A vestige of Earth's oldest ophiolite

A sheeted-dike complex within the approximately 3.8-billion-year-old Isua supracrustal belt (ISB) in southwest Greenland provides the oldest evidence of oceanic crustal accretion by spreading. The geochemistry of the dikes and associated pillow lavas demonstrates an intraoceanic island arc and mid-ocean ridge-like setting, and their oxygen isotopes suggest a hydrothermal ocean-floor-type metamorphism. The pillows and dikes are associated with gabbroic and ultramafic rocks that together make up an ophiolitic association: the Paleoarchean Isua ophiolite complex. These sheeted dikes offer evidence for remnants of oceanic crust formed by sea-floor spreading of the earliest intact rocks on Earth.     

GOAnnotator: linking protein GO annotations to evidence text

Background

Annotation of proteins with gene ontology (GO) terms is ongoing work and a complex task. Manual GO annotation is precise and precious, but it is time-consuming. Therefore, instead of curated annotations most of the proteins come with uncurated annotations, which have been generated automatically. Text-mining systems that use literature for automatic annotation have been proposed but they do not satisfy the high quality expectations of curators.

Results

In this paper we describe an approach that links uncurated annotations to text extracted from literature. The selection of the text is based on the similarity of the text to the term from the uncurated annotation. Besides substantiating the uncurated annotations, the extracted texts also lead to novel annotations. In addition, the approach uses the GO hierarchy to achieve high precision. Our approach is integrated into GOAnnotator, a tool that assists the curation process for GO annotation of UniProt proteins.

Conclusion

The GO curators assessed GOAnnotator with a set of 66 distinct UniProt/SwissProt proteins with uncurated annotations. GOAnnotator provided correct evidence text at 93% precision. This high precision results from using the GO hierarchy to only select GO terms similar to GO terms from uncurated annotations in GOA. Our approach is the first one to achieve high precision, which is crucial for the efficient support of GO curators. GOAnnotator was implemented as a web tool that is freely available at http://xldb.di.fc.ul.pt/rebil/tools/goa/.

     

Tagging of juvenile lobsters (Homarus gammarus (L.)) with visible implant fluorescent elastomer tags

Visible implant fluorescent elastomer (VIFE) tags were implanted beneath the epidermal layer within the abdomen of 25 juvenile lobsters. After three molts the tag retention was 100% and the total survival 92%. The results suggest that VIFE tags could be an effective tool when assessing the feasibility of enhancing natural lobster stocks.     

Photoperiod in recirculation aquaculture systems and timing of seawater transfer affect seawater growth performance of Atlantic salmon (Salmo salar)

Production of Atlantic salmon smolts in recirculation aquaculture systems (RAS) is growing, and novel production protocols using continuous light in RAS are being implemented in the industry. In the present study, Atlantic Salmon parr were exposed to either a traditional protocol (short-day winter signal [12:12 L:D] for 6 weeks) or to continuous light. Both photoperiods were applied in freshwater (FW) and brackish water RAS. Salmon from all treatments were transferred to seawater pens at 200 and 600 g and grown until slaughter size. A control group was smoltified with a 6-week short-day winter signal and kept in FW until sea transfer at 100 g. Continuous light gave a higher growth rate in RAS but reduced feed intake and growth and increased feed conversion ratio during the first 8 weeks in seawater. However, at slaughter, fish exposed to continuous light was bigger than fish given a winter signal because of the higher growth rate in RAS. Slaughter weight was lowest in fish transferred to sea at 600 g, despite having the highest day-degree sum during their life span. The best performing group was the control group transferred at 100 g. All treatments handled transfer to seawater and survival and maturation were not affected by the treatments in RAS. The immune status was examined with a multigene expression assay on BioMark HD platform from parr stage to 5–7 months after seawater transfer. Overall, there was no significant effect of photoperiod or salinity on the expression of the selected immune genes. In sum, the results from this study indicate that using continuous light in RAS may have negative effects on performance shortly after transfer in fish transferred to sea at 200 g, whereas at 600 g, all treatments had reduced growth after transfer irrespective of treatment in RAS.     

Decreased concentration of hemoglobin,accumulation of lipid oxidation products and unchanged skeletal muscle in Atlantic salmon (Salmo salar) fed low dietary vitamin E

Atlantic salmon (Salmo salar) fry, initial weight 0.16 g, were fed a semipurified diet with 0, 15, 30, 60 or 120 mg dl-α-tocopheryl acetate/kg. After 24 weeks, the first two of these groups were extinct, and the fish receiving 30 mg/kg were clearly vitamin E deficient. Vitamin E deficient fish had low hemoglobin levels, characterized by a combination of reduced cellular hemoglobin concentration, red cell volume and red cell number, and an increased number and fraction of immature red blood cells. The hemoglobin concentration decreased over the decreasing range of experimental dl-ga-tocopheryl acetate levels. Therefore, even if 60 mg dl-α-tocopheryl acetate/kg gave good survival, this level was clearly physiologically suboptimal. Ceroid accumulated in the liver of fish fed 30 mg vitamin E/kg, and autofluorescent inclusions were found in the red blood cells of fish fed 30 and 60 mg vitamin E/kg. Degeneration of skeletal muscle was not observed in the present study.     

The Potential Effects of Social Interactions on Reproductive Efficiency of Stallions

The reproductive efficiency of stabled domestic stallions is often lower than what could be expected from observations in feral herds. In the wild, stallions typically live with mares in harem bands, with other stallions in bachelor bands, or occasionally in mixed-sex transitional bands. We, therefore, argue that permanent contact with mares may increase reproductive efficiency of stallions suffering from low libido and/or fertility. We also provide a summary of our present knowledge of natural conditions, management, and husbandry of domestic stallions, and of intra- and intersexual behavioral interactions in horses.     

Highly characteristic and individual specific telomere length patterns in cattle

A combined primed in situ labelling (PRINS)/4',6-diamino-2-phenylindole (DAPI)/propidium iodide (PI)-fluorescence-banding method was used to characterise telomeres, identify their specific chromosomes and visualise neighbouring heterochromatin in 25 artificial insemination (AI) bulls. A highly heterogeneous telomere length pattern was found in cattle. Each bull possessed his own characteristic, specific telomere length pattern.     

Soil organic C as affected by silvicultural and exploitative interventions in Nothofagus pumilio forests of the Chilean Patagonia

This study evaluates the effect of silvicultural and exploitative interventions on soil organic carbon (SOC) in Chilean Lenga (Nothofagus pumilio (Poepp et Endl.) Krasser) forests in south Patagonia. We analyzed SOC and the organic soil horizons in five stands at different stages of development: intact native forest (NI); a 3-year-old shelterwood stand (S3); an 8-year-old shelterwood stand (S8); a 14-year-old stand that was initially treated with shelterwood and subsequently final cut (10 years after the first intervention) (S14), and a 25-year-old stand subject to a exploitative intervention (E25). The SOC under the forest stands, down to a depth of 50 cm (including the Oi horizon), was 60, 55, 71, 85, and 67 Mg ha⁻¹ for the NI, S3, S8, S14, and E25 forest stands, respectively. A significant decrease in SOC occurred 3 years after an intensive shelterwood cut (S3), particularly in the first 5 cm of the mineral soil. Slightly higher carbon contents were observed in the upper horizons of the mineral soil in both the S8 and S14 stands. Consequently, the applied shelterwood system appears to generate only short-term losses of SOC in the Lenga forest. Soil organic carbon increased over the medium term but decreased to the level observed in intact native forests over the long term. Regeneration, which influences stand microclimate (a factor in SOC storage) and provides an important source of organic soil material, was identified as one of the most important factors influencing SOC.     

Linking fluorescence induction curve and biomass in herbicide screening

A suite of dose-response bioassays with white mustard (Sinapis alba L) and sugar beet (Beta vulgaris L) in the greenhouse and with three herbicides was used to analyse how the fluorescence induction curves (Kautsky curves) were affected by the herbicides. Bentazone, a photosystem II (PSII) inhibitor, completely blocked the normal fluorescence decay after the P-step. In contrast, fluorescence decay was still obvious for flurochloridone, a PDS inhibitor, and glyphosate, an EPSP inhibitor, which indicated that PSII inhibition was incomplete. From the numerous parameters that can be derived from OJIP-steps of the Kautsky curve the relative changes at the J-step [Fvj = (Fm - Fj)/Fm] was selected to be a common response parameter for the herbicides and yielded consistent dose-response relationships. Four hours after treatment, the response Fvj on the doses of bentazone and flurochloridone could be measured. For glyphosate, the changes of the Kautsky curve could similarly be detected 4 h after treatment in sugar beet, but only after 24 hs in S alba. The best prediction of biomass in relation to Fvj was found for bentazone. The experiments were conducted between May and August 2002 and showed that the ambient temperature and solar radiation in the greenhouse could affect dose-response relationships. If the Kautsky curve parameters should be used to predict the outcome of herbicide screening experiments in the greenhouse, where ambient radiation and temperature can only partly be controlled, it is imperative that the chosen fluorescence parameters can be used to predict accurately the resulting biomass used in classical bioassays.