First Microsatellite Markers Developed From Cupuassu Ests: Application In Diversity Analysis And Cross-species Transferability To Cacao

The cupuassu tree (Theobroma grandiflorum) (Willd. ex Spreng.) Schum. is a fruitful species from the Amazon with great economical potential, due to the multiple uses of its fruit's pulp and seeds in the food and cosmetic industries, including the production of cupulate, an alternative to chocolate. In order to support the cupuassu breeding program and to select plants presenting both pulp/seed quality and fungal disease resistance, SSRs from Next Generation Sequencing ESTs were obtained and used in diversity analysis. From 8,330 ESTs, 1,517 contained one or more SSRs (1,899 SSRs identified). The most abundant motifs identified in the EST-SSRs were hepta-And trinucleotides, and they were found with a minimum and maximum of 2 and 19 repeats, respectively. From the 1,517 ESTs containing SSRs, 70 ESTs were selected based on their functional annotation, focusing on pulp and seed quality, as well as resistance to pathogens. The 70 ESTs selected contained 77 SSRs, and among which, 11 were polymorphic in cupuassu genotypes. These EST-SSRs were able to discriminate the cupuassu genotype in relation to resistance/susceptibility to witches' broom disease, as well as to pulp quality (SST/ATT values). Finally, we showed that these markers were transferable to cacao genotypes, and that genome availability might be used as a predictive tool for polymorphism detection and primer design useful for both Theobroma species. To our knowledge, this is the first report involving EST-SSRs from cupuassu and is also a pioneer in the analysis of marker transferability from cupuassu to cacao. Moreover, these markers might contribute to develop or saturate the cupuassu and cacao genetic maps, respectively. The cupuassu tree (Theobroma grandiflorum) (Willd. ex Spreng.) Schum. is a fruitful species from the Amazon with great economical potential, due to the multiple uses of its fruit's pulp and seeds in the food and cosmetic industries, including the production of cupulate, an alternative to chocolate. In order to support the cupuassu breeding program and to select plants presenting both pulp/seed quality and fungal disease resistance, SSRs from Next Generation Sequencing ESTs were obtained and used in diversity analysis. From 8,330 ESTs, 1,517 contained one or more SSRs (1,899 SSRs identified). The most abundant motifs identified in the EST-SSRs were hepta-And trinucleotides, and they were found with a minimum and maximum of 2 and 19 repeats, respectively. From the 1,517 ESTs containing SSRs, 70 ESTs were selected based on their functional annotation, focusing on pulp and seed quality, as well as resistance to pathogens. The 70 ESTs selected contained 77 SSRs, and among which, 11 were polymorphic in cupuassu genotypes. These EST-SSRs were able to discriminate the cupuassu genotype in relation to resistance/susceptibility to witches' broom disease, as well as to pulp quality (SST/ATT values). Finally, we showed that these markers were transferable to cacao genotypes, and that genome availability might be used as a predictive tool for polymorphism detection and primer design useful for both Theobroma species. To our knowledge, this is the first report involving EST-SSRs from cupuassu and is also a pioneer in the analysis of marker transferability from cupuassu to cacao. Moreover, these markers might contribute to develop or saturate the cupuassu and cacao genetic maps, respectively. © 2016 Ferraz dos Santos et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.11

Numerical comparison of two approaches for the study of phase transitions in small systems

We compare two recently proposed methods for the characterization of phase transitions in small systems. The validity and usefulness of these approaches are studied for the case of the q=4 and q=5 Potts model, i.e. systems where a thermodynamic limit and exact results exist. Guided by this analysis we discuss then the helix-coil transition in polyalanine, an example of structural transitions in biological molecules.Comment: 16 pages and 7 figure

Prompt atmospheric neutrinos and muons: dependence on the gluon distribution function

We compute the next-to-leading order QCD predictions for the vertical flux of atmospheric muons and neutrinos from decays of charmed particles, for different PDF's (MRS-R1, MRS-R2, CTEQ-4M and MRST) and different extrapolations of these at small partonic momentum fraction x. We find that the predicted fluxes vary up to almost two orders of magnitude at the largest energies studied, depending on the chosen extrapolation of the PDF's. We show that the spectral index of the atmospheric leptonic fluxes depends linearly on the slope of the gluon distribution function at very small x. This suggests the possibility of obtaining some bounds on this slope in ``neutrino telescopes'', at values of x not reachable at colliders, provided the spectral index of atmospheric leptonic fluxes could be determined.Comment: 20 pages including 8 figure

AAV-CRB2 protects against vision loss in an inducible CRB1 retinitis pigmentosa mouse model

Loss of Crumbs homolog 1 (CRB1) or CRB2 proteins in Muller cells or photoreceptors in the mouse retina results in a CRB dose-dependent retinal phenotype. In this study, we present a novel Muller cell-specific Crb1(KO)Crb2(LowMGC) retinitis pigmentosa mouse model (complete loss of CRB1 and reduced levels of CRB2 specifically in Muller cells). The Crb double mutant mice showed deficits in electroretinography, optokinetic head tracking, and retinal morphology. Exposure of retinas to low levels of DL-alpha-aminoadipate acid induced gliosis and retinal disorganization in Crb1(KO)Crb2(LowMGC) retinas but not in wild-type or Crb1-deficient retinas. Crb1(KO)Crb2(LowMGC) mice showed a substantial decrease in inner/outer photoreceptor segment length and optokinetic head-tracking response. Intravitreal application of rAAV vectors expressing human CRB2 (hCRB2) in Muller cells of Crb1(KO)Crb2(LowMGC) mice subsequently exposed to low levels of DL-alpha-aminoadipate acid prevented loss of vision, whereas recombinant adeno-associated viral (rAAV) vectors expressing human CRB1 (hCRB1) did not. Both rAAV vectors partially protected the morphology of the retina. The results suggest that hCRB expression in Muller cells is vital for control of retinal cell adhesion at the outer limiting membrane, and that the rAAV-cytomegalovirus (CMV)-hCRB2 vector is more potent than rAAV-minimal CMV (CMVmin)-hCRB1 in protection against loss of vision.Ophthalmic researc

The leading particle effect from light quark fragmentation in charm hadroproduction

The asymmetry of $D^-$ and $D^+$ meson production in $\pi^-N$ scattering observed by the E791 experiment is a typical phenomenon known as the leading particle effect in charm hadroproducton. We show that the phenomenon can be explained by the effect of light quark fragmentation into charmed hadrons (LQF). Meanwhile, the size of the LQF effect is estimated from data of the E791 experiment. A comparison is made with the estimate of the LQF effect from prompt like-sign dimuon rate in neutrino experiments. The influence of the LQF effect on the measurement of nucleon strange distribution asymmetry from charged current charm production processes is briefly discussed.Comment: 6 latex pages, 1 figure, to appear in EPJ

Tree canopy enhances Collembola functional richness and diversity across typical habitats of the Gorongosa National Park (Mozambique)

ABSTRACT: The role of tree canopies in protecting soil functional diversity is essential for ecosystems threatened by the longer lasting periods of drought, which are predicted to increase in the southern afro-tropical region. Nonetheless, biodiversity inventories of soil mesofauna are scarce in afro-tropical ecosystems, even in emblematic and well-studied protected areas, such as the Gorongosa National Park (GNP). Understanding the interrelationships between tree canopies and soil fauna functional diversity can provide insightful information for future adaptive management to protect wildlife and ecosystem services in the GNP, in the context of climate change. Here we assessed collembolan functional type richness and functional diversity in the dry period and during the rainfall across major GNP habitat types: miombo forests, mixed forests, and open savanna/floodplains. Besides the significant positive influence of rainfall, habitat types also influenced functional type’ richness and diversity of collembolan life-forms. Environmental gradients across habitat types, namely the area of tree canopy cover and its indirect effect on soil local conditions (pH and nutrient availability), explained collembolan functional parameters. Calcium concentrations and soil alkalinity significantly enhanced collembolan functional type richness and functional diversity, respectively. Collembola survival across GNP habitats depended on the canopy buffering in the dry sampling period. These results highlight the key role of tree canopies in creating suitable microhabitat conditions supporting soil functional diversity and the sustainability of soil processes and ecosystem services in GNP.info:eu-repo/semantics/publishedVersio

Microarray and morphological analysis of early postnatal CRB2 mutant retinas on a pure C57BL/6J genetic background

In humans, the Crumbs homologue-1 (CRB1) gene is mutated in progressive types of autosomal recessive retinitis pigmentosa and Leber congenital amaurosis. Th