Large multi-gene phylogenetic trees of the grasses (Poaceae): progress towards complete tribal and generic level sampling.

In this paper we included a very broad representation of grass family diversity (84% of tribes and 42% of genera). Phylogenetic inference was based on three plastid DNA regions rbcL, matK and trnL-F, using maximum parsimony and Bayesian methods. Our results resolved most of the subfamily relationships within the major clades (BEP and PACCMAD), which had previously been unclear, such as, among others the: (i) BEP and PACCMAD sister relationship, (ii) composition of clades and the sister-relationship of Ehrhartoideae and Bambusoideae + Pooideae, (iii) paraphyly of tribe Bambuseae, (iv) position of Gynerium as sister to Panicoideae, (v) phylogenetic position of Micrairoideae. With the presence of a relatively large amount of missing data, we were able to increase taxon sampling substantially in our analyses from 107 to 295 taxa. However, bootstrap support and to a lesser extent Bayesian inference posterior probabilities were generally lower in analyses involving missing data than those not including them. We produced a fully resolved phylogenetic summary tree for the grass family at subfamily level and indicated the most likely relationships of all included tribes in our analysis.

A Novel Pulse-Chase SILAC Strategy Measures Changes in Protein Decay and Synthesis Rates Induced by Perturbation of Proteostasis with an Hsp90 Inhibitor.

Standard proteomics methods allow the relative quantitation of levels of thousands of proteins in two or more samples. While such methods are invaluable for defining the variations in protein concentrations which follow the perturbation of a biological system, they do not offer information on the mechanisms underlying such changes. Expanding on previous work [1], we developed a pulse-chase (pc) variant of SILAC (stable isotope labeling by amino acids in cell culture). pcSILAC can quantitate in one experiment and for two conditions the relative levels of proteins newly synthesized in a given time as well as the relative levels of remaining preexisting proteins. We validated the method studying the drug-mediated inhibition of the Hsp90 molecular chaperone, which is known to lead to increased synthesis of stress response proteins as well as the increased decay of Hsp90 "clients". We showed that pcSILAC can give information on changes in global cellular proteostasis induced by treatment with the inhibitor, which are normally not captured by standard relative quantitation techniques. Furthermore, we have developed a mathematical model and computational framework that uses pcSILAC data to determine degradation constants kd and synthesis rates Vs for proteins in both control and drug-treated cells. The results show that Hsp90 inhibition induced a generalized slowdown of protein synthesis and an increase in protein decay. Treatment with the inhibitor also resulted in widespread protein-specific changes in relative synthesis rates, together with variations in protein decay rates. The latter were more restricted to individual proteins or protein families than the variations in synthesis. Our results establish pcSILAC as a viable workflow for the mechanistic dissection of changes in the proteome which follow perturbations. Data are available via ProteomeXchange with identifier PXD000538.

Latest Miocene - Pliocene Larger Foraminifera and depositional environments of the carbonate bank of La Désirade Island, Guadeloupe (French Antilles)

In this paper we present first results of the study of planktonic Foraminifera, large benthic Foraminifera and carbonate facies of La Désirade, aiming at a definition of the age and depositional environments of the Neogene carbonates of this island. The study of planktonic Foraminifera from the Detrital Offshore Limestones (DOL) of the Anciènne Carrière allows to constrain the biochronology of this formation to the lower Zone N19 and indicates a latest Miocene to early Pliocene (5.48 - 4.52 Ma) age. Large benthic Foraminifera were studied both as isolated and often naturally split specimens from the DOL, and in thin sections of limestones from the DOL and the Limestone Table (LT). The assemblages of Foraminifera include Nummulitidae, Amphisteginidae, Asterigerinidae, Peneroplidae, Soritidae, Rotalidae (Globigerinidae: Globigerinoides, Sphaeroidenellopsis, Orbulina) and incrusting Foraminifera (Homotrema and Sporadotrema). The genera Amphistegina, Archaias and Operculina are discussed. Concerning the Nummulitidae we include both "Paraspiroclypeus" chawneri and "Nummulites" cojimarensis, as well as a newly described species, Operculina desiradensis new species, in the genus Operculina, because the differences between these 3 species are rather on the specific than the generic level, while their morphology, studied by SEM, is compatible with the definition of the genus Operculina (D'Orbigny1826, emend. Hottinger 1977). The three species can be easily distinguished on the basis of their differences in spiral growth: while O. desiradensis has an overall logarithmic spiral growth, O. cojimarensis and especially O. chawneri show a tighter and more geometric spiral growth. O. cojimarensis and O. chawneri were originally described from Cuba in outcrops originally dated as Oligocene and later redated as early Pliocene. Therefore, O. chawneri was considered until now as restricted to the early Pliocene. However, in the absence of a detailed morphometric and biostratigraphic study of the Caribbean Neogene nummulitids, it is difficult to evaluate the biochronologic range of these species.The history of the carbonates begins with the initial tectonic uplift and erosion of the Jurassic igneous basement of La Désirade, that must have occurred at latest in late Miocene times, when sea-level oscillated around a long term stable mean. The rhythmic deposition of the Désirade Limestone Table (LT) can be explained by synsedimentary subsidence in a context of rapidly oscillating sea-level due to precession-driven (19-21 kyr) glacio-eustatic sea-level changes during the latest Miocene- Pliocene. Except for a thin reef cap present at the eastern edge of the LT, no other in-place reefal constructions have been observed in the LT. The DOL of western Désirade are interpreted as below wave base gravity deposits that accumulated beneath a steep fore-reef slope. They document the mobilisation of carbonate material (including Larger Foraminifera) from an adjacent carbonate platform by storms and their gravitational emplacement as debris and grain flows. The provenance of both the reefal carbonate debris and the tuffaceous components redeposited in the carbonates of La Désirade must be to the west, i. e. the carbonate platforms of Marie Galante and Grande Terre.

Paleohydrological Reconstruction from Late Holocene Records in Interdune Lakes (N'Guigmi, Northern Bank of the Lake Chad, Niger)

An old erg covers the northern part of the Lake Chad basin. This dune landform allowed the formation of many inter- dune ponds of various sizes. Still present in certain zones where the groundwater level is high (e.g. Kanem, southern Manga), these ponds formed in the past a vast network of lacustrine microsystems, as shown by the nature and the dis- tribution of their deposits. In the Manga, these interdune deposits represent the main sedimentary records of the Holo- cene environmental succession. Their paleobiological (pollens, diatoms, ostracods) and geochemical (δ18O, δ13C, Sr/ Ca) contents are often the basis for paleoenvironmental reconstruction. On the other hand, their sedimentological char- acters are rarely exploited. This study of palustro-lacustrine deposits of the Holocene N'Guigmi lake (northern bank of the Lake Chad; Niger) is based on the relationships between the sedimentological features and the climato-hydrological fluctuations. The mineralogical parameters (e.g. calcium carbonate content, clay mineralogy) and the nature of autoch- thonous mineralization (i.e. amorphous silica, clays, calcium carbonates) can be interpreted using a straightforward hy- dro-sedimentary model. Established to explain the geochemical dynamics of Lake Chad, this model is based on a bio- geochemical cycle of the main elements (i.e. silicium, calcium) directly controlled by the local hydrological balance (i.e. rainfall/evaporation ratio). All these results show that a detailed study of sedimentological features can provide impor- tant paleohydrological informations about the regional aridification since ca 6500 14C BP.