The genome of the non-cultured,bacterial-like organism associated with citrus greening disease contains thenusG-rplKAJL-rpoBC gene cluster and the gene for a bacteriophage type DNA polymerase

We have recently cloned three DNA fragments (In-2.6, In-1.0, and In-0.6) of the noncultured, bacterial-like organism (BLO) associated with citrus greening disease. Nucleotide sequence determination has shown that fragment In-2.6 is part of therplKAJL-rpoBC gene cluster, a well-known operon in eubacteria. The DNA fragment upstream of and partially overlapping with In-2.6 could be isolated and was shown to be thenusG gene. InEscherichia coli, nusG is also immediately upstream ofrplKAJL-rpoBC. Fragment In-1.0 carries the gene for a bacteriophage type DNA polymerase. Fragment In-0.6 could not be identified.When In-2.6 was used, at high stringency, as a probe to detect greening BLO strains in infected plants, hybridization was obtained with all Asian strains tested, but not with the African strain examined. At lower stringencies, In-2.6 was able to detect also the African strain. The implications of these reults in the taxonomical position of the greening BLO are discussed.     

Trade-offs and synergies between ecosystem productivity and stability in temperate grasslands

Aim

It is crucial to monitor how the productivity of grasslands varies with its temporal stability for management of these ecosystems. However, identifying the direction of the productivity–stability relationship remains challenging because ecological stability has multiple components that can display neutral, positive or negative covariations. Furthermore, evidence suggests that the direction of the productivity–stability relationship depends on the biotic interactions and abiotic conditions that underlie ecosystem productivity and stability. We decipher the relationships between grassland productivity and two components of its stability in four habitat types with contrasting environments and flora.

Location

France.

Time period

2000–2020.

Major taxa

Grassland plant species.

Methods

We used c. 20,000 vegetation plots spread across French permanent grasslands and remotely sensed vegetation indices to quantify grassland productivity and temporal stability. We decomposed stability into constancy (i.e., temporal invariability) and resistance (i.e., maximum deviation from average) and deciphered the direct and indirect effects of abiotic (namely growing season length and nitrogen input) and biotic (namely plant taxonomic diversity, trait diversity and community-weighted mean traits) factors on productivity–stability relationships using structural equation models.

Results

We found a positive relationship between productivity and constancy and a negative relationship between productivity and resistance in all habitats. Abiotic factors had stronger effects on productivity and stability compared with biotic factors. A longer growing season enhanced grassland productivity and constancy. Nitrogen input had positive and negative effects on grassland productivity and resistance, respectively. Trait values affected the constancy and resistance of grassland more than taxonomic and trait diversity, with effects varying from one habitat to another. Productivity was not related to any biotic factor.

Main conclusions

Our findings reveal how vital it is to consider both the multiple components of stability and the interaction between environment and biodiversity to gain an understanding of the relationships between productivity and stability in real-world ecosystems, which is a crucial step for sustainable grassland management.     

Modeling of protein loops by simulated annealing.

A method is presented to model loops of protein to be used in homology modeling of proteins. This method employs the ESAP program of Higo et al. (Higo, J., Collura, V., & Garnier, J., 1992, Biopolymers 32, 33-43) and is based on a fast Monte Carlo simulation and a simulated annealing algorithm. The method is tested on different loops or peptide segments from immunoglobulin, bovine pancreatic trypsin inhibitor, and bovine trypsin. The predicted structure is obtained from the ensemble average of the coordinates of the Monte Carlo simulation at 300 K, which exhibits the lowest internal energy. The starting conformation of the loop prior to modeling is chosen to be completely extended, and a closing harmonic potential is applied to N, CA, C, and O atoms of the terminal residues. A rigid geometry potential of Robson and Platt (1986, J. Mol. Biol. 188, 259-281) with a united atom representation is used. This we demonstrate to yield a loop structure with good hydrogen bonding and torsion angles in the allowed regions of the Ramachandran map. The average accuracy of the modeling evaluated on the eight modeled loops is 1 A root mean square deviation (rmsd) for the backbone atoms and 2.3 A rmsd for all heavy atoms.     

Inferring landscape resistance to gene flow when genetic drift is spatially heterogeneous

In connectivity models, land cover types are assigned cost values characterizing their resistance to species movements. Landscape genetic methods infer these values from the relationship between genetic differentiation and cost distances. The spatial heterogeneity of population sizes, and consequently genetic drift, is rarely included in this inference although it influences genetic differentiation. Similarly, migration rates and population spatial distributions potentially influence this inference. Here, we assessed the reliability of cost value inference under several migration rates, population spatial patterns and degrees of population size heterogeneity. Additionally, we assessed whether considering intra-population variables, here using gravity models, improved the inference when drift is spatially heterogeneous. We simulated several gene flow intensities between populations with varying local sizes and spatial distributions. We then fit gravity models of genetic distances as a function of (i) the ‘true’ cost distances driving simulations or alternative cost distances, and (ii) intra-population variables (population sizes, patch areas). We determined the conditions making the identification of the ‘true’ costs possible and assessed the contribution of intra-population variables to this objective. Overall, the inference ranked cost scenarios reliably in terms of similarity with the ‘true’ scenario (cost distance Mantel correlations), but this ‘true’ scenario rarely provided the best model goodness of fit. Ranking inaccuracies and failures to identify the ‘true’ scenario were more pronounced when migration was very restricted (<4 dispersal events/generation), population sizes were most heterogeneous and some populations were spatially aggregated. In these situations, considering intra-population variables helps identify cost scenarios reliably, thereby improving cost value inference from genetic data.     

Phylogenomic study of Amorphophallus (Alismatales; Araceae): When plastid DNA gene sequences help to resolve the backbone subgeneric delineation

Encompassing ca. 200 species distributed in paleotropical Africa and Asia, Amorphophallus is one of the largest genera of Araceae. In spite of the great economic interest in its glucomannan production, only a few studies have attempted to grasp the evolutionary history of this genus. In the current state of knowledge, four main clades, mostly linked to biogeographical delineation, have been identified from phylogenies based on a few genes. However, relationships among and within these clades still remain unclear, due to the rapid radiation that occurred during the early evolutionary history of the genus. Here, we generated genome skimming libraries for 43 specimens from 36 species distributed across the 4 clades, which allowed us to produce a phylogenetic matrix for a set of 71 plastid genes. Our phylogenies confirm the monophyly of these clades but show a new and well-resolved arrangement among these clades. Our analyses therefore provide a new scenario and timeline for the evolution of the main Amorphophallus clades, consistent with the morphological characteristics of the clades. The inferred scenario is also in agreement with climate dynamics and the onset of long-distance dispersal by the earliest migratory birds near the Oligocene/Miocene transition around 23 million years ago. Our study provides an up-to-date baseline to understand biogeographic and ecological processes that shaped the current diversity and distribution of Amorphophallus, paving the way for larger-scale phylogenomic studies based on plastid and nuclear genomes.     

Transferrin, somatomedins and growth

Plasma transferrin is significantly positively correlated to the growth velocity in normal children and children with various growth disorders. In hypopituitary dwarfs, both plasma transferrin and somatomedin are significantly lower than in controls. Acute variations of the plasma transferrin levels could be involved in the regulation of the GH secretion by a feedback mechanism. Yet, transferrin is neither a somatomedin or a somatomedin-binding protein, and the mechanisms relating growth to transferrin remain unknown.     

Scent-marking in free-ranging coyotes, Canis latrans

From November 1977 to March 1978 we recorded the scent-marking behaviour of free-ranging coyotes in southern Québec. Fourteen animals were marked by foot-pad ablation, which made it possible to recognize individuals' tracks in the snow and therefore to relate scent-marking with social organization. We observed 949 scent-marks. The identity of the animals was known for 50% of the tracking distances. Animals living in territorial groups (pairs and pairs with juveniles) marked more than twice as much as solitary non-territorial individuals. In addition the former used stronger forms of marking significantly more often than the latter.     

The dimerization of protochlorophyll pigments in non-polar solvents

The infrared, visible and nuclear magnetic resonance spectra of protochlorophyll a and vinylprotochlorophyll a in dry non-polar solvents (carbon tetrachloride, chloroform, cyclohexane) are presented and interpreted in terms of dimer interaction.

The infrared spectra in the 1600–1800 cm⁻¹ region clearly show the existence of a coordination interaction between the C-9 ketone oxygen function of one molecule and the central magnesium atom of another molecule. Infrared spectra in the OH stretching region (3200–3800 cm⁻¹) provide a valuable test of the water content in the samples.

The analysis of the absorption and circular dichroism spectra of protochlorophyll a and vinylprotochlorophyll a in carbon tetrachloride demonstrates the existence of a monomer-dimer equilibrium in the concentration range from 10⁻⁶ to 5 · 10⁻⁴ M. The dimerization constants are (6±2) · 10⁵ 1 · M⁻¹ for protochlorophyll a and (4.5±2) · 10⁵ 1 · M⁻¹ for vinylprotochlorophyll a at 20 °C. The deconvolution of visible spectra in the red region has been performed in order to obtain quantitative information on the dimer structure. Two models involving a parallel or a perpendicular arrangement of the associated molecules are considered.

From ¹H NMR spectra, it appears that the region of overlap occurs near ring V, in agreement with the interpretation of the infrared spectra.     

The protein structure code: what is its present status?

Current methods of prediction of protein conformation are reviewedand the algorithms on which they rely are presented. For non-homologousproteins and after cross-validation the reported methods exhibita probability index, i.e. the per cent of correctly predictedresidues per predicted residues, of 63–65% with a standarddeviation of the order of 7% for three conformational states—helix,ß-strand and coil. This present limitation in theaccuracy of predictions that use only the information of thelocal sequence can be related essentially to the effect of long-rangeinteractions specific for each protein family. The methods basedon sequence similarity can improve the accuracy of predictionby expressing explicitly the homology of the protein to be predictedwith proteins in the database. In these circumstances the probabilityindex can reach 87% with a standard deviation of 6.6%. Thisproperty can be used for modeling homologous proteins by aidingin amino acid sequence alignments. The prediction of the tertiarystructure of a protein is still limited to the case of modelinga structure based on the known three-dimensional structure ofa homologous protein.