Selection of miRNA reference genes for plant defence studies in rice (Oryza sativa)

RT-qPCR is a widely used method to investigate the expression levels of genes under certain conditions. A key step, however, to have reliable results is the normalization of expression. For every experimental condition, suitable reference genes must be chosen. These reference genes must not be affected by differences in experimental conditions. MicroRNAs are regulatory RNA molecules, able to direct the expression levels of protein coding genes. In plants, their attributed functions range from roles in development to immunity. In this work, microRNAs (miRNAs) are evaluated for their suitability as reference genes in rice after infection with root-knot nematode Meloidogyne graminicola or after priming with beta-amino butyric acid. The evaluation was based on their amplification efficiency and their stability estimates according to geNorm, NormFinder and BestKeeper. All tested miRNAs, excluding one, were considered acceptable for normalization. Furthermore, miRNAs were validated using miRNA sequencing data. The set of microRNAs miR390-5p and miR7694-3p was found to be the most stable combination under the tested conditions. Another miRNA set consisting of miR7694-3p, miR1868 and miR1849 also shows potential to be used for miRNA expression normalization under experimental conditions beyond the scope of this study. This work is the first report on reference miRNAs in rice for the purpose of plant defence studies

OERopoly: A game to generate collective intelligence around OER

Collective Intelligence (CI ) is a phenomenon that emerges at the crossroads of three worlds: Open Educational Resources (OER), Web 2.0 technologies and Online Learning Communities. Building CI for the OER movement means capturing the richness of information, experiences, knowledge and resources, that the movement is constantly generating, in a way that they can be shared and reused for the benefit of the movement itself. The organisation of CI starts from collecting the knowledge and experiences of OER's practitioners and scholars in new creative forms, and then situating this knowledge in a collective 'pot' from where it can be leveraged with new 'intelligent' meanings and toward new 'intelligent' goals. This workshop is an attempt to do so by engaging participants in a CI experience, in which they will contribute to, and at the same time take something from, the existing CI around OER, Web 2.0 technologies and Online Learning Communities

Systemic suppression of the shoot metabolism upon rice root nematode infection

Hirschmanniella oryzae is the most common plant-parasitic nematode in flooded rice cultivation systems. These migratory animals penetrate the plant roots and feed on the root cells, creating large cavities, extensive root necrosis and rotting. The objective of this study was to investigate the systemic response of the rice plant upon root infection by this nematode. RNA sequencing was applied on the above-ground parts of the rice plants at 3 and 7 days post inoculation. The data revealed significant modifications in the primary metabolism of the plant shoot, with a general suppression of for instance chlorophyll biosynthesis, the brassinosteroid pathway, and amino acid production. In the secondary metabolism, we detected a repression of the isoprenoid and shikimate pathways. These molecular changes can have dramatic consequences for the growth and yield of the rice plants, and could potentially change their susceptibility to above-ground pathogens and pests

Robustness of fossil fish teeth for seawater neodymium isotope reconstructions under variable redox conditions in an ancient shallow marine setting

Fossil fish teeth from pelagic open ocean settings are considered a robust archive for preserving the neodymium (Nd) isotopic composition of ancient seawater. However, using fossil fish teeth as an archive to reconstruct seawater Nd isotopic compositions in different sedimentary redox environments and in terrigenous‐dominated, shallow marine settings is less proven. To address these uncertainties, fish tooth and sediment samples from a middle Eocene section deposited proximal to the East Antarctic margin at Integrated Ocean Drilling Program Site U1356 were analyzed for major and trace element geochemistry, and Nd isotopes. Major and trace element analyses of the sediments reveal changing redox conditions throughout deposition in a shallow marine environment. However, variations in the Nd isotopic composition and rare earth element (REE) patterns of the associated fish teeth do not correspond to redox changes in the sediments. REE patterns in fish teeth at Site U1356 carry a typical mid‐REE‐enriched signature. However, a consistently positive Ce anomaly marks a deviation from a pure authigenic origin of REEs to the fish tooth. Neodymium isotopic compositions of cleaned and uncleaned fish teeth fall between modern seawater and local sediments and hence could be authigenic in nature, but could also be influenced by sedimentary fluxes. We conclude that the fossil fish tooth Nd isotope proxy is not sensitive to moderate changes in pore water oxygenation. However, combined studies on sediments, pore waters, fish teeth, and seawater are needed to fully understand processes driving the reconstructed signature from shallow marine sections in proximity to continental sources

Interactions between the oomycete Pythium arrhenomanes and the rice root-knot nematode Meloidogyne graminicola in aerobic Asian rice varieties

Background: Aerobic rice fields are frequently infested by pathogenic oomycetes (Pythium spp.) and the rice root-knot nematode Meloidogyne graminicola. Here, the interaction between Pythium arrhenomanes and Meloidogyne graminicola was studied in rice roots of two aerobic rice varieties. In different experimental set-ups and infection regimes, plant growth, rice yield, Pythium colonization, as well as establishment, development and reproduction of M. graminicola were studied. Results: In this study, it is shown that the presence of P. arrhenomanes delays the establishment, development and reproduction of M. graminicola compared to single nematode infected plants. The delay in establishment and development of M. graminicola becomes stronger with higher P. arrhenomanes infection pressure. Conclusions: Our data indicate that P. arrhenomanes antagonizes M. graminicola in the rice root and that the plant benefits from this antagonism as shown by the yield data, especially when either of the pathogens is present in high levels

Internalizing and externalizing correlates of parental overprotection as measured by the EMBU:A systematic review and meta-analysis

Aspects of parenting including overprotection explain individual differences in child adjustment. This review and meta-analysis summarizes studies on parental overprotection and internalizing and externalizing problems. To ensure that findings could be compared as systematically as possible, the focus was on studies that used the overprotection scale of the Egna Minnen Beträffande Uppfostran (“Memories of my Parents’ Upbringing”) (EMBU) questionnaire, a popular instrument to measure parental overprotection. In total, we extracted 176 effects from 29 studies. A modified version of the Newcastle-Ottawa Scale was used to perform quality assessments for the included studies. Parental overprotection was associated positively with offspring internalizing and externalizing problems, with overall estimates ranging from r =.14 to.18. Moderator analyses suggested that effects of maternal were larger than effects of paternal overprotection. Other factors that moderated the strength of the association between overprotection and maladjustment included whether outcomes were self-reported or parent-reported, the design was cross-sectional or longitudinal, and publication year. Cultural context, age at exposure, and child sex did not explain differences between effect sizes. Most findings were based on cross-sectional studies and therefore do not constitute proof of causal relations. Many studies were of less-than-satisfactory quality regarding representativeness of the sample, descriptions of the data collection, and statistical analyses. There is a clear need for well-powered longitudinal studies to strengthen inferences about associations between parental overprotection and internalizing and externalizing problems

Redirection of auxin flow in Arabidopsis thaliana roots after infection by root-knot nematodes

Plant auxin efflux and influx proteins redirect the plant hormone auxin towards the feeding site upon root-knot nematode infection in Arabidopsis thaliana roots.Plant-parasitic root-knot nematodes induce the formation of giant cells within the plant root, and it has been recognized that auxin accumulates in these feeding sites. Here, we studied the role of the auxin transport system governed by AUX1/LAX3 influx proteins and different PIN efflux proteins during feeding site development in Arabidopsis thaliana roots. Data generated via promoter-reporter line and protein localization analyses evoke a model in which auxin is being imported at the basipetal side of the feeding site by the concerted action of the influx proteins AUX1 and LAX3, and the efflux protein PIN3. Mutants in auxin influx proteins AUX1 and LAX3 bear significantly fewer and smaller galls, revealing that auxin import into the feeding sites is needed for their development and expansion. The feeding site development in auxin export (PIN) mutants was only slightly hampered. Expression of some PINs appears to be suppressed in galls, probably to prevent auxin drainage. Nevertheless, a functional PIN4 gene seems to be a prerequisite for proper nematode development and gall expansion, most likely by removing excessive auxin to stabilize the hormone level in the feeding site. Our data also indicate a role of local auxin peaks in nematode attraction towards the root