The 2HA line of Medicago truncatula has characteristics of an epigenetic mutant that is weakly ethylene insensitive

BACKGROUND The Medicago truncatula 2HA seed line is highly embryogenic while the parental line Jemalong rarely produces embryos. The 2HA line was developed from one of the rare Jemalong regenerates and this method for obtaining a highly regenerable genotype in M. truncatula is readily reproducible suggesting an epigenetic mechanism. Microarray transcriptomic analysis showed down regulation of an ETHYLENE INSENSITIVE 3-like gene in 2HA callus which provided an approach to investigating epigenetic regulation of genes related to ethylene signalling and the 2HA phenotype. Ethylene is involved in many developmental processes including somatic embryogenesis (SE) and is associated with stress responses. RESULTS Microarray transcriptomic analysis showed a significant number of up-regulated transcripts in 2HA tissue culture, including nodule and embryo specific genes and transposon-like genes, while only a few genes were down-regulated, including an EIN3-like gene we called MtEIL1. This reduced expression was associated with ethylene insensitivity of 2HA plants that was further investigated. The weak ethylene insensitivity affected root and nodule development. Sequencing of MtEIL1 found no difference between 2HA and wild-type plants. DNA methylation analysis of MtEIL1 revealed significant difference between 2HA and wild-type plants. Tiling arrays demonstrated an elevated level of miRNA in 2HA plants that hybridised to the antisense strand of the MtEIL1 gene. AFLP-like methylation profiling revealed more differences in DNA methylation between 2HA and wild-type. Segregation analysis demonstrated the recessive nature of the eil1 phenotype and the dominant nature of the SE trait. CONCLUSIONS We have demonstrated that EIL1 of Medicago truncatula (MtEIL1) is epigenetically silenced in the 2HA seed line. The possible cause is an elevated level of miRNA that targets its 3'UTR and is also associated with DNA methylation of MtEIL1. Down regulation of MtEIL1 makes it possible to form nodules in the presence of ethylene and affects root growth under normal conditions. Segregation analysis showed no association between MtEIL1 expression and SE in culture but the role and mechanism of ethylene signalling in the process of plant regeneration through SE requires further investigation. The work also suggests that epigenetic changes to a particular gene induced in culture can be fixed in regenerated plants.This work was funded by the Australian Research Council (CEO348212) through the ARC Centre of Excellence for Integrative Legume Research (CILR)

Validation of a FFQ for estimating whole-grain cereal food intake

Estimation of whole-grain (WG) food intake in epidemiological and nutritional studies is normally based on general diet FFQ, which are not designed to specifically capture WG intake. To estimate WG cereal intake, we developed a forty-three-item FFQ focused on cereal product intake over the past month. We validated this questionnaire against a 3-d-weighed food record (3DWFR) in thirty-one subjects living in the French-speaking part of Switzerland (nineteen female and twelve male). Subjects completed the FFQ on day 1 (FFQ1), the 3DWFR between days 2 and 13 and the FFQ again on day 14 (FFQ2). The subjects provided a fasting blood sample within 1 week of FFQ2. Total cereal intake, total WG intake, intake of individual cereals, intake of different groups of cereal products and alkylresorcinol (AR) intake were calculated from both FFQ and the 3DWFR. Plasma AR, possible biomarkers for WG wheat and rye intake were also analysed. The total WG intake for the 3DWFR, FFQ1, FFQ2 was 26 (sd 22), 28 (sd 25) and 21 (sd 16)g/d, respectively. Mean plasma AR concentration was 55·8 (sd 26·8)nmol/l. FFQ1, FFQ2 and plasma AR were correlated with the 3DWFR (r 0·72, 0·81 and 0·57, respectively). Adjustment for age, sex, BMI and total energy intake did not affect the results. This FFQ appears to give a rapid and adequate estimate of WG cereal intake in free-living subject

Calling in Call-out Culture: An Analysis on Call-out Culture and its influence on Filipino Twitter

Call-out culture has become a questionable phenomenon in and out of Filipino Twitter due to the differing ideologies that participants have perpetuated, separating Filipino communities based on their standing on certain topics on the internet. The reason it has become dubious is due to the bullying that occurs because of the call-outs. Previous research had stated that call-outs have started shifting from being a tool used to oppose abuse into an accessory for building fame on the internet. The researchers used Foucauldian Discourse Analysis to analyze several replies, tweets, and quoted tweets from Filipinos on Twitter. The data was put under the lens of the synopticon theory and Althusser’s concept of the Ideological State Apparatus. The analysis has led to the conclusion that there is an evident divide between Filipino communities, and, amid the discord with themes of colonialism and racism, public figures can use it as a device to manipulate the mindset of the masses

Phenotypic and genotypic characterization of Bradyrhizobia nodulating the leguminous tree Acacia albida

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Functional variants of human papillomavirus type 16 demonstrate host genome integration and transcriptional alterations corresponding to their unique cancer epidemiology

BACKGROUND: Human papillomaviruses (HPVs) are a worldwide burden as they are a widespread group of tumour viruses in humans. Having a tropism for mucosal tissues, high-risk HPVs are detected in nearly all cervical cancers. HPV16 is the most common high-risk type but not all women infected with high-risk HPV develop a malignant tumour. Likely relevant, HPV genomes are polymorphic and some HPV16 single nucleotide polymorphisms (SNPs) are under evolutionary constraint instigating variable oncogenicity and immunogenicity in the infected host. RESULTS: To investigate the tumourigenicity of two common HPV16 variants, we used our recently developed, three-dimensional organotypic model reminiscent of the natural HPV infectious cycle and conducted various “omics” and bioinformatics approaches. Based on epidemiological studies we chose to examine the HPV16 Asian-American (AA) and HPV16 European Prototype (EP) variants. They differ by three non-synonymous SNPs in the transforming and virus-encoded E6 oncogene where AAE6 is classified as a high- and EPE6 as a low-risk variant. Remarkably, the high-risk AAE6 variant genome integrated into the host DNA, while the low-risk EPE6 variant genome remained episomal as evidenced by highly sensitive Capt-HPV sequencing. RNA-seq experiments showed that the truncated form of AAE6, integrated in chromosome 5q32, produced a local gene over-expression and a large variety of viral-human fusion transcripts, including long distance spliced transcripts. In addition, differential enrichment of host cell pathways was observed between both HPV16 E6 variant-containing epithelia. Finally, in the high-risk variant, we detected a molecular signature of host chromosomal instability, a common property of cancer cells. CONCLUSIONS: We show how naturally occurring SNPs in the HPV16 E6 oncogene cause significant changes in the outcome of HPV infections and subsequent viral and host transcriptome alterations prone to drive carcinogenesis. Host genome instability is closely linked to viral integration into the host genome of HPV-infected cells, which is a key phenomenon for malignant cellular transformation and the reason for uncontrolled E6 oncogene expression. In particular, the finding of variant-specific integration potential represents a new paradigm in HPV variant biology. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-016-3203-3) contains supplementary material, which is available to authorized users

The ISLAndS project II: The Lifetime Star Formation Histories of Six Andromeda dSphs

The Initial Star formation and Lifetimes of Andromeda Satellites (ISLAndS) project uses Hubble Space Telescope imaging to study a representative sample of six Andromeda dSph satellite companion galaxies. The main goal of the program is to determine whether the star formation histories (SFHs) of the Andromeda dSph satellites demonstrate significant statistical differences from those of the Milky Way, which may be attributable to the different properties of their local environments. Our observations reach the oldest main sequence turn-offs, allowing a time resolution at the oldest ages of ~ 1 Gyr, which is comparable to the best achievable resolution in the MW satellites. We find that the six dSphs present a variety of SFHs that are not strictly correlated with luminosity or present distance from M31. Specifically, we find a significant range in quenching times (lookback times from 9 to 6 Gyr), but with all quenching times more than ~ 6 Gyr ago. In agreement with observations of Milky Way companions of similar mass, there is no evidence of complete quenching of star formation by the cosmic UV background responsible for reionization, but the possibility of a degree of quenching at reionization cannot be ruled out. We do not find significant differences between the SFHs of the three members of the vast, thin plane of satellites and the three off-plane dSphs. The primary difference between the SFHs of the ISLAndS dSphs and Milky Way dSph companions of similar luminosities and host distances is the absence of very late quenching (< 5 Gyr ago) dSphs in the ISLAndS sample. Thus, models that can reproduce satellite populations with and without late quenching satellites will be of extreme interest.Comment: 24 pages, 11 figures, 3 tables, submitted to the Ap

The ISLANDS project I: Andromeda XVI, An Extremely Low Mass Galaxy not Quenched by Reionization

Based on data aquired in 13 orbits of HST time, we present a detailed evolutionary history of the M31 dSph satellite Andromeda XVI, including its life-time star formation history, the spatial distribution of its stellar populations, and the properties of its variable stars. And XVI is characterized by prolonged star formation activity from the oldest epochs until star formation was quenched ~6 Gyr ago, and, notably, only half of the mass in stars of And XVI was in place 10 Gyr ago. And XVI appears to be a low mass galaxy for which the early quenching by either reionization or starburst feedback seems highly unlikely, and thus, is most likely due to an environmental effect (e.g., an interaction), possibly connected to a late infall in the densest regions of the Local Group. Studying the star formation history as a function of galactocentric radius, we detect a mild gradient in the star formation history: the star formation activity between 6 and 8 Gyr ago is significantly stronger in the central regions than in the external regions, although the quenching age appears to be the same, within 1 Gyr. We also report the discovery of 9 RR Lyrae stars, 8 of which belong to And XVI. The RR Lyrae stars allow a new estimate of the distance, (m-M)0= 23.72+/-0.09 mag, which is marginally larger than previous estimates based on the tip of the red giant branch.Comment: Accepted for publication on Ap

Predicting mental imagery based BCI performance from personality, cognitive profile and neurophysiological patterns

Mental-Imagery based Brain-Computer Interfaces (MI-BCIs) allow their users to send commands to a computer using their brain-activity alone (typically measured by ElectroEncephaloGraphy— EEG), which is processed while they perform specific mental tasks. While very promising, MI-BCIs remain barely used outside laboratories because of the difficulty encountered by users to control them. Indeed, although some users obtain good control performances after training, a substantial proportion remains unable to reliably control an MI-BCI. This huge variability in user-performance led the community to look for predictors of MI-BCI control ability. However, these predictors were only explored for motor-imagery based BCIs, and mostly for a single training session per subject. In this study, 18 participants were instructed to learn to control an EEG-based MI-BCI by performing 3 MI-tasks, 2 of which were non-motor tasks, across 6 training sessions, on 6 different days. Relationships between the participants’ BCI control performances and their personality, cognitive profile and neurophysiological markers were explored. While no relevant relationships with neurophysiological markers were found, strong correlations between MI-BCI performances and mental-rotation scores (reflecting spatial abilities) were revealed. Also, a predictive model of MI-BCI performance based on psychometric questionnaire scores was proposed. A leave-one-subject-out cross validation process revealed the stability and reliability of this model: it enabled to predict participants’ performance with a mean error of less than 3 points. This study determined how users’ profiles impact their MI-BCI control ability and thus clears the way for designing novel MI-BCI training protocols, adapted to the profile of each user

Magnetoconductance anisotropy of a polymer thin film at the onset of metallicity

Thin films of poly(2,5-bis(3-dodecyl-2-yl)-thieno[3,2-b] thiophene) (C12-PBTTT) polymer under electrolyte gating and doping are investigated as model systems for organic thin films devices approaching the metallic side of a metal-insulator (M-I) transition. For the most doped samples, with an estimated density reaching 8 x 10(20) cm(-3) holes and a conductivity exceeding 1000 S cm(-1), a positive high-field magnetoconductance is found in a limited temperature range window and only when the field is perpendicular to the sample plane. This signature of weak localization, combined with indications of finite zero-temperature conductivity, allows us to identify delocalized metallic-like transport in these thin films, even though the conductivity decreases when cooling down the samples. (C) 2015 AIP Publishing LLC