represented by the SHR, BN, LEW, and F344 strains. In the current study, we investigated the metabolic and hemodynamic effects of the SHR vs. LEW mitochondrial genomes by comparing the SHR to a new SHR conplastic strain, SHR-mt(LEW); these strains are genetically identical except for their mitochondrial genomes. Complete mitochondrial DNA (mtDNA) sequence analysis comparing the SHR and LEW strains revealed gene variants encoding amino acid substitutions limited to a single mitochondrial enzyme complex, NADH dehydrogenase (complex I), affecting subunits 2, 4, and 5. Two of the variants in the mt-Nd4 subunit gene are located close to variants known to be associated with exercise intolerance and diabetes mellitus in humans. No variants were found in tRNA or rRNA genes. These variants in mt-Nd2, mt-Nd4, and mt-Nd5 in the SHR-mt(LEW) conplastic strain were linked to reductions in oxidative and nonoxidative glucose metabolism in skeletal muscle. In addition, SHR-mt(LEW) conplastic rats showed increased serum nonesterified fatty acid levels and resistance to insulin stimulated incorporation of glucose into adipose tissue lipids. These results provide evidence that inherited variation in mitochondrial genes encoding respiratory chain complex I subunits, in the absence of variation in the nuclear genome and other confounding factors, can influence glucose and lipid metabolism when expressed on the nuclear genetic background of the SHR strain.     

Interplay of Ca2+ and cAMP signaling in the insulin-secreting MIN6 beta-cell line

Ca2+ and cAMP are important second messengers that regulate multiple cellular processes. Although previous studies have suggested direct interactions between Ca2+ and cAMP signaling pathways, the underlying mechanisms remain unresolved. In particular, direct evidence for Ca2+-regulated cAMP production in living cells is incomplete. Genetically encoded fluorescence resonance energy transfer-based biosensors have made possible real-time imaging of spatial and temporal gradients of intracellular cAMP concentration in single living cells. Here, we used confocal microscopy, fluorescence resonance energy transfer, and insulin-secreting MIN6 cells expressing Epac1-camps, a biosynthetic unimolecular cAMP indicator, to better understand the role of intracellular Ca2+ in cAMP production. We report that depolarization with high external K+, tolbutamide, or glucose caused a rapid increase in cAMP that was dependent on extracellular Ca2+ and inhibited by nitrendipine, a Ca2+ channel blocker, or 2',5'-dideoxyadenosine, a P-site antagonist of transmembrane adenylate cyclases. Stimulation of MIN6 cells with glucose in the presence of tetraethylammonium chloride generated concomitant Ca2+ and cAMP oscillations that were abolished in the absence of extracellular Ca2+ and blocked by 2',5'-dideoxyadenosine or 3-isobutyl-1-methylxanthine, an inhibitor of phosphodiesterase. Simultaneous measurements of Ca2+ and cAMP concentrations with Fura-2 and Epac1-camps, respectively, revealed a close temporal and causal interrelationship between the increases in cytoplasmic Ca2+ and cAMP levels following membrane depolarization. These findings indicate highly coordinated interplay between Ca2+ and cAMP signaling in electrically excitable endocrine cells and suggest that Ca2+-dependent cAMP oscillations are derived from an increase in adenylate cyclase activity and periodic activation and inactivation of cAMP-hydrolyzing phosphodiesterase.     

Deep sympatric mitochondrial divergence without reproductive isolation in the common redstart Phoenicurus phoenicurus

Mitochondrial DNA usually shows low sequence variation within and high sequence divergence among species, which makes it a useful marker for phylogenetic inference and DNA barcoding. A previous study on the common redstart (Phoenicurus phoenicurus) revealed two very different mtDNA haplogroups (5% K2P distance). This divergence is comparable to that among many sister species; however, both haplogroups coexist and interbreed in Europe today. Herein, we describe the phylogeographic pattern of these lineages and test hypotheses for how such high diversity in mtDNA has evolved. We found no evidence for mitochondrial pseudogenes confirming that both haplotypes are of mitochondrial origin. When testing for possible reproductive barriers, we found no evidence for lineage‐specific assortative mating and no difference in sperm morphology, indicating that they are not examples of cryptic species, nor likely to reflect the early stages of speciation. A gene tree based on a short fragment of cytochrome c oxidase subunit 1 from the common redstart and 10 other Phoenicurus species, showed no introgression from any of the extant congenerics. However, introgression from an extinct congeneric cannot be excluded. Sequences from two nuclear introns did not show a similar differentiation into two distinct groups. Mismatch distributions indicated that the lineages have undergone similar demographic changes. Taken together, these results confirm that deeply divergent mitochondrial lineages can coexist in biological species. Sympatric mtDNA divergences are relatively rare in birds, but the fact that they occur argues against the use of threshold mtDNA divergences in species delineation.     

Metabolism of gibberellin A19 is under photoperiodic control in Populus, Salix and Betula, but not in daylength-insensitive Populus overexpressing phytochrome A

Application experiments have suggested that short‐day‐induced cessation of elongation growth in trees is caused by photoperiodic regulation of the conversion of gibberellin GA₁₉ to GA₂₀. In the present study we examined further the photoperiodic control of GA metabolism in trees with focus on the conversion of GA₁₉ in Salix pentandra, hybrid aspen (Populus tremula × tremuloides) and silver birch (Betula pendula) using [17,17‐²H₂]‐GA₁₉ or unlabelled GAs in application studies. GA₂₀ and GA₁ were able to restore growth also in hybrid aspen and silver birch under short days (SD), whereas GA₁₉ had no or only a very small activity. Contrary to hybrid aspen and S. pentandra, the activity of GA₂₀ in silver birch was significantly lower than that of GA₁. Gas chromatography‐mass spectrometry (GC‐MS) analysis revealed a smaller turnover of [²H₂]‐GA₁₉ in SD than in long days (LD) in hybrid aspen. No such difference in turnover of [²H₂]‐GA₁₉ was observed in photoperiod‐insensitive hybrid aspen overexpressing PHYA. Application of unlabelled GAs to seedlings of S. pentandra, hybrid aspen and silver birch under SD followed by quantification of metabolites by GC‐MS analysis, showed that applied GA₁₉ was not readily converted to GA₂₀ and GA₁. Although the sensitivity to GAs is also known to decrease under SD, the present data are in favour of a photoperiodic regulation of the metabolism of GA₁₉in vivo in the woody species S. pentandra, hybrid aspen and silver birch. The data might also suggest that silver birch differs from S. pentandra and hybrid aspen by exhibiting a possible photoperiodic control also of the conversion of GA₂₀ to GA₁.     

Chemotaxonomic discrimination among the fungal genera Tolypocladium, beauveria and Paecilomyces

Fungi of the genera Beauveria and Paecilomyces were found to produce cyclotetradepsipeptides, beauverolides. Production of beauverolides was not detected at the genus Tolypocladium. Analysis of beauverolides therefore provides a very simple chemotaxonomic test which seems to be suitable for fast discrimination between the genera Beauveria vs Tolypocladium and complementing morphological examination. A GC-MS study of β-hydroxy acid distribution in the beauverolide hydrolyzates revealed that all strains prdouce γ-methyl-β-hydroxy acids only. Their occurrence thus cannot be used as a taxonomic marker of different species within the genera Beauveria and Paecilomyces.     

Population characteristics predict responses in moose body mass to temporal variation in the environment

1. A general problem in population ecology is to predict under which conditions stochastic variation in the environment has the stronger effect on ecological processes. By analysing temporal variation in a fitness-related trait, body mass, in 21 Norwegian moose Alces alces (L.) populations, we examined whether the influence of temporal variation in different environmental variables were related to different parameters that were assumed to reflect important characteristics of the fundamental niche space of the moose. 2. Body mass during autumn was positively related to early access to fresh vegetation in spring, and to variables reflecting slow phenological development (low June temperature, a long spring with a slow plant progression during spring). In contrast, variables related to food quantity and winter conditions had only a minor influence on temporal variation in body mass. 3. The magnitude of the effects of environmental variation on body mass was larger in populations with small mean body mass or living at higher densities than in populations with large-sized individuals or living at lower densities. 4. These results indicate that the strongest influence of environmental stochasticity on moose body mass occurs towards the borders of the fundamental niche space, and suggests that populations living under good environmental conditions are partly buffered against fluctuations in environmental conditions.