Ontwikkeling epifauna, infauna en kreeften (T0, T1, T2) op een ecologisch aantrekkelijke vooroeverbestorting (Schelphoek, Oosterschelde) : monitoring Building for Nature proefvak Schelphoek

Rijkswaterstaat voert vooroeverbestortingen uit op het deel van de dijk dat onder water ligt in de Oosteren Westerschelde. Dit is nodig om de stabiliteit van de dijk en daarmee de waterveiligheid te kunnen blijven garanderen. Eerst werd hierbij alleen op veiligheidsdoelen gelet. Nieuw inzicht is dat je door gebruik van bepaalde materialen ook de natuur kunt faciliteren, dit principe wordt ‘Building for Nature’ genoemd. In 2014 is bij de oostelijke strekdam van locatie Schelphoek in de Oosterschelde een bestorting van zeegrind uitgevoerd. In het oorspronkelijke ontwerp was een basis van staalslakken voorzien, maar bij de uitvoering van het werk is vanwege beperkte beschikbaarheid van staalslakken voor zeegrind gekozen. Op het zeegrind zijn riffen van twee verschillende typen breuksteen gestort: kalksteen en zandsteen. Er is gekozen voor deze aangepaste bestorting om de ecologische meerwaarde van dit ontwerp te kunnen onderzoeken. Doel van dit onderzoek is om de rekolonisatie en ontwikkeling van hardsubstraatsoorten (epifauna) en soorten die leven in het sediment (infauna), en het voorkomen van kreeften op de nieuwe bestorting van kalksteen, zandsteen en zeegrind bij de locatie Schelphoek gedurende twee jaar na bestorting te volgen (T1-2015 en T2-2016) en te vergelijken met de situatie voor bestorten (T0-situatie in 2014)

Learning biophysically-motivated parameters for alpha helix prediction

<p>Abstract</p> <p>Background</p> <p>Our goal is to develop a state-of-the-art protein secondary structure predictor, with an intuitive and biophysically-motivated energy model. We treat structure prediction as an optimization problem, using parameterizable cost functions representing biological "pseudo-energies". Machine learning methods are applied to estimate the values of the parameters to correctly predict known protein structures.</p> <p>Results</p> <p>Focusing on the prediction of alpha helices in proteins, we show that a model with 302 parameters can achieve a Q_{<it>α </it>}value of 77.6% and an SOV_{<it>α </it>}value of 73.4%. Such performance numbers are among the best for techniques that do not rely on external databases (such as multiple sequence alignments). Further, it is easier to extract biological significance from a model with so few parameters.</p> <p>Conclusion</p> <p>The method presented shows promise for the prediction of protein secondary structure. Biophysically-motivated elementary free-energies can be learned using SVM techniques to construct an energy cost function whose predictive performance rivals state-of-the-art. This method is general and can be extended beyond the all-alpha case described here.</p

Haliclona (Halichoclona) vansoesti n. sp., a new chalinid sponge species (Porifera, Demospongiae, Haplosclerida) from the Caribbean

A new sponge species, Haliclona (Halichoclona) vansoesti n.sp., belonging to the family Chalinidae of the order Haplosclerida, is described from Curaçao and other Caribbean localities. The subgenus name Halichoclona de Laubenfels is for the first time applied to a species of the “fistulosa” group ( “Pellina” of authors), one of eight species groups which came out as monophyletic groups during an earlier phylogenetic analysis of the genus Haliclona. Justification for devoting a separate paper to a single species follows from recent findings of interesting secondary metabolites produced by this sponge. Chemistry and cell biology research necessitates to have a proper name for the species available

Ontwikkeling epifauna, infauna en kreeften (T0, T1, T2) op een ecologisch aantrekkelijke vooroeverbestorting (Schelphoek, Oosterschelde) : monitoring Building for Nature proefvak Schelphoek

Rijkswaterstaat voert vooroeverbestortingen uit op het deel van de dijk dat onder water ligt in de Oosteren Westerschelde. Dit is nodig om de stabiliteit van de dijk en daarmee de waterveiligheid te kunnen blijven garanderen. Eerst werd hierbij alleen op veiligheidsdoelen gelet. Nieuw inzicht is dat je door gebruik van bepaalde materialen ook de natuur kunt faciliteren, dit principe wordt ‘Building for Nature’ genoemd. In 2014 is bij de oostelijke strekdam van locatie Schelphoek in de Oosterschelde een bestorting van zeegrind uitgevoerd. In het oorspronkelijke ontwerp was een basis van staalslakken voorzien, maar bij de uitvoering van het werk is vanwege beperkte beschikbaarheid van staalslakken voor zeegrind gekozen. Op het zeegrind zijn riffen van twee verschillende typen breuksteen gestort: kalksteen en zandsteen. Er is gekozen voor deze aangepaste bestorting om de ecologische meerwaarde van dit ontwerp te kunnen onderzoeken. Doel van dit onderzoek is om de rekolonisatie en ontwikkeling van hardsubstraatsoorten (epifauna) en soorten die leven in het sediment (infauna), en het voorkomen van kreeften op de nieuwe bestorting van kalksteen, zandsteen en zeegrind bij de locatie Schelphoek gedurende twee jaar na bestorting te volgen (T1-2015 en T2-2016) en te vergelijken met de situatie voor bestorten (T0-situatie in 2014)

Cellular location of (2R, 3R, 7Z)-2-aminotetradec-7-ene-1, 3-diol, a potent antimicrobial metabolite produced by the Caribbean sponge Haliclona vansoesti

SCOPUS: ar.jinfo:eu-repo/semantics/publishe

New sesquiterpene/quinones from two sponges of the genus Hyrtios

SCOPUS: ar.jinfo:eu-repo/semantics/publishe

Localization and ecological significance of oroidin and sceptrin in the Caribbean sponge Agelas conifera

The Caribbean sponge Agelas conifera was found to produce a mixture of previously described bromopyrrole alkaloids of which oroidin (1) and sceptrin (2) were predominant. This sponge harboured large populations of heterotrophic bacteria but no photosynthetic symbionts (cyanobacteria). However, 1 and 2 were not associated with the bacteria but with the sponge cells as shown by their distribution in enriched cell fractions obtained by differential centrifugation and Ficoll density gradients. Spherulous cells, found in great abundance in the sponge ectosome, were assumed to be involved in the production of 1 and 2. The target compounds were detected, although in small amounts, in short-term cultures of sponge cells, validating the possibility of a continuous cell culture source. Laboratory assays showed that organic sponge extracts affected the behaviour of the coral Madracis mirabilis in causing closure and retraction of the polyps at concentrations of the combined compounds 1 and 2 (1:3.3) as low as 0.7 mg/l (0.0125% of the concentration in whole sponges). At higher concentrations (1.4 mg/l) no recovery of the polyps occurred. The extracts, at almost natural concentrations of 1 and 2, deterred feeding by the predatory reef fish Stegastis partitus, supporting other reported research. In field experiments, wounding induced a sharp increase of 1 and 2 in the sponge tissues but prolonged predator exclusion by caging and forced confrontation with coral neighbours did not yield measurable changes in 1 and 2 concentrations. All sponges were found to release measurable amounts of bromopyrrole alkaloids in seawater conditioned for 30 min. Crude and fractionated sponge extracts and pure sceptrin (2) were active against bacteria, yeast and filamentous fungi. Taken together, these results support a role of oroidin (1) and sceptrin (2) in defence mechanisms against predators and possibly against space competitors and invaing and fouling organisms. © 2003 Elsevier Science Ltd. All rights reserved.SCOPUS: ar.jinfo:eu-repo/semantics/publishe

Sponge invaders in Dutch coastal waters

Continuous monitoring by scientists and volunteers of the Biological Working Group of the Dutch SubAqua Union and the 'Anemoon' Foundation over the past four years, yielded a surprising six new records of sponges for Dutch coastal waters. Oscarella lobularis, Celtodoryx girardae, Suberites virgultosus, Haliclona (Haliclona) simulans, Halisarca aff. dujardini, and a species identified as Leucosolenia somesii were unknown from Dutch coastal waters before 2000. The latter is a giant calcareous sponge, seemingly belonging to the common Leucosolenia variabilis, but here assumed to be an invader as well, as it has spicular characters well outside the variation found in the majority of Dutch L. variabilis specimens. It is likely a member of a 'forgotten' species, L. somesii. Habit photographs, SEM images of the spicules, and for O. lobularis and H. aff. dujardini, photographs of histological sections are provided to substantiate these new records. With the exception of C. girardae, most of the species resemble previously described widespread north-east Atlantic species, occurring in the area to the south and west of the Netherlands, so it is assumed pending future genetic research that at least several of the invaders comprise range extensions related to rising winter temperatures. Possibly, recent shellfish imports may be an additional causal agent. We also report the occurrence of unprecedented spicular deviations observed in three sponge species commonly occurring in Dutch waters, Halichondria (Halichondria) panicea, Hymeniacidon perlevis and Haliclona (Soestella) xena, which grew in small inland water bodies. Possibly, the limited space in these inland waters with possible stress factors for sponges such as reduced water exchange, and deviating chemistry, have caused the sponges to form stunted growth in spicules varying from rhabds with rounded endings to silica spheroids. We provide an updated list of sponges found in Dutch waters and a list of suspected or proven invaders of Dutch waters