Functional proteome analysis of the banana plant (Musa spp.) using de novo sequence analysis of derivatized peptides

We report the use of chemical derivatization with MALDI-MS/MS analysis for de novo sequence analysis. Using three frequently used homology-based search algorithms, we were able to identify more than 40 proteins from banana, a nonmodel plant with unsequenced genome. Furthermore, this approach allowed the identification of different isoforms. We also observed that the identification score obtained varied according to the position of the peptide sequences in the query using the MS-Blast algorithm.     

Ecology,conservation, and phylogenetic position of the Madagascar Jacana Actophilornis albinucha

The Madagascar Jacana Actophilornis albinucha (Jacanidae) is an endemic shorebird found in the threatened wetlands of western Madagascar. This species is presumed to exhibit classical polyandry; however, few data are available to support that assumption. More generally, a lack of basic understanding of this species hinders conservation efforts. We conducted the most extensive study of the Madagascar Jacana to date, and report on its: 1) distribution, population size and density; 2) degree of sexual size dimorphism; and 3) phylogenetic position. The surveys were conducted at 54 lakes, between January and October in 2016. Madagascar Jacana were found at 22 lakes, and within these were distributed at a mean density of 3.5 ± 0.74 [SE] individuals per hectare of surveyed habitat. We estimate the global population size to be between 975 and 2 064 individuals, and habitat destruction appears to be the main threat to the species. Females were significantly larger than males, consistent with reports for other Jacanidae species. Using a mitochondrial DNA fragment, we expanded the Jacanidae genetic phylogeny, and confirmed that Madagascar Jacana is the sister species to the African Jacana Actophilornis africanus. Further studies are urgently needed to thoroughly re-assess the threat status and population trend of the Madagascar Jacana.     

A comprehensive examination of the network position hypothesis across multiple river metacommunities

The hierarchical branching nature of river networks can have a strong influence on the assembly of freshwater communities. This unique structure has spurred the development of the network position hypothesis (NPH), which states that the strength of different assembly processes depends on the community position in the river network. Specifically, it predicts that 1) headwater communities should be exclusively controlled by the local environment given that they are more isolated and environmentally heterogeneous relative to downstream reaches. In contrast, 2) downstream communities should be regulated by both environmental and dispersal processes due to increased connectivity given their central position in the riverscape. Although intuitive, the NPH has only been evaluated on a few catchments and it is not yet clear whether its predictions are generalizable. To fill this gap, we tested the NPH on river dwelling fishes using an extensive dataset from 28 French catchments. Stream and climatic variables were assembled to characterize environmental conditions and graph theory was applied on river networks to create spatial variables. We tested both predictions using variation partitioning analyses separately for headwater and downstream sites in each catchment. Only 10 catchments supported both predictions, 11 failed to support at least one of them, while in 7 the NPH was partially supported given that spatial variables were also significant for headwater communities. We then assembled a dataset at the catchment scale (e.g. topography, environmental heterogeneity, network connectivity) and applied a classification tree analysis (CTA) to determine which regional property could explain these results. The CTA showed that the NPH was not supported in catchments with high heterogeneity in connectivity among sites. In more homogeneously connected catchments, the NPH was only supported when headwaters were more environmentally heterogeneous than downstream sites. We conclude that the NPH is context dependent even for taxa dispersing exclusively within streams.     

Inhibition of NF-kappaB activity by IkappaBbeta in association with kappaB-Ras

IkappaBbeta, one of the major IkappaB proteins, is only partially degraded in response to most extracellular signals. However, the molecular mechanism of this event is unknown. We show here that IkappaBbeta exists in at least two different forms: one that is bound to the NF-kappaB dimer and the other bound to both NF-kappaB and kappaB-Ras, a Ras-like small G protein. Removal of cellular kappaB-Ras enhances whereas excess kappaB-Ras blocks induced IkappaBbeta degradation. Remarkably, kappaB-Ras functions in both GDP- and GTP-bound states, and mutations of the conserved guanine-binding residues of kappaB-Ras abrogate its ability to block degradation of IkappaBbeta. kappaB-Ras also directly blocks the in vitro phosphorylation of IkappaBbeta by IKKbeta. These observations suggest that IkappaBbeta in the ternary complex is resistant to degradation by most signals. We suggest that specific signals, in addition to those that activate only IKK, are essential for the complete degradation of IkappaBbeta.     

Diterpenes from the leaves of Croton zambesicus

Two new trachylobane- and one isopimarane-type diterpenoids: ent-18-hydroxy-trachyloban-3-one; ent-trachyloban-3-one; isopimara-7,15-dien-3beta-ol, were isolated from the leaves of Croton zambesicus, together with trans-phytol, beta-sitosterol, alpha-amyrin and stigmasterol. The structures were determined by extensive NMR techniques and X-ray analysis. The cytotoxicity of these compounds has been evaluated on cancer and non-cancer cell-lines.     

Docking study of ligands into the colchicine binding site of tubulin

Cancer is a major cause of mortality in developed countries, following only cardiovascular diseases. Death of cancerous cells can be achieved by stopping mitosis and the antimitotic class of drugs formed by the spindle poisons can be used for this purpose. Their role is to disorganize the mitotic spindle by targeting its main constituent, the microtubules, themselves made of heterodimers of alpha and beta-tubulin. They disrupt the dynamics of the microtubules either by stabilizing them, as do paclitaxel or epothilones, or destabilizing them, as do colchicine. The binding site of colchicine seems to lie between the two units of the tubulin dimer. Here, we report on the characterization of this site by the docking of a series of reference compounds, and the subsequent docking of ligands prepared in our laboratory.     

RNAi-mediated Hip1R silencing results in stable association between the endocytic machinery and the actin assembly machinery

Actin filaments transiently associate with the endocytic machinery during clathrin-coated vesicle formation. Although several proteins that might mediate or regulate this association have been identified, in vivo demonstration of such an activity has not been achieved. Huntingtin interacting protein 1R (Hip1R) is a candidate cytoskeletal-endocytic linker or regulator because it binds to clathrin and actin. Here, Hip1R levels were lowered by RNA interference (RNAi). Surprisingly, rather than disrupting the transient association between endocytic and cytoskeletal proteins, clathrin-coated structures (CCSs) and their endocytic cargo became stably associated with dynamin, actin, the Arp2/3 complex, and its activator, cortactin. RNAi double-depletion experiments demonstrated that accumulation of the cortical actin-endocytic complexes depended on cortactin. Fluorescence recovery after photobleaching showed that dynamic actin filament assembly can occur at CCSs. Our results provide evidence that Hip1R helps to make the interaction between actin and the endocytic machinery functional and transient.     

Real-Time State Estimation in a Flight Simulator Using fNIRS

Working memory is a key executive function for flying an aircraft. This function is particularly critical when pilots have to recall series of air traffic control instructions. However, working memory limitations may jeopardize flight safety. Since the functional near-infrared spectroscopy (fNIRS) method seems promising for assessing working memory load, our objective is to implement an on-line fNIRS-based inference system that integrates two complementary estimators. The first estimator is a real-time state estimation MACD-based algorithm dedicated to identifying the pilot’s instantaneous mental state (not-on-task vs. on-task). It does not require a calibration process to perform its estimation. The second estimator is an on-line SVM-based classifier that is able to discriminate task difficulty (low working memory load vs. high working memory load). These two estimators were tested with 19 pilots who were placed in a realistic flight simulator and were asked to recall air traffic control instructions. We found that the estimated pilot’s mental state matched significantly better than chance with the pilot’s real state (62% global accuracy, 58% specificity, and 72% sensitivity). The second estimator, dedicated to assessing single trial working memory loads, led to 80% classification accuracy, 72% specificity, and 89% sensitivity. These two estimators establish reusable blocks for further fNIRS-based passive brain computer interface development.