HETEROFOR 1.0: A spatially explicit model for exploring the response of structurally complex forests to uncertain future conditions-Part 2: Phenology and water cycle

Climate change affects forest growth in numerous and sometimes opposite ways, and the resulting trend is often difficult to predict for a given site. Integrating and structuring the knowledge gained from the monitoring and experimental studies into process-based models is an interesting approach to predict the response of forest ecosystems to climate change. While the first generation of models operates at stand level, one now needs spatially explicit individual-based approaches in order to account for individual variability, local environment modification and tree adaptive behaviour in mixed and uneven-Aged forests that are supposed to be more resilient under stressful conditions. The local environment of a tree is strongly influenced by the neighbouring trees, which modify the resource level through positive and negative interactions with the target tree. Among other things, drought stress and vegetation period length vary with tree size and crown position within the canopy. In this paper, we describe the phenology and water balance modules integrated in the tree growth model HETEROFOR (HETEROgenous FORest) and evaluate them on six heterogeneous sessile oak and European beech stands with different levels of mixing and development stages and installed on various soil types. More precisely, we assess the ability of the model to reproduce key phenological processes (budburst, leaf development, yellowing and fall) as well as water fluxes. Two two-phase models differing regarding their response function to temperature during the chilling period (optimum and sigmoid functions) and a simplified one-phase model are. used to predict budburst date. The two-phase model with the optimum function is the least biased (overestimation of 2.46 d), while the one-phase model best accounts for the interannual variability (Pearson's r D 0:68). For the leaf development, yellowing and fall, predictions and observations are in accordance. Regarding the water balance module, the predicted throughfall is also in close agreement with the measurements (Pearson's r D 0:856; biasD 1:3 %), and the soil water dynamics across the year are well reproduced for all the study sites (Pearson's r was between 0.893 and 0.950, and bias was between 1:81 and 9:33 %). The model also reproduced well the individual transpiration for sessile oak and European beech, with similar performances at the tree and stand scale (Pearson's r of 0.84 0.85 for sessile oak and 0.88 0.89 for European beech). The good results of the model assessment will allow us to use it reliably in projection studies to evaluate the impact of climate change on tree growth in structurally complex stands and test various management strategies to improve forest resilience. © 2020 Author(s)

Software for the frontiers of quantum chemistry:An overview of developments in the Q-Chem 5 package

This article summarizes technical advances contained in the fifth major release of the Q-Chem quantum chemistry program package, covering developments since 2015. A comprehensive library of exchange–correlation functionals, along with a suite of correlated many-body methods, continues to be a hallmark of the Q-Chem software. The many-body methods include novel variants of both coupled-cluster and configuration-interaction approaches along with methods based on the algebraic diagrammatic construction and variational reduced density-matrix methods. Methods highlighted in Q-Chem 5 include a suite of tools for modeling core-level spectroscopy, methods for describing metastable resonances, methods for computing vibronic spectra, the nuclear–electronic orbital method, and several different energy decomposition analysis techniques. High-performance capabilities including multithreaded parallelism and support for calculations on graphics processing units are described. Q-Chem boasts a community of well over 100 active academic developers, and the continuing evolution of the software is supported by an “open teamware” model and an increasingly modular design

Comparison of the genomes of pathogenic treponemes of human and animal origin.

The aim of this study was to compare the genomes of two strains of intestinal treponemes, which were isolated from patients suffering from intestinal disorders, with that of Treponema hyodysenteriae, the known etiological agent of swine dysentery (bloody scours). The guanine-plus-cytosine contents of the three DNAs were found to be 28.5 to 30.0%. DNA-DNA hybridization in liquid phase indicated a high degree of homology (56 to 95%) among the human strains and with T. hyodysenteriae. One of the human strains in particular displayed a very high homology (91 to 95%) with T. hyodysenteriae. The overall conclusion is that treponemal strains pathogenic for humans and animals are clustered within the same species (we propose T. hyodysenteriae), which suggests the possibility of exchange of pathogenic microorganisms between domestic animals and humans

Demonstration of peptidoglycan-associated Brucella outer-membrane proteins by use of monoclonal antibodies.

A monoclonal antibody (3D6) was produced which reacted only with Brucella sonicated cell extracts that had been lysozyme-treated after sonication. The monoclonal antibody (mAb) reacted with the three major outer-membrane proteins (OMPs) of B. melitensis B115 in Western blots. A large number of reactive bands ranging from 12 to 43 kDa were present in lysozyme-treated Escherichia coli and Yersinia enterocolitica sonicated cell extracts. In a latex agglutination inhibition immunoassay, mAb 3D6 showed better reactivity with purified peptidoglycan (PG) of B. melitensis B115 than with that of Escherichia coli. This mAb was also used in immunogold electron microscopy with whole Brucella cells and sections. No binding was observed on whole cells and immunogold labelling in sections was observed close to the outer membrane, in the periplasmic space and in the cytoplasm. These findings indicate that mAb 3D6 is specific for PG subunits. Immunoblot analysis of B. melitensis B115 rough sonicated cell extracts after SDS-PAGE, with or without lysozyme treatment, was performed using mAbs specific for Brucella OMPs of molecular masses of 10, 16.5, 19, 25-27, 31-34, 36-38 and 89 kDa, for PG and for rough lipopolysaccharide (R-LPS) and smooth lipopolysaccharide (S-LPS). mAbs specific for the 25-27, 31-34 and 36-38 kDa OMPs reacted with three to six bands. All of them except the band of lowest molecular mass reacted with the PG-specific mAb and not with R-LPS- and S-LPS-specific mAbs.(ABSTRACT TRUNCATED AT 250 WORDS

The origins of marine bioluminescence: turning oxygen defence mechanisms into deep-sea communication tools.

Bioluminescence, the emission of ecologically functional light by living organisms, emerged independently on several occasions, yet the evolutionary origins of most bioluminescent systems remain obscure. We propose that the luminescent substrates of the luminous reactions (luciferins) are the evolutionary core of most systems, while luciferases, the enzymes catalysing the photogenic oxidation of the luciferin, serve to optimise the expression of the endogenous chemiluminescent properties of the luciferin. Coelenterazine, a luciferin occurring in many marine bioluminescent groups, has strong antioxidative properties as it is highly reactive with reactive oxygen species such as the superoxide anion or peroxides. We suggest that the primary function of coelenterazine was originally the detoxification of the deleterious oxygen derivatives. The functional shift from its antioxidative to its light-emitting function might have occurred when the strength of selection for antioxidative defence mechanisms decreased. This might have been made possible when marine organisms began colonising deeper layers of the oceans, where exposure to oxidative stress is considerably reduced because of reduced light irradiance and lower oxygen levels. A reduction in metabolic activity with increasing depth would also have decreased the endogenous production of reactive oxygen species. Therefore, in these organisms, mechanisms for harnessing the chemiluminescence of coelenterazine in specialised organs could have developed, while the beneficial antioxidative properties were maintained in other tissues. The full range of graded irradiance in the mesopelagic zone, where the majority of organisms are bioluminescent, would have provided a continuum for the selection and improvement of proto-bioluminescence. Although the requirement for oxygen or reactive oxygen species observed in bioluminescent systems reflects the high energy required to produce visible light, it may suggest that oxygen-detoxifying mechanisms provided excellent foundations for the emergence of many bioluminescent systems