Organic matter processing and soil evolution in a braided river system

Traditionally, braided river research has considered flow, sediment transport processes and, recently, vegetation dynamics in relation to river morphodynamics. However, if considering the development of woody vegetated patches over a time scale of decades, we must consider the extent to which soil forming processes, particularly related to soil organic matter, impact the alluvial geomorphic-vegetation system. Here we quantify the soil organic matter processing (humification) that occurs on young alluvial landforms. We sampled different geomorphic units, ranging from the active river channel to established river terraces in a braided river system. For each geomorphic unit, soil pits were used to sample sediment/soil layers that were analysed in terms of grain size (<2mm) and organic matter quantity and quality (RockEval method). A principal components analysis was used to identify patterns in the dataset. Results suggest that during the succession from bare river gravels to a terrace soil, there is a transition from small amounts of external organic matter supply provided by sedimentation processes (e.g. organic matter transported in suspension and deposited on bars), to large amounts of autogenic in situ organic matter production due to plant colonisation. This appears to change the time scale and pathways of alluvial succession (bio-geomorphic succession). However, this process is complicated by: the ongoing possibility of local sedimentation, which can serve to isolate surface layers via aggradation from the exogenic supply; and erosion which tends to create fresh deposits upon which organic matter processing must re-start. The result is a complex pattern of organic matter states as well as a general lack of any clear chronosequence within the active river corridor. This state reflects the continual battle between deposition events that can isolate organic matter from the surface, erosion events that can destroy accumulating organic matter and the early ecosystem processes necessary to assist the co-evolution of soil and vegetation. A key question emerges over the extent to which the fresh organic matter deposited in the active zone is capable of significantly transforming the local geochemical environment sufficiently to accelerate soil development.

Blue light activates a specific protein kinase in higher plants.

Blue light mediates the phosphorylation of a membrane protein in seedlings from several plant species. When crude microsomal membrane proteins from dark-grown pea (Pisum sativum L.), sunflower (Helianthus annuus L.), zucchini (Cucurbita pepo L.), Arabidopsis (Arabidopsis thaliana L.), or tomato (Lycopersicon esculentum L.) stem segments, or from maize (Zea mays L.), barley (Hordeum vulgare L.), oat (Avena sativa L.), wheat (Triticum aestivum L.), or sorghum (Sorghum bicolor L.) coleoptiles are illuminated and incubated in vitro with [gamma-(32)P]ATP, a protein of apparent molecular mass from 114 to 130 kD is rapidly phosphorylated. Hence, this system is probably ubiquitous in higher plants. Solubilized maize membranes exposed to blue light and added to unirradiated solubilized maize membranes show a higher level of phosphorylation of the light-affected protein than irradiated membrane proteins alone, suggesting that an unirradiated substrate is phosphorylated by a light-activated kinase. This finding is further demonstrated with membrane proteins from two different species, where the phosphorylated proteins are of different sizes and, hence, unambiguously distinguishable on gel electrophoresis. When solubilized membrane proteins from one species are irradiated and added to unirradiated membrane proteins from another species, the unirradiated protein becomes phosphorylated. These experiments indicate that the irradiated fraction can store the light signal for subsequent phosphorylation in the dark. They also support the hypothesis that light activates a specific kinase and that the systems share a close functional homology among different higher plants.

Working memory in schizophrenia: dynamic visuo-spatial information processing

Working memory, commonly defined as the ability to hold mental representations on line transiently and to manipulate these representations, is known to be a core deficit in schizophrenia. The aim of the present study was to investigate the visuo-spatial component of the working memory in schizophrenia, and more precisely to what extent the dynamic visuo-spatial information processing is impaired in schizophrenia patients. For this purpose we used a computerized paradigm in which 29 patients with schizophrenia (DSMIV, Diagnostic Interview for Genetic Studies) and 29 age and sex matched control subjects (DIGS) had to memorize a plane moving across the computer screen and to identify the observed trajectory among 9 plots proposed together. Each trajectory could be seen max. 3 times if needed. The results showed no difference between schizophrenia patients and controls regarding the number of correct trajectory identified after the first presentation. However, when we determine the mean number of correct trajectories on the basis of 3 trials, we observed that schizophrenia patients are significantly less performant than controls (Mann-Whitney, p _ 0.002). These findings suggest that, although schizophrenia patients are able to memorize some dynamic trajectories as well as controls, they do not profit from the repetition of the trajectory presentation. These findings are congruent with the hypothesis that schizophrenia could induce an unbalance between local and global information processing: the patients may be able to focus on details of the trajectory which could allow them to find the right target (bottom-up processes), but may show difficulty to refer to previous experience in order to filter incoming information (top-down processes) and enhance their visuo-spatial working memory abilities.

In vivo brain macromolecule signals in healthy and glioblastoma mouse models: (1) H magnetic resonance spectroscopy, post-processing and metabolite quantification at 14.1 T.

In (1) H magnetic resonance spectroscopy, macromolecule signals underlay metabolite signals, and knowing their contribution is necessary for reliable metabolite quantification. When macromolecule signals are measured using an inversion-recovery pulse sequence, special care needs to be taken to correctly remove residual metabolite signals to obtain a pure macromolecule spectrum. Furthermore, since a single spectrum is commonly used for quantification in multiple experiments, the impact of potential macromolecule signal variability, because of regional differences or pathologies, on metabolite quantification has to be assessed. In this study, we introduced a novel method to post-process measured macromolecule signals that offers a flexible and robust way of removing residual metabolite signals. This method was applied to investigate regional differences in the mouse brain macromolecule signals that may affect metabolite quantification when not taken into account. However, since no significant differences in metabolite quantification were detected, it was concluded that a single macromolecule spectrum can be generally used for the quantification of healthy mouse brain spectra. Alternatively, the study of a mouse model of human glioma showed several alterations of the macromolecule spectrum, including, but not limited to, increased mobile lipid signals, which had to be taken into account to avoid significant metabolite quantification errors.

Chemical and physical composition of grain-type and food-type soybean for food processing

The objective of this work was to evaluate the chemical and physical characteristics of grains of soybean (Glycine max) cultivars for food processing. The soybean cultivars evaluated were: grain-type - BRS 133 and BRS 258; food-type - BRS 213 (null lipoxygenases), BRS 267 (vegetable-type) and BRS 216 (small grain size). BRS 267 and BRS 216 cultivars showed higher protein content, indicating that they could promote superior nutritional value. BRS 213 cultivar showed the lowest lipoxygenase activity, and BRS 267, the lowest hexanal content. These characteristics can improve soyfood flavor. After cooking, BRS 267 cultivar grains presented a higher content of aglycones (more biologically active form of isoflavones) and oleic acid, which makes it proper for functional foods and with better stability for processing, and also showed high content of fructose, glutamic acid and alanine, compounds related to the soybean mild flavor. Because of its large grain size, BRS 267 is suitable for tofu and edamame, while small-grain-sized BRS 216 is good for natto and for soybean sprouts production. BRS 216 and BRS 213 cultivars presented shorter cooking time, which may be effective for reducing processing costs.

Oligogalacturonide defense signals in plants: large fragments interact with the plasma membrane in vitro.

Oligogalacturonides are plant cell wall-derived regulatory molecules which stimulate defense gene expression during pathogenesis. In vitro, these compounds enhance the phosphorylation of an approximately 34-kDa protein (pp34) in purified plasma membranes from potato and tomato leaves. We now show that polygalacturonate-enhanced phosphorylation of pp34 occurs in plasma membranes purified from tomato roots, hypocotyls, and stems and from undifferentiated potato cells. Furthermore, a similar phosphorylation is detected in leaf plasma membranes from soybean, a plant distantly related to tomato. Purified oligogalacturonides 13 to at least 26 residues long stimulate pp34 thiophosphorylation in vitro. This stimulation pattern differs from the induction of many known defense responses in vivo, where a narrower range of smaller fragments, between approximately 10 and 15 residues long, are active. On the basis of these differences we suggest that observed effects of applied exogenous oligogalacturonides on defense responses may not necessarily reflect the situation during pathogenesis. The cell wall could act as a barrier to many exogenous oligo- and polygalacturonides as well as other large regulatory ligands.

Towards a diffusion image processing validation and accuracy prediction framework

Validation is the main bottleneck preventing theadoption of many medical image processing algorithms inthe clinical practice. In the classical approach,a-posteriori analysis is performed based on someobjective metrics. In this work, a different approachbased on Petri Nets (PN) is proposed. The basic ideaconsists in predicting the accuracy that will result froma given processing based on the characterization of thesources of inaccuracy of the system. Here we propose aproof of concept in the scenario of a diffusion imaginganalysis pipeline. A PN is built after the detection ofthe possible sources of inaccuracy. By integrating thefirst qualitative insights based on the PN withquantitative measures, it is possible to optimize the PNitself, to predict the inaccuracy of the system in adifferent setting. Results show that the proposed modelprovides a good prediction performance and suggests theoptimal processing approach.

Molecular characterization of the processing of arenavirus envelope glycoprotein precursors by subtilisin kexin isozyme-1/site-1 protease.

A crucial step in the life cycle of arenaviruses is the biosynthesis of the mature fusion-active viral envelope glycoprotein (GP) that is essential for virus-host cell attachment and entry. The maturation of the arenavirus GP precursor (GPC) critically depends on proteolytic processing by the cellular proprotein convertase (PC) subtilisin kexin isozyme-1 (SKI-1)/site-1 protease (S1P). Here we undertook a molecular characterization of the SKI-1/S1P processing of the GPCs of the prototypic arenavirus lymphocytic choriomeningitis virus (LCMV) and the pathogenic Lassa virus (LASV). Previous studies showed that the GPC of LASV undergoes processing in the endoplasmic reticulum (ER)/cis-Golgi compartment, whereas the LCMV GPC is cleaved in a late Golgi compartment. Herein we confirm these findings and provide evidence that the SKI-1/S1P recognition site RRLL, present in the SKI-1/S1P prodomain and LASV GPC, but not in the LCMV GPC, is crucial for the processing of the LASV GPC in the ER/cis-Golgi compartment. Our structure-function analysis revealed that the cleavage of arenavirus GPCs, but not cellular substrates, critically depends on the autoprocessing of SKI-1/S1P, suggesting differences in the processing of cellular and viral substrates. Deletion mutagenesis showed that the transmembrane and intracellular domains of SKI-1/S1P are dispensable for arenavirus GPC processing. The expression of a soluble form of the protease in SKI-I/S1P-deficient cells resulted in the efficient processing of arenavirus GPCs and rescued productive virus infection. However, exogenous soluble SKI-1/S1P was unable to process LCMV and LASV GPCs displayed at the surface of SKI-I/S1P-deficient cells, indicating that GPC processing occurs in an intracellular compartment. In sum, our study reveals important differences in the SKI-1/S1P processing of viral and cellular substrates.

Do geographic distribution, niche property and life form explain plants' vulnerability to global change?

We modelled the future distribution in 2050 of 975 endemic plant species in southern Africa distributed among seven life forms, including new methodological insights improving the accuracy and ecological realism of predictions of global changes studies by: (i) using only endemic species as a way to capture the full realized niche of species, (ii) considering the direct impact of human pressure on landscape and biodiversity jointly with climate, and (iii) taking species' migration into account. Our analysis shows important promises for predicting the impacts of climate change in conjunction with land transformation. We have shown that the endemic flora of Southern Africa on average decreases with 41% in species richness among habitats and with 39% on species distribution range for the most optimistic scenario. We also compared the patterns of species' sensitivity with global change across life forms, using ecological and geographic characteristics of species. We demonstrate here that species and life form vulnerability to global changes can be partly explained according to species' (i) geographical distribution along climatic and biogeographic gradients, like climate anomalies, (ii) niche breadth or (iii) proximity to barrier preventing migration. Our results confirm that the sensitivity of a given species to global environmental changes depends upon its geographical distribution and ecological proprieties, and makes it possible to estimate a priori its potential sensitivity to these changes.

Software for interpolation of vegetative growth of yerba mate plants in 3D

The objective of this work was to build mock-ups of complete yerba mate plants in several stages of development, using the InterpolMate software, and to compute photosynthesis on the interpolated structure. The mock-ups of yerba-mate were first built in the VPlants software for three growth stages. Male and female plants grown in two contrasting environments (monoculture and forest understory) were considered. To model the dynamic 3D architecture of yerba-mate plants during the biennial growth interval between two subsequent prunings, data sets of branch development collected in 38 dates were used. The estimated values obtained from the mock-ups, including leaf photosynthesis and sexual dimorphism, are very close to those observed in the field. However, this similarity was limited to reconstructions that included growth units from original data sets. The modeling of growth dynamics enables the estimation of photosynthesis for the entire yerba mate plant, which is not easily measurable in the field. The InterpolMate software is efficient for building yerba mate mock-ups.

Neural networks complemented with genetic algorithms and fuzzy systems for predicting nitrogenous effluent variables in wastewater treatment plants

This work focuses on the prediction of the two main nitrogenous variables that describe the water quality at the effluent of a Wastewater Treatment Plant. We have developed two kind of Neural Networks architectures based on considering only one output or, in the other hand, the usual five effluent variables that define the water quality: suspended solids, biochemical organic matter, chemical organic matter, total nitrogen and total Kjedhal nitrogen. Two learning techniques based on a classical adaptative gradient and a Kalman filter have been implemented. In order to try to improve generalization and performance we have selected variables by means genetic algorithms and fuzzy systems. The training, testing and validation sets show that the final networks are able to learn enough well the simulated available data specially for the total nitrogen

Development and fruit yield of strawberry plants as affected by crown diameter and plantlet growing period

The objective of this work was to evaluate the influence of crown diameter and growing period of runner tips in 128 cell-trays on growth and yield of strawberry in the field. Treatments consisted of three classes of runner tip crown diameters, between 2.0 to 3.9 mm; 4.0 to 5.5 mm and 5.6 to 7.0 mm, respectively, and four growing periods in trays, 24; 39; 54 and 69 days, respectively. Higher shoot dry mass of transplants at planting and earlier yield of plants in the field were obtained in transplants grown for 69 days in trays. Larger runner tips lead to more vigorous transplants at planting and plants with higher vegetative growth in the field, with minor impact on yield. Increasing the growing time of runner tips in trays improved early fruit yield and decreased plant vegetative growth in the field.

Bacterial spot and early blight biocontrol by epiphytic bacteria in tomato plants

The objective of this work was to evaluate in vitro and in vivo biocontrol of bacterial spot (Xanthomonas vesicatoria) and early blight (Alternaria solani) by the epiphytic bacteria Paenibacillus macerans and Bacillus pumilus. Tomato plants were previously sprayed with epiphytic bacteria, benzalkonium chloride and PBS buffer and, after four days, they were inoculated with A. solani and X. vesicatoria. To determine the phytopathogenic bacteria population, leaflet samples were collected from each treatment every 24 hours, for seven days, and plated on semi-selective medium. The effect of epiphytic bacteria over phytopathogens was performed by the antibiosis test and antagonistic activity measured by inhibition zone diameter. The epiphytic and benzalkonium chloride drastically reduced the severity of early blight and bacterial spot in comparison to the control (PBS). In detached leaflets, the epiphytic bacteria reduced in 70% the number of phytopathogenic bacteria cells in the phylloplane. The antibiosis test showed that the epiphytic bacteria efficiently inhibit the phytopathogens growth. In all the bioassays, the epiphytic bacteria protect tomato plants against the phytopathogens

Decision-theoretic reflections on processing a fingermark

A recent publication in this journal [Neumann et al., Forensic Sci. Int. 212 (2011) 32-46] presented the results of a field study that revealed the data provided by the fingermarks not processed in a forensic science laboratory. In their study, the authors were interested in the usefulness of this additional data in order to determine whether such fingermarks would have been worth submitting to the fingermark processing workflow. Taking these ideas as a starting point, this communication here places the fingermark in its context of a case brought before a court, and examines the question of processing or not processing a fingermark from a decision-theoretic point of view. The decision-theoretic framework presented provides an answer to this question in the form of a quantified expression of the expected value of information (EVOI) associated with the processed fingermark, which can then be compared with the cost of processing the mark.