RNA delivery by extracellular vesicles in mammalian cells and its applications.

The term 'extracellular vesicles' refers to a heterogeneous population of vesicular bodies of cellular origin that derive either from the endosomal compartment (exosomes) or as a result of shedding from the plasma membrane (microvesicles, oncosomes and apoptotic bodies). Extracellular vesicles carry a variety of cargo, including RNAs, proteins, lipids and DNA, which can be taken up by other cells, both in the direct vicinity of the source cell and at distant sites in the body via biofluids, and elicit a variety of phenotypic responses. Owing to their unique biology and roles in cell-cell communication, extracellular vesicles have attracted strong interest, which is further enhanced by their potential clinical utility. Because extracellular vesicles derive their cargo from the contents of the cells that produce them, they are attractive sources of biomarkers for a variety of diseases. Furthermore, studies demonstrating phenotypic effects of specific extracellular vesicle-associated cargo on target cells have stoked interest in extracellular vesicles as therapeutic vehicles. There is particularly strong evidence that the RNA cargo of extracellular vesicles can alter recipient cell gene expression and function. During the past decade, extracellular vesicles and their RNA cargo have become better defined, but many aspects of extracellular vesicle biology remain to be elucidated. These include selective cargo loading resulting in substantial differences between the composition of extracellular vesicles and source cells; heterogeneity in extracellular vesicle size and composition; and undefined mechanisms for the uptake of extracellular vesicles into recipient cells and the fates of their cargo. Further progress in unravelling the basic mechanisms of extracellular vesicle biogenesis, transport, and cargo delivery and function is needed for successful clinical implementation. This Review focuses on the current state of knowledge pertaining to packaging, transport and function of RNAs in extracellular vesicles and outlines the progress made thus far towards their clinical applications

American oil palm from Brazil: genetic diversity, population structure, and core collection.

The American oil palm [Elaeis oleifera (Knuth) Cortés] has pronounced importance in oil palm breeding programs. Here, a germplasm bank (GB) of E. oleifera plants collected in the Amazon rainforest in Brazil was submitted to single nucleotide polymorphism (SNP) marker identification, selection, and use, aiming to characterize genetic diversity and population structure and to design a core collection (CC). Five hundred and fifty-three plants from 206 subsamples, collected at 19 localities spread throughout six geographic regions, were submitted to genotyping-by-sequencing analysis. A set of 1,827 high-quality SNP markers was then selected and used to run the genetic diversity and population structure analysis. The genetic diversity found is of moderate degree, and probably only a small portion of the species diversity is represented in the collection. The possible reason for that is the collecting strategy used, which collected subsamples only around the most prominent watercourses in the region. The average degree of genetic differentiation among subsamples is very high, indicating the presence of high interpopulation differentiation. The collection showed a low level of endogamy. The low average gene flow found indicates that genetic isolation caused by drift is occurring, and there is a need to review the conservation strategy. A set of 245 SNPs distributed throughout all 16 chromosomes was used to design CC based on maximizing the strategy of diversity. The optimal adjustment of the validated parameters, maintained while taking fewest subsamples, led to the choice of a model containing 20% of the entire collection as the ideal to form the CC

Contrasting patterns of historical colonization in white oaks (Quercus spp.) in California and Europe

Phylogeography allows the inference of evolutionary processes that have shaped the current distribution of genealogical lineages across a landscape. In this perspective, comparative phylogeographical analyses are useful in detecting common historical patterns by either comparing different species within the same area within a continent or by comparing similar species in different areas. Here, we analyse one taxon (the white oak, genus Quercus , subgenus Quercus , section Quercus ) that is widespread worldwide, and we evaluate its phylogeographical pattern on two different continents: western North America and Western Europe. The goals of the present study are: (i) to compare the chloroplast genetic diversity found in one California oak species vs. that found in the extensively studied European oak species (in France and the Iberian Peninsula); (ii) to contrast the geographical structure of haplotypes between these two taxa and test for a phylogeographical structure for the California species. For this purpose, we used the same six maternally inherited chloroplast microsatellite markers and a similar sampling strategy. The haplotype diversity within site as well as the differentiation among sites was alike in both taxa, but the Californian species has higher allelic richness with a greater number of haplotypes (39 vs. 11 in the European white oak complex). Furthermore, in California these 39 haplotypes are distributed locally in patches while in the European oaks haplotypes are distributed into lineages partitioned longitudinally. These contrasted patterns could indicate that gene movement in California oak populations have been more stable in response to past climatic and geological events, in contrast to their European counterparts

Impact of asymmetric male and female gamete dispersal on allelic diversity and spatial genetic structure in valley oak (Quercus lobata Née)

The distribution and abundance of genetic diversity in plant populations is initiated by sexually asymmetric propagule dispersal through pollen and seeds. Because these processes occur serially, it is not transparent how each contributes to subsequent patterns of genetic diversity. Using combined seedling/seed coat assay for naturally distributed seedlings of Quercus lobata Née, we extracted male and female gametic genotypes, and then assessed (wind-vectored) paternal and (gravity- and animal-vectored) maternal contributions to spatially distributed allelic diversity. We evaluated 200 naturally recruited seedlings from 4 open patches away from any adult canopies (denoted ‘open’), and 174 seedlings from 14 patches immediately beneath adult canopies (denoted ‘canopy’). The open patches included 19 % long distant dispersal events of >1 km while the canopy patches contained seedlings from one tree overhead. For each patch type, we partitioned average allelic diversity for six microsatellite loci for the whole study site (γ) into separate within-patch (α) and among-patch (β) components, translated into among-patch divergence (δ). We found that α-diversity resulting from seed dispersal was much less than that from pollen dispersal in both patch types, while total γ-diversity across the site was similar. Divergence (δ) among canopy patches was significantly greater than δ among open patches. We then evaluated spatial genetic autocorrelation (kinship) patterns for both open and canopy strata, separately for male and female gametes. Female gametes showed sharply declining kinship with increasing distance for canopy patches and modestly for open patches. In sharp contrast, male gametes from both patches showed only subtle decline of kinship, but seedlings still showed significant structure across patch types. On balance, sexual asymmetry in propagule dispersal shapes both the abundance and distribution of allelic diversity, with pollen dispersal promoting overall diversity but reducing spatial structure, but seed-dispersal reduces overall diversity and markedly increases spatial genetic structure. © 2015, Springer International Publishing Switzerland

Using seedling and pericarp tissues to determine maternal parentage of dispersed valley oak recruits

The spatial pattern of established seedlings yields valuable information about variation in fecundity, dispersal, and spatial structure of distributed recruits, but separating maternal and paternal contributions in monoecious species has been hampered by the "2 parent" problem. It is now possible to determine the maternal parentage of established recruits with genetic assay of maternally derived tissues of the seed or fruit, but the DNA of weathered maternal tissues often yields unreliable genotypes, reducing the practical range of such assay. We develop a mixed assay of seedling and seed (pericarp) tissues and illustrate it with distributed recruits of California valley oak (Quercus lobata Née). Detailed analysis indicates correct maternal assignment rates of canopy patch recruits of 56% (seedling assay only) versus 94% (mixed assay). For open patch recruits, maternal assignment rates were less than 50% (seedling assay only) versus 91% (mixed assay). The strategy of choice is to use seedling genotypes to identify a small set of credible parental candidates and then deploy 3-4 well-chosen pericarp/endocarp loci to reduce that list to a single obvious maternal candidate. The increase in the number of recruits available for subsequent analysis is pronounced, increasing precision and statistical power for subsequent inference. © The American Genetic Association. 2012. All rights reserved

PSA Software for parental structure analysis of seed or seedling patches

Parental structure analysis (PSA) is a computer program to analyse separate contributions of paternal and maternal parents to postdispersal plant offspring. The program provides joint estimates of maternal, paternal and cross-parental correlations within and among a set of predefined groups of seeds or seedlings, as well as derivative estimates of effective parental numbers. PSA utilizes data sets that distinguish between maternal and paternal contributions to the genotype of each offspring in the sample, but does not require parental samples per se. The approach requires assay of codominant diploid markers from both seed coat (maternally inherited) and seedling/embryo (biparentally inherited) tissues for each offspring. A simulation analysis of PSA's performance shows that it provides fairly accurate parental correlation estimates from affordable sampling effort. PSA should be of interest to plant biologists studying the interplay between dispersal, demography and genetics, as well as plant-animal interactions. © 2012 Blackwell Publishing Ltd