Fish perform spatial pattern recognition and abstraction by exclusive use of active electrolocation

The field generated by the electric organ of weakly electric fish varies with the electrical properties of nearby objects. Correspondingly, current fluxes in this field differentially stimulate the electroreceptors in the fish's skin. Thus, resistors are to conductors and insulators as gray is to black and white in optics. Additionally, the capacitances of plants and insect larvae contrast with those of water or stones, giving effects comparable to "coloration". Receptors arrayed over a large area of the skin act like a retina upon which the discharge projects "electric images". By further central processing, the fish also discriminate between objects according to their composition, size, or distance, a procedure termed "electrolocation", analogous to echolocation in bats. Here we demonstrate that G. petersii and S. macrurus can also recognize 3D orientations and configurations and extract and generalize spatial features solely with their electrical sense. We presented fish with virtual electrical "objects" formed from electrodes set flush in the inner surface of a Y maze with various patterns of external connectivity. With reward and aversion training, the fish could recognize similar electrode configurations and extract a feature, e.g., a vertical connectivity, present in various novel configurations. Previously, shape recognition has only been shown in electrolocating fish when they are in full mechanical contact with solid objects.     

Identification of six loci in which mutations partially restore peroxisome biogenesis and/or alleviate the metabolic defect of pex2 mutants in podospora

Peroxins (PEX) are proteins required for peroxisome biogenesis. Mutations in PEX genes cause lethal diseases in humans, metabolic defects in yeasts, and developmental disfunctions in plants and filamentous fungi. Here we describe the first large-scale screening for suppressors of a pex mutation. In Podospora anserina, pex2 mutants exhibit a metabolic defect [inability to grow on medium containing oleic acid (OA medium) as sole carbon source] and a developmental defect (inability to differentiate asci in homozygous crosses). Sixty-three mutations able to restore growth of pex2 mutants on OA medium have been analyzed. They fall in six loci (suo1 to suo6) and act as dominant, allele-nonspecific suppressors. Most suo mutations have pleiotropic effects in a pex2(+) background: formation of unripe ascospores (all loci except suo5 and suo6), impaired growth on OA medium (all loci except suo4 and suo6), or sexual defects (suo4). Using immunofluorescence and GFP staining, we show that peroxisome biogenesis is partially restored along with a low level of ascus differentiation in pex2 mutant strains carrying either the suo5 or the suo6 mutations. The data are discussed with respect to beta-oxidation of fatty acids, peroxisome biogenesis, and cell differentiation.     

Screening the Sargasso Sea metagenome for data to investigate genome evolution in Ostreococcus (Prasinophyceae, Chlorophyta)

The Sargasso Sea water shotgun sequencing unveiled an unprecedented glimpse of marine prokaryotic diversity and gene content. The sequence data was gathered from 0.8 microm filtered surface water extracts, and revealed picoeukaryotic (cell size<2 microm) sequences alongside the prokaryotic data. We used the available genome sequence of the picoeukaryote Ostreococcus tauri (Prasinophyceae, Chlorophyta) as a benchmark for the eukaryotic sequence content of the Sargasso Sea metagenome. Sequence data from at least two new Ostreococcus strains were identified and analyzed, and showed a bias towards higher coverage of the AT-rich organellar genomes. The Ostreococcus nuclear sequence data retrieved from the Sargasso metagenome is divided onto 731 scaffolds of average size 3917 bp, and covers 23% of the complete nuclear genome and 14% of the total number of protein coding genes in O. tauri. We used this environmental Ostreococcus sequence data to estimate the level of constraint on intronic and intergenic sequences in this compact genome.     

A skin substitute based on human amniotic membrane

Human amniotic membrane (HAM) has biological properties which are useful for wound healing. HAM is notably one of the therapeutic alternatives for venous leg ulcer care. Indeed, a prospective clinical study has demonstrated that cryopreserved HAM transplantation for leg ulcer is feasible, safe and has beneficial effects: 80 % of the patients had a significant clinical response. Nevertheless, at the end of the 3-month follow-up period, only 20 % of the ulcers were totally closed. The aim of this work was to create and characterize a model of epidermized HAM. The method of HAM desepithelialization was validated by histology, immunohistochemistry and scanning electron microscopy. Then, de-epithelialized HAM was seeded with primary keratinocytes. After 21 days of culture, 15 at the air–liquid interface, the model obtained was analyzed histologically and by immunohistochemistry. The amniotic basement membrane was preserved during enzymatic desepithelialization of HAM. Primary keratinocytes proliferated on HAM: the model obtained showed involucrin expression and had a good basement membrane. As re-epithelialization is an important step for ulcer closure, a model of epidermized HAM could be used to speed up the healing of such wounds.     

Interacting Microbe and Litter Quality Controls on Litter Decomposition: A Modeling Analysis

The decomposition of plant litter in soil is a dynamic process during which substrate chemistry and microbial controls interact. We more clearly quantify these controls with a revised version of the Guild-based Decomposition Model (GDM) in which we used a reverse Michaelis-Menten approach to simulate short-term (112 days) decomposition of roots from four genotypes of Zea mays that differed primarily in lignin chemistry. A co-metabolic relationship between the degradation of lignin and holocellulose (cellulose+hemicellulose) fractions of litter showed that the reduction in decay rate with increasing lignin concentration (LCI) was related to the level of arabinan substitutions in arabinoxylan chains (i.e., arabinan to xylan or A∶X ratio) and the extent to which hemicellulose chains are cross-linked with lignin in plant cell walls. This pattern was consistent between genotypes and during progressive decomposition within each genotype. Moreover, decay rates were controlled by these cross-linkages from the start of decomposition. We also discovered it necessary to divide the Van Soest soluble (labile) fraction of litter C into two pools: one that rapidly decomposed and a second that was more persistent. Simulated microbial production was consistent with recent studies suggesting that more rapidly decomposing materials can generate greater amounts of potentially recalcitrant microbial products despite the rapid loss of litter mass. Sensitivity analyses failed to identify any model parameter that consistently explained a large proportion of model variation, suggesting that feedback controls between litter quality and microbial activity in the reverse Michaelis-Menten approach resulted in stable model behavior. Model extrapolations to an independent set of data, derived from the decomposition of 12 different genotypes of maize roots, averaged within <3% of observed respiration rates and total CO₂ efflux over 112 days.     

A Multilocus Phylogeny of the World Sycoecinae Fig Wasps (Chalcidoidea: Pteromalidae)

The Sycoecinae is one of five chalcid subfamilies of fig wasps that are mostly dependent on Ficus inflorescences for reproduction. Here, we analysed two mitochondrial (COI, Cytb) and four nuclear genes (ITS2, EF-1α, RpL27a, mago nashi) from a worldwide sample of 56 sycoecine species. Various alignment and partitioning strategies were used to test the stability of major clades. All topologies estimated using maximum likelihood and Bayesian methods were similar and well resolved but did not support the existing classification. A high degree of morphological convergence was highlighted and several species appeared best described as species complexes. We therefore proposed a new classification for the subfamily. Our analyses revealed several cases of probable speciation on the same host trees (up to 8 closely related species on one single tree of F. sumatrana), which raises the question of how resource partitioning occurs to avoid competitive exclusion. Comparisons of our results with fig phylogenies showed that, despite sycoecines being internally ovipositing wasps host-switches are common incidents in their evolutionary history. Finally, by studying the evolutionary properties of the markers we used and profiling their phylogenetic informativeness, we predicted their utility for resolving phylogenetic relationships of Chalcidoidea at various taxonomic levels.     

Formation and volatilisation of alkyl-iodidesand -selenides in macrotidal estuaries

The occurrence of alkylated volatile iodide andselenide species was evidenced and investigatedin water, sediments and overlying atmosphere ofthree major European estuaries, such as theGironde (F), the Rhine (NL) and the Scheldt(B/NL), along with the salinity gradient. Foriodine, up to eight volatile species wereobserved as alkyl-iodides in estuarine waters.The major one (ca. 40%) was methyl-iodide(MeI) with average seasonal concentrationsranging from 1 to 100 pmol l^–1. Otherspecies observed were found to correspond toseveral halomethane derivatives and lightalkyl-iodide species. For selenium, dimethylselenide (Me₂Se) was the main compound(ca. 90%) over three methyl-selenidesencountered in estuarine waters. Me₂Seaverage seasonal concentrations were found torange between 0.2 and 100 pmol l^–1 in thewater column. The occurrence of methylatediodides and selenides seems to be mainlyrelated to the algae's biomass turnover asindicated by photosynthetic pigment tracers(i.e. chlorophyll a and phaeopigments) andseasonal variation of surface waterconcentrations. The production and release ofgaseous iodide and selenide compounds may thenresult from natural biological pathways leadingto the methylation of their inorganic form.Finally, significant volatilisation rates wereevaluated leading to average seasonal fluxrates for total volatile iodide and selenidecompounds ranging from 4 to 100 and from 1 to75 nmol m^–2 d^–1, respectively.Estuarine mass balance estimated from MeI andMe₂Se distributions indicates thatvolatilisation to the atmosphere represents aprimary sink for MeI and Me₂Se fromestuarine surface waters.     

Scaling up ideals to freedom: are densities of red knots across western Europe consistent with ideal free distribution?

Local studies have shown that the distribution of red knots Calidris canutus across intertidal mudflats is consistent with the predictions of an ideal distribution, but not a free distribution. Here, we scale up the study of feeding distributions to their entire wintering area in western Europe. Densities of red knots were compared among seven wintering sites in The Netherlands, UK and France, where the available mollusc food stocks were also measured and from where diets were known. We tested between three different distribution models that respectively assumed (i) a uniform distribution of red knots over all areas, (ii) a uniform distribution across all suitable habitat (based on threshold densities of harvestable mollusc prey), and (iii) an ideal and free distribution (IFD) across all suitable habitats. Red knots were not homogeneously distributed across the different European wintering areas, also not when considering suitable habitats only. Their distribution was best explained by the IFD model, suggesting that the birds are exposed to interference and have good knowledge about their resource landscape at the spatial scale of NW Europe, and that the costs of movement between estuaries, at least when averaged over a whole winter, are negligible.