Fatal attraction: the intuitive appeal of GMO opposition

Public opposition to genetically modified organisms (GMOs) remains strong. By contrast, studies demonstrate again and again that GM crops make a valuable contribution to the development of a sustainable type of agriculture. The discrepancy between public opinion and the scientific evidence requires an explanation. We argue that intuitive expectations about the world render the human mind vulnerable to particular misrepresentations of GMOs. We explain how the involvement of particular intuitions accounts for the popularity, persistence, and typical features of GM opposition and tackle possible objections to our approach. To conclude, we discuss the implications for science education, science communication, and the environmental movement

Reactive oxygen species in plant development

Reactive oxygen species (ROS) are produced by metabolic pathways in almost all cells. As signaling components, ROS are best known for their roles in abiotic and biotic stress-related events. However, recent studies have revealed that they are also involved in numerous processes throughout the plant life cycle, from seed development and germination, through to root, shoot and flower development. Here, we provide an overview of ROS production and signaling in the context of plant growth and development, highlighting the key functions of ROS and their interactions with plant phytohormonal networks

Genome-wide RNAi screen reveals a role for multipass membrane proteins in endosome-to-golgi retrieval.

Endosome-to-Golgi retrieval is an essential membrane trafficking pathway required for many important physiological processes and linked to neurodegenerative disease and infection by bacterial and viral pathogens. The prototypical cargo protein for this pathway is the cation-independent mannose 6-phosphate receptor (CIMPR), which delivers lysosomal hydrolases to endosomes. Efficient retrieval of CIMPR to the Golgi requires the retromer complex, but other aspects of the endosome-to-Golgi retrieval pathway are poorly understood. Employing an image-based antibody-uptake assay, we conducted a genome-wide RNAi loss-of-function screen for novel regulators of this trafficking pathway and report ∼90 genes that are required for endosome-to-Golgi retrieval of a CD8-CIMPR reporter protein. Among these regulators of endosome-to-Golgi retrieval are a number of multipass membrane-spanning proteins, a class of proteins often overlooked with respect to a role in membrane trafficking. We further demonstrate a role for three multipass membrane proteins, SFT2D2, ZDHHC5, and GRINA, in endosome-to-Golgi retrieval.This work was financially supported through a Medical Research Council Senior Research Fellowship awarded to MNJS. Work in the CIMR is also supported by a Welcome Trust Strategic Award (100140).This is the final version of the article. It first appeared from Cell Press via http://dx.doi.org/10.1016/j.celrep.2014.10.05

A chemoselective and continuous synthesis of m-sulfamoylbenzamide analogues

For the synthesis of m-sulfamoylbenzamide analogues, small molecules which are known for their bioactivity, a chemoselective procedure has been developed starting from m-(chlorosulfonyl) benzoyl chloride. Although a chemoselective process in batch was already reported, a continuous-flow process reveals an increased selectivity at higher temperatures and without catalysts. In total, 15 analogues were synthesized, using similar conditions, with yields ranging between 65 and 99%. This is the first automated and chemoselective synthesis of m- sulfamoylbenzamide analogues

Analysis of novel endosome-to-Golgi retrieval genes reveals a role for PLD3 in regulating endosomal protein sorting and amyloid precursor protein processing

The processing of amyloid precursor protein (APP) to the neurotoxic pro-aggregatory Aβ peptide is controlled by the mechanisms that govern the trafficking and localisation of APP. We hypothesised that genes involved in endosomal protein sorting could play an important role in regulating APP processing and therefore analysed ~40 novel endosome-to-Golgi retrieval genes previously identified in a genome-wide siRNA screen. We report that phospholipase D3 (PLD3), a type II membrane protein, functions in endosomal protein sorting and plays an important role in regulating APP processing. PLD3 colocalises with APP in endosomes and loss of PLD3 function results in reduced endosomal tubules, impaired trafficking of several membrane proteins and reduced association of sortilin-like 1 (SorL1) with APP.MNJS is supported by funding from the Medical Research Council (Grant no.: MR/L007533/1). Work at the Cambridge Institute for Medical Research is aided by a Wellcome Trust Strategic award

The ROS wheel: refining ROS transcriptional footprints

In the last decade, microarray studies have delivered extensive inventories of transcriptome-wide changes in messenger RNA levels provoked by various types of oxidative stress in Arabidopsis (Arabidopsis thaliana). Previous cross-study comparisons indicated how different types of reactive oxygen species (ROS) and their subcellular accumulation sites are able to reshape the transcriptome in specific manners. However, these analyses often employed simplistic statistical frameworks that are not compatible with large-scale analyses. Here, we reanalyzed a total of 79 Affymetrix ATH1 microarray studies of redox homeostasis perturbation experiments. To create hierarchy in such a high number of transcriptomic data sets, all transcriptional profiles were clustered on the overlap extent of their differentially expressed transcripts. Subsequently, meta-analysis determined a single magnitude of differential expression across studies and identified common transcriptional footprints per cluster. The resulting transcriptional footprints revealed the regulation of various metabolic pathways and gene families. The RESPIRATORY BURST OXIDASE HOMOLOG F-mediated respiratory burst had a major impact and was a converging point among several studies. Conversely, the timing of the oxidative stress response was a determining factor in shaping different transcriptome footprints. Our study emphasizes the need to interpret transcriptomic data sets in a systematic context, where initial, specific stress triggers can converge to common, aspecific transcriptional changes. We believe that these refined transcriptional footprints provide a valuable resource for assessing the involvement of ROS in biological processes in plants

Traffic modeling and state feedback control for metro lines

Abstract-This paper deals with traffic modeling and control design for high-frequency metro lines. A complete discrete-event traffic model pointing out the natural instability of metro lines is presented. The traffic stability properties are analyzed and easyto-implement state feedback traffic control algorithms are designed, which guarantee the system stability. Simulations illustrate the methodology. I

Mitochondrial and chloroplast stress responses are modulated in distinct touch and chemical inhibition phases

Previous studies have identified a range of transcription factors that modulate retrograde regulation of mitochondrial and chloroplast functions in Arabidopsis (Arabidopsis thaliana). However, the relative importance of these regulators and whether they act downstream of separate or overlapping signaling cascades is still unclear. Here, we demonstrate that multiple stress-related signaling pathways, with distinct kinetic signatures, converge on overlapping gene sets involved in energy organelle function. The transcription factor ANAC017 is almost solely responsible for transcript induction of marker genes around 3 to 6 h after chemical inhibition of organelle function and is a key regulator of mitochondrial and specific types of chloroplast retrograde signaling. However, an independent and highly transient gene expression phase, initiated within 10 to 30 min after treatment, also targets energy organelle functions, and is related to touch and wounding responses. Metabolite analysis demonstrates that this early response is concurrent with rapid changes in tricarboxylic acid cycle intermediates and large changes in transcript abundance of genes encoding mitochondrial dicarboxylate carrier proteins. It was further demonstrated that transcription factors AtWRKY15 and AtWRKY40 have repressive regulatory roles in this touch-responsive gene expression. Together, our results show that several regulatory systems can independently affect energy organelle function in response to stress, providing different means to exert operational control

N-terminal proteomics assisted profiling of the unexplored translation initiation landscape in Arabidopsis thaliana

Proteogenomics is an emerging research field yet lacking a uniform method of analysis. Proteogenomic studies in which N-terminal proteomics and ribosome profiling are combined, suggest that a high number of protein start sites are currently missing in genome annotations. We constructed a proteogenomic pipeline specific for the analysis of N-terminal proteomics data, with the aim of discovering novel translational start sites outside annotated protein coding regions. In summary, unidentified MS/MS spectra were matched to a specific N-terminal peptide library encompassing protein N termini encoded in the Arabidopsis thaliana genome. After a stringent false discovery rate filtering, 117 protein N termini compliant with N-terminal methionine excision specificity and indicative of translation initiation were found. These include N-terminal protein extensions and translation from transposable elements and pseudogenes. Gene prediction provided supporting protein-coding models for approximately half of the protein N termini. Besides the prediction of functional domains (partially) contained within the newly predicted ORFs, further supporting evidence of translation was found in the recently released Araport11 genome re-annotation of Arabidopsis and computational translations of sequences stored in public repositories. Most interestingly, complementary evidence by ribosome profiling was found for 23 protein N termini. Finally, by analyzing protein N-terminal peptides, an in silico analysis demonstrates the applicability of our N-terminal proteogenomics strategy in revealing protein-coding potential in species with well-and poorly-annotated genomes