Relations Between River Plant Richness in the Portuguese Floodplains and the Widespread Water Knotgrass <Emphasis Type="Italic">(Paspalum Paspalodes</Emphasis>)

We examined the variability of macroinvertebrate assemblage structure, species identities, and functional feeding group composition in relation to stream size, tributary position, and in-stream factors in a boreal watershed in Finland. Our study included three riffle sites in each of three stream sections in each of three stream size classes. Multi-response permutation procedure, indicator value method, and canonical correspondence analysis revealed clear differences in assemblage structure among the stream size classes, with a gradual increase of species richness as the stream size increased. Significant differences in assemblage structure were also found among the tributary river systems. The functional feeding group composition broadly followed the river continuum concept, i.e., headwaters were dominated by shredders, gatherers, or filterers, whereas scrapers increased in relative abundance with stream size. There was, however, considerable variation in the functional feeding group composition both among and within the headwater stream sections. Our findings refer to a strong influence of stream size on macroinvertebrate assemblages, but also factors prevailing at the scale of individual riffles should be considered in biodiversity conservation of lotic ecosystems.     

Recruitment of C-terminal Src kinase by the leukocyte inhibitory receptor CD85j

The CD85j inhibitory receptor (also termed ILT2 or LIR-1) is a type-I transmembrane protein that belongs to the Ig superfamily and is expressed by different leukocyte lineages. The extracellular region of CD85j binds HLA class I molecules and its cytoplasmic domain displays four immunoreceptor tyrosine-based inhibition motifs (ITIM). Upon tyrosine phosphorylation CD85j recruits the SHP-1 tyrosine phosphatase, involved in negative signaling. In order to identify other molecules to which CD85j might interact with in a phosphotyrosine-dependent manner, a cDNA B-cell library was screened in a three-hybrid system in yeast using the CD85j cytoplasmic tail as bait in the presence of the Src-kinase c-fyn420, 531Y-F, 176R-Q mutant. In this system, the C-terminal Src kinase (Csk) was shown to interact with CD85j. Phosphorylation-dependent recruitment of Csk to the CD85j cytoplasmic tail was confirmed in CD85j-transfected mammalian cells by immunoprecipitation and Western blot analysis. Mutational analyses and phospho-peptide mapping suggested that the SH2 domain of Csk may preferentially bind to ITIM Y562 of CD85j; yet, mutation to phenylalanine of Y533, Y614, and Y644 also significantly reduced Csk recruitment by CD85j. Even though CD85j was detected in both anti-SHP1 and CSK immunoprecipitates, these two molecules did not co-precipitate together with CD85j. Our data support the possibility that Csk regulates the function of CD85j.     

Phenylalanine promotes interaction of transmembrane domains via GxxxG motifs

Interactions of transmembrane helices play a crucial role in the folding and oligomerisation of integral membrane proteins. In order to uncover novel sequence motifs mediating these interactions, we randomised one face of a transmembrane helix with a set of non-polar or moderately polar amino acids. Those sequences capable of self-interaction upon integration into bacterial inner membranes were selected by means of the ToxR/POSSYCCAT system. A comparison between low/medium-affinity and high-affinity sequences reveals that high-affinity sequences are strongly enriched in phenylalanine residues that are frequently observed at the − 3 position of GxxxG motifs, thus yielding FxxGxxxG motifs. Mutation of Phe or GxxxG in selected sequences significantly reduces self-interaction of the transmembrane domains without affecting their efficiency of membrane integration. Conversely, grafting FxxGxxxG onto unrelated transmembrane domains strongly enhances their interaction. Further, we find that FxxGxxxG is significantly over-represented in transmembrane domains of bitopic membrane proteins. The same motif contributes to self-interaction of the vesicular stomatitis virus G protein transmembrane domain. We conclude that Phe stabilises membrane-spanning GxxxG motifs. This is one example of how the role of certain side-chains in helix-helix interfaces is modulated by sequence context.     

The extremely halophilic bacterium Salicola marasensis IC10 accumulates the compatible solute betaine

The extremely halophilic bacterium strain IC10 was isolated from a solar saltern on Isla Cristina (southern Spain). Phylogenetic, genotypic and phenotypic data supported the inclusion of this strain in the species Salicola marasensis. An analysis of intracellular organic osmotic solutes showed glycine betaine to be present, contributing to the overall osmotic balance, and this was the only compatible solute accumulated when S. marasensis IC10 was grown over a wide range of external NaCl concentrations (10–25%, w/v).     

An important step forward for the future development of an easy and fast procedure for identifying the most dangerous wine spoilage yeast,Dekkera bruxellensis,in wine environment

Dekkera bruxellensis is the main reason for spoilage in the wine industry. It renders the products unacceptable leading to large economic losses. Fluorescence In Situ Hybridization (FISH) technique has the potential for allowing its specific detection. Nevertheless, some experimental difficulties can be encountered when FISH technique is applied in the wine environment (e.g. matrix and cells’ autofluorescence, fluorophore inadequate selection and probes’ low specificity to the target organisms). An easy and fast in-suspension RNA-FISH procedure was applied for the first time for identifying D. bruxellensis in wine. A previously designed RNA-FISH probe to detect D. bruxellensis (26S D. brux.5.1) was used, and the matrix and cells’ fluorescence interferences, the influence of three fluorophores in FISH performance and the probe specificity were evaluated. The results revealed that to apply RNA-FISH technique in the wine environment, a red-emitting fluorophore should be used. Good probe performance and specificity were achieved with 25% of formamide. The resulting RNA-FISH protocol was applied in wine samples artificially inoculated with D. bruxellensis. This spoilage microorganism was detected in wine at cell densities lower than those associated with phenolic off-flavours. Thus, the RNA-FISH procedure described in this work represents an advancement to facilitate early detection of the most dangerous wine spoilage yeast and, consequently, to reduce the economic losses caused by this yeast to the wine industry.     

Assessment of Real-time PCR Based Methods for Quantification of Pollen-mediated Gene Flow from GM to Conventional Maize in a Field Study

Maize is one of the main crops worldwide and an increasing number of genetically modified (GM) maize varieties are cultivated and commercialized in many countries in parallel to conventional crops. Given the labeling rules established e.g. in the European Union and the necessary coexistence between GM and non-GM crops, it is important to determine the extent of pollen dissemination from transgenic maize to other cultivars under field conditions. The most widely used methods for quantitative detection of GMO are based on real-time PCR, which implies the results are expressed in genome percentages (in contrast to seed or grain percentages). Our objective was to assess the accuracy of real-time PCR based assays to accurately quantify the contents of transgenic grains in non-GM fields in comparison with the real cross-fertilization rate as determined by phenotypical analysis. We performed this study in a region where both GM and conventional maize are normally cultivated and used the predominant transgenic maize Mon810 in combination with a conventional maize variety which displays the characteristic of white grains (therefore allowing cross-pollination quantification as percentage of yellow grains). Our results indicated an excellent correlation between real-time PCR results and number of cross-fertilized grains at Mon810 levels of 0.1–10%. In contrast, Mon810 percentage estimated by weight of grains produced less accurate results. Finally, we present and discuss the pattern of pollen-mediated gene flow from GM to conventional maize in an example case under field conditions.     

Adult:Child Differences in the Intraspecies Uncertainty Factor: A Case Study Using Lead

Adults and children differ in their susceptibility to the toxic effects of lead. Lead was therefore used as a case study to evaluate intraspecies differences by comparing the adult and child minimal Lowest Observed Adverse Effect Level (LOAEL) or the No Observed Adverse Effect Level (NOAEL), allowing an evaluation of the ten-fold intraspecies uncertainty factor (UF). The lead intakes (in µg/kg/d) necessary to achieve target blood lead (PbB) levels reflecting the minimal LOAEL or NOAEL were determined using biokinetic slope factors (BKSFs), which relate lead uptake to PbB levels. The analyses assumed chronic, low-level oral exposure to lead, and the response of a typical adult and child. Child analyses used a target geometric mean (GM) PbB of 4.6?µg/dL (95% of population <10?µg/dL), resulting in lead intakes of 1.9?µg/kg/day (assuming 100% soluble lead) and 4.9?µg/kg/day (assuming 25% soluble lead and 75 % soil lead). Adult analyses assumed intake of 100 % soluble lead, and used target GM PbB levels of 4.2?µg/dL (95% of population <11.1 µg/dL) and 11.4?µg/dL (95% of population <30?µg/dL), resulting in lead intakes of 1.9?µg/kg/day and 5.1?µg/kg/day, respectively. The results indicate that despite the greater vulnerability of young children to the effects of lead as compared to adults, the minimal LOAEL or NOAEL for lead is remarkably similar between children and adults. In this case, the application of a tenfold intraspecies uncertainty factor to adjust the adult minimal LOAEL or NOAEL for a child would be unnecessary, despite the well-established vulnerability of children to lead.     

Afforestation effects on SOC in former cropland: oak and spruce chronosequences resampled after 13 years

Chronosequences are commonly used to assess soil organic carbon (SOC) sequestration after land‐use change, but SOC dynamics predicted by this space‐for‐time substitution approach have rarely been validated by resampling. We conducted a combined chronosequence/resampling study in a former cropland area (Vestskoven) afforested with oak (Quercus robur) and Norway spruce (Picea abies) over the past 40 years. The aims of this study were (i) to compare present and previous chronosequence trends in forest floor and top mineral soil (0–25 cm) C stocks; (ii) to compare chronosequence estimates with current rates of C stock change based on resampling at the stand level; (iii) to estimate SOC changes in the subsoil (25–50 cm); and (iv) to assess the influence of two tree species on SOC dynamics. The two chronosequence trajectories for forest floor C stocks revealed consistently higher rates of C sequestration in spruce than oak. The chronosequence trajectory was validated by resampling and current rates of forest floor C sequestration decreased with stand age. Chronosequence trends in topsoil SOC in 2011 did not differ significantly from those reported in 1998, however, there was a shift from a negative rate (1998: ?0.3 Mg C ha^?1 yr^?1) to no change in 2011. In contrast SOC stocks in the subsoil increased with stand age, however, not significantly (P = 0.1), suggesting different C dynamics in and below the former plough layer. Current rates of C change estimated by repeated sampling decreased with stand age in forest floors but increased in the topsoil. The contrasting temporal change in forest floor and mineral soil C sequestration rates indicate a shift in C source‐sink strength after approximately 40 years. We conclude that afforestation of former cropland within the temperate region may induce soil C loss during the first decades followed by a recovery phase of yet unknown duration.