jMHC: software assistant for multilocus genotyping of gene families using next-generation amplicon sequencing

Genotyping of multilocus gene families, such as the major histocompatibility complex (MHC), may be challenging because of problems with assigning alleles to loci and copy number variation among individuals. Simultaneous amplification and genotyping of multiple loci may be necessary, and in such cases, next-generation deep amplicon sequencing offers a great promise as a genotyping method of choice. Here, we describe jMHC, a computer program developed for analysing and assisting in the visualization of deep amplicon sequencing data. Software operates on FASTA files; therefore, output from any sequencing technology may be used. jMHC was designed specifically for MHC studies but it may be useful for analysing amplicons derived from other multigene families or for genotyping other polymorphic systems. The program is written in Java with user-friendly graphical interface (GUI) and can be run on Microsoft Windows, Linux OS and Mac OS.     

Halimodendrin I, a new acylated triterpene glycoside from Halimodendron halodendron (Fabaceae)

Halimodendrin I, a new acylated triterpene glycoside (1), was isolated and chemically characterized as 3β-O-palmitoyl-28-[3′-palmitoyl-β-d-glucopyranosyl]-olean-12-en-28-oic acid from the aerial part of Halimodendron halodendron (Fabaceae) by IR, 1D and 2D NMR, HR-ESI-MS and LR-ESI-MS experiments. In addition, seven known compounds were isolated and identified as: palmitic acid, glycerol-2-linoleneate, glycerol-1,3-dilinoleneate, ferulic acid, 3-O-methylquercetin, β-sitosterol, and β-sitosterol-3-O-β-d-glucopyranoside. Nine fatty acids were identified and quantified in the saponifiable matter of the hexane extract. These fatty acids are: myristic, n-pentadecanoic, palmitoleic, palmitic, linoleic, oleic, stearic, arachidic, and behenic acids. The volatile oil was isolated by hydrodistillation (0.013%, w/w) with unpleasant smell. Twenty-seven components were identified in the oil by GC/MS.     

Cleavage of prothrombin bound in immune complexes results in high thrombin enzymatic activity.

Thrombin plays a pivotal role in blood clotting as well as in the regulation of vascular remodeling and oxidative stress. Recent evidence suggests that auto-antibodies directed against prothrombin, may play an important role in the pathogenesis of atherosclerosis. It is however not clear, if prothrombin bound in an immune complex retains its clotting and regulatory properties or acts solely by increasing vascular inflammation. In order to answer this question, we used a newly developed stain for the detection of thrombin activity of such complexes. Plasma and serum samples were subjected to rocket immunoelectrophoresis in an anti-prothrombin antiserum containing agarose gel. Gel plates, covered with a nitrocellulose membrane were soaked with chromogenic thrombin substrate. The product of thrombin activity was diazotized to red azo dye bound to nitrocellulose. Activity stain revealed barely discernible rockets in plasma, but heavily stained ones in serum. Pre-incubation with trypsin enhanced activity of immunoprecipitates deriving from plasma, but not from serum. Densitometric analysis showed, that the trypsin-enhanced activity in plasma derived immune complexes was twice as high as in serum derived immunoprecipitates. Thrombin active centre is not blocked by anti-prothrombin antiserum allowing to retain thrombin activity. Moreover, prothrombin in immunoprecipitate is readily cleaved by proteolytic enzymes. This cleavage could potentially be enhanced by antibody binding, although these results need to be confirmed using different antibodies.     

Enhancing the growth of Vicia faba plants by microbial inoculation to improve their phytoremediation potential for oily desert areas

Two experiments were conducted to investigate the effect of inoculating Vicia faba plants (broad beens) raised in clean and oily sand with nodule-forming rhizobia and plant-growth-promoting rhizobacteria (PGPR) on growth of these plants in sand and to test whether this can improve the phytoremediation potential of this crop for oily desert areas. It was found that crude oil in sand at concentrations < 1.0% (w/w) enhanced the plant heights, their fresh and dry weights, the total nodule weights per plant, and the nitrogen contents of shoots and fruits. Similar enhancing effects were recorded when roots of the young plants were inoculated with nodule bacteria alone, PGPR alone, or a mixture of one strain of nodule bacteria and one of the PGPR. Such plant growth effects were associated with a better phytoremediation potential of V. faba plants for oily sand. The total numbers of oil-utilizing bacteria increased in the rhizosphere and more hydrocarbons were eliminated in sand close to the roots. The nodule bacteria tested were two strains of Rhizobium leguminosarum and the PGPR were Pseudomonas aeruginosa and Serratia liquefaciens. The four strains were found to use crude oil, n-octadecane, and phenanthrene as sole sources of carbon and energy. It was concluded that coinoculation of V. faba plant roots in oily sand with nodule bacteria and PGPR enhances the phytoremediation potential of this plant for oily desert sand through improving plant growth and nitrogen fixation.     

Resistance of sunflower to the biotrophic oomycete Plasmopara halstedii is associated with a delayed hypersensitive response within the hypocotyls

The biotrophic oomycete Plasmopara halstedii is the causal agent of downy mildew in sunflower. It penetrates the roots of both susceptible and resistant sunflower lines and grows through the hypocotyls towards the upper part of the seedling. RT-PCR analysis has shown that resistance is associated with the activation of a hsr203J-like gene, which is a molecular marker of the hypersensitive reaction in tobacco. Activation of this gene was specifically observed during the incompatible interaction and coincided with cell collapse in the hypocotyls. This HR was also associated with the early and local activation of the NPR1 gene which is a key component in the establishment of the SAR. No such HR or a significant activation of the hsr203J-like gene were observed during the compatible combination. These results suggest that the resistance of sunflower to P. halstedii is associated with an HR which fails to halt the parasite. By contrast, this HR triggers a SAR which takes places in the upper part of the hypocotyls and eventually leads to the arrest of parasite growth. A model describing the resistance of plants to root-infecting oomycetes is proposed.     

SEXUAL SELECTION COUNTERACTS EXTINCTION OF SMALL POPULATIONS OF THE BULB MITES

Genetic drift in small populations can increase frequency of deleterious recessives and consequently lead to inbreeding depression and population extinction. On the other hand, as homozygosity at deleterious recessives increases, they should be purged from populations more effectively by selection. Sexual selection has been postulated to strengthen selection against deleterious mutations, and should thus decrease extinction rate and intensify purging of inbreeding depression. We tested these predictions in the bulb mite Rhizoglyphus robini. We created 100 replicate lines of small populations (five males and five females) and in half of them experimentally removed sexual selection by enforcing monogamy. The lines were propagated for eight generations and then assayed for purging of inbreeding depression. We found that proportion of lines which went extinct was lower with sexual selection than without. We also found evidence for purging of inbreeding depression in the lines with sexual selection, but not in lines without sexual selection. Our results suggest that purging of inbreeding depression was more effective against mutations with relatively large deleterious effects. Thus, although our data clearly indicate a positive impact of sexual selection on short‐term survival of bottlenecked populations, long‐term consequences are less clear as they may be negatively impacted by accumulation of deleterious mutations of small effect.     

Meta-analysis suggests choosy females get sexy sons more than "good genes"

Female preferences for specific male phenotypes have been documented across a wide range of animal taxa, including numerous species where males contribute only gametes to offspring production. Yet, selective pressures maintaining such preferences are among the major unknowns of evolutionary biology. Theoretical studies suggest that preferences can evolve if they confer genetic benefits in terms of increased attractiveness of sons ("Fisherian" models) or overall fitness of offspring ("good genes" models). These two types of models predict, respectively, that male attractiveness is heritable and genetically correlated with fitness. In this meta-analysis, we draw general conclusions from over two decades worth of empirical studies testing these predictions (90 studies on 55 species in total). We found evidence for heritability of male attractiveness. However, attractiveness showed no association with traits directly associated with fitness (life-history traits). Interestingly, it did show a positive correlation with physiological traits, which include immunocompetence and condition. In conclusion, our results support "Fisherian" models of preference evolution, while providing equivocal evidence for "good genes." We pinpoint research directions that should stimulate progress in our understanding of the evolution of female choice.