Remarks on the tight-binding model of graphene

We address a simple but fundamental issue arising in the study of graphene, as well as of other systems that have a crystalline structure with more than one atom per unit cell. For these systems, the choice of the tight-binding basis is not unique. For monolayer graphene two bases are widely used in the literature. While the expectation values of operators describing physical quantities should be independent of basis, the form of the operators may depend on the basis, especially in the presence of disorder or of an applied magnetic field. Using the inappropriate form of certain operators may lead to erroneous physical predictions. We discuss the two bases used to describe monolayer graphene, as well as the form of the most commonly used operators in the two bases. We repeat our analysis for the case of bilayer graphene.Comment: 15 pages, 4 figure

Complete Genome Sequence of \u3ci\u3eBurkholderia phymatum\u3c/i\u3e STM815T , a Broad Host Range and Efficient Nitrogen-Fixing Symbiont of \u3ci\u3eMimosa\u3c/i\u3e Species

Burkholderia phymatum is a soil bacterium able to develop a nitrogen-fixing symbiosis with species of the legume genus Mimosa, and is frequently found associated specifically with Mimosa pudica. The type strain of the species, STM 815T , was isolated from a root nodule in French Guiana in 2000. The strain is an aerobic, motile, non-spore forming, Gram-negative rod, and is a highly competitive strain for nodulation compared to other Mimosa symbionts, as it also nodulates a broad range of other legume genera and species. The 8,676,562 bp genome is composed of two chromosomes (3,479,187 and 2,697,374 bp), a megaplasmid (1,904,893 bp) and a plasmid hosting the symbiotic functions (595,108 bp)

Recombinaison, spécialisation et spéciation chez les symbiotes du genre Sinorhizobium associés aux plantes de genre Medicago (des patrons de diversité aux hypothèses évolutives)

MONTPELLIER-BU Sciences (341722106) / SudocSudocFranceF

Medicago – Sinorhizobium symbiotic specificity evolution and the geographic expansion of Medicago

International audienceThe legume genus Medicago interacts with soil bacteria commonly referred to as rhizobia, in a nitrogen fixing symbiosis. We analysed the diversity of symbiotic association specificity among the two organisms, and its evolution in the plant genus. Nitrogen fixation tests and molecular phylogenetic reconstructions revealed that the genus Medicago includes more symbiotic specificity groups than previously suggested and that plant specificity is highly unstable and has repeatedly switched along the diversification of this genus. A phylogenetic analysis including geographical data shows that bacterial geographical diversity distribution has a strong influence on the geographic distribution of plant species and their ability to colonize new areas. Multiple other modifications of specificity occurred along the diversification of the genus, presumably due to selection for specialization to a single bacterial biovar. Codivergence between plants and bacteria may also have taken place

Phylogéographie, compétition et sélection chez les bactéries symbiotiques Sinorhizobium meliloti et Sinorhizobium medicae

Les deux espèces bactériennes, Sinorhizobium meliloti et S. medicae forment une symbiose efficace avec Medicago truncatula, tout en présentant un polymorphisme de fixation d'azote. Nous n'avons pas pu confirmer dans ce modèle l'existence de mécanismes de sanction des symbiotes non-fixateurs décrits théoriquement et expérimentalement chez d'autres couples symbiotiques. Les deux espèces bactériennes pourraient alors être maintenues en sympatrie avec la même plante-hôte du fait d'avantages sélectifs différents : S. meliloti serait plus compétitrice pour la nodulation de la plante, alors que S. medicae présenterait un plus fort potentiel de fixation. Essentiellement du fait de son fort taux de recombinaison, S. medicae est l'espèce présentant le plus de diversité génotypique. A l'échelle du bassin méditerranéen S. medicae a une structure panmictique se rapprochant d'une métapopulation, expliquant le profil phylogéographique décelé sur cette espèce. Sa forte expansion démographique pourrait également suggérer une spécialisation symbiotique en cours. S. meliloti a une structure génétique épidémique, avec de probables adaptations locales, mais qui n'ont pas pu être décelées. Aucun isolement par la distance ne permet d'expliquer la répartition spatiale de la diversité bactérienne, tant intra- que interspécifique. Cependant, certains paramètres physico-chimiques du sol, ainsi que le couvert végétal, même à l'échelle de la lignée, ont une influence sur la structuration de la diversité bactérienne. Des manipulations d'évolution expérimentale ont été entreprises pour évaluer l'impact de la plante-hôte sur la capacité mutationnelle de ces bactéries symbiotiques associéesThe two bacterial species, Sinorhizobium meliloti and S. medicae form an efficient symbiosis with Medicago truncatula, while presenting a polymorphism for nitrogen fixation. We could not confirm in this biological model the existence of mechanisms of sanctions against non-fixing symbionts, theoretically and experimentally described for other symbiotic couples. Both bacterial species might then be maintained in sympatry with the same plant-host because of different selective advantages: S. meliloti would be more competitive for plant nodulation, while S. medicae would present a better potential of fixation. Mostly because of its strong rate of recombination, S. medicae is the species presenting the more genotypic diversity. At the scale of the Mediterranean basin, S. medicae show a panmictic structure converging towards a metapopulation structuration, explaining the phylogeographic pattern revealed on this species. Its strong demographic expansion could also suggest an ongoing symbiotic specialization. S. meliloti displays an epidemic genetic structure, with possible local adaptations that however could not be proven. Lack of isolation by distance could not help in explaining the spatial distribution of the bacterial diversity, both at an intra- and interspecific scale. However, several physical and chemical soil parameters, as well as the plant cover, even on the scale of the fixed line, have an influence on the structuration of the bacterial diversity. Bacterial artificial evolution experiments were initiated to estimate the impact of the plant-host on the mutational process of these associated symbiotic bacteriaMONTPELLIER-BU Sciences (341722106) / SudocSudocFranceF

Ribosomal External and Internal Transcribed Spacers: Combined Use in the Phylogenetic Analysis of Medicago ( Leguminosae )

International audienceWe have estimated the potential phylogenetic utility of the ribosomal external transcribed spacer (ETS) from the nuclear ribosomal region. The ETS was sequenced from 13 annual Medicago (Fabaceae) species upstream a highly conserved motive which was found among many different organisms. In the genus Medicago, the ETS was found to evolve 1.5 times faster than the internal transcribed spacer and to be 1.5 times more informative. Reduced ribosomal maturation process constraints on ETS are proposed to explain the different evolutionary rates between the two spacers. Maximal phylogenetic resolution and support was obtained when the two spacers were analyzed together. No incongruence between the two spacers was found and ETS appears to be a valuable source of information for solidifying ITS plant phylogeny. The phylogeny obtained in Medicago suggests that none of the three subsections included in the study is monophyletic

Evolution of Annual Species of the Genus Medicago: A Molecular Phylogenetic Approach

International audienceWe performed a molecular phylogenetic study based on the nuclear ribosomal internal and external transcribed spacer (ITS and ETS). Thirty-one annualMedicagospecies were included in the study, representing more than half of the genus and 85% of the annuals of the genus. Major incongruences were found between phylogenetic relationships and morphological classification of the genus. Morphological and cytological traits were mapped onto the phylogeny. The most parsimonious reconstruction suggested an ancestral spiny state and a recurrent transition from spiny to spineless state. From the ancestral state of 2n=16, three loss events of chromosomes must have occurred leading to the same specific number of 14 chromosomes whereas species having 30 chromosomes form a monophyletic clade

The Spatial Structure of Sexual and Cytonuclear Polymorphism in the Gynodioecious Beta vulgaris ssp. maritima: I/ at a Local Scale

International audienceWe have analyzed the spatial distribution of the sex phenotypes and of mitochondrial, chloroplast, and nuclear markers within two gynodioecious populations of Beta vulgaris ssp. maritima. Within both populations , sexual phenotype variation is controlled mainly by the cytoplasmic genotype, although in one study population a joint polymorphism of cytonuclear factors is clearly involved. In spite of contrasts in the ecology (mainly due to different habitats), a clear common feature in both populations is the highly patchy distribution of cytoplasmic haplotypes, contrasting with the wide distribution of nuclear diversity. This high contrast between cytoplasmic vs. nuclear spatial structure may have important consequences for the maintenance of gynodioecy. It provides opportunities for differential selection since nuclear restorer alleles are expected to be selected for in the presence of their specific cytoplasmic male sterile (CMS) type, but to be neutral (or selected against if there is a cost of restoration) in the absence of their CMS type. Selective processes in such a cytonuclear landscape may explain the polymorphism we observed at restorer loci for two CMS types

Genotypic and symbiotic diversity of <em>Rhizobium</em> populations associated with cultivated lentil and pea in sub-humid and semi-arid regions of Eastern Algeria

International audienceThe genetic structure of rhizobia nodulating pea and lentil in Algeria, Northern Africa was determined. A total of 237 isolates were obtained from root nodules collected on lentil (Lens culinaris), proteaginous and forage pea (Pisum sativum) growing in two eco-climatic zones, sub-humid and semi-arid, in Eastern Algeria. They were characterised by PCR-restriction fragment length polymorphism (RFLP) of the 16S-23S rRNA intergenic region (IGS), and the nodD-F symbiotic region. The combination of these haplotypes allowed the isolates to be clustered into 26 distinct genotypes, and all isolates were classified as Rhizobium leguminosarum. Symbiotic marker variation (nodD-F) was low but with the predominance of one nod haplotype (g), which had been recovered previously at a high frequency in Europe. Sequence analysis of the IGS further confirmed its high variability in the studied strains. An AMOVA analysis showed highly significant differentiation in the IGS haplotype distribution between populations from both eco-climatic zones. This differentiation was reflected by differences in dominant genotype frequencies. Conversely, no host plant effect was detected. The nodD gene sequence-based phylogeny suggested that symbiotic gene diversity in pea and lentil nodulating rhizobial populations in Algeria was low compared to that reported elsewhere in the world

Recovery of symbiotic nitrogen fixing acacia rhizobia from Merzouga Desert sand dunes in South East Morocco - Identification of a probable new species of <em>Ensifer</em> adapted to stressed environments

Moulin Patricia: present address: Institut de Recherche pour le Développement (IRD), UMR210Eco&Sols, Campus SupAgro, Place Viala, bât. 12, 34060 Montpellier Cedex 2, France. Bena Gilles: present address: Institut de Recherche pour le Développement (IRD), UMR186IPME, Centre IRD France-Sud, 911, avenue Agropolis, BP 64501, 34394 Montpellier cedex 5, France.International audienceBacteria capable of nodulating Acacia tortilis and A. gummifera could be recovered from sand dunes collected in the Moroccan Merzouga desert. The trapping approach enabled the recovery of 17 desert rhizobia that all clustered within the Ensifer (Sinorhizobium) genus. Four isolates of the dominant genotype comprising 15 strains as well as 2 divergent strains were further characterized by MESA. Phylogenetic analyzes indicated that the dominant genetic type was belonging to a new and yet undefined species within the Ensifer genus. Interestingly, housekeeping gene phylogenies showed that this possibly new species is also present in another desert but in India. Phylogenetic analyses of nifH and nodC sequences showed high sequence conservation among the Moroccan strains belonging to the dominant genotype but high divergence with sequences from Indian isolates suggesting acquisition of symbiotic genes through Horizontal Gene Transfer. These desert rhizobia were capable of growing in media containing high salt concentrations, under high pH and most of the strains showed growth at 45 degrees C. Only recovered from desert type of Biome, yet, this new taxon appears particularly adapted to such harsh environment