Authenticated DNA from Ancient Wood Remains

• Background The reconstruction of biological processes and human activities during the last glacial cycle relies mainly on data from biological remains. Highly abundant tissues, such as wood, are candidates for a genetic analysis of past populations. While well-authenticated DNA has now been recovered from various fossil remains, the final ‘proof' is still missing for wood, despite some promising studies. • Scope The goal of this study was to determine if ancient wood can be analysed routinely in studies of archaeology and palaeogenetics. An experiment was designed which included blind testing, independent replicates, extensive contamination controls and rigorous statistical tests. Ten samples of ancient wood from major European forest tree genera were analysed with plastid DNA markers. • Conclusions Authentic DNA was retrieved from wood samples up to 1000 years of age. A new tool for real-time vegetation history and archaeology is ready to us

Thorough assessment of DNA preservation from fossil bone and sediments excavated from a late Pleistocenee-Holocene cave deposit on Kangaroo Island, South Australia

Fossils and sediments preserved in caves are an excellent source of information for investigating impacts of past environmental changes on biodiversity. Until recently studies have relied on morphology-based palaeontological approaches, but recent advances in molecular analytical methods offer excellent potential for extracting a greater array of biological information from these sites. This study presents a thorough assessment of DNA preservation from late Pleistocene-Holocene vertebrate fossils and sediments from Kelly Hill Cave Kangaroo Island, South Australia. Using a combination of extraction techniques and sequencing technologies, ancient DNA was characterised from over 70 bones and 20 sediment samples from 15 stratigraphic layers ranging in age from >20 ka to ~6.8 ka. A combination of primers targeting marsupial and placental mammals, reptiles and two universal plant primers were used to reveal genetic biodiversity for comparison with the mainland and with the morphological fossil record for Kelly Hill Cave. We demonstrate that Kelly Hill Cave has excellent long-term DNA preservation, back to at least 20 ka. This contrasts with the majority of Australian cave sites thus far explored for ancient DNA preservation, and highlights the great promise Kangaroo Island caves hold for yielding the hitherto-elusive DNA of extinct Australian Pleistocene species

The precursors of chocolate aroma.

The subject of this research was an experimental study of the development of chocolate aroma during the commercial processing of cocoa beans. The components of unroasted aroma cocoa beans have been fractionated, and the various groups of substances obtained tested for the development of aroma when roasted. The results obtained provide further evidence of the involvement of simple amino acids, reducing sugars and flavonoids in the formation of the primary aroma of chocolate products, and a mechanism for the formation and mixing of these substances during cocoa fermentation is described. Model mixtures of these compounds have been examined in order to assess the extent of the contribution of individual compounds to the production of the aroma. The reaction of these model mixtures have also been examined under the conditions obtaining during commercial bean roasting, and combined gas chromstography-mase spectrometry has been used to compare their volatile reaction products with these present in roasted cocoa beans. The results of these studies indicate the importance of the natural environment of the precursors in the control of the extent of subsequent reactions, and the consequences of the 'dry state' reaction conditions in this respect. Various types of compound formed in these reactions are described and their possible importance in the recognition of chocolate aroma is discussed. The experimental results are discussed in terms of literature surveys of the current state of knowledge of both chocolate aroma development, and the aroma potential of amino acid-reducing sugar reactions

High-Throughput Sequencing of Six Bamboo Chloroplast Genomes: Phylogenetic Implications for Temperate Woody Bamboos (Poaceae: Bambusoideae)

BACKGROUND: Bambusoideae is the only subfamily that contains woody members in the grass family, Poaceae. In phylogenetic analyses, Bambusoideae, Pooideae and Ehrhartoideae formed the BEP clade, yet the internal relationships of this clade are controversial. The distinctive life history (infrequent flowering and predominance of asexual reproduction) of woody bamboos makes them an interesting but taxonomically difficult group. Phylogenetic analyses based on large DNA fragments could only provide a moderate resolution of woody bamboo relationships, although a robust phylogenetic tree is needed to elucidate their evolutionary history. Phylogenomics is an alternative choice for resolving difficult phylogenies. METHODOLOGY/PRINCIPAL FINDINGS: Here we present the complete nucleotide sequences of six woody bamboo chloroplast (cp) genomes using Illumina sequencing. These genomes are similar to those of other grasses and rather conservative in evolution. We constructed a phylogeny of Poaceae from 24 complete cp genomes including 21 grass species. Within the BEP clade, we found strong support for a sister relationship between Bambusoideae and Pooideae. In a substantial improvement over prior studies, all six nodes within Bambusoideae were supported with ≥0.95 posterior probability from Bayesian inference and 5/6 nodes resolved with 100% bootstrap support in maximum parsimony and maximum likelihood analyses. We found that repeats in the cp genome could provide phylogenetic information, while caution is needed when using indels in phylogenetic analyses based on few selected genes. We also identified relatively rapidly evolving cp genome regions that have the potential to be used for further phylogenetic study in Bambusoideae. CONCLUSIONS/SIGNIFICANCE: The cp genome of Bambusoideae evolved slowly, and phylogenomics based on whole cp genome could be used to resolve major relationships within the subfamily. The difficulty in resolving the diversification among three clades of temperate woody bamboos, even with complete cp genome sequences, suggests that these lineages may have diverged very rapidly

Deciduous Trees and the Application of Universal DNA Barcodes: A Case Study on the Circumpolar Fraxinus

The utility of DNA barcoding for identifying representative specimens of the circumpolar tree genus Fraxinus (56 species) was investigated. We examined the genetic variability of several loci suggested in chloroplast DNA barcode protocols such as matK, rpoB, rpoC1 and trnH-psbA in a large worldwide sample of Fraxinus species. The chloroplast intergenic spacer rpl32-trnL was further assessed in search for a potentially variable and useful locus. The results of the study suggest that the proposed cpDNA loci, alone or in combination, cannot fully discriminate among species because of the generally low rates of substitution in the chloroplast genome of Fraxinus. The intergenic spacer trnH-psbA was the best performing locus, but genetic distance-based discrimination was moderately successful and only resulted in the separation of the samples at the subgenus level. Use of the BLAST approach was better than the neighbor-joining tree reconstruction method with pairwise Kimura's two-parameter rates of substitution, but allowed for the correct identification of only less than half of the species sampled. Such rates are substantially lower than the success rate required for a standardised barcoding approach. Consequently, the current cpDNA barcodes are inadequate to fully discriminate Fraxinus species. Given that a low rate of substitution is common among the plastid genomes of trees, the use of the plant cpDNA “universal” barcode may not be suitable for the safe identification of tree species below a generic or sectional level. Supplementary barcoding loci of the nuclear genome and alternative solutions are proposed and discussed

Détermination d'une loi de comportement pour le cisaillement des sols pulvérulents

La définition, pour un sol, de la loi liant les contraintes aux déformations permet, grâce au calcul sur ordinateur, de prévoir le comportement d'ouvrages complexes.La présente communication résoud théoriquement le problème de l'écrouissage, dans le cas de la contrainte moyenne constante ou variant peu. La démonstration s'appuie sur la formule de Frydman qui exprime la variation de l'énergie de déformation du sol. On en déduit la direction de la déformation plastique, puis sa longueur. Les formules obtenues sont directement applicables à la méthode des contraintes initiales dans un calcul par éléments finis.On étudie ensuite la direction de la déformation plastique à la rupture, ce qui permet de compléter le modèle théorique présenté grâce à l'hypothèse de la plasticité non standard.Les calculs de plusieurs séries d'essais triaxiaux, réalisés sur des matériaux divers (de façon à faire varier les quatre paramètres), montrent la bonne coïncidence entre les résultats théoriques et expérimentaux. Ceci permet de conclure à la validité de la loi proposée

Geographic isolation and evolution of Mediterranean endemic Cyclamen: insights from chloroplast trnL (UAA) intron sequence variation

International audienceIn this study we construct a phylogenetic hypothesis for the relatedness among disjunct subspecies of Cyclamen repandum and its two allopatric congeners, C. creticum and C. balearicum in order to examine the evolutionary divergence of currently isolated populations across the western Mediterranean. The most parsimonious phylogenetic tree obtained from sequencing the cpDNA trnL (UAA) intron suggests a major phylogeographic divide in southern Greece between two clades. The first clade comprises samples of C. repandum subsp. peloponnesiacum (from the Peloponnese) and C. creticum (from Crete). The second comprises samples of C. repandum subsp. repandum (from Croatia, Italy, southern France, Corsica, Sardinia and Sicily), C. repandum subsp. rhodense (from Rhodes and Kos) and C. balearicum (from the Balearic Islands and southern France). These data suggest that C. creticum has evolved in allopatry from C. repandum subsp. peloponnesiacum and that C. balearicum and C. repandum ssp. rhodense have diverged from C. repandum subsp. repandum at its western and eastern distribution limits. At one small site on Corsica, a population of C. repandum may have introgressed with relictual populations of C. balearicum. These divergence patterns illustrate how a phylogenetic perspective can be used to better understand the evolution of endemism in the Mediterranean flora

Universal Primers For Amplification Of 3 Noncoding Regions Of Chloroplast Dna

Times Cited: 1334International audienceSix primers for the amplification of three non-coding regions of chloroplast DNA via the polymerase chain reaction (PCR) have been designed. In order to find out whether these primers were universal, we used them in an attempt to amplify DNA from various plant species. The primers worked for most species tested including algae, bryophytes, pteridophytes, gymnosperms and angiosperms. The fact that they amplify chloroplast DNA non-coding regions over a wide taxonomic range means that these primers may be used to study the population biology (in supplying markers) and evolution (inter- and probably intraspecific phylogenies) of plants

Étude et réalisation de la boîte à plan de cisaillement vertical

Afin de représenter le mode réel de rupture lors d’un glissement d’un remblai, un essai de cisaillement original « à plan de cisaillement vertical » a été mis au point. Pour cela, un appareil a été conçu et construit. Les caractéristiques mécaniques du sol utilisé, obtenues à l’aide de cette boîte, sont comparées à celles obtenues à la boîte à plan de cisaillement horizontal. Les déchets de matières plastiques peuvent constituer des nappes de renforts discontinues pour améliorer les caractéristiques mécaniques des sols des remblais. Des essais effectués sur la nouvelle boîte de cisaillement ont permis de quantifier la résistance à la traction apportée par ces renforts. Une correspondance a été établie avec les valeurs obtenues pour des nappes continues