The rice functional genomics (refuge) platform, an international hosting platform for elucidating gene function using rice as a model system

REFUGE is an international hosting platform for the elucidation of gene function using rice as a model species. It offers international scientists, notably nonrice specialists, an access to know-how, bioinformatic, biological, and molecular resources, allowing the use of rice as a model system to investigate gene function through functional genomics strategies. PhD and postdoctoral researchers, notably from the South, are the first target beneficiaries of this initiative. Visiting scientists have access to REFUGE's know-how, including bioinformatic searches, preparation of T-DNA vectors, high-throughput production of rice transformants, molecular characterization of transformants, genotyping of insertion lines from local and international collections; growth, crossing, and phenotyping in containment greenhouse; and access to cell imaging and genotyping platforms. Hosted scientists have the opportunity to carry out one to several visits from 1 to 3 months, the REFUGE staff taking care of the materials produced between two visits. The REFUGE platform provides supervision of the hosted scientists or students and covers bench fees. Visitors have to find their own travel and subsistence funds. However, REFUGE can provide assistance to scientists notably from South countries, to find an appropriate funding source for travel and subsistence. Applications should be submitted at http://www.refuge-platform.org and will be readily examined by the REFUGE scientific committee. Funded by Agropolis Fondation, http://www.agropolis-fondation.fr/, REFUGE is a collaborative venture between the joint research unit DAP -INRA, CIRAD and Montpellier University and Agronomy School- and the 'Plant genome and development' laboratory at IRD and Perpignan University. (Texte intégral

Unleashing meiotic recombinaton in plants. [W1068]

Meiotic crossovers shuffle parental genetic information, providing novel combinations of alleles on which natural or artificial selection can act. However, crossover events are relatively rare, typically one to three exchange points per chromosome pair. Recent work has identified three pathways limiting meiotic crossovers in Arabidopsis thaliana that rely on the activity of FANCM [Crismani W, et al. (2012) Science 336:1588-1590], RECQ4 [Séguéla-Arnaud M, et al. (2015) Proc Natl Acad Sci USA 112:4713-4718], and FIGL1 [Girard C, et al. (2015) PLoS Genet 11:e1005369]. We analyzed recombination in Arabidopsis plants in which one, two, or all three of these pathways were disrupted in both pure line and hybrid contexts. The greatest effect was observed when combining recq4 and figl1 mutations, which increased the hybrid genetic map length from 389 to 3,037 cM. This corresponds to an unprecedented 7.8-fold increase in crossover frequency. We then showed that recombination can be massively increased in crop species. These results open the possibility of manipulating recombination to enhance plant breeding efficiency. (Résumé d'auteur

Klimawandel und biologische Invasion: eine soziologische Längsschnittstudie der Ausbreitungsüberwachung der Asiatische Tigermücke in Europa

The consequences of climate change on public health can be direct or indirect such as, for example, by modifying vector species distribution. This is the case with Aedes albopictus, a mosquito that is a vector for dengue fever, chikungunya, and potentially the Zika virus. This article focuses on the Alpes-Maritimes department, the first French department affected by the introduction of A. albopictus, i.e., the “Asian tiger mosquito”. It draws on qualitative and quantitative diachronic research conducted from 2009 to 2014 to provide a time-dependent sociological analysis of the implementation of chikungunya and dengue prevention policies and their reception by the population of the Alpes-Maritimes. The article first compares scientific expertise and the discourse of inhabitants regarding the climatic and anthropogenic factors that have encouraged the introduction and proliferation of tiger mosquitoes. It then highlights how both policy-makers and inhabitants must mediate between the epidemic-related and environmental challenges that have accompanied the spread of A. albopictus. Finally, the paper examines the (un)acceptance of the population vis-à-vis this invasive exotic species and points to the unequal capacity of different inhabitants to react when confronted with an environmental and health-related risk.Posljedice klimatskih promjena po zdravlje ljudi mogu biti izravne ali i neizravne kao što je, primjerice, raspodjela vektorskih vrsta. Takav je slučaj s komarcem Aedes albopictus, koji je vektor Denge virusa, Chikungunya virusa, a potencijalno i Zika virusa. U ovom se radu istražuje pojava A. albopictusa, ili “azijskog tigrastog komarca”, u francuskom departmanu Alpes-Maritimes u kojem se u Francuskoj prvi put pojavio. Rad se temelji na kvalitativnom i kvantitativnom dijakroničnom istraživanju provedenom između 2009. i 2014. godine s ciljem davanja vremenski ovisne sociološke analize implementacije preventivnih politika protiv Chikungunya i Denge virusa, kao i njihovog prihvaćanja među stanovništvom ovog departmana. U radu se prvo uspoređuju znanstveni diskurs i diskurs lokalnog stanovništva o klimatskim i antropogenim čimbenicima koji su doveli do pojave i širenja tigrastih komaraca. Nadalje, ističe se činjenica da i donositelji mjera i lokalno stanovništvo moraju uzeti u obzir i epidemiološke i okolišne izazove koji prate širenje A. albopictusa. Konačno, u radu se istražuje (ne)prihvaćanje stanovnika prema ovoj invazivnoj egzotičnoj vrsti, te se ukazuje na nejednakosti među dijelovima populacije s obzirom na mogućnosti rješavanja ovog pitanja okolišne i zdravstvene ugroze.Die Auswirkungen des Klimawandels auf die menschliche Gesundheit können direkt aber auch indirekt sein, wie z.B. die Verteilung von Vektorarten. Um einen solchen Fall handelt es sich bei der Mücke aedes albopictus, die das Dengue-Virus, das Chikungunya-Virus, und vielleicht auch das Zika-Virus überträgt. In dieser Arbeit befassen wir uns mit der aedes albopictus, der “asiatischen Tigermücke”, im französischen Département Alpes-Maritimes, wo sie in Frankreich zum ersten Mal gesichtet wurde. Die Arbeit beruht auf einer zwischen 2009 und 2014 durchgeführten qualitativen und quantitativen diachronischen Untersuchung, die es zum Ziel hatte,eine zeitabhängige soziologische Analyse der Implementierung von Präventionspolitiken gegen das Chikungunya- und das Dengue-Virus, sowie deren Rezeption von der Bevölkerung des Départements durchzuführen. In der Arbeit wird zuerst der wissenschaftliche Diskurs mit dem Diskurs der lokalen Bevölkerung verglichen, hinsichtlich der klimatischen und anthropogenen Faktoren, die zum Erscheinen und zur Verbreitung von Tigermücken beigetragen haben. Weiterhin wird die Tatsache hervorgehoben, dass sowohl die Maßnahmenträger als auch die lokale Bevölkerung epidemiologische und ökologische die Verbreitung von aedes albopictus begleitende Herausforderungen berücksichtigen müssen. Schließlich wird die (Nicht-) Akzeptierung dieser invasiven exotischen Art von der Bevölkerung erforscht, es wird auch auf die ungleichen Möglichkeiten der Bevölkerungsteile hingewiesen im Hinblick auf die Lösung dieses Problems der Umwelt- und Gesundheitsgefährdung

Folate polyglutamylation is required for rice seed development

In plants, polyglutamylated folate forms account for a significant proportion of the total folate pool. Polyglutamylated folate forms are produced by the enzyme folylpolyglutamate synthetase (FPGS). The FPGS enzyme is encoded by two genes in rice, Os03g02030 and Os10g35940. Os03g02030 represents the major expressed form in developing seed. To determine the function of this FPGS gene in rice, a T-DNA knockout line was characterised. Disrupting Os03g02030 gene expression resulted in delayed seed filling. LC-MS/MS-based metabolite profiling revealed that the abundance of mono- and polyglutamylated folate forms was significantly decreased in seeds of the knockout line. RT-qPCR detected an increase in the transcript abundance of folate biosynthesis genes in seed of the knockout plant, whereas the folate deglutamating enzyme ?-glutamyl hydrolase mRNA level was reduced. Our study has uncovered a novel role for folate polyglutamylation during rice seed development and a potential feedback mechanism to maintain folate abundance.(Résumé d'auteur

A highly mutagenised barley (cv. Golden Promise) TILLING population coupled with strategies for screening-by-sequencing

Background:We developed and characterised a highly mutagenised TILLING population of the barley (Hordeum vulgare) cultivar Golden Promise. Golden Promise is the 'reference' genotype for barley transformation and a primary objective of using this cultivar was to be able to genetically complement observed mutations directly in order to prove gene function. Importantly, a reference genome assembly of Golden Promise has also recently been developed. As our primary interest was to identify mutations in genes involved in meiosis and recombination, to characterise the population we focused on a set of 46 genes from the literature that are possible meiosis gene candidates. Results:Sequencing 20 plants from the population using whole exome capture revealed that the mutation density in this population is high (one mutation every 154 kb), and consequently even in this small number of plants we identified several interesting mutations. We also recorded some issues with seed availability and germination. We subsequently designed and applied a simple two-dimensional pooling strategy to identify mutations in varying numbers of specific target genes by Illumina short read pooled-amplicon sequencing and subsequent deconvolution. In parallel we assembled a collection of semi-sterile mutants from the population and used a custom exome capture array targeting the 46 candidate meiotic genes to identify potentially causal mutations. Conclusions:We developed a highly mutagenised barley TILLING population in the transformation competent cultivar Golden Promise. We used novel and cost-efficient screening approaches to successfully identify a broad range of potentially deleterious variants that were subsequently validated by Sanger sequencing. These resources combined with a high-quality genome reference sequence opens new possibilities for efficient functional gene validation.Miriam Schreiber, Abdellah Barakate, Nicola Uzrek, Malcolm Macaulay, Adeline Sourdille, Jenny Morris, Pete E. Hedley, Luke Ramsay and Robbie Waug

New Strategies in Sport Nutrition to Increase Exercise Performance.

Despite over 50 years of research, the field of sports nutrition continues to grow at a rapid rate. Whilst the traditional research focus was one that centred on strategies to maximize competition performance, emerging data in the last decade has demonstrated how both macronutrient and micronutrient availability can play a prominent role in regulating those cell signalling pathways that modulate skeletal muscle adaptations to endurance and resistance training. Nonetheless, in the context of exercise performance, it is clear that carbohydrate (but not fat) still remains king and that carefully chosen ergogenic aids (e.g. caffeine, creatine, sodium bicarbonate, beta-alanine, nitrates) can all promote performance in the correct exercise setting. In relation to exercise training, however, it is now thought that strategic periods of reduced carbohydrate and elevated dietary protein intake may enhance training adaptations whereas high carbohydrate availability and antioxidant supplementation may actually attenuate training adaptation. Emerging evidence also suggests that vitamin D may play a regulatory role in muscle regeneration and subsequent hypertrophy following damaging forms of exercise. Finally, novel compounds (albeit largely examined in rodent models) such as epicatechins, nicotinamide riboside, resveratrol, β-hydroxy β-methylbutyrate, phosphatidic acid and ursolic acid may also promote or attenuate skeletal muscle adaptations to endurance and strength training. When taken together, it is clear that sports nutrition is very much at the heart of the Olympic motto, Citius, Altius, Fortius (faster, higher, stronger)

Dietary Restriction Depends on Nutrient Composition to Extend Chronological Lifespan in Budding Yeast Saccharomyces cerevisiae

10.1371/journal.pone.0064448PLoS ONE85

Metabolism via arginase or nitric oxide synthase: two competing arginine pathways in macrophages

Macrophages play a major role in the immune system, both as antimicrobial effector cells and as immunoregulatory cells, which induce, suppress or modulate adaptive immune responses. These key aspects of macrophage biology are fundamentally driven by the phenotype of macrophage arginine metabolism that is prevalent in an evolving or ongoing immune response. M1 macrophages express the enzyme nitric oxide synthase, which metabolizes arginine to nitric oxide (NO) and citrulline. NO can be metabolized to further downstream reactive nitrogen species, while citrulline might be reused for efficient NO synthesis via the citrulline–NO cycle. M2 macrophages are characterized by expression of the enzyme arginase, which hydrolyzes arginine to ornithine and urea. The arginase pathway limits arginine availability for NO synthesis and ornithine itself can further feed into the important downstream pathways of polyamine and proline syntheses, which are important for cellular proliferation and tissue repair. M1 versus M2 polarization leads to opposing outcomes of inflammatory reactions, but depending on the context, M1 and M2 macrophages can be both pro- and anti-inflammatory. Notably, M1/M2 macrophage polarization can be driven by microbial infection or innate danger signals without any influence of adaptive immune cells, secondarily driving the T helper (Th)1/Th2 polarization of the evolving adaptive immune response. Since both arginine metabolic pathways cross-inhibit each other on the level of the respective arginine break-down products and Th1 and Th2 lymphocytes can drive or amplify macrophage M1/M2 dichotomy via cytokine activation, this forms the basis of a self-sustaining M1/M2 polarization of the whole immune response. Understanding the arginine metabolism of M1/M2 macrophage phenotypes is therefore central to find new possibilities to manipulate immune responses in infection, autoimmune diseases, chronic inflammatory conditions, and cancer

Metabolomic analyses of Leishmania reveal multiple species differences and large differences in amino acid metabolism

Comparative genomic analyses of Leishmania species have revealed relatively minor heterogeneity amongst recognised housekeeping genes and yet the species cause distinct infections and pathogenesis in their mammalian hosts. To gain greater information on the biochemical variation between species, and insights into possible metabolic mechanisms underpinning visceral and cutaneous leishmaniasis, we have undertaken in this study a comparative analysis of the metabolomes of promastigotes of L. donovani, L. major and L. mexicana. The analysis revealed 64 metabolites with confirmed identity differing 3-fold or more between the cell extracts of species, with 161 putatively identified metabolites differing similarly. Analysis of the media from cultures revealed an at least 3-fold difference in use or excretion of 43 metabolites of confirmed identity and 87 putatively identified metabolites that differed to a similar extent. Strikingly large differences were detected in their extent of amino acid use and metabolism, especially for tryptophan, aspartate, arginine and proline. Major pathways of tryptophan and arginine catabolism were shown to be to indole-3-lactate and arginic acid, respectively, which were excreted. The data presented provide clear evidence on the value of global metabolomic analyses in detecting species-specific metabolic features, thus application of this technology should be a major contributor to gaining greater understanding of how pathogens are adapted to infecting their hosts

Arabica-like flavour in a heat tolerant wild coffee species

There are numerous factors to consider when developing climate resilient coffee crops, including the ability to tolerate altered climatic conditions, meet agronomic and value chain criteria, and satisfy consumer preferences for flavour (aroma and taste). We evaluated the sensory characteristics and key environmental requirements for the enigmatic narrow-leaved coffee (Coffea stenophylla), a wild species from Upper West Africa1. We confirm historical reports of a superior flavour1-3, and uniquely and remarkably, reveal a sensory profile analogous to high quality Arabica coffee. We demonstrate that this species grows and crops under the same range of key climatic conditions as (sensorially inferior) robusta and Liberica coffee4-9, and has a mean annual temperature 6.2–6.8⁰C higher than Arabica coffee, even under equivalent rainfall conditions. This species substantially broadens the climate envelope for high quality coffee, and could provide an important resource for the development of climate resilient coffee crop plants