The scale of population structure in Arabidopsis thaliana

The population structure of an organism reflects its evolutionary history and influences its evolutionary trajectory. It constrains the combination of genetic diversity and reveals patterns of past gene flow. Understanding it is a prerequisite for detecting genomic regions under selection, predicting the effect of population disturbances, or modeling gene flow. This paper examines the detailed global population structure of Arabidopsis thaliana. Using a set of 5,707 plants collected from around the globe and genotyped at 149 SNPs, we show that while A. thaliana as a species self-fertilizes 97% of the time, there is considerable variation among local groups. This level of outcrossing greatly limits observed heterozygosity but is sufficient to generate considerable local haplotypic diversity. We also find that in its native Eurasian range A. thaliana exhibits continuous isolation by distance at every geographic scale without natural breaks corresponding to classical notions of populations. By contrast, in North America, where it exists as an exotic species, A. thaliana exhibits little or no population structure at a continental scale but local isolation by distance that extends hundreds of km. This suggests a pattern for the development of isolation by distance that can establish itself shortly after an organism fills a new habitat range. It also raises questions about the general applicability of many standard population genetics models. Any model based on discrete clusters of interchangeable individuals will be an uneasy fit to organisms like A. thaliana which exhibit continuous isolation by distance on many scales

Reference Gene Validation for RT-qPCR, a Note on Different Available Software Packages

Background: An appropriate normalization strategy is crucial for data analysis from real time reverse transcription polymerase chain reactions (RT-qPCR). It is widely supported to identify and validate stable reference genes, since no single biological gene is stably expressed between cell types or within cells under different conditions. Different algorithms exist to validate optimal reference genes for normalization. Applying human cells, we here compare the three main methods to the online available RefFinder tool that integrates these algorithms along with R-based software packages which include the NormFinder and GeNorm algorithms. Results: 14 candidate reference genes were assessed by RT-qPCR in two sample sets, i.e. a set of samples of human testicular tissue containing carcinoma in situ (CIS), and a set of samples from the human adult Sertoli cell line (FS1) either cultured alone or in co-culture with the seminoma like cell line (TCam-2) or with equine bone marrow derived mesenchymal stem cells (eBM-MSC). Expression stabilities of the reference genes were evaluated using geNorm, NormFinder, and BestKeeper. Similar results were obtained by the three approaches for the most and least stably expressed genes. The R-based packages NormqPCR, SLqPCR and the NormFinder for R script gave identical gene rankings. Interestingly, different outputs were obtained between the original software packages and the RefFinder tool, which is based on raw Cq values for input. When the raw data were reanalysed assuming 100% efficiency for all genes, then the outputs of the original software packages were similar to the RefFinder software, indicating that RefFinder outputs may be biased because PCR efficiencies are not taken into account. Conclusions: This report shows that assay efficiency is an important parameter for reference gene validation. New software tools that incorporate these algorithms should be carefully validated prior to use

Solvent Extraction of Magnesium by Cyanex 272: Experimental study and modeling

International audienc

Extraction of Nb(v) by quaternary ammonium-based solvents: toward organic hexaniobate systems.

Solvent extraction of Nb(v) from alkaline aqueous media using quaternary ammonium solutions, especially Aliquat® 336 diluted in an aliphatic diluent, was investigated. The hexaniobate ions (HxNb6O19x-8) were extracted into the organic phase with very high yields at room temperature and within a few minutes, affording easy access to organic solutions of hexaniobates. Several parameters were found to influence the extraction of HxNb6O19x-8 including the nature and concentration of alkali cations, confirming subtle effects previously described for polyoxoniobates such as ion-pairing with alkali ions. The extraction of HxNb6O19x-8 with Aliquat® 336 is also influenced if competing anions are present in the aqueous phase (NO3-, Cl-, C2O42-, SO42- and CO32-) and varies with the pH mainly due to the competitive extraction of hydroxide ions at high pH. The co-extraction of sodium ions with HxNb6O19x-8 was observed as well as the co-extraction of water molecules, suggesting a self-association of the extractant. The proposed liquid-liquid extraction generic system paves the way for innovative niobium (and potentially tantalum) hydrometallurgical processes and it may also afford more direct routes for exploring the chemistry of hexaniobates in organic solvents

On the origin of germ cell neoplasia in situ: Dedifferentiation of human adult Sertoli cells in cross talk with seminoma cells in vitro

Germ cell neoplasia in situ (GCNIS) is the noninvasive precursor of testicular germ cell tumors type II, the most common cancer in young men, which originates from embryonic germ cells blocked in their maturation. GCNIS is associated with impaired Sertoli cells (SCs) that express fetal keratin 18 (KRT18) and the pluripotency factor SRY-Box transcription factor 2 (SOX2). According to the current theory concerning the origin of GCNIS, these SCs are prepubertal cells arrested in their maturation due to (epi)genetic anomalies and/or environmental antiandrogens. Thus, they are unable to support the development of germ cells, which leads to their maturational block and further progresses into GCNIS. Alternatively, these SCs are hypothesized to be adult cells dedifferentiating secondarily under the influence of GCNIS. To examine whether tumor cells can dedifferentiate SCs, we established a coculture model of adult human SCs (FS1) and a seminoma cell line similar to GCNIS (TCam-2). After 2 wk of coculture, FS1 cells showed progressive expression of KRT18 and SOX2, mimicking the in vivo changes. TCam-2 cells showed SOX2 expression and upregulation of further pluripotency- and reprogramming-associated genes, suggesting a seminoma to embryonal carcinoma transition. Thus, our FS1/TCam-2 coculture model is a valuable tool for investigating interactions between SCs and seminoma cells. Our immunohistochemical and ultrastructural studies of human testicular biopsies with varying degrees of GCNIS compared to biopsies from fetuses, patients with androgen insensitivity syndrome, and patients showing normal spermatogenesis further suggest that GCNIS-associated SCs represent adult cells undergoing progressive dedifferentiation

Prédiction infrarouge des teneurs en lactoferrine dans le lait: potentiel indicateur de mammite

peer reviewe

BestKeeper outputs of reference genes ranked by the correlation coefficients (A&C) or by their standard deviation (B&D) for the two datasets, i.e. FS1 (A&B) and CIS (C&D).

<p>BestKeeper outputs of reference genes ranked by the correlation coefficients (A&C) or by their standard deviation (B&D) for the two datasets, i.e. FS1 (A&B) and CIS (C&D).</p

geNorm outputs with efficiency corrected data (A&C) and without efficiency corrected data (B&D) for the two datasets, i.e. FS1 (A&B) and CIS (C&D).

<p>geNorm outputs with efficiency corrected data (A&C) and without efficiency corrected data (B&D) for the two datasets, i.e. FS1 (A&B) and CIS (C&D).</p