Belowground mutualists and the invasive ability of Acacia longifolia in coastal dunes of Portugal

The ability to form symbiotic associations with soil microorganisms and the consequences for plant growth were studied for three woody legumes grown in five different soils of a Portuguese coastal dune system. Seedlings of the invasive Acacia longifolia and the natives Ulex europaeus and Cytisus grandiflorus were planted in the five soil types in which at least one of these species appear in the studied coastal dune system. We found significant differences between the three woody legumes in the number of nodules produced, final plant biomass and shoot ¹⁵N content. The number of nodules produced by A. longifolia was more than five times higher than the number of nodules produced by the native legumes. The obtained ¹⁵N values suggest that both A. longifolia and U. europaeus incorporated more biologically-fixed nitrogen than C. grandiflorus which is also the species with the smallest distribution. Finally, differences were also found between the three species in the allocation of biomass in the different studied soils. Acacia longifolia displayed a lower phenotypic plasticity than the two native legumes which resulted in a greater allocation to aboveground biomass in the soils with lower nutrient content. We conclude that the invasive success of A. longifolia in the studied coastal sand dune system is correlated to its capacity to nodulate profusely and to use the biologically-fixed nitrogen to enhance aboveground growth in soils with low N content.     

NO3 −/NO2 − assimilation in halophilic archaea: physiological analysis, nasA and nasD expressions

The haloarchaeon Haloferax mediterranei is able to assimilate nitrate or nitrite using the assimilatory nitrate pathway. An assimilatory nitrate reductase (Nas) and an assimilatory nitrite reductase (NiR) catalyze the first and second reactions, respectively. The genes involved in this process are transcribed as two messengers, one polycistronic (nasABC; nasA encodes Nas) and one monocistronic (nasD; codes for NiR). Here we report the Hfx mediterranei growth as well as the Nas and NiR activities in presence of high nitrate, nitrite and salt concentrations, using different approaches such as physiological experiments and enzymatic activities assays. The nasA and nasD expression profiles are also analysed by real-time quantitative PCR. The results presented reveal that the assimilatory nitrate/nitrite pathway in Hfx mediterranei takes place even if the salt concentration is higher than those usually present in the environments where this microorganism inhabits. This haloarchaeon grows in presence of 2 M nitrate or 50 mM nitrite, which are the highest nitrate and nitrite concentrations described from a prokaryotic microorganism. Therefore, it could be attractive for bioremediation applications in sewage plants where high salt, nitrate and nitrite concentrations are detected in wastewaters and brines.     

The Not-so-Dark Ages: ecology for human growth in medieval and early twentieth century Portugal as inferred from skeletal growth profiles

This study attempts to address the issue of relative living standards in Portuguese medieval and early 20th century periods. Since the growth of children provides a good measure of environmental quality for the overall population, the skeletal growth profiles of medieval Leiria and early 20th century Lisbon were compared. Results show that growth in femur length of medieval children did not differ significantly from that of early 20th century children, but after puberty medieval adolescents seem to have recovered, as they have significantly longer femora as adults. This is suggestive of greater potential for catch-up growth in medieval adolescents. We suggest that this results from distinct child labor practices, which impact differentially on the growth of Leiria and Lisbon adolescents. Work for medieval children and adolescents were related to family activities, and care and attention were provided by family members. Conversely, in early 20th century Lisbon children were more often sent to factories at around 12 years of age as an extra source of family income, where they were exploited for their labor. Since medieval and early 20th century children were stunted at an early age, greater potential for catch-up growth in medieval adolescents results from exhausting work being added to modern adolescent's burdens of disease and poor diet, when they entered the labor market. Although early 20th century Lisbon did not differ in overall unfavorable living conditions from medieval Leiria, after puberty different child labor practices may have placed modern adolescents at greater risk of undernutrition and poor growth.     

Effects of vessel compliance on flow pattern in porcine epicardial right coronary arterial tree

The compliance of the vessel wall affects hemodynamic parameters which may alter the permeability of the vessel wall. Based on experimental measurements, the present study established a finite element (FE) model in the proximal elastic vessel segments of epicardial right coronary arterial (RCA) tree obtained from computed tomography. The motion of elastic vessel wall was measured by an impedance catheter and the inlet boundary condition was measured by an ultrasound flow probe. The Galerkin FE method was used to solve the Navier–Stokes and Continuity equations, where the convective term in the Navier–Stokes equation was changed in the arbitrary Lagrangian–Eulerian (ALE) framework to incorporate the motion due to vessel compliance. Various hemodynamic parameters (e.g., wall shear stress—WSS, WSS spatial gradient—WSSG, oscillatory shear index—OSI) were analyzed in the model. The motion due to vessel compliance affects the time-averaged WSSG more strongly than WSS at bifurcations. The decrease of WSSG at flow divider in elastic bifurcations, as compared to rigid bifurcations, implies that the vessel compliance decreases the permeability of vessel wall and may be atheroprotective. The model can be used to predict coronary flow pattern in subject-specific anatomy as determined by noninvasive imaging.     

The Membrane-binding Motif of the Chloroplast Signal Recognition Particle Receptor (cpFtsY) Regulates GTPase Activity

The chloroplast signal recognition particle (cpSRP) and its receptor (cpFtsY) function in thylakoid biogenesis to target integral membrane proteins to thylakoids. Unlike cytosolic SRP receptors in eukaryotes, cpFtsY partitions between thylakoid membranes and the soluble stroma. Based on sequence alignments, a membrane-binding motif identified in Escherichia coli FtsY appears to be conserved in cpFtsY, yet whether the proposed motif is responsible for the membrane-binding function of cpFtsY has yet to be shown experimentally. Our studies show that a small N-terminal region in cpFtsY stabilizes a membrane interaction critical to cpFtsY function in cpSRP-dependent protein targeting. This membrane-binding motif is both necessary and sufficient to direct cpFtsY and fused passenger proteins to thylakoids. Our results demonstrate that the cpFtsY membrane-binding motif may be functionally replaced by the corresponding region from E. coli, confirming that the membrane-binding motif is conserved among organellar and prokaryotic homologs. Furthermore, the capacity of cpFtsY for lipid binding correlates with liposome-induced GTP hydrolysis stimulation. Mutations that debilitate the membrane-binding motif in cpFtsY result in higher rates of GTP hydrolysis, suggesting that negative regulation is provided by the intact membrane-binding region in the absence of a bilayer. Furthermore, NMR and CD structural studies of the N-terminal region and the analogous region in the E. coli SRP receptor revealed a conformational change in secondary structure that takes place upon lipid binding. These studies suggest that the cpFtsY membrane-binding motif plays a critical role in the intramolecular communication that regulates cpSRP receptor functions at the membrane.Proper compartmentalization of proteins relies on the ability of protein localization pathways to transport proteins efficiently from their sites of synthesis to their sites of function. The signal recognition particle (SRP)² and its receptor function in every kingdom of life to target proteins to the endoplasmic reticulum (eukaryotes), cytoplasmic membrane (prokaryotes), and thylakoid membrane (chloroplasts) (1). The targeting function of SRP relies on a conserved 54-kDa SRP subunit (SRP54; Ffh in Escherichia coli and cpSRP54 in chloroplasts) as well as a conserved SRP receptor (SRα; FtsY in E. coli and cpFtsY in chloroplasts). For cytosolic SRPs (SRP54 and Ffh), interactions with a substrate signal sequence and an SRP RNA moiety are prerequisite for interaction with the SRP receptor (SRα and FtsY) (2). GTP binding and hydrolysis by both SRP54 and SRα coordinate substrate release from SRP to the translocon and release of SRP from SRα. In chloroplasts, cpFtsY functions along with a unique SRP (cpSRP) to post-translationally target nuclear encoded proteins to thylakoid membranes (3). Light-harvesting chlorophyll a/b-binding proteins (LHCPs) imported into the chloroplast stroma are bound by cpSRP to form a soluble targeting complex, which directs the LHCP substrate to the thylakoid membrane translocon Alb3 (Albino3) in a GTP- and cpFtsY-dependent manner (14, 36). Although many general steps of SRP protein targeting seem largely conserved across evolutionary boundaries, the nature and dynamics of the receptor appear to have diverged.In eukaryotic systems, SRα is peripherally bound to the membrane through association with the integral membrane subunit SRβ. In contrast, no chloroplast or bacterial homolog of SRβ has been identified. cpFtsY and E. coli FtsY (EcFtsY) are found partitioned between the membrane and the stroma or cytosol, respectively. The membrane-binding capacity of EcFtsY serves to stimulate GTPase activity and appears critical in that only membrane-associated EcFtsY supports the release of nascent chains from SRP to the translocon (4, 5). However, the partitioning activity is not strictly required because EcFtsY tethered to the membrane is functional in vivo (37). Given the conserved nature of partitioning among bacterial and chloroplast SRP receptors, partitioning may play an, as of yet, unidentified role in protein targeting by SRP. Nevertheless, differences in lipid composition between bacterial and thylakoid membranes make it interesting to speculate that there are mechanistic differences in membrane partitioning.Like many prokaryotic FtsY homologs (e.g. Thermus aquaticus), cpFtsY lacks the N-terminal acidic domain (A domain) implicated in EcFtsY membrane binding (6). Although the highly conserved FtsY GTPase domain (NG domain) of EcFtsY (EcFtsY_NG) fails to support protein targeting, the addition of the last A domain residue, Phe-196 of a conserved double-Phe motif (EcFtsY_NG+1), restores protein targeting in vivo (7). In vitro studies also show that EcFtsY_NG+1 retains the capacity to bind membranes and support integration of SRP-dependent substrates, although at significantly reduced levels compared with full-length EcFtsY (8). A resolved structure of EcFtsY_NG+1 suggests that the amphipathic nature of the region containing Phe-196 plays a critical role in membrane association (9). Furthermore, it has been demonstrated that liposomes stimulate GTP hydrolysis rates of SRP with EcFtsY_NG+1, but not with EcFtsY_NG, supporting the idea that the A domain in its entirety is not strictly required.For cpFtsY, the necessity and functional role(s) of partitioning between a thylakoid-bound and a soluble phase, as well as the role of N-terminal residues in these functions, remain unknown. In addition, both the conformational state of membrane-bound cpFtsY and EcFtsY and the mechanism responsible for controlling membrane partitioning and altered GTPase activity remain unclear. Because of the gain of function exhibited by EcFtsY_NG+1 and the conserved nature of the surrounding motif (9), it seems likely that this conserved region is necessary to support membrane binding and corresponding functions not only in EcFtsY but also in FtsY homologs.To examine the functional role of the N-terminal region of cpFtsY, we have utilized deletion and point mutants in assays that reconstitute cpFtsY activities, including the cpSRP-dependent integration of LHCP. Together, our data indicate that the conserved lipid-binding motif identified in bacterial FtsY homologs is present in cpFtsY and is both necessary and sufficient for thylakoid binding and critical for LHCP targeting.     

A chip‐based amide‐HILIC LC/MS platform for glycosaminoglycan glycomics profiling

A key challenge to investigations into the functional roles of glycosaminoglycans (GAGs) in biological systems is the difficulty in achieving sensitive, stable, and reproducible mass spectrometric analysis. GAGs are linear carbohydrates with domains that vary in the extent of sulfation, acetylation, and uronic acid epimerization. It is of particular importance to determine spatial and temporal variations of GAG domain structures in biological tissues. In order to analyze GAGs from tissue, it is useful to couple MS with an on‐line separation system. The purposes of the separation system are both to remove components that inhibit GAG ionization and to enable the analysis of very complex mixtures. This contribution presents amide–silica hydrophilic interaction chromatography (HILIC) in a chip‐based format for LC/MS of heparin, heparan sulfate (HS) GAGs. The chip interface yields robust performance in the negative ion mode that is essential for GAGs and other acidic glycan classes while the built‐in trapping cartridge reduces background from the biological tissue matrix. The HILIC chromatographic separation is based on a combination of the glycan chain lengths and the numbers of hydrophobic acetate (Ac) groups and acidic sulfate groups. In summary, chip based amide‐HILIC LC/MS is an enabling technology for GAG glycomics profiling.     

Sex differences in obesity rates in poor countries: Evidence from South Africa

Globally, men and women face markedly different risks of obesity. In all but of handful of (primarily Western European) countries, obesity is much more prevalent among women than men. We examine several potential explanations for this phenomenon. We analyze differences between men and women in reports and effects of potential underlying causes of obesity—childhood and adult poverty, depression, and attitudes about obesity. We evaluate the evidence for each explanation using data collected in an urban African township in the Cape Town metropolitan area. Three factors explain the greater obesity rates we find among women. Women who were nutritionally deprived as children are significantly more likely to be obese as adults, while men who were deprived as children face no greater risk. In addition, women of higher adult socioeconomic status are significantly more likely to be obese, which is not true for men. These two factors - childhood circumstances and adult SES - can fully explain the difference in obesity rates between men and women that we find in our sample. More speculatively, in South Africa, women's perceptions of an ‘ideal’ female body are larger than men's perceptions of the ‘ideal’ male body, and individuals with larger ‘ideal’ body images are significantly more likely to be obese.     

Mapping field-scale spatial patterns of size and activity of the denitrifier community

There is ample evidence that microbial processes can exhibit large variations in activity on a field scale. However, very little is known about the spatial distribution of the microbial communities mediating these processes. Here we used geostatistical modelling to explore spatial patterns of size and activity of the denitrifying community, a functional guild involved in N-cycling, in a grassland field subjected to different cattle grazing regimes. We observed a non-random distribution pattern of the size of the denitrifier community estimated by quantification of the denitrification genes copy numbers with a macro-scale spatial dependence (6–16 m) and mapped the distribution of this functional guild in the field. The spatial patterns of soil properties, which were strongly affected by presence of cattle, imposed significant control on potential denitrification activity, potential N₂O production and relative abundance of some denitrification genes but not on the size of the denitrifier community. Absolute abundance of most denitrification genes was not correlated with the distribution patterns of potential denitrification activity or potential N₂O production. However, the relative abundance of bacteria possessing the nosZ gene encoding the N₂O reductase in the total bacterial community was a strong predictor of the N₂O/(N₂ + N₂O) ratio, which provides evidence for a relationship between bacterial community composition based on the relative abundance of denitrifiers in the total bacterial community and ecosystem processes. More generally, the presented geostatistical approach allows integrated mapping of microbial communities, and hence can facilitate our understanding of relationships between the ecology of microbial communities and microbial processes along environmental gradients.     

Crystal structure of CbpF,a bifunctional choline‐binding protein and autolysis regulator from Streptococcus pneumoniae

Phosphorylcholine, a crucial component of the pneumococcal cell wall, is essential in bacterial physiology and in human pathogenesis because it binds to serum components of the immune system and acts as a docking station for the family of surface choline‐binding proteins. The three‐dimensional structure of choline‐binding protein F (CbpF), one of the most abundant proteins in the pneumococcal cell wall, has been solved in complex with choline. CbpF shows a new modular structure composed both of consensus and non‐consensus choline‐binding repeats, distributed along its length, which markedly alter its shape, charge distribution and binding ability, and organizing the protein into two well‐defined modules. The carboxy‐terminal module is involved in cell wall binding and the amino‐terminal module is crucial for inhibition of the autolytic LytC muramidase, providing a regulatory function for pneumococcal autolysis.