Carbohydrate degradation and methane production during fermentation ofLaminaria saccharina (Laminariales,Phaeophyceae)

Anaerobic digestion of the brown algaLaminaria saccharina (L.) Lamour. harvested in spring and autumn was carried out at controlled laboratory conditions in stirred fermentor systems. Due to the normal seasonal variations, the autumn material had a much higher content of carbohydrates such as mannitol and laminaran. Both batch and semi-continuous feeding conditions were investigated for periods up to 800 h, with inoculum provided from previous kelp fermentations. In batch cultures, the methane yield from the autumn material was doubled compared to that of the spring material. Semi-continuous conditions gave more similar methane yields for both raw materials, 0.22 and 0.27 l CH₄ per g VS for spring and autumn material, respectively. In all experiments, mannitol and laminaran were reduced to less than 5 of the initial values within 24–48 hours after inoculation, whereas 30 of the alginate content was detectable even after 30 days. Viscometry revealed that this material was severely depolymerized, and alginate lyase activity was found to develop rapidly in all cultures. Although mannitol and laminaran were fermented much faster than alginate, the total accumulated methane yields seemed to be determined by the total carbohydrate content of the raw material during extended semi-continuous feeding.(*author for correspondence)     

The contributions of protein disulfide isomerase and its homologues to oxidative protein folding in the yeast endoplasmic reticulum

In vitro, protein disulfide isomerase (Pdi1p) introduces disulfides into proteins (oxidase activity) and provides quality control by catalyzing the rearrangement of incorrect disulfides (isomerase activity). Protein disulfide isomerase (PDI) is an essential protein in Saccharomyces cerevisiae, but the contributions of the catalytic activities of PDI to oxidative protein folding in the endoplasmic reticulum (ER) are unclear. Using variants of Pdi1p with impaired oxidase or isomerase activity, we show that isomerase-deficient mutants of PDI support wild-type growth even in a strain in which all of the PDI homologues of the yeast ER have been deleted. Although the oxidase activity of PDI is sufficient for wild-type growth, pulse-chase experiments monitoring the maturation of carboxypeptidase Y reveal that oxidative folding is greatly compromised in mutants that are defective in isomerase activity. Pdi1p and one or more of its ER homologues (Mpd1p, Mpd2p, Eug1p, Eps1p) are required for efficient carboxypeptidase Y maturation. Consistent with its function as a disulfide isomerase in vivo, the active sites of Pdi1p are partially reduced (32 +/- 8%) in vivo. These results suggest that PDI and its ER homologues contribute both oxidase and isomerase activities to the yeast ER. The isomerase activity of PDI can be compromised without affecting growth and viability, implying that yeast proteins that are essential under laboratory conditions may not require efficient disulfide isomerization.     

Food‐web structure and mercury dynamics in a large subarctic lake following multiple species introductions

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Climate change at northern latitudes: rising atmospheric humidity decreases transpiration, N-uptake and growth rate of hybrid aspen

At northern latitudes a rise in atmospheric humidity and precipitation is predicted as a consequence of global climate change. We studied several growth and functional traits of hybrid aspen (Populus tremula L.×P. tremuloides Michx.) in response to elevated atmospheric humidity (on average 7% over the ambient level) in a free air experimental facility during three growing seasons (2008-2010) in Estonia, which represents northern temperate climate (boreo-nemoral zone). Data were collected from three humidified (H) and three control (C) plots, and analysed using nested linear models. Elevated air humidity significantly reduced height, stem diameter and stem volume increments and transpiration of the trees whereas these effects remained highly significant also after considering the side effects from soil-related confounders within the 2.7 ha study area. Tree leaves were smaller, lighter and had lower leaf mass per area (LMA) in H plots. The magnitude and significance of the humidity treatment effect - inhibition of above-ground growth rate - was more pronounced in larger trees. The lower growth rate in the humidified plots can be partly explained by a decrease in transpiration-driven mass flow of NO(3) (-) in soil, resulting in a significant reduction in the measured uptake of N to foliage in the H plots. The results suggest that the potential growth improvement of fast-growing trees like aspens, due to increasing temperature and atmospheric CO(2) concentration, might be smaller than expected at high latitudes if a rise in atmospheric humidity simultaneously takes place.     

Substrate specificities of bacterial and human AlkB proteins

Methylating agents introduce cytotoxic 1-methyladenine (1-meA) and 3-methylcytosine (3-meC) residues into nucleic acids, and it was recently demonstrated that the Escherichia coli AlkB protein and two human homologues, hABH2 and hABH3, can remove these lesions from DNA by oxidative demethylation. Moreover, AlkB and hABH3 were also found to remove 1-meA and 3-meC from RNA, suggesting that cellular RNA repair can occur. We have here studied the preference of AlkB, hABH2 and hABH3 for single-stranded DNA (ssDNA) or double-stranded DNA (dsDNA), and show that AlkB and hABH3 prefer ssDNA, while hABH2 prefers dsDNA. This was consistently observed with three different oligonucleotide substrates, implying that the specificity for single-stranded versus double-stranded DNA is sequence independent. The dsDNA preference of hABH2 was observed only in the presence of magnesium. The activity of the enzymes on single-stranded RNA (ssRNA), double-stranded RNA (dsRNA) and DNA/RNA hybrids was also investigated, and the results generally confirm the notion that while AlkB and hABH3 tend to prefer single-stranded nucleic acids, hABH2 is more active on double-stranded substrates. These results may contribute to identifying the main substrates of bacterial and human AlkB proteins in vivo.     

Impact of emotion on consciousness: positive stimuli enhance conscious reportability

Emotion and reward have been proposed to be closely linked to conscious experience, but empirical data are lacking. The anterior cingulate cortex (ACC) plays a central role in the hedonic dimension of conscious experience; thus potentially a key region in interactions between emotion and consciousness. Here we tested the impact of emotion on conscious experience, and directly investigated the role of the ACC. We used a masked paradigm that measures conscious reportability in terms of subjective confidence and objective accuracy in identifying the briefly presented stimulus in a forced-choice test. By manipulating the emotional valence (positive, neutral, negative) and the presentation time (16 ms, 32 ms, 80 ms) we measured the impact of these variables on conscious and subliminal (i.e. below threshold) processing. First, we tested normal participants using face and word stimuli. Results showed that participants were more confident and accurate when consciously seeing happy versus sad/neutral faces and words. When stimuli were presented subliminally, we found no effect of emotion. To investigate the neural basis of this impact of emotion, we recorded local field potentials (LFPs) directly in the ACC in a chronic pain patient. Behavioural findings were replicated: the patient was more confident and accurate when (consciously) seeing happy versus sad faces, while no effect was seen in subliminal trials. Mirroring behavioural findings, we found significant differences in the LFPs after around 500 ms (lasting 30 ms) in conscious trials between happy and sad faces, while no effect was found in subliminal trials. We thus demonstrate a striking impact of emotion on conscious experience, with positive emotional stimuli enhancing conscious reportability. In line with previous studies, the data indicate a key role of the ACC, but goes beyond earlier work by providing the first direct evidence of interaction between emotion and conscious experience in the human ACC.     

Base water potential of Picea abies as a characteristic of the soil water status

Variation in base water potential (Ψ_b, a daily maximum level of plant water potential, which is presumed to correspond to the condition of equilibrium between the soil and plant water potentials) was examined in shoots of Norway spruce trees growing in well-drained and waterlogged soils. The influence of soil water content, air temperature, and vapour pressure deficit of the atmosphere on Ψ_b was studied using the pressure chamber technique. Maximum daily water potentials were not always observable before dawn; some were registered up to two hours later. This tendency being characteristic of trees growing under stress (shade, waterlogging) conditions, increased with declining soil water availability. In trees growing in well-drained soil, Ψ_b depended asymptotically on the available soil water storage (R²=0.73), while the values were slightly influenced by vapour pressure deficit of the atmosphere as well. In trees growing in waterlogged soil, Ψ_b was independent of the soil water storage, but sensitive to the vapour pressure deficit.     

A DNA barcode library for Germany′s mayflies,stoneflies and caddisflies (Ephemeroptera,Plecoptera and Trichoptera)

Mayflies, stoneflies and caddisflies (Ephemeroptera, Plecoptera and Trichoptera) are prominent representatives of aquatic macroinvertebrates, commonly used as indicator organisms for water quality and ecosystem assessments. However, unambiguous morphological identification of EPT species, especially their immature life stages, is a challenging, yet fundamental task. A comprehensive DNA barcode library based upon taxonomically well‐curated specimens is needed to overcome the problematic identification. Once available, this library will support the implementation of fast, cost‐efficient and reliable DNA‐based identifications and assessments of ecological status. This study represents a major step towards a DNA barcode reference library as it covers for two‐thirds of Germany's EPT species including 2,613 individuals belonging to 363 identified species. As such, it provides coverage for 38 of 44 families (86%) and practically all major bioindicator species. DNA barcode compliant sequences (≥500 bp) were recovered from 98.74% of the analysed specimens. Whereas most species (325, i.e., 89.53%) were unambiguously assigned to a single Barcode Index Number (BIN) by its COI sequence, 38 species (18 Ephemeroptera, nine Plecoptera and 11 Trichoptera) were assigned to a total of 89 BINs. Most of these additional BINs formed nearest neighbour clusters, reflecting the discrimination of geographical subclades of a currently recognized species. BIN sharing was uncommon, involving only two species pairs of Ephemeroptera. Interestingly, both maximum pairwise and nearest neighbour distances were substantially higher for Ephemeroptera compared to Plecoptera and Trichoptera, possibly indicating older speciation events, stronger positive selection or faster rate of molecular evolution.