Restoring natural seepage conditions on former agricultural grasslands does not lead to reduction of organic matter decomposition and soil nutrient dynamics

In the central part of the Netherlands, wetland restoration projects involve the rewetting of former agricultural land, where low water levels were artificially maintained (polders). Many of these projects do not result in the expected reduction of nitrogen and phosphorus availability and subsequent re-establishment of a diverse wetland vegetation. The aim of the present study was to investigate which mechanisms are responsible for this lack of success. Thereto, we studied the effect of rewetting of former agricultural grasslands on acidified peat soil (pH = 3.5) on organic matter decomposition, nitrogen cycling and phosphorus availability in the soil for three seasons. To provide an explanation for the observed effects, we simultaneously studied a set of potentially controlling abiotic soil conditions that were expected to change after rewetting. It was found that rewetting of these grasslands with natural, unpolluted seepage water did not affect nitrogen cycling, but raised decomposition rates and almost doubled phosphorus availability. The main cause of these effects is a raise of soil pH to about 7 due to the hydrochemical composition of the soil pore water after rewetting, which reflects groundwater with high amounts of buffering ions. This effect overruled any reduction in process rates by the lowered soil redox potential. The counterintuitive finding of eutrophication after rewetting with natural and unpolluted water is considered to represent a new form of internal eutrophication, triggered by the restoration of natural site conditions of former agricultural land on acid peat soil.     

Carbohydrate metabolism is perturbed in peroxisome-deficient hepatocytes due to mitochondrial dysfunction, AMP-activated protein kinase (AMPK) activation, and peroxisome proliferator-activated receptor γ coactivator 1α (PGC-1α) suppression

Hepatic peroxisomes are essential for lipid conversions that include the formation of mature conjugated bile acids, the degradation of branched chain fatty acids, and the synthesis of docosahexaenoic acid. Through unresolved mechanisms, deletion of functional peroxisomes from mouse hepatocytes (L-Pex5(-/-) mice) causes severe structural and functional abnormalities at the inner mitochondrial membrane. We now demonstrate that the peroxisomal and mitochondrial anomalies trigger energy deficits, as shown by increased AMP/ATP and decreased NAD(+)/NADH ratios. This causes suppression of gluconeogenesis and glycogen synthesis and up-regulation of glycolysis. As a consequence, L-Pex5(-/-) mice combust more carbohydrates resulting in lower body weights despite increased food intake. The perturbation of carbohydrate metabolism does not require a long term adaptation to the absence of functional peroxisomes as similar metabolic changes were also rapidly induced by acute elimination of Pex5 via adenoviral administration of Cre. Despite its marked activation, peroxisome proliferator-activated receptor α (PPARα) was not causally involved in these metabolic perturbations, because all abnormalities still manifested when peroxisomes were eliminated in a peroxisome proliferator-activated receptor α null background. Instead, AMP-activated kinase activation was responsible for the down-regulation of glycogen synthesis and induction of glycolysis. Remarkably, PGC-1α was suppressed despite AMP-activated kinase activation, a paradigm not previously reported, and they jointly contributed to impaired gluconeogenesis. In conclusion, lack of functional peroxisomes from hepatocytes results in marked disturbances of carbohydrate homeostasis, which are consistent with adaptations to an energy deficit. Because this is primarily due to impaired mitochondrial ATP production, these L-Pex5-deficient livers can also be considered as a model for secondary mitochondrial hepatopathies.     

Electron microscopic study of DNA complexes with proteins from the Archaebacterium Sulfolobus acidocaldarius

DNA-protein complexes formed in vitro with isolated DNA-binding proteins from the thermoacidophilic archaebacterium Sulfolobus acidocaldarius were analyzed by electron microscopy. Two of the proteins (10a and 10b) formed specific structures after incubation with DNA. Protein 10a, at low protein concentrations, showed individual small spots on the DNA and at high concentrations evenly covered doublestranded DNA. Protein 10b showed three different types of regular structures: one with single-stranded and two with double-stranded DNA. Using double-stranded DNA, 10b first bound cooperatively to two strands forming long, plait-like structures only slightly shorter than respective free DNA. The complex consists of two right-handed, interwound fibers, with a helical pitch of 26 nm and a diameter of ~10-11 nm. At higher protein concentration than needed to package all DNA into the complex with two double-stranded DNAs, the two DNAs were separated again and a new structure was formed evenly covering only one DNA strand. Both structures showed no significant contraction of the length of the DNA covered in the complex. Nucleoprotein formed with single-stranded ΦX174 DNA had a diameter of ~11 nm and could form circles with a contour length of 0.5 μm.     

Distribution of "classic" virulence factors among Salmonella spp

Whether an infection with Salmonella spp. leads to a disease largely depends on the virulence of the strain and the constitution of the host. The virulence of the strain is determined by so-called virulence factors. Whereas a number of virulence factors of Salmonella have been identified only recently, others have been studied for decades. These latter virulence factors i.e., virulence-plasmids, toxins, fimbriae and flagella are therefore referred to as "classic" virulence factors. Here we present an overview on the distribution of (genes coding for) these virulence factors among Salmonella spp. The pathogenicity islands of Salmonella are also reviewed, all be it briefly, since they contain a major part of the virulence genes.     

Characterization of the protonation and hydrogen bonding state of the histidine residues in IIAmtl, a domain of the phosphoenolpyruvate-dependent mannitol-specific transport protein.

The A domain of the mannitol-specific EII, IIAmtl, was subcloned and proven to be functional in the isolated form (Van Weeghel et al., 1991). It contains a histidine phosphorylation site, the first of two phosphorylation sites in the parent protein. In this paper, we describe the characterization of the three histidine residues in IIAmtl with respect to their protonation and hydrogen bonding state, using 1H[15N] heteronuclear NMR techniques and protein selectively enriched with [delta 1,epsilon 2-15N]histidine. The active site residue has a low pKa (less than 5.8) and shows no hydrogen bond interactions. The proton in the neutral ring is located at the N epsilon 2 position, which also proved to be the site of phosphorylation. The phosphorylation raises the pKa of the active site histidine considerably but does not change the hydrogen bond situation. The other two histidine residues, one of which is probably located on the surface of the protein, were also characterized. Both show hydrogen bond interactions in the unphosphorylated protein, but these are disturbed by the phosphorylation process. These observations, combined with small changes in pKa and titration behavior, indicate that the IIAmtl changes its conformation upon phosphorylation.     

Identification of RFLP markers closely linked to the bolting gene B and their significance for the study of the annual habit in beets (Beta vulgaris L.)

The annual habit in beet is due to complete or partial absence of the vernalization requirement and can cause severe problems in the beet crop. The absolute vernalization requirement in beet is controlled by a major geneB (bolting), known to be linked to the geneR (red hypocotyl color), in linkage group I. Segregation for theB andR genes was studied in several beet progenies. Penetrance of the annual habit inBb genotypes was affected by both environmental and genetic factors. The precise location in linkage group I of the major geneB was found by restriction fragment length polymorphism (RFLP) analysis in a back-cross progeny exhibiting partial penetrance of the annual habit. The linkage value betweenB andR was in good accordance with previous estimations. Use of the closest RFLP marker (pKP591: 3.8 recombination units) allowed us to estimate the penetrance of the annual habit in this back-cross as 0.62. Evidence of pseudo-compatibility was found in the wild coastal beet (Beta vulgaris sspmaritima) used as the mother plant of the back-cross: the selfing rate was estimated as 7%.     

Evidence of genetic change in the flowering phenology of sea beets along a latitudinal cline within two decades

Sea beets grown from seeds collected in 1989 and 2009 along the coasts of France and adjacent regions were compared for flowering date under controlled conditions. Seeds from both collection years were sown simultaneously and cultivated under the same glasshouse conditions. Date of flowering onset and year of first flowering were recorded. There was an overall northward shift in flowering time of about 0.35° latitude (i.e. 39 km) over the 20‐year period. The southern portion of the latitudinal gradient – that is, from 44.7°N to 47.28°N – flowered significantly later by a mean of 1.78 days, equivalent to a 43.2‐km northward shift of phenotypes. In the northern latitudes between 48.6°N and 52°N, flowering date was significantly earlier by a mean of 4.04 days, corresponding to a mean northward shift of 104.9 km, and this shift was apparently due to a diminished requirement of exposure to cold temperatures (i.e. vernalization), for which we found direct and indirect evidence. As all plants were grown from seed under identical conditions, we conclude that genetic changes occurred in the sensitivity to environmental cues that mediate the onset of flowering in both the northern and the southern latitudes of the gradient. Microevolution and gene flow may have contributed to this change. There was no significant change in the frequency of plants that flowered without vernalization. The lack of vernalization requirement may be associated with environmental instability rather than with climate conditions.