The transposable element-rich genome of the cereal pest Sitophilus oryzae

Background The rice weevil Sitophilus oryzae is one of the most important agricultural pests, causing extensive damage to cereal in fields and to stored grains. S. oryzae has an intracellular symbiotic relationship (endosymbiosis) with the Gram-negative bacterium Sodalis pierantonius and is a valuable model to decipher host-symbiont molecular interactions. Results We sequenced the Sitophilus oryzae genome using a combination of short and long reads to produce the best assembly for a Curculionidae species to date. We show that S. oryzae has undergone successive bursts of transposable element (TE) amplification, representing 72% of the genome. In addition, we show that many TE families are transcriptionally active, and changes in their expression are associated with insect endosymbiotic state. S. oryzae has undergone a high gene expansion rate, when compared to other beetles. Reconstruction of host-symbiont metabolic networks revealed that, despite its recent association with cereal weevils (30 kyear), S. pierantonius relies on the host for several amino acids and nucleotides to survive and to produce vitamins and essential amino acids required for insect development and cuticle biosynthesis. Conclusions Here we present the genome of an agricultural pest beetle, which may act as a foundation for pest control. In addition, S. oryzae may be a useful model for endosymbiosis, and studying TE evolution and regulation, along with the impact of TEs on eukaryotic genomes.Funding for this project was provided by the Fondation de l’Institut National des Sciences Appliquées-Lyon (INSA-Lyon), the research direction of INSA-Lyon, the Santé des Plantes et Environnement (SPE) department at the Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (INRAE), the French ANR-10-BLAN-1701 (ImmunSymbArt), the French ANR-13-BSV7-0016-01 (IMetSym), the French ANR-17_CE20_0031_01 (GREEN), and a grant from la Région Rhône-Alpes (France) to AH. RR received funding from the French ANR-17-CE20-0015 (UNLEASH) and the IDEX-Lyon PALSE IMPULSION initiative. The project was also funded by European Regional Development Fund (ERDF) and Ministerio de Ciencia, Innovación y Universidades (Spain) PGC2018-099344-B-I00 to AL, and PID2019-105969GB-I00 to AM and Conselleria d’Educació, Generalitat Valenciana (Spain), grant number PROMETEO/2018/133 to AM. CV-C was a recipient of a fellowship from the Ministerio de Economía y Competitividad (Spain) and a grant from la Région Rhône-Alpes (France).Peer Reviewed"Article signat per 47 autors/es: Nicolas Parisot, Carlos Vargas-Chávez, Clément Goubert, Patrice Baa-Puyoulet, Séverine Balmand, Louis Beranger, Caroline Blanc, Aymeric Bonnamour, Matthieu Boulesteix, Nelly Burlet, Federica Calevro, Patrick Callaerts, Théo Chancy, Hubert Charles, Stefano Colella, André Da Silva Barbosa, Elisa Dell’Aglio, Alex Di Genova, Gérard Febvay, Toni Gabaldón, Mariana Galvão Ferrarini, Alexandra Gerber, Benjamin Gillet, Robert Hubley, Sandrine Hughes, Emmanuelle Jacquin-Joly, Justin Maire, Marina Marcet-Houben, Florent Masson, Camille Meslin, Nicolas Montagné, Andrés Moya, Ana Tereza Ribeiro de Vasconcelos, Gautier Richard, Jeb Rosen, Marie-France Sagot, Arian F. A. Smit, Jessica M. Storer, Carole Vincent-Monegat, Agnès Vallier, Aurélien Vigneron, Anna Zaidman-Rémy, Waël Zamoum, Cristina Vieira, Rita Rebollo, Amparo Latorre & Abdelaziz Heddi"Postprint (published version

COLLARES project report - Strengthening collaborative food waste prevention in Colombia: towards responsible consumption and production

Throwing away food which could be eaten or otherwise put to good use should no longer be tolerated. Simply deemed as ‘food waste’, this practice is meeting with increasing disfavour from governments, householders and businesses alike (World Food Security, 2014; WRAP, 2013). Advocates are increasing calling for a move towards a circular economy by designing out waste, wherever possible, at every stage of handling resources (European Commission, 2014a; LWARB, 2017; Vilariño et al., 2017; Food Citizenship, 2019; Camilleri, 2021). In this respect, Colombia has joined other regional LAC countries by aiming to halve per capita food waste by 2025 (FAO, 2016). Circular practice in food preparation entails basic moves such as combating kitchen waste. Therefore, when it comes to food businesses and the wider hospitality sector (HaFS), preventing wastage or loss would be also strategic. The central aim would be to capture residual food value and, to keep consumable foodstuff from being discarded (usually in forms of landfill). It is towards this end that the project COLLARES aims to promote action against food waste in Colombia and Peru. COLLARES was implemented in 2021 by a cross-sector partnership of academic, business and other stakeholders. Data collection and business engagement was conducted primarily between February and July 2021 and was therefore impacted significantly by the COVID 19 pandemic. Despite this, COLLARES achieved engagement and exchange with over 160 HaFS businesses across the two DAC countries. COVID 19 effects on these businesses was generally sobering. At the same time, COVID 19 restrictions helped to trigger innovative responses including; improved management; new food handling techniques, and new distribution models. This document reports only on the findings from Colombia, based on the city of Medellín. An accompanying report on the work in Peru can be found on the project website (www.collaresproject.org). In addition to a literature review, we generated primary data from three main stages of the project. These encompassed an online quantitative survey, a series of qualitative expert interviews and an online workshop for HaFS representatives in Medellín. The latter involved a mixed grouping of participants with contributions from HaFS business representatives, academics and, specialists in food waste reduction and the circular economy

Physical, physiological and sanitary quality of canola seeds after the application of maturing herbicides.

The use of herbicides to anticipate harvesting in species with easy seed dehiscence may be an alternative to avoid maturation losses. However, the appropriate time for herbicide application is extremely important as it prevents the seeds from remaining in the field for long periods. The objective of this study was to evalu ate the efficiency of the application of maturing herbicides in two distinct seasons, and their effects on the physical, physiological, and sanitary quality of canola seeds. A randomized block experimental design arranged in a factorial scheme (herbicide x season + control) with four replications was used. Hybrid 50 canola plants were matured with the herbicides: glufosinate, paraquat, glyphosate, diquat, saflufenacil, 2,4 D, and paraquat + diuron twice during the crop cycle, G3 and G4, and two controls wit hout applicati on for each epoch, with the first being harvested the day of product application, and the second kept in the field until the final crop cycle. Analyses of one thousand seed weight, electrical conductivity, emergence speed index, and a sanity test were performed. The application of maturing herbicides to canola increases the one thousand seed weight and rate of emergence speed. At the same time, it increases electrical conductivity and the incidence of ungi. Plants that remained in the field u ntil the end of the crop cycle and did not receive herbicide application resulted in higher quality seeds. The most appropriate moment to apply maturation herbicides to canola is in the G4 season.herbicides to canola is in the G4 season

Autogenic Training Relaxation Helping Postpartum Mothers to Achieve Successful Breastfeeding on Early Lactation Period

Introduction: The numbers of breastfeeding failures are mostly caused by mothers` disbelief to themselves. One method that can be done to overcome these problems in accordance with the self-care nursing theory is the autogenic training relaxation. This method teaches mothers to be self-sufficient in building a positive intention and motivation to help the process of breastfeeding. This study aimed to examine the influence of autogenic training relaxation to the effectiveness of breastfeeding and the enhancement of breast milk volume on maternal postpartum. Method: By using an experimental posttest only-non equivalent control group design, 26 samples were taken based on the criteria and divided into two groups by matching technuiqe. autogenic training was given through MP3 Player for 3 weeks. Post-test observation conducted on the third week by home visit. Via Christi Breastfeeding Assessment Tool Jan Riordan modifications used to assess the effectiveness of breastfeeding, and to measure the milk ejection volume, used weighing test using electronic baby scales. Data were analyzed using one-tailed independent t test with α ≤ 0.05. Result: The analysis showed that mothers who did autogenic training relaxation could breastfeed more effectively and had greater average volume of milk ejection than the control group (p = 0.000 and p = 0.001). Discussion: It can be concluded that autogenic relaxation training techniques affect the effectiveness of breastfeeding and breast milk volume. These results can be considered that autogenic training as an intervention in program of support for breastfeeding mothers

Transport and Recovery of Gilthead Seabream (Sparus aurata L.) Sedated With Clove Oil and MS-222: Effects on Stress Axis Regulation and Intermediary Metabolism

Transport processes between aquaculture facilities activate the stress response in fish. To deal with these situations, the hypothalamic-pituitary-interrenal (HPI) axis releases cortisol, leading to an increase in circulating energy resources to restore homeostasis. However, if the allostatic load generated exceeds fish tolerance limits, stress-related responses will compromise health and welfare of the animals. In this context, anesthetics have arisen as potential agents aiming to reduce negative effects of stress response. Here we assessed the effects of a sedative dose of clove oil (CO) and MS-222 on hallmarks involved in HPI axis regulation and energy management after simulated transport, and further recovery, in gilthead seabream (Sparus aurata L.) juveniles. Fish were placed in a mobile setup of water tanks where transport conditions were simulated for 6 h. Sedation doses of either CO (2.5 mg L−1) or MS-222 (5 mg L−1) were added in the water tanks. A control group without anesthetics was also included in the setup. Half of the animals (n = 12 per group) were sampled immediately after transport, while remaining animals were allowed to recover for 18 h in clean water tanks and then sampled. Our results showed that the HPI axis response was modified at peripheral level, with differences depending on the anesthetic employed. Head kidney gene-expressions related to cortisol production (star and cyp11b1) matched concomitantly with increased plasma cortisol levels immediately after transport in CO-sedated fish, but these levels remained constant in MS-222-sedated fish. Differential changes in the energy management of carbohydrates, lipids and amino acids, depending on the anesthetic employed, were also observed. The use of CO stimulated amino acids catabolism, while MS-222-sedated fish tended to consume liver glycogen and mobilize triglycerides. Further studies, including alternative doses of both anestethics, as well as the assessment of time-course HPI activation and longer recovery periods, are necessary to better understand if the use of clove oil and MS-222 is beneficial for S. aurata under these circumstances

Glial contribution to excitatory and inhibitory synapse loss in neurodegeneration

Synapse loss is an early feature shared by many neurodegenerative diseases, and it represents the major correlate of cognitive impairment. Recent studies reveal that microglia and astrocytes play a major role in synapse elimination, contributing to network dysfunction associated with neurodegeneration. Excitatory and inhibitory activity can be affected by glia-mediated synapse loss, resulting in imbalanced synaptic transmission and subsequent synaptic dysfunction. Here, we review the recent literature on the contribution of glia to excitatory/inhibitory imbalance, in the context of the most common neurodegenerative disorders. A better understanding of the mechanisms underlying pathological synapse loss will be instrumental to design targeted therapeutic interventions, taking in account the emerging roles of microglia and astrocytes in synapse remodeling

The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics.

ABSTRACT: A global genome database of all of Earth’s species diversity could be a treasure trove of scientific discoveries. However, regardless of the major advances in genome sequencing technologies, only a tiny fraction of species have genomic information available. To contribute to a more complete planetary genomic database, scientists and institutions across the world have united under the Earth BioGenome Project (EBP), which plans to sequence and assemble high-quality reference genomes for all ∼1.5 million recognized eukaryotic species through a stepwise phased approach. As the initiative transitions into Phase II, where 150,000 species are to be sequenced in just four years, worldwide participation in the project will be fundamental to success. As the European node of the EBP, the European Reference Genome Atlas (ERGA) seeks to implement a new decentralised, accessible, equitable and inclusive model for producing high-quality reference genomes, which will inform EBP as it scales. To embark on this mission, ERGA launched a Pilot Project to establish a network across Europe to develop and test the first infrastructure of its kind for the coordinated and distributed reference genome production on 98 European eukaryotic species from sample providers across 33 European countries. Here we outline the process and challenges faced during the development of a pilot infrastructure for the production of reference genome resources, and explore the effectiveness of this approach in terms of high-quality reference genome production, considering also equity and inclusion. The outcomes and lessons learned during this pilot provide a solid foundation for ERGA while offering key learnings to other transnational and national genomic resource projects.info:eu-repo/semantics/publishedVersio

Identification of novel risk loci, causal insights, and heritable risk for Parkinson's disease: a meta-analysis of genome-wide association studies

Background Genome-wide association studies (GWAS) in Parkinson's disease have increased the scope of biological knowledge about the disease over the past decade. We aimed to use the largest aggregate of GWAS data to identify novel risk loci and gain further insight into the causes of Parkinson's disease. Methods We did a meta-analysis of 17 datasets from Parkinson's disease GWAS available from European ancestry samples to nominate novel loci for disease risk. These datasets incorporated all available data. We then used these data to estimate heritable risk and develop predictive models of this heritability. We also used large gene expression and methylation resources to examine possible functional consequences as well as tissue, cell type, and biological pathway enrichments for the identified risk factors. Additionally, we examined shared genetic risk between Parkinson's disease and other phenotypes of interest via genetic correlations followed by Mendelian randomisation. Findings Between Oct 1, 2017, and Aug 9, 2018, we analysed 7·8 million single nucleotide polymorphisms in 37 688 cases, 18 618 UK Biobank proxy-cases (ie, individuals who do not have Parkinson's disease but have a first degree relative that does), and 1·4 million controls. We identified 90 independent genome-wide significant risk signals across 78 genomic regions, including 38 novel independent risk signals in 37 loci. These 90 variants explained 16–36% of the heritable risk of Parkinson's disease depending on prevalence. Integrating methylation and expression data within a Mendelian randomisation framework identified putatively associated genes at 70 risk signals underlying GWAS loci for follow-up functional studies. Tissue-specific expression enrichment analyses suggested Parkinson's disease loci were heavily brain-enriched, with specific neuronal cell types being implicated from single cell data. We found significant genetic correlations with brain volumes (false discovery rate-adjusted p=0·0035 for intracranial volume, p=0·024 for putamen volume), smoking status (p=0·024), and educational attainment (p=0·038). Mendelian randomisation between cognitive performance and Parkinson's disease risk showed a robust association (p=8·00 × 10−7). Interpretation These data provide the most comprehensive survey of genetic risk within Parkinson's disease to date, to the best of our knowledge, by revealing many additional Parkinson's disease risk loci, providing a biological context for these risk factors, and showing that a considerable genetic component of this disease remains unidentified. These associations derived from European ancestry datasets will need to be followed-up with more diverse data. Funding The National Institute on Aging at the National Institutes of Health (USA), The Michael J Fox Foundation, and The Parkinson's Foundation (see appendix for full list of funding sources)