Identification and characterization of extensive intra-molecular associations between 3′-UTRs and their ORFs

During eukaryotic translation, mRNAs may form intra-molecular interactions between distant domains. The 5′-cap and the polyA tail were shown to interact through their associated proteins, and this can induce physical compaction of the mRNA in vitro. However, the stability of this intra-molecular association in translating mRNAs and whether additional contacts exist in vivo are largely unknown. To explore this, we applied a novel approach in which several endogenous polysomal mRNAs from Saccharomyces cerevisiae were cleaved near their stop codon and the resulting 3′-UTR fragments were tested either for co-sedimentation or co-immunoprecipitation (co-IP) with their ORFs. In all cases a significant fraction of the 3′-UTR fragments sedimented similarly to their ORF-containing fragments, yet the extent of co-sedimentation differed between mRNAs. Similar observations were obtained by a co-IP assay. Interestingly, various treatments that are expected to interfere with the cap to polyA interactions had no effect on the co-sedimentation pattern. Moreover, the 3′-UTR appeared to co-sediment with different regions from within the ORF. Taken together, these results indicate extensive physical associations between 3′-UTRs and their ORFs that vary between genes. This implies that polyribosomal mRNAs are in a compact configuration in vivo

Viscous fingering and a shape of an electronic droplet in the Quantum Hall regime

We show that the semiclassical dynamics of an electronic droplet confined in the plane in a quantizing inhomogeneous magnetic field in the regime when the electrostatic interaction is negligible is similar to viscous (Saffman-Taylor) fingering on the interface between two fluids with different viscosities confined in a Hele-Shaw cell. Both phenomena are described by the same equations with scales differing by a factor of up to $10^{-9}$. We also report the quasiclassical wave function of the droplet in an inhomogeneous magnetic field.Comment: 4 pages, 1 eps figure include

EULAR recommendations for the management of familial Mediterranean fever

Familial Mediterranean fever (FMF) is the most common monogenic autoinflammatory disease, but many rheumatologists are not well acquainted with its management. The objective of this report is to produce evidence-based recommendations to guide rheumatologists and other health professionals in the treatment and follow-up of patients with FMF. A multidisciplinary panel, including rheumatologists, internists, paediatricians, a nurse, a methodologist and a patient representative, was assembled. Panellists came from the Eastern Mediterranean area, Europe and North America. A preliminary systematic literature search on the pharmacological treatment of FMF was performed following which the expert group convened to define aims, scope and users of the guidelines and established the need for additional reviews on controversial topics. In a second meeting, recommendations were discussed and refined in light of available evidence. Finally, agreement with the recommendations was obtained from a larger group of experts through a Delphi survey. The level of evidence (LoE) and grade of recommendation (GR) were then incorporated. The final document comprises 18 recommendations, each presented with its degree of agreement (0-10), LoE, GR and rationale. The degree of agreement was greater than 7/10 in all instances. The more controversial statements were those related to follow-up and dose change, for which supporting evidence is limited. A set of widely accepted recommendations for the treatment and monitoring of FMF is presented, supported by the best available evidence and expert opinion. It is believed that these recommendations will be useful in guiding physicians in the care of patients with FMF

High-Throughput GoMiner, an 'industrial-strength' integrative gene ontology tool for interpretation of multiple-microarray experiments, with application to studies of Common Variable Immune Deficiency (CVID)

BACKGROUND: We previously developed GoMiner, an application that organizes lists of 'interesting' genes (for example, under-and overexpressed genes from a microarray experiment) for biological interpretation in the context of the Gene Ontology. The original version of GoMiner was oriented toward visualization and interpretation of the results from a single microarray (or other high-throughput experimental platform), using a graphical user interface. Although that version can be used to examine the results from a number of microarrays one at a time, that is a rather tedious task, and original GoMiner includes no apparatus for obtaining a global picture of results from an experiment that consists of multiple microarrays. We wanted to provide a computational resource that automates the analysis of multiple microarrays and then integrates the results across all of them in useful exportable output files and visualizations. RESULTS: We now introduce a new tool, High-Throughput GoMiner, that has those capabilities and a number of others: It (i) efficiently performs the computationally-intensive task of automated batch processing of an arbitrary number of microarrays, (ii) produces a human-or computer-readable report that rank-orders the multiple microarray results according to the number of significant GO categories, (iii) integrates the multiple microarray results by providing organized, global clustered image map visualizations of the relationships of significant GO categories, (iv) provides a fast form of 'false discovery rate' multiple comparisons calculation, and (v) provides annotations and visualizations for relating transcription factor binding sites to genes and GO categories. CONCLUSION: High-Throughput GoMiner achieves the desired goal of providing a computational resource that automates the analysis of multiple microarrays and integrates results across all of the microarrays. For illustration, we show an application of this new tool to the interpretation of altered gene expression patterns in Common Variable Immune Deficiency (CVID). High-Throughput GoMiner will be useful in a wide range of applications, including the study of time-courses, evaluation of multiple drug treatments, comparison of multiple gene knock-outs or knock-downs, and screening of large numbers of chemical derivatives generated from a promising lead compound

Investigating cooperation with robotic peers

We explored how people establish cooperation with robotic peers, by giving participants the chance to choose whether to cooperate or not with a more/less selfish robot, as well as a more or less interactive, in a more or less critical environment. We measured the participants' tendency to cooperate with the robot as well as their perception of anthropomorphism, trust and credibility through questionnaires. We found that cooperation in Human-Robot Interaction (HRI) follows the same rule of Human-Human Interaction (HHI), participants rewarded cooperation with cooperation, and punished selfishness with selfishness. We also discovered two specific robotic profiles capable of increasing cooperation, related to the payoff. A mute and non-interactive robot is preferred with a high payoff, while participants preferred a more human-behaving robot in conditions of low payoff. Taken together, these results suggest that proper cooperation in HRI is possible but is related to the complexity of the task

The contributions of biodiversity to the sustainable intensification of food production:Thematic Study to support the State of the World’s Biodiversity for Food and Agriculture

Biodiversity supports sustainable food production, although recognition of its roles has been relatively neglected in the sustainable intensification literature. In the current study, the roles of biodiversity in sustainable food production are considered, assessing how these roles can be measured, the current state of knowledge and opportunities for intervention. The trajectory of global food production, and the challenges and opportunities this presents for the roles of biodiversity in production, are also considered, as well as how biodiversitybased interventions fit within wider considerations for sustainable food systems. The positive interactions between a diverse array of organisms, including annual crops, animal pollinators, trees, micro-organisms, livestock and aquatic animals, support food production globally. To support these interactions, a range of interventions related to access to materials and practices are required. For annual crops, major interventions include breeding crops for more positive crop–crop interactions, and the integration of a wider range of crops into production systems. For animal pollinators, major interventions include the introduction of pollinator populations into production landscapes and the protection and improvement of pollinator habitat. For trees, a major required intervention is the greater integration of perennial legumes into farmland. For micro-organisms, the implementation of agronomic practices that support beneficial crop-microbe interactions is crucial. For livestock production, breed and crop feedstock diversification are essential, and the implementation of improved methods for manure incorporation into cropland. Finally, in the case of aquatic production, it is essential to support the wider adoption of multi-trophic production systems and to diversify crop- and animal-based feed resources. These and other interventions, and the research needs around them, are discussed. Looking to the future, understanding the drivers behind trends in food systems is essential for determining the options for biodiversity in supporting sustainable food production. The increased dominance of a narrow selection of foods globally indicates that efforts to more sustainably produce these foods are crucial. From a biodiversity perspective, this means placing a strong emphasis on breeding for resource use efficiency and adaptation to climate change. It also means challenging the dominance of these foods through focusing on productivity improvements for other crop, livestock and aquaculture species, so that they can compete successfully and find space within production systems. New biodiversity-based models that support food production need not only to be productive but to be profitable. Thus, as well as describing appropriate production system management practices that enhance production and support the environment, the labour, knowledge, time required to operationalize, and other costs of new production approaches, must be considered and minimized. To support the future roles of biodiversity in sustainable food production, we recommend that particular attention be given to the longitudinal analysis of food sectors to determine how the diversity of foods consumed from these sectors has changed over time. Analysis is already available for crops, but related research is needed for livestock and aquaculture sectors. This analysis will then support more optimal cross-sectoral interactions, in terms of the contributions each sector provides to supplying the different components of human diets. Additional meta-analyses and synthetic reviews of case studies are required as an evidence base for biodiversity-based food production system interventions, but future studies should pay more attention to articulating the potential biases in case study compilation (the problem of ‘cherry picking’ positive examples) and the measures that have been taken to minimize such effects

Imaging Pulmonary NF-kappaB Activation and Therapeutic Effects of MLN120B and TDZD-8

NF-κB activation is a critical signaling event in the inflammatory response and has been implicated in a number of pathological lung diseases. To enable the assessment of NF-κB activity in the lungs, we transfected a luciferase based NF-κB reporter into the lungs of mice or into Raw264.7 cells in culture. The transfected mice showed specific luciferase expression in the pulmonary tissues. Using these mouse models, we studied the kinetics of NF-κB activation following exposure to lipopolysaccharide (LPS). The Raw264.7 cells expressed a dose-dependent increase in luciferase following exposure to LPS and the NF-κB reporter mice expressed luciferase in the lungs following LPS challenge, establishing that bioluminescence imaging provides adequate sensitivity for tracking the NF-κB activation pathway. Interventions affecting the NF-κB pathway are promising clinical therapeutics, thus we further examined the effect of IKK-2 inhibition by MLN120B and glycogen synthase kinase 3 beta inhibition by TDZD-8 on NF-κB activation. Pre-treatment with either MLN120B or TDZD-8 attenuated NF-κB activation in the pulmonary tissues, which was accompanied with suppression of pro-inflammatory chemokine MIP-1ß and induction of anti-inflammatory cytokine IL-10. In summary, we have established an imaging based approach for non-invasive and longitudinal assessment of NF-κB activation and regulation during acute lung injury. This approach will potentiate further studies on NF-κB regulation under various inflammatory conditions

p53 Plays a Role in Mesenchymal Differentiation Programs, in a Cell Fate Dependent Manner

Background: The tumor suppressor p53 is an important regulator that controls various cellular networks, including cell differentiation. Interestingly, some studies suggest that p53 facilitates cell differentiation, whereas others claim that it suppresses differentiation. Therefore, it is critical to evaluate whether this inconsistency represents an authentic differential p53 activity manifested in the various differentiation programs. Methodology/Principal Findings: To clarify this important issue, we conducted a comparative study of several mesenchymal differentiation programs. The effects of p53 knockdown or enhanced activity were analyzed in mouse and human mesenchymal cells, representing various stages of several differentiation programs. We found that p53 downregulated the expression of master differentiation-inducing transcription factors, thereby inhibiting osteogenic, adipogenic and smooth muscle differentiation of multiple mesenchymal cell types. In contrast, p53 is essential for skeletal muscle differentiation and osteogenic re-programming of skeletal muscle committed cells. Conclusions: These comparative studies suggest that, depending on the specific cell type and the specific differentiatio