Kernel regression methods for the prediction of wood properties of Pinus taeda using near infrared spectroscopy

Near infrared diffuse reflectance spectra collected in 10-mm sections were used for the estimation of air-dry density (AD), microfibril angle (MFA), stiffness (MOE), tracheid coarseness (COARS), and tracheid wall thickness (WTHICK) in wood radial strip samples obtained at breast height (1.4 m) from 60 Pinus taeda trees. Calibration models were developed using traditional partial least squares (PLS) and kernel regression. The kernel methods included radial basis functions-partial least squares (RBF-PLS) and least-squares support vector machines (LS-SVM). RBF-PLS and LS-SVM models outperformed PLS-CV calibrations in terms of fit statistics. MFA and MOE, two properties that exhibited nonlinearity, showed the most significant improvements compared to PLS. In terms of predictive ability RBF-PLS performed better than PLS for the prediction of MFA, MOE, and COARS. LS-SVM showed better prediction statistics in all cases, except for WTHICK that gave similar statistics compared to PLS and was superior to RBF-PLS. By adding statistically significant factors to the PLS regressions, it was possible to capture some of the nonlinear features of the data and improve the predictive ability of the PLS models.     

Is spawning stock biomass a robust proxy for reproductive potential?

Reference points based on fishing mortality (F) and spawning stock biomass (SSB) are a requirement of many fisheries management frameworks. SSB is assumed to be a proxy for stock reproductive potential (SRP). Limit reference points based on SSB are used to indicate the level of biomass below which productivity is affected. SSB fails to account for changes in fecundity, egg viability and sex ratio, and it has been argued that total egg production (TEP) provides a better reflection of SRP. We explore how accounting for TEP impacts limit reference points and evidence for a relationship between stock and recruit. Time series of SSB and TEP are compared for three North Sea stocks: cod (Gadus morhua), herring (Clupea harengus) and plaice (Pleuronectes platessa). Dynamics based on TEP are different from those based on SSB for cod and plaice, but the stock–recruit relationships were not ‘improved’ using TEP. Shifts in productivity (spawner per recruit) occur in all three time series and SSB underestimated uncertainty. Yet again, it was shown that assumptions of stationarity about fish population productivity are incorrect. We argue that the use of TEP does improve the realism in our understanding of stock dynamics, and demographically, more complex management strategy evaluation is required to develop management procedures that are robust to uncertainty and integrate F and the demographic health of a stock. Empirical feedback control systems based on fisheries independent indices including surveys of eggs, larvae, recruits, juveniles or spawning adults should be evaluated and compared to traditional approaches.     

Is crop N demand more closely related to dry matter accumulation or leaf area expansion during vegetative growth?

The critical crop nitrogen uptake is defined as the minimum nitrogen uptake necessary to achieve maximum biomass accumulation (W). Across a range of crops, the critical N uptake is related to W by a power function with a coefficient less than unity that suggests crop N uptake is co-regulated by both soil N supply and biomass accumulation. However, crop N demand is also often linearly related to the expansion of the leaf area index (LAI) during the vegetative growth period. This suggests that crop N demand could be also linked with LAI extension. In this paper, we develop theory to combine these two concepts within a common framework. The aim of this paper is to determine whether generic relationships between N uptake, biomass accumulation, and LAI expansion could be identified that would be robust across both species and environment types. To that end, we used the framework to analyze data on a range of species, including C₃ and C₄ ones and mono- and di-cotyledonous crops. All crops were grown in either temperate or tropical and subtropical environments without limitations on N supply. The relationship between N uptake and biomass was more robust, across environment types, than the relationship of LAI with biomass. In general, C₃ species had a higher N uptake per unit biomass than C₄ species, whereas dicotyledonous species tended to have higher LAI per unit biomass than monocotyledonous ones. Species differences in N uptake per unit biomass were partly associated with differences in LAI and N-partitioning. Consequently the critical leaf-N uptake per unit LAI (specific leaf nitrogen, SLN) was relatively constant across species at 1.8–2.0 g m⁻², a value that was close to published data on the critical SLN of new leaves at the top of the canopy. Our results indicate that critical N uptake curves as a function of biomass accumulation may provide a robust platform for simulating N uptake of a species. However, if crop simulation models are to capture the genotypic and environmental control of crop N dynamics in a physiologically functional manner, plant growth has to be considered as the sum of a metabolic (e.g. leaves) and a structural (e.g. stems) compartment, each with its own demand for metabolic and structural N.     

Vibrational circular-dichroism spectroscopy of homologous cyclic peptides designed to fold into β helices of opposite chirality

Cyclic β-helical peptides have been developed as model structured biomolecules for examining peptide adsorption and conformation on surfaces. As a key prerequisite to circular-dichroism (CD) analysis of these model peptides on surfaces, their conformations and the corresponding vibrational spectra in the 1400-1800 cm?1 range were analyzed by vibrational circular-dichroism (VCD) spectroscopy in solution. The two model peptides ("β Leu and β Val") were examined in chloroform, where they each fold into a homogeneous well-defined antiparallel double-stranded β-helical species, as determined previously by NMR and electronic CD spectroscopy. Because the β-helical conformations of β Leu and β Val are well characterized, the VCD spectra of these peptides can be unambiguously correlated with their structures. In addition, these two β-helical peptides differ from one another in two key respects that make them uniquely advantageous for CD analysis--first, while their backbone conformations are topologically similar, β Leu and β Val form helices of opposite chiralities; second, the two peptides differ in their sequences, i.e., composition of the side chains attached to the backbone. The observed VCD spectra for β Leu and β Val are roughly mirror images of each other, indicating that the VCD features are dominated by the chirality and conformation of the peptide backbone rather than by the peptide sequence. Accordingly, spectra similarly characteristic of peptide secondary structure can be expected for peptides designed to be structural analogs of β Leu and β Val while incorporating a variety of side chains for studies of surface adsorption from organic and aqueous solvents.     

Ostreid herpesvirus 1 detection and relationship with Crassostrea gigas spat mortality in France between 1998 and 2006

ABSTRACT: Since its molecular characterisation, Ostreid herpesvirus 1 (OsHV-1) has been regularly detected in Crassostrea gigas in France. Although its pathogenicity was demonstrated on larval stages, its involvement during mortality outbreaks at the juvenile stage was highly suspected but not evidenced. To investigate mortality outbreaks, the French National Network for Surveillance and Monitoring of Mollusc Health (REPAMO) carried out two surveys in juvenile C. gigas. The first survey lasted from 1998 to 2006 and was an epidemiological inquiry occurring when oyster farmers reported mortality outbreaks. The second survey, a longitudinal one, was set up in 1998 to complete the network observations on OsHV-1. Data analysis showed a specific pattern of mortality outbreaks associated with OsHV-1 detection. Ostreid herpesvirus 1 detection mainly appeared during the summer, suggesting the influence of the seawater temperature on its occurrence. It mostly presented a patchy distribution in the field in contrast to the nursery. Significant relationship between OsHV-1 detection and spat mortality was found, preferentially in sheltered and closed environments. The longitudinal survey confirmed most of the network observations. Although subsequent works particularly epidemiological surveys would be useful to confirm the causal link between the detection of OsHV-1 and the mortality outbreaks in juvenile C. gigas, the role of OsHV-1 in oyster mortality is progressing.     

Marker-assisted selection efficiency in multiple connected populations: a simulation study based on the results of a QTL detection experiment in maize

Many studies already investigated marker-assisted selection (MAS) efficiency but mainly in biparental populations. Connected multiparental populations address a broader diversity and confer a gain of power for QTL detection which must be beneficial for MAS. Our objective was to compare multiparental connected designs to biparental populations taken separately for MAS and phenotypic selection. We first detected QTL for flowering time and grain yield in an experimental maize design involving four parental inbred lines crossed to produce six different biparental populations and confirmed the advantage of multiparental connected designs over biparental populations for QTL detection. Based on these results we performed stochastic simulations to evaluate the expected efficiency of four generations of MAS and phenotypic selection. Different parameters were considered: trait heritability, genetic architecture and whether QTL were assumed to be known or have to be detected. Genetic gains were higher in the multiparental design than on average over the biparental populations considered separately, especially when favourable alleles were equally distributed among parental lines. When QTL detection was included in the simulation process, we found that type I error risk considered for declaring QTL as significant should be adapted to the design. Type I error risks leading to the best response were higher for the biparental populations than for the multiparental design. Besides addressing a broader diversity, multiparental designs increase the power of QTL detection, which reinforces their superiority over biparental designs for MAS. Application of MAS to multiparental designs therefore appears promising to accelerate genetic gain in plant breeding programs.     

A new bioclimatic model calibrated with vegetation for Mediterranean forest areas

? Water availability is one of the main factors explaining flora composition and growth in Mediterranean regions, where it may decline with climate change.

? Our goal was to develop a model for forest site assessment in Mediterranean environments, focusing on water availability to assess potential vegetation composition and productivity in any places, whatever their level of disturbance.

? We designed a statistical model, using global climatic and geographic variables, as well as detailed local topographic and edaphic variables, to compute a bioclimatic index for Mediterranean forest environments. This model was calibrated in France with a flora index from 325 old forests. The model explained 80.3% of the flora index variance. The method fills a gap in existing models, bridging scales from the region to forest sites.

? Beyond its theoretical aspect, it was designed to allow practical tools to be derived from it for decision-making and management, such as the assessment of climate change impact on vegetation, and of forest productivity. Its development and adaptation is possible in other Mediterranean regions, and in any region where water is one of the main limiting factors.