Resource availability affects the structure of a natural bacteria-bacteriophage community

Antagonistic networks are known to be structured in the wild, but knowledge on how this structure may change as a response to environmental perturbations is scarce. We describe a natural bipartite network between bacteria and lytic bacteriophages, and investigate how it is affected by environmental productivity in the form of different resource levels for the bacteria. We report that low amounts of resource decrease phage generality and lead to less robust and less stable communities. We discuss how resource levels in nature may alter the structure of complex communities.     

Dietary Abrasiveness Is Associated with Variability of Microwear and Dental Surface Texture in Rabbits

Dental microwear and 3D surface texture analyses are useful in reconstructing herbivore diets, with scratches usually interpreted as indicators of grass dominated diets and pits as indicators of browse. We conducted feeding experiments with four groups of rabbits (Oryctolagus cuniculus) each fed a different uniform, pelleted diet (lucerne, lucerne & oats, grass & oats, grass). The lowest silica content was measured in the lucerne and the highest in the grass diet. After 25 weeks of exposure to the diets, dental castings were made of the rabbit''s lower molars. Occlusal surfaces were then investigated using dental microwear and 3D areal surface texture analysis. In terms of traditional microwear, we found our hypothesis supported, as the grass group showed a high proportion of (long) “scratches” and the lucerne group a high proportion of “pits”. Regardless of the uniform diets, variability of microwear and surface textures was higher when silica content was low. A high variability in microwear and texture analysis thus need not represent dietary diversity, but can also be related to a uniform, low-abrasion diet. The uniformity or variability of microwear/texture analysis results thus might represent varying degrees of abrasion and attrition rather than a variety of diet items per se.     

Tree diversity and conservation value of Ngovayang’s lowland forests,Cameroon

The Ngovayang Massif of southern Cameroon is a range of small hills near the Atlantic coast, in the Lower Guinea floristic region. This region is known to harbor forests with high levels of biodiversity and endemism, but this Massif is botanically poorly known. We assessed tree species diversity, floristic composition and level of endemism of the Ngovayang forest, comparing it with other sites in Central Africa. Five 1-ha permanent plots within old-growth lowland forests of the Ngovayang Massif were censused. A total of 2,658 individuals with dbh ≥ 10 cm were recorded, belonging to 293 species, 170 genera and 60 families. The mean number of stems was 532 ± 75 stems ha⁻¹. Taking into account other data available, the list of vascular plants known in the Massif reaches a total of 450 species. We found 47 species of high conservation value, including Cameroon endemics and other rare and threatened species. Species richness and endemism are comparable to those of the richest known sites in Central African forests. The forests of Ngovayang were found to be particularly rich in Fabaceae-Caesalpinioideae. Topographic heterogeneity, high precipitation and atmospheric humidity owing to the proximity of the ocean, and permanence of a forest cover during past geological times probably all contribute to explaining the Massif’s high tree diversity and endemism. This study highlights the botanical importance of the poorly studied Ngovayang forest within the Lower Guinea region, justifying efforts for improved assessment of this value and for the development of suitable national conservation strategies.     

Phosphorylation-dependent structure of ATF4 peptides derived from a human ATF4 protein, a member of the family of transcription factors

ATF4 plays a crucial role in the cellular response to stress and the F-box protein β-TrCP, the receptor component of the SCF E3 ubiquitin ligase responsible for ATF4 degradation by the proteasome, binds to ATF4, and controls its stability. Association between the two proteins depends on ATF4 phosphorylation of serine residues 219 and 224 present in the context of DpSGXXXpS, which is similar but not identical to the DpSGXXpS motif found in most other substrates of β-TrCP. We used NMR spectroscopy to analyze the structure of the 23P-ATF4 peptide. The 3D structure of the ligand was determined on the basis of NOESY restraints that provide an hairpin loop structure. In contrast, no ordered structure was observed in the NMR experiments for the nonphosphorylated 23-ATF4 in solution. This structural study provides information, which could be used to study the β-TrCP receptor–ligand interaction in docking procedure. Docking studies showed that the binding epitope of the ligand, is represented by the DpSGIXXpSXE motif. 23P-ATF4 peptide fits the binding pocket of protein β-TrCP very well, considering that the DpSGIXXpSXE motif adopts an S-turning conformation contrary to the extended DpSGXXpS motif in the other known β-TrCP ligands.     

Spatial and temporal ecological diversity amongst Eocene primates of France: evidence from teeth

Diet is of paramount importance in the life of a primate. It is also highly variable, as potential food sources vary in spatial distribution and availability over time. The fossil record, due to its fragmentary nature, offers few possibilities to assess the dietary range of a given primate across its spatial and temporal distribution. Here we focus on three taxa, Leptadapis magnus (Adapidae, Adapiformes), Necrolemur cf. antiquus (Microchoeridae, Omomyiformes), and Pseudoloris parvulus (Microchoeridae, Omomyiformes). These taxa occur at different localities of the Late Eocene in the south of France ranging from MP16 (Robiac, Lavergne; 39 Ma), MP17a (La Bouffie, Euzet, Fons 4; 38 Ma) to MP17b (Perrière; 37 Ma). Diets of fossil taxa are assessed here by dental microwear analysis using a comparative database of 11 species of living strepsirhines. On the whole, leaves were a preferred food for the large-bodied Leptadapis (4-5 kg). However, the diet of this taxon varied from a mix of leaves and fruit at La Bouffie, a closed tropical rain forest environment, to a strictly leaf-eating one in the more open environment of Perrière. Based on body mass (200-350 g) and dental microwear patterns, Necrolemur had a mainly fruit-based diet, perhaps supplemented by insects. However, the comparison of the different localities reveals the dietary range of this small-bodied omomyiform which seems to vary between insects and a much softer diet. Pseudoloris had a diet strictly based on insects. Contrary to Leptadapis or Necrolemur, its diet seems to have been confined to insects whatever the locality considered.     

Dental microwear textural analyses to track feeding ecology of reindeer: a comparison of two contrasting populations in Norway

Using dental microwear textural analysis, we aim to explore variations in feeding habits within and between wild reindeer populations (Rangifer tarandus) in Norway. Specimens from the two wild reindeer areas of Knutshø and Hardangervidda were hunted between late August and the end of September 2014, and found to share very similar topological and ecological characteristics (continental alpine tundra). Despite the homogenisation of plant resources at the end of the snow-free period, dental microwear textural analysis on cheek teeth indicates differences in feeding behaviors between the two populations, in that reindeer from Knutshø might display a more “grazing” signal than the ones from Hardangervidda. Such differences in dental microwear textures reflect the differences in feeding habits that could be linked with differences in population density of reindeer. The Knutshø reindeer density is lower than at Hardangervidda, where primary food resources like grasses, sedges, and lichens are less abundant. Analyses also show the differences in gender for the population of Knutshø, but more studies are necessary for the clearest interpretation of data. Our results emphasize the need to explore local variations at a monthly time frame in order to better assess the versatility of dental microwear textures before applying this kind of analysis to either extant or extinct multi-population scales.     

Tracking a refined eIF4E-binding motif reveals Angel1 as a new partner of eIF4E

The initiation factor 4E (eIF4E) is implicated in most of the crucial steps of the mRNA life cycle and is recognized as a pivotal protein in gene regulation. Many of these roles are mediated by its interaction with specific proteins generally known as eIF4E-interacting partners (4E-IPs), such as eIF4G and 4E-BP. To screen for new 4E-IPs, we developed a novel approach based on structural, in silico and biochemical analyses. We identified the protein Angel1, a member of the CCR4 deadenylase family. Immunoprecipitation experiments provided evidence that Angel1 is able to interact in vitro and in vivo with eIF4E. Point mutation variants of Angel1 demonstrated that the interaction of Angel1 with eIF4E is mediated through a consensus eIF4E-binding motif. Immunofluorescence and cell fractionation experiments showed that Angel1 is confined to the endoplasmic reticulum and Golgi apparatus, where it partially co-localizes with eIF4E and eIF4G, but not with 4E-BP. Furthermore, manipulating Angel1 levels in living cells had no effect on global translation rates, suggesting that the protein has a more specific function. Taken together, our results illustrate that we developed a powerful method for identifying new eIF4E partners and open new perspectives for understanding eIF4E-specific regulation.     

Solution structure of a peptide derived from the oncogenic protein beta-Catenin in its phosphorylated and nonphosphorylated states

Beta-Catenin plays an essential role in the Wingless/Wnt signaling cascade. Phosphorylation of beta-Catenin in its N-terminal region by the kinase GSK-3beta is required for the interaction with the SCF-beta-TrCP protein complex that targets beta-Catenin for proteasome degradation. In the present work, we used two peptides of 32 amino acids referred to beta-Cat17-48 and P-beta-Cat17-48 for the phosphorylated peptide at the two sites Ser33 and Ser37. Circular dichroism and NMR techniques were used to assess the influence of the phosphorylation. The spectra of the peptides at pH 7.2 were completely assigned. Analysis of the medium-range NOE connectivities indicated that beta-Cat17-48 seems to be only poorly folded. These data are in agreement with the result of structure calculations. P-beta-Cat17-48 possesses two helical segments around the DpSGXXpS motif, which forms a large bent with the phosphate groups pointing out of the structure. On the contrary, beta-Cat17-48 shows less well-defined secondary structures and appears as a more flexible peptide, but adopts in the motif DSGXXS a more compact conformation than P-beta-Cat17-48. Differences in this molecular region suggest that conformational changes of phosphorylated beta-Catenin play an important role for the interaction with the SCF-beta-TrCP protein complex.