Quantification of protopectinase SE, an endopolygalacturonase with pectin-releasing activity from Geotrichum klebahnii

Pectin releasing activity of protopectinase SE (PPase-SE) from Geotrichum klebahnii (= G. penicillatum = Trichosporon penicillatum) ATCC 42397 was determined using different batches of lemon protopectin as substrate. Results obtained showed a high degree of variability depending on the batch of protopectin used. As PPase-SE also shows polygalacturonase (PGase) activity, a method for the assay of this activity was optimised. The best assay conditions were: substrate (polygalacturonic acid) concentration of 2.0 g 1^–1, reaction time of 10 min and up to 0.17 PGase units per test tube.     

Determining the quality and complexity of next-generation sequencing data without a reference genome

We describe an open-source kPAL package that facilitates an alignment-free assessment of the quality and comparability of sequencing datasets by analyzing k-mer frequencies. We show that kPAL can detect technical artefacts such as high duplication rates, library chimeras, contamination and differences in library preparation protocols. kPAL also successfully captures the complexity and diversity of microbiomes and provides a powerful means to study changes in microbial communities. Together, these features make kPAL an attractive and broadly applicable tool to determine the quality and comparability of sequence libraries even in the absence of a reference sequence. kPAL is freely available at https://github.com/LUMC/kPAL.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-014-0555-3) contains supplementary material, which is available to authorized users.     

Streams dry and ecological uniqueness rise: environmental selection drives aquatic insect patterns in a stream network prone to intermittence

Hydrobiologia - The study of variation of species composition among sites is key to understanding community ecology, but few studies have assessed beta diversity patterns in highly dynamic stream...     

Sesquiterpene lactone from Wunderlichia crulsiana inhibits the respiratory burst of leukocytes triggered by distinct biochemical pathways

The sesquiterpene lactone tubiferin was chemically purified from the brazilian native plant Wunderlichia crulsiana and identified by NMR and GC/MS data. Its ability to inhibit the respiratory burst of peritoneal inflammatory polymorphonuclear leukocytes (PMN) stimulated upon addition of phorbol miristate acetate (PMA), opsonized zymosan (OZ), and N-formyl-methionyl-leucyl-phenylalanine (fMLP) was evaluated. The tubiferin inhibition was more pronounced when PMN were stimulated through the protein kinase C pathway (PMA) compared to the alternative complement pathway (OZ). The inhibition when PMN were triggered by a chemoattractant stimulus (fMLP) was similar to that achieved with OZ-stimulated phagocytes. Tubiferin showed dose-dependent effects on the PMN respiratory burst triggered by the three different substances, and also decreased substantially the carrageenan-induced mice paw edema.     

Measuring cortisol in fish scales to study stress in wild tropical tuna

Environmental Biology of Fishes - Cortisol is recognized as a physiological indicator of stress in fish. However, this hormone is typically measured in plasma samples. In this study, cortisol...     

Xenochironomus ceciliae (Diptera: Chironomidae), a new chironomid species inhabiting freshwater sponges in Brazil

Chironomids living inside freshwater sponges are scarcely known, particularly in the Neotropical region where most of them are to be described. Here, male and female adults, pupa and 4th instar larva of Xenochironomus ceciliae sp. n., living in freshwater sponges of the Paraná River (Brazil) are described. The larval labrum with its several densely setose or combed structures somewhat resembling the filtering structures of simuliid larvae and the predominance of fine detritus in the larval gut contents, may indicate that the larvae of Xenochironomus ceciliae sp. n. are collector-filterers and they might be favored by the aquifer systems of the sponges.     

Monospecies and multispecies probiotic formulations produce different systemic and local immunostimulatory effects in the gilthead seabream (Sparus aurata L.)

The effects of the oral administration of heat-inactivated Lactobacillus delbrüeckii ssp. lactis and Bacillus subtilis, individually or combined, on gilthead seabream immune responses were investigated both systemically and locally in the gut. In a first experiment, seabream (65 g) were fed for 3 weeks different diets supplemented with 1 x 10(7)CFU g(-1)Lactobacillus, 1 x 10(7)CFU g(-1)Bacillus, or 0.5 x 10(7)CFU g(-1)Lactobacillus plus 0.5 x 10(7)CFU g(-1)Bacillus. Controls were fed non-supplemented diet. Six fish per group were sampled at the end of the trial and some humoral and cellular systemic innate immune parameters were evaluated. Feeding the mixture of the two killed bacteria species significantly increased natural complement, serum peroxidase and phagocytic activities compared with controls. In a second experiment, juvenile seabream (13 g) were fed for 3 weeks the same experimental diets and total serum IgM and numbers of gut IgM(+) cells and acidophilic granulocytes were evaluated. All these parameters were significantly higher in the multispecies probiotic group compared to monospecies and control fed groups. The advantages provided by administration of killed probiotic bacteria as well as multispecies versus monospecies formulations are discussed in light of the results obtained and for their possible application in aquacultural practices.     

The role of niche measures in explaining the abundance–distribution relationship in tropical lotic chironomids

In situ measurements of both community metabolism (primary production and respiration) and PAM fluorometry were conducted during emersion on intertidal sediments in the Mont Saint-Michel Bay, in areas where oysters and mussels were cultivated. Results highlighted a low benthic metabolism compared to other intertidal areas previously investigated with the same methods. Comparisons between gross community primary production and relative electron transport rates confirmed this statement. More specifically, primary productivity remained very low all over the year, whereas the associated microalgal biomass was estimated to be high. We suggest that the microphytobenthic community studied was characterized by a self-limitation of its primary productivity by its own biomass, as previously shown in Marennes-Oléron Bay for example. The almost permanent high biomass would represent a limiting factor for micromigration processes within the first millimetres of the sediment. This could be explained by very low resuspension processes occurring in the western part of the bay, enhanced by the occurrence of numerous aquaculture structures that could decrease tidal currents in the benthic boundary layer. Handling editor: N. Desroy     

The fission yeast XMAP215 homolog Dis1p is involved in microtubule bundle organization

Microtubules are essential for a variety of fundamental cellular processes such as organelle positioning and control of cell shape. Schizosaccharomyces pombe is an ideal organism for studying the function and organization of microtubules into bundles in interphase cells. Using light microscopy and electron tomography we analyzed the bundle organization of interphase microtubules in S. pombe. We show that cells lacking ase1p and klp2p still contain microtubule bundles. In addition, we show that ase1p is the major determinant of inter-microtubule spacing in interphase bundles since ase1 deleted cells have an inter-microtubule spacing that differs from that observed in wild-type cells. We then identified dis1p, a XMAP215 homologue, as factor that promotes the stabilization of microtubule bundles. In wild-type cells dis1p partially co-localized with ase1p at regions of microtubule overlap. In cells deleted for ase1 and klp2, dis1p accumulated at the overlap regions of interphase microtubule bundles. In cells lacking all three proteins, both microtubule bundling and inter-microtubule spacing were further reduced, suggesting that Dis1p contributes to interphase microtubule bundling.     

Effectiveness of wood ash containing charcoal as a fertilizer for a forest plantation in a temperate region

Amendment of forest soils with mixed wood ash (MWA) generated in biomass power plants can prevent the depletion of soil nutrients that results from the intensive harvesting of forest plantations. Unlike fly wood ash, MWA contains charcoal and is characterized by a lower release of nutrients, so that it might be useful as a long term source of nutrients and soil organic matter. However, in order to use MWA as a fertilizer in forest systems, its effectiveness as regards supplying P and N must be improved. These aspects were studied in a 4 year-trial carried out in a Pinus radiata plantation. MWA was added alone or with mineral P, and the results were compared with those obtained with a combination of Ca(OH)₂ and mineral P. The application of MWA together with mineral P fertilizer increased the nutrient supply to the trees, as revealed by the changes in nutrient concentrations, lower values of resorption efficiencies and improved tree growth. The results showed that the amounts of Ca, Mg and K supplied by the MWA were suitable for maintenance of soil reserves. However, the presence of charcoal may have decreased the availability of P. The application of the MWA led to lower soil N mineralization rates and mineral N concentrations, which may affect N-limited systems. The use of density-dependent single tree increment models enabled the positive effects on tree growth of fertilization and thinning to be distinguished. For the treatments supplemented with mineral P, multiplicative factors of 1.13 to 1.15 can be applied to obtain post-thinning predictions of 4-year single-tree basal area increments. Although MWA can be used as a long term source of nutrients, charcoal temporarily reduces the availability of P and N.