Latent Dirichlet Allocation reveals spatial and taxonomic structure in a DNA‐based census of soil biodiversity from a tropical forest

High‐throughput sequencing of amplicons from environmental DNA samples permits rapid, standardized and comprehensive biodiversity assessments. However, retrieving and interpreting the structure of such data sets requires efficient methods for dimensionality reduction. Latent Dirichlet Allocation (LDA) can be used to decompose environmental DNA samples into overlapping assemblages of co‐occurring taxa. It is a flexible model‐based method adapted to uneven sample sizes and to large and sparse data sets. Here, we compare LDA performance on abundance and occurrence data, and we quantify the robustness of the LDA decomposition by measuring its stability with respect to the algorithm's initialization. We then apply LDA to a survey of 1,131 soil DNA samples that were collected in a 12‐ha plot of primary tropical forest and amplified using standard primers for bacteria, protists, fungi and metazoans. The analysis reveals that bacteria, protists and fungi exhibit a strong spatial structure, which matches the topographical features of the plot, while metazoans do not, confirming that microbial diversity is primarily controlled by environmental variation at the studied scale. We conclude that LDA is a sensitive, robust and computationally efficient method to detect and interpret the structure of large DNA‐based biodiversity data sets. We finally discuss the possible future applications of this approach for the study of biodiversity.     

Agonistic and proximity patterns in enclosed mouflon (Ovis gmelini) ewes in relation to age, reproductive status and kinship

Agonistic and proximity patterns of mouflon sheep (Ovis gmelini) were studied in a group of enclosed females during two lambing periods. A non-random linear-tending hierarchy almost stable over the 2-years was found. Age was correlated to social rank and to the distribution of agonistic acts by females. The rank of the yearling females was linked to the rank of their mothers. The age of the animal and the degree of relatedness with its congeners appeared as main determinants of the proximity patterns of ewes. Strong associations between closely related females (especially mothers and daughters), brought out the existence of a familial structure in mouflon. Otherwise, we found a strong inter-attraction between yearlings, which received a large number of aggressions from older females. That revealed peer grouping superimposed on familial structures. Age also seemed to influence ‘sociality’ of females, older females tending to associate less with conspecifics than younger ones.     

Monophyly and relationships of the tribe Exaceae (Gentianaceae) inferred from nuclear ribosomal and chloroplast DNA sequences

Both chloroplast trnL (UAA) intron and nuclear ribosomal ITS sequences highly confirmed the monophyly of the tribes of the Gentianaceae defined by the recent classification, and revealed the tribe Exaceae as a basal clade just next to the basal-most lineage, the tribe Saccifolieae. Within the tribe Exaceae, Sebaea (except Sebaea madagascariensis) appeared as the most basal clade as the sister group to the rest of the tribe. The Madagascan endemic genera Gentianothamnus and Tachiadenus were very closely related to each other, together standing as sister to a clade comprising Sebaea madagascariensis, Ornichia, and Exacum. The saprophytic genus Cotylanthera nested deeply inside Exacum. Sebaea madagascariensis was shown closer to the Madagascan endemic genus Ornichia than to any other sampled Sebaea species. Exacum appeared as the most derived taxon within this tribe. The topology of the phylogenetic trees conform with the Gondwana vicariance hypothesis regarding the biogeography of Exaceae. However, no evidence for matching the older relationships within the family to the tectonic history could be corroborated with various divergence time analyses. Divergence dating estimated a post-Gondwana diverging of the Gentianaceae about 50 million years ago (MYA), and the tribe Exaceae as about 40 MYA. The Mozambique Channel land-bridge could have played an important role in the biogeographic history of the tribe Exaceae.     

Systematic capsule gene disruption reveals the central role of galactose metabolism on Cryptococcus neoformans virulence

The polysaccharidic capsule is the main virulence factor of Cryptococcus neoformans. It primarily comprised of two polysaccharides: glucuronoxylomannan (GXM, 88% of the capsule mass) and galactoxylomannan (GalXM, 7% of the capsule mass). We constructed a large collection of mutant strains in which genes potentially involved in capsule biosynthesis were deleted. We used a new post-genomic approach to study the virulence of the strains. Primers specific for unique tags associated with the disruption cassette were used in a real-time PCR virulence assay to measure the fungal burden of each strain in different organs of mice in multi-infection experiments. With this very sensitive assay, we identified a putative UDP-glucose epimerase (Uge1p) and a putative UDP-galactose transporter (Ugt1p) essential for C. neoformans virulence. The uge1Delta and ugt1Delta strains are temperature sensitive and do not produce GalXM but synthesize a larger capsule. These mutant strains (GalXM negative, GXM positive) are not able to colonize the brain even at the first day of infection whereas GXM-negative strains (GalXM positive) can still colonize the brain, although less efficiently than the wild-type strain.     

Fibropapillomatosis Prevalence and Distribution in Immature Green Turtles (Chelonia mydas) in Martinique Island (Lesser Antilles)

Fibropapillomatosis (FP) threatens the survival of green turtle (Chelonia mydas) populations at a global scale, and human activities are regularly pointed as causes of high FP prevalence. However, the association of ecological factors with the disease’s severity in complex coastal systems has not been well established and requires further studies. Based on a set of 405 individuals caught over ten years, this preliminary study provides the first insight of FP in Martinique Island, which is a critical development area for immature green turtles. Our main results are: (i) 12.8% of the individuals were affected by FP, (ii) FP has different prevalence and temporal evolution between very close sites, (iii) green turtles are more frequently affected on the upper body part such as eyes (41.4%), fore flippers (21.9%), and the neck (9.4%), and (iv) high densities of individuals are observed on restricted areas. We hypothesise that turtle’s aggregation enhances horizontal transmission of the disease. FP could represent a risk for immature green turtles’ survival in the French West Indies, a critical development area, which replenishes the entire Atlantic population. Continuing scientific monitoring is required to identify which factors are implicated in this panzootic disease and ensure the conservation of the green turtle at an international scale.

     

Delineation of the roles of paracrine and autocrine interleukin-6 (IL-6) in myeloma cell lines in survival versus cell cycle. A possible model for the cooperation of myeloma cell growth factors

Primary myeloma cells rapidly apoptose as soon as they are removed from their bone-marrow environment. A likely explanation is that the tumor environment produces survival factors that may counteract a spontaneous activation of pro-apoptotic program. Additional factors may trigger cell cycling in surviving myeloma cells. Interleukin-6 (IL-6) is a well recognized myeloma cell growth factor produced mainly by the tumor environment. However, myeloma cells themselves may produce low levels of autocrine IL-6. The respective roles of paracrine versus autocrine IL-6 are a matter of debate. We investigated these roles using the XG-6 myeloma cell line whose growth is dependent on addition of exogenous IL-6, despite its weak IL-6 mRNA and protein expression. The apoptosis induced by exogenous IL-6 deprivation was blocked by transferring the Mcl-1 gene coding for an anti-apoptotic protein in XG-6 cells. An XG-6Mcl-1 cell line which can survive and grow without adding IL-6 was obtained. We show that anti-IL-6 or anti-gp130 antibodies abrogated cell cycling whereas they did not affect cell survival. These data indicate that the weak autocrine IL-6 produced by myeloma cells is sufficient to trigger cell cycling whereas their survival requires large exogenous IL-6 concentrations. This important role of autocrine IL-6 has to be considered when evaluating the mechanism of action of myeloma cell growth factors. These factors may actually block an activated pro-apoptotic program, making possible a weak production of autocrine IL-6 to promote cell cycling.     

Analysis of protein contacts into Protein Units

Three-dimensional structures of proteins are the support of their biological functions. Their folds are maintained by inter-residue interactions which are one of the main focuses to understand the mechanisms of protein folding and stability. Furthermore, protein structures can be composed of single or multiple functional domains that can fold and function independently. Hence, dividing a protein into domains is useful for obtaining an accurate structure and function determination.     

In Vivo Characterization of Dynein-Driven nanovectors Using Drosophila Oocytes

Molecular motors transport various cargoes including vesicles, proteins and mRNAs, to distinct intracellular compartments. A significant challenge in the field of nanotechnology is to improve drug nuclear delivery by engineering nanocarriers transported by cytoskeletal motors. However, suitable in vivo models to assay transport and delivery efficiency remain very limited. Here, we develop a fast and genetically tractable assay to test the efficiency and dynamics of fluospheres (FS) using microinjection into Drosophila oocytes coupled with time-lapse microscopy. We designed dynein motor driven FS using a collection of dynein light chain 8 (LC8) peptide binding motifs as molecular linkers and characterized in real time the efficiency of the FS movement according to its linker’s sequence. Results show that the conserved LC8 binding motif allows fast perinuclear nanoparticle''s accumulation in a microtubule and dynein dependent mechanism. These data reveal the Drosophila oocyte as a new valuable tool for the design of motor driven nanovectors.