Organic in Europe: Recent Developments

In 2017, the European organic food and farming sector continued to excel both in terms of organic production and market growth. Data for 2017 (for full data see page 216) shows the European organic food market recording significant growth – increasing by more than ten percent to 37.3 billion. At the same time, the organic sector faces a number of challenges, notably that the growth rates in organic area, in spite of recent stronger growth, continues to lag behind the dynamic growth seen within the organic food market (Figure 68). A major milestone in 2018 was the publication of the new European Union rules on organic production and labelling of organic products in May, and in June 2018, the European Commission launched its proposal for the Common Agricultural Policy for the period 2021 to 2027

Deep Super-SAGE transcriptomic analysis of cold acclimation in lentil (Lens culinaris Medik.)

[EN] Background: Frost is one of the main abiotic stresses limiting plant distribution and crop production. To cope with the stress, plants evolved adaptations known as cold acclimation or chilling tolerance to maximize frost tolerance. Cold acclimation is a progressive acquisition of freezing tolerance by plants subjected to low non-freezing temperatures which subsequently allows them to survive exposure to frost. Lentil is a cool season grain legume that is challenged by winter frost in some areas of its cultivation. Results: To better understand the genetic base of frost tolerance differential gene expression in response to cold acclimation was investigated. Recombinant inbred lines (RILs) from the cross Precoz x WA8649041 were first classified as cold tolerant or cold susceptible according to their response to temperatures between -3 to -15 °C. Then, RILs from both extremes of the response curve were cold acclimated and the leaf transcriptomes of two bulks each of eight frost tolerant and seven cold susceptible RILs were investigated by Deep Super-SAGE transcriptome profiling. Thus, four RNA bulks were analysed: the acclimated susceptible, the acclimated tolerant and the respective controls (non-acclimated susceptible and non-acclimated tolerant). Approximately 16.5 million 26 nucleotide long Super-SAGE tags were sequenced in the four sets (between ~3 and 5.4 millions). In total, 133,077 different unitags, each representing a particular transcript isoform, were identified in these four sets. Tags which showed a significantly different abundance in any of the bulks (fold change ≥4.0 and a significant p-value <0.001) were selected and used to identify the corresponding lentil gene sequence. Three hundred of such lentil sequences were identified. Most of their known homologs coded for glycine-rich, cold and drought-regulated proteins, dormancy-associated proteins, proline-rich proteins (PRPs) and other membrane proteins. These were generally but not exclusively over-expressed in the acclimated tolerant lines. Conclusions: This set of candidate genes implicated in the response to frost in lentil represents an useful base for deeper and more detailed investigations into this important agronomic trait in futureSIThis work was supported by the E.U. ERA-PG 075B LEGRESIST project, the AGL2013-44714-R project from the Spanish Ministerio de Economía y Competitividad (co-financed with FEDER funds), and a predoctoral fellowship (A. Barrios) from the ITACyL

HTS YBCO Resonator Configuration with Coplanar Optimized Flux Concentrator Strongly Coupled to rf SQUID

We developed a novel magnetic coupling module formed of a monolayer superconducting flux concentrator, which is integrated with a coplanar resonator strongly coupled to HTS rf-SQUID. Three types of resonators, including a long stripline resonator between input loop and pick-up loop of the flux concentrator, a complementary split ring resonator (CSRR), and also a spiral shape inside the input loop are explored. The resonance quality factors as well as the coupling to the SQUID of different patterns of these three types of the resonators is evaluated using Finite Element Method (FEM) simulations. Several readout methods to couple the electronic system to the resonators are tested, including inductive (coil) and capacitive (transmission line) couplings, and the optimum readout is reported for each of the resonators. Among the evaluated resonator types, a spiral shape resonator with optimal design showing the highest quality factor (5900) together with the strongest coupling to the SQUID (-0.5 dB) at resonance frequency of 836 MHz, is fabricated using 200 nm thick superconducting YBCO on a 1 mm thick crystalline LaAlO3 substrate. The flux concentrator of the module is optimized by the variation of its linewidths and also its input loop radius to obtain maximum flux transformation efficiency.Comment: 5 page

New insights on phylogeography and distribution of painted frogs (Discoglossus) in northern Africa and the Iberian Peninsula

Painted frogs (Discoglossus) contain five to six species of Western Palearctic anurans that are mainly distributed in allopatry. We here provide the first comprehensive assessment of the phylogeography of the Moroccan species D. scovazzi and geographically characterize its contact zone with D. pictus in Eastern Morocco. Discoglossus scovazzi shows, in general, a weak phylogeographic structure across Morocco on the basis of mitochondrial DNA sequences of the cytochrome b gene, with only populations centered in the Atlas Mountains characterized by the presence of slightly divergent haplotypes. In eastern Morocco, all populations east of the Moulouya River were clearly assignable to D. pictus. This species was also found along the Mediterranean coast west of the Moulouya, in the cities of Nador and Melilla, suggesting that not the river itself but the wide arid valley extending along much of the river (except close to the estuary) acts as a possible distributional barrier to these frogs. No sympatry of D. scovazzi with D. pictus was observed, and all specimens were concordantly assigned to either species by DNA sequences of cytochrome b and of the nuclear marker RAG1. Species distribution models of the two taxa show largely overlapping areas of suitable habitat, and the two species’ niches are significantly more similar than would be expected given the underlying environmental differences between the regions in which they occur. Comparative data are also presented from the southern Iberian contact zone of D. galganoi galganoi and D. g. jeanneae. These taxa showed less clear-cut distributional borders, extensively shared RAG1 haplotypes, and had instances of sympatric occurrence on the basis of cytochrome b haplotypes, in agreement with the hypothesis of a yet incomplete speciation. In this wide contact zone area we found mitochondrial sequences containing double peaks in electropherograms, suggesting nuclear pseudogenes or (less likely) heteroplasmy, possibly related to the ongoing admixture among the lineagesPeer reviewe

The stellar occultations by the largest satellite of the dwarf planet Haumea, Hi'iaka

Two stellar occultations by the largest satellite of the dwarf planet Haumea, Hi'iaka, were predicted to happen on April, 6th and 16th, 2021. Additional high accuracy astrometric analysis was carried out in order to refine the prediction for April 6th, using several telescopes in the 1.2-m to 2-m range, with the final shadow path crossing North Africa. We successfully detected the first event from TRAPPIST-North telescope at Oukaïmeden Observatory (Morocco). Although it was recorded from only one site, this first detection allowed us to improve the prediction for the second that crossed North America from East to West. We had a good success recording six positive detections and several negative detections that constrain the shape and size of the body. The light curves obtained from the different observatories provide the time at which the star disappears and reappears, which are translated into chords (the projected lines on the sky-plane as observed from each location). Additionally, we carried out a campaign to study Hi'iaka's rotational light-curve, studying the residuals of Haumea's rotational light-curve to a four-order Fourier fit. We obtained the rotational phases at the times of the occultations, which is critical for the analysis of the occultations, given that Hi'iaka is clearly non-spherical. Our preliminary results show that Hi'iaka indeed has a triaxial shape with a larger effective diameter than what has been published so far. The preliminary results and their implications will be discussed in this talk

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts

Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas

Although theMYConcogene has been implicated incancer, a systematic assessment of alterations ofMYC, related transcription factors, and co-regulatoryproteins, forming the proximal MYC network (PMN),across human cancers is lacking. Using computa-tional approaches, we define genomic and proteo-mic features associated with MYC and the PMNacross the 33 cancers of The Cancer Genome Atlas.Pan-cancer, 28% of all samples had at least one ofthe MYC paralogs amplified. In contrast, the MYCantagonists MGA and MNT were the most frequentlymutated or deleted members, proposing a roleas tumor suppressors.MYCalterations were mutu-ally exclusive withPIK3CA,PTEN,APC,orBRAFalterations, suggesting that MYC is a distinct onco-genic driver. Expression analysis revealed MYC-associated pathways in tumor subtypes, such asimmune response and growth factor signaling; chro-matin, translation, and DNA replication/repair wereconserved pan-cancer. This analysis reveals insightsinto MYC biology and is a reference for biomarkersand therapeutics for cancers with alterations ofMYC or the PMN

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin

Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images

Beyond sample curation and basic pathologic characterization, the digitized H&E-stained images of TCGA samples remain underutilized. To highlight this resource, we present mappings of tumorinfiltrating lymphocytes (TILs) based on H&E images from 13 TCGA tumor types. These TIL maps are derived through computational staining using a convolutional neural network trained to classify patches of images. Affinity propagation revealed local spatial structure in TIL patterns and correlation with overall survival. TIL map structural patterns were grouped using standard histopathological parameters. These patterns are enriched in particular T cell subpopulations derived from molecular measures. TIL densities and spatial structure were differentially enriched among tumor types, immune subtypes, and tumor molecular subtypes, implying that spatial infiltrate state could reflect particular tumor cell aberration states. Obtaining spatial lymphocytic patterns linked to the rich genomic characterization of TCGA samples demonstrates one use for the TCGA image archives with insights into the tumor-immune microenvironment

A collaboratively derived environmental research agenda for Galapagos

Galápagos is one of the most pristine archipelagos in the world and its conservation relies upon research and sensible management. In recent decades both the interest in, and the needs of, the islands have increased, yet the funds and capacity for necessary research have remained limited. It has become, therefore, increasingly important to identify areas of priority research to assist decision-making in Galápagos conservation. This study identified 50 questions considered priorities for future research and management. The exercise involved the collaboration of policy makers, practitioners and researchers from more than 30 different organisations. Initially, 360 people were consulted to generate 781 questions. An established process of preworkshop voting and three rounds to reduce and reword the questions, followed by a two-day workshop, was used to produce the final 50 questions. The most common issues raised by this list of questions were human population growth, climate change and the impact of invasive alien species. These results have already been used by a range of organisations and politicians and are expected to provide the basis for future research on the islands so that its sustainability may be enhanced. </jats:p