Improvement of BDNF signalling by P42 peptide in Huntington's disease.

Huntington's disease (HD) is caused by a mutation in the Huntingtin (HTT) protein. We previously reported that the 23aa peptide of HTT protein, P42, is preventing HD pathological phenotypes, such as aggregation, reduction of motor performances and neurodegeneration. A systemic treatment with P42 during the pre-symptomatic phase of the disease showed therapeutic potential in R6/2 mice. We here tested P42 effects when administered during the post-symptomatic phase. The P42 treatment alleviated deficits in motor performances, even when symptoms have already started. Because changes in the level and activity of brain-derived neurotrophic factor (BDNF) have been shown to play a central role in HD, we analysed the influence of P42 on BDNF deficit and associated phenotypes. Our data suggest that P42 is involved in the spatio-temporal control of bdnf and trkB mRNA and their protein levels. Related to this enhancement of BDNF-TrkB signalling, R6/2 mice treated with P42, exhibit reduced anxiety, better learning and memory performances, and better long-term potentiation (LTP) response. Finally we identified a direct influence of P42 peptide on neuronal plasticity and activity. These results suggest that P42 offers an efficient therapeutic potential not only by preventing aggregation of mutant HTT at early stages of the disease, but also by favouring some physiological functions of normal HTT, as P42 is naturally part of it, at the different stages of the disease. This makes P42 peptide potentially suitable not only to prevent, but also to treat HD.

How deep can ectomycorrhizas go? A case study on Pisolithus down to 4 meters in a Brazilian eucalypt plantation.

Despite the strong ecological importance of ectomycorrhizal (ECM) fungi, their vertical distribution remains poorly understood. To our knowledge, ECM structures associated with trees have never been reported in depths below 2 meters. In this study, fine roots and ECM root tips were sampled down to 4-m depth during the digging of two independent pits differing by their water availability. A meta-barcoding approach based on Illumina sequencing of internal transcribed spacers (ITS1 and ITS2) was carried out on DNA extracted from root samples (fine roots and ECM root tips separately). ECM fungi dominated the root-associated fungal community, with more than 90% of sequences assigned to the genus Pisolithus. The morphological and barcoding results demonstrated, for the first time, the presence of ECM symbiosis down to 4-m. The molecular diversity of Pisolithus spp. was strongly dependent on depth, with soil pH and soil water content as primary drivers of the Pisolithus spp. structure. Altogether, our results highlight the importance to consider the ECM symbiosis in deep soil layers to improve our understanding of fine roots functioning in tropical soils.

Control of nerve cord formation by Engrailed and Gooseberry-Neuro: A multi-step, coordinated process.

One way to better understand the molecular mechanisms involved in the construction of a nervous system is to identify the downstream effectors of major regulatory proteins. We previously showed that Engrailed (EN) and Gooseberry-Neuro (GsbN) transcription factors act in partnership to drive the formation of posterior commissures in the central nervous system of Drosophila. In this report, we identified genes regulated by both EN and GsbN through chromatin immunoprecipitation ("ChIP on chip") and transcriptome experiments, combined to a genetic screen relied to the gene dose titration method. The genomic-scale approaches allowed us to define 175 potential targets of EN-GsbN regulation. We chose a subset of these genes to examine ventral nerve cord (VNC) defects and found that half of the mutated targets show clear VNC phenotypes when doubly heterozygous with en or gsbn mutations, or when homozygous. This strategy revealed new groups of genes never described for their implication in the construction of the nerve cord. Their identification suggests that, to construct the nerve cord, EN-GsbN may act at three levels, in: (i) sequential control of the attractive-repulsive signaling that ensures contralateral projection of the commissural axons, (ii) temporal control of the translation of some mRNAs, (iii) regulation of the capability of glial cells to act as commissural guideposts for developing axons. These results illustrate how an early, coordinated transcriptional control may orchestrate the various mechanisms involved in the formation of stereotyped neuronal networks. They also validate the overall strategy to identify genes that play crucial role in axonal pathfinding.

DigR: a generic model and its open source simulation software to mimic three-dimensional root-system architecture diversity.

Background and Aims: Many studies exist in the literature dealing with mathematical representations of root systems, categorized, for example, as pure structure description, partial derivative equations or functional-structural plant models. However, in these studies, root architecture modelling has seldom been carried out at the organ level with the inclusion of environmental influences that can be integrated into a whole plant characterization. Methods: We have conducted a multidisciplinary study on root systems including field observations, architectural analysis, and formal and mathematical modelling. This integrative and coherent approach leads to a generic model (DigR) and its software simulator. Architecture analysis applied to root systems helps at root type classification and architectural unit design for each species. Roots belonging to a particular type share dynamic and morphological characteristics which consist of topological and geometric features. The DigR simulator is integrated into the Xplo environment, with a user interface to input parameter values and make output ready for dynamic 3-D visualization, statistical analysis and saving to standard formats. DigR is simulated in a quasi-parallel computing algorithm and may be used either as a standalone tool or integrated into other simulation platforms. The software is open-source and free to download at http://amapstudio.cirad.fr/soft/xplo/download. Key Results: DigR is based on three key points: (1) a root-system architectural analysis, (2) root type classification and modelling and (3) a restricted set of 23 root type parameters with flexible values indexed in terms of root position. Genericity and botanical accuracy of the model is demonstrated for growth, branching, mortality and reiteration processes, and for different root architectures. Plugin examples demonstrate the model's versatility at simulating plastic responses to environmental constraints. Outputs of the model include diverse root system structures such as tap-root, fasciculate, tuberous, nodulated and clustered root systems. Conclusions: DigR is based on plant architecture analysis which leads to specific root type classification and organization that are directly linked to field measurements. The open source simulator of the model has been included within a friendly user environment. DigR accuracy and versatility are demonstrated for growth simulations of complex root systems for both annual and perennial plants.

Increased light-use efficiency sustains net primary productivity of shaded coffee plants in agroforestry system.

In agroforestry systems, shade trees strongly affect the physiology of the undergrown crop. However, a major paradigm is that the reduction in absorbed photosynthetically active radiation is, to a certain extent, compensated by an increase in light-use efficiency, thereby reducing the difference in net primary productivity between shaded and non-shaded plants. Due to the large spatial heterogeneity in agroforestry systems and the lack of appropriate tools, the combined effects of such variables have seldom been analysed, even though they may help understand physiological processes underlying yield dynamics. In this study, we monitored net primary productivity, during two years, on scales ranging from individual coffee plants to the entire plot. Absorbed radiation was mapped with a 3D model (MAESPA). Light-use efficiency and net assimilation rate were derived for each coffee plant individually. We found that although irradiance was reduced by 60% below crowns of shade trees, coffee light-use efficiency increased by 50%, leaving net primary productivity fairly stable across all shade levels. Variability of aboveground net primary productivity of coffee plants was caused primarily by the age of the plants and by intraspecific competition among them (drivers usually overlooked in the agroforestry literature) rather than by the presence of shade trees.

Root biomass, turnover and net primary productivity of a coffee agroforestry system in Costa Rica: effects of soil depth, shade trees, distance to row and coffee age.

Background and Aims In Costa Rica, coffee (Coffea arabica) plants are often grown in agroforests. However, it is not known if shade-inducing trees reduce coffee plant biomass through root competition, and hence alter overall net primary productivity (NPP). We estimated biomass and NPP at the stand level, taking into account deep roots and the position of plants with regard to trees. Methods Stem growth and root biomass, turnover and decomposition were measured in mixed coffee/tree (Erythrina poeppigiana) plantations. Growth ring width and number at the stem base were estimated along with stem basal area on a range of plant sizes. Root biomass and fine root density were measured in trenches to a depth of 4 m. To take into account the below-ground heterogeneity of the agroforestry system, fine root turnover was measured by sequential soil coring (to a depth of 30 cm) over 1 year and at different locations (in full sun or under trees and in rows/inter-rows). Allometric relationships were used to calculate NPP of perennial components, which was then scaled up to the stand level. Key Results Annual ring width at the stem base increased up to 2·5 mm yr-1 with plant age (over a 44-year period). Nearly all (92 %) coffee root biomass was located in the top 1·5 m, and only 8 % from 1·5 m to a depth of 4 m. Perennial woody root biomass was 16 t ha-1 and NPP of perennial roots was 1·3 t ha-1 yr-1. Fine root biomass (0-30 cm) was two-fold higher in the row compared with between rows. Fine root biomass was 2·29 t ha-1 (12 % of total root biomass) and NPP of fine roots was 2·96 t ha-1 yr-1 (69 % of total root NPP). Fine root turnover was 1·3 yr-1 and lifespan was 0·8 years. Conclusions Coffee root systems comprised 49 % of the total plant biomass; such a high ratio is possibly a consequence of shoot pruning. There was no significant effect of trees on coffee fine root biomass, suggesting that coffee root systems are very competitive in the topsoil.

Measured and modeled interactive effects of potassium deficiency and water deficit on gross primary productivity and light-use efficiency in Eucalyptus grandis plantations.

Global climate change is expected to increase the length of drought periods in many tropical regions. Although large amounts of potassium (K) are applied in tropical crops and planted forests, little is known about the interaction between K nutrition and water deficit on the physiological mechanisms governing plant growth. A process-based model (MAESPA) parameterized in a split-plot experiment in Brazil was used to gain insight into the combined effects of K deficiency and water deficit on absorbed radiation (aPAR), gross primary productivity (GPP), and light-use efficiency for carbon assimilation and stem biomass production (LUEC and LUEs ) in Eucalyptus grandis plantations. The main-plot factor was the water supply (undisturbed rainfall vs. 37% of throughfall excluded) and the subplot factor was the K supply (with or without 0.45 mol K m(-2 ) K addition). Mean GPP was 28% lower without K addition over the first 3 years after planting whether throughfall was partly excluded or not. K deficiency reduced aPAR by 20% and LUEC by 10% over the whole period of growth. With K addition, throughfall exclusion decreased GPP by 25%, resulting from a 21% decrease in LUEC at the end of the study period. The effect of the combination of K deficiency and water deficit was less severe than the sum of the effects of K deficiency and water deficit individually, leading to a reduction in stem biomass production, gross primary productivity and LUE similar to K deficiency on its own. The modeling approach showed that K nutrition and water deficit influenced absorbed radiation essentially through changes in leaf area index and tree height. The changes in gross primary productivity and light-use efficiency were, however, driven by a more complex set of tree parameters, especially those controlling water uptake by roots and leaf photosynthetic capacities.

Mixing Eucalyptus and Acacia trees leads to fine root over-yielding and vertical segregation between species.

The consequences of diversity on belowground processes are still poorly known in tropical forests. The distributions of very fine roots (diameter <1 mm) and fine roots (diameter <3 mm) were studied in a randomized block design close to the harvest age of fast-growing plantations. A replacement series was set up in Brazil with mono-specific Eucalyptus grandis (100E) and Acacia mangium (100A) stands and a mixture with the same stocking density and 50% of each species (50A:50E). The total fine root (FR) biomass down to a depth of 2 m was about 27% higher in 50A:50E than in 100A and 100E. Fine root over-yielding in 50A:50E resulted from a 72 % rise in E. grandis fine root biomass per tree relative to 100E, whereas A. mangium FR biomass per tree was 17% lower than in 100A. Mixing A. mangium with E. grandis trees led to a drop in A. mangium FR biomass in the upper 50 cm of soil relative to 100A, partially balanced by a rise in deep soil layers. Our results highlight similarities in the effects of directional resources on leaf and FR distributions in the mixture, with A. mangium leaves below the E. grandis canopy and a low density of A. mangium fine roots in the resource-rich soil layers relative to monospecific stands. The vertical segregation of resource-absorbing organs did not lead to niche complementarity expected to increase the total biomass production.

Is the simple auger coring method reliable for below-ground standing biomass estimation in Eucalyptus forest plantations?

BACKGROUND AND AIMS: Despite their importance for plant production, estimations of below-ground biomass and its distribution in the soil are still difficult and time consuming, and no single reliable methodology is available for different root types. To identify the best method for root biomass estimations, four different methods, with labour requirements, were tested at the same location. METHODS: The four methods, applied in a 6-year-old Eucalyptus plantation in Congo, were based on different soil sampling volumes: auger (8 cm in diameter), monolith (25 × 25 cm quadrate), half Voronoi trench (1·5 m(3)) and a full Voronoi trench (3 m(3)), chosen as the reference method. KEY RESULTS: With the reference method (0-1m deep), fine-root biomass (FRB, diameter <2 mm) was estimated at 1·8 t ha(-1), medium-root biomass (MRB diameter 2-10 mm) at 2·0 t ha(-1), coarse-root biomass (CRB, diameter >10 mm) at 5·6 t ha(-1) and stump biomass at 6·8 t ha(-1). Total below-ground biomass was estimated at 16·2 t ha(-1) (root : shoot ratio equal to 0·23) for this 800 tree ha(-1) eucalypt plantation density. The density of FRB was very high (0·56 t ha(-1)) in the top soil horizon (0-3 cm layer) and decreased greatly (0·3 t ha(-1)) with depth (50-100 cm). Without labour requirement considerations, no significant differences were found between the four methods for FRB and MRB; however, CRB was better estimated by the half and full Voronoi trenches. When labour requirements were considered, the most effective method was auger coring for FRB, whereas the half and full Voronoi trenches were the most appropriate methods for MRB and CRB, respectively. CONCLUSIONS: As CRB combined with stumps amounted to 78 % of total below-ground biomass, a full Voronoi trench is strongly recommended when estimating total standing root biomass. Conversely, for FRB estimation, auger coring is recommended with a design pattern accounting for the spatial variability of fine-root distribution.

The Mi-2 nucleosome remodeler and the Rpd3 histone deacetylase are involved in piRNA-guided heterochromatin formation.

In eukaryotes, trimethylation of lysine 9 on histone H3 (H3K9) is associated with transcriptional silencing of transposable elements (TEs). In drosophila ovaries, this heterochromatic repressive mark is thought to be deposited by SetDB1 on TE genomic loci after the initial recognition of nascent transcripts by PIWI-interacting RNAs (piRNAs) loaded on the Piwi protein. Here, we show that the nucleosome remodeler Mi-2, in complex with its partner MEP-1, forms a subunit that is transiently associated, in a MEP-1 C-terminus-dependent manner, with known Piwi interactors, including a recently reported SUMO ligase, Su(var)2-10. Together with the histone deacetylase Rpd3, this module is involved in the piRNA-dependent TE silencing, correlated with H3K9 deacetylation and trimethylation. Therefore, drosophila piRNA-mediated transcriptional silencing involves three epigenetic effectors, a remodeler, Mi-2, an eraser, Rpd3 and a writer, SetDB1, in addition to the Su(var)2-10 SUMO ligase.

Impact of tapping and soil water status on fine root dynamics in a rubber tree plantation in Thailand.

Fine roots (FR) play a major role in the water and nutrient uptake of plants and contribute significantly to the carbon and nutrient cycles of ecosystems through their annual production and turnover. FR growth dynamics were studied to understand the endogenous and exogenous factors driving these processes in a 14-year-old plantation of rubber trees located in eastern Thailand. FR dynamics were observed using field rhizotrons from October 2007 to October 2009. This period covered two complete dry seasons (November to March) and two complete rainy seasons (April to October), allowing us to study the effect of rainfall seasonality on FR dynamics. Rainfall and its distribution during the two successive years showed strong differences with 1500 and 950 mm in 2008 and 2009, respectively. FR production (FRP) completely stopped during the dry seasons and resumed quickly after the first rains. During the rainy seasons, FRP and the daily root elongation rate (RER) were highly variable and exhibited strong annual variations with a total FRP of 139.8 and 40.4 mm(-) (2) and an average RER of 0.16 and 0.12 cm day(-) (1) in 2008 and 2009, respectively. The significant positive correlations found between FRP, RER, the appearance of new roots, and rainfall at monthly intervals revealed the impact of rainfall seasonality on FR dynamics. However, the rainfall patterns failed to explain the weekly variations of FR dynamics observed particularly during the rainy seasons. At this time step, FRP, RER, and the appearance of new FR were negatively correlated to the average soil matric potential measured at a depth of between 30 and 60 cm. In addition, our study revealed a significant negative correlation between FR dynamics and the monthly production of dry rubber. Consequently, latex harvesting might disturb carbon dynamics in the whole tree, far beyond the trunk where the tapping was performed. These results exhibit the impact of climatic conditions and tapping system in the carbon budget of rubber plantations.

Dynamics of soil exploration by fine roots down to a depth of 10 m throughout the entire rotation in Eucalyptus grandis plantations.

Although highly weathered soils cover considerable areas in tropical regions, little is known about exploration by roots in deep soil layers. Intensively managed Eucalyptus plantations are simple forest ecosystems that can provide an insight into the belowground growth strategy of fast-growing tropical trees. Fast exploration of deep soil layers by eucalypt fine roots may contribute to achieving a gross primary production that is among the highest in the world for forests. Soil exploration by fine roots down to a depth of 10 m was studied throughout the complete cycle in Eucalyptus grandis plantations managed in short rotation. Intersects of fine roots, less than 1 mm in diameter, and medium-sized roots, 1-3 mm in diameter, were counted on trench walls in a chronosequence of 1-, 2-, 3.5-, and 6-year-old plantations on a sandy soil, as well as in an adjacent 6-year-old stand growing in a clayey soil. Two soil profiles were studied down to a depth of 10 m in each stand (down to 6 m at ages 1 and 2 years) and 4 soil profiles down to 1.5-3.0 m deep. The root intersects were counted on 224 m(2) of trench walls in 15 pits. Monitoring the soil water content showed that, after clear-cutting, almost all the available water stored down to a depth of 7 m was taken up by tree roots within 1.1 year of planting. The soil space was explored intensively by fine roots down to a depth of 3 m from 1 year after planting, with an increase in anisotropy in the upper layers throughout the rotation. About 60% of fine root intersects were found at a depth of more than 1 m, irrespective of stand age. The root distribution was isotropic in deep soil layers and kriged maps showed fine root clumping. A considerable volume of soil was explored by fine roots in eucalypt plantations on deep tropical soils, which might prevent water and nutrient losses by deep drainage after canopy closure and contribute to maximizing resource uses.

Differential gene expression in different types of Hevea brasiliensis roots.

Three types of roots (taproots, first order laterals and second order laterals) were functionally characterized on 7-month-old in vitro plantlets regenerated by somatic embryogenesis in Hevea brasiliensis. A histological analysis revealed different levels of differentiation depending on root diameter. A primary structure was found in first and second order lateral roots, while taproots displayed a secondary structure. The expression of 48 genes linked to some of the regulatory pathways acting in roots was compared in leaves, stems and the different types of roots by real-time RT-PCR. Thirteen genes were differentially expressed in the different organs studied in plants grown under control conditions. Nine additional other genes were differentially regulated between organs under water deficit conditions. In addition, 10 genes were significantly regulated in response to water deficit, including 8 regulated mainly in lateral roots types. Our results suggest that the regulation of gene expression in lateral roots is different than that in taproots, which have a main role in nutrient uptake and transport, respectively.

Two independent estimations of stand-level root respiration on clonal Eucalyptus stands in Congo: up scaling of direct measurements on roots versus the trenched-plot technique.

Root respiration at the level of a forest stand, an important component of ecosystem carbon balance, has been estimated in the past using various methods, most of them being indirect and relying on soil respiration measurements. On a 3-yr-old Eucalyptus stand in Congo-Brazzaville, a method involving the upscaling of direct measurements made on roots in situ, was compared with an independent approach using soil respiration measurements conducted on control and trenched plots (i.e. without living roots). The first estimation was based on the knowledge of root-diameter distribution and on a relationship between root diameter and specific respiration rates. The direct technique involving the upscaling of direct measurements on roots resulted in an estimation of 1.53 micromol m(-2) s(-1), c. 50% higher than the mean estimation obtained with the indirect technique (1.05 micromol m(-2) s(-1)). Monte-Carlo simulations showed that the results carried high uncertainty, but this uncertainty was no higher for the direct method than for the trenched-plot method. The reduction of the uncertainties on upscaled results requires more extensive knowledge of temperature sensitivity and more confidence and precision on the respiration rates and biomasses of fine roots.