Nitrogen supply method affects growth, yield and must composition of young grape vines (Vitis vinifera L. cv Alicante Bouschet) in southern Brazil.

The aim of this study was to evaluate yield and chemical composition of the must in grapevines subjected to Nitrogen (N) supply methods in sandy soils. The vineyard cultivar was ?Alicante Bouschet? (Vitis vinifera L.) grafted on 1103 Paulsen rootstock, in southern Brazil. The treatments consisted of the application of 20+20 kg N ha−1 without irrigation (NWI), 20+20 kg N ha−1 followed by irrigation (NFI), 20+20 kg N ha−1 via fertigation (NF), 20 kg N ha−1 via fertigation (½NF), and a control (C) without N application. The study was conducted during four crop seasons. Leaves were collected at flowering and veraison to determination N concentration. Stem diameter, grape yield and its components were determined. In the must were evaluated the total soluble solids (TSS), pH, total titratable acidity (TTA) and total anthocyanins (TA). The concentration of nitrate and ammonium in soil solution was determined. N application followed by irrigation or N supplied via fertigation provided to the vines larger stem diameters and leaf N concentrations, in most crop seasons. Grapevines submitted to N application via fertigation or followed by irrigation presented higher yields than conventional application without irrigation, and between two and three times higher than the control. N supply methods little affected total soluble solids contents. The application of N to the soil, regardless of the N supply method, decreased the anthocyanin concentration in the grape must, due to the dilution effect on the pulp/skin ratio, promoted by the yield increase

Twist exome capture allows for lower average sequence coverage in clinical exome sequencing

Background Exome and genome sequencing are the predominant techniques in the diagnosis and research of genetic disorders. Sufficient, uniform and reproducible/consistent sequence coverage is a main determinant for the sensitivity to detect single-nucleotide (SNVs) and copy number variants (CNVs). Here we compared the ability to obtain comprehensive exome coverage for recent exome capture kits and genome sequencing techniques. Results We compared three different widely used enrichment kits (Agilent SureSelect Human All Exon V5, Agilent SureSelect Human All Exon V7 and Twist Bioscience) as well as short-read and long-read WGS. We show that the Twist exome capture significantly improves complete coverage and coverage uniformity across coding regions compared to other exome capture kits. Twist performance is comparable to that of both short- and long-read whole genome sequencing. Additionally, we show that even at a reduced average coverage of 70× there is only minimal loss in sensitivity for SNV and CNV detection. Conclusion We conclude that exome sequencing with Twist represents a significant improvement and could be performed at lower sequence coverage compared to other exome capture techniques

Solving patients with rare diseases through programmatic reanalysis of genome-phenome data.

Funder: EC | EC Seventh Framework Programm | FP7 Health (FP7-HEALTH - Specific Programme "Cooperation": Health); doi: https://doi.org/10.13039/100011272; Grant(s): 305444, 305444Funder: Ministerio de Economía y Competitividad (Ministry of Economy and Competitiveness); doi: https://doi.org/10.13039/501100003329Funder: Generalitat de Catalunya (Government of Catalonia); doi: https://doi.org/10.13039/501100002809Funder: EC | European Regional Development Fund (Europski Fond za Regionalni Razvoj); doi: https://doi.org/10.13039/501100008530Funder: Instituto Nacional de Bioinformática ELIXIR Implementation Studies Centro de Excelencia Severo OchoaFunder: EC | EC Seventh Framework Programm | FP7 Health (FP7-HEALTH - Specific Programme "Cooperation": Health)Reanalysis of inconclusive exome/genome sequencing data increases the diagnosis yield of patients with rare diseases. However, the cost and efforts required for reanalysis prevent its routine implementation in research and clinical environments. The Solve-RD project aims to reveal the molecular causes underlying undiagnosed rare diseases. One of the goals is to implement innovative approaches to reanalyse the exomes and genomes from thousands of well-studied undiagnosed cases. The raw genomic data is submitted to Solve-RD through the RD-Connect Genome-Phenome Analysis Platform (GPAP) together with standardised phenotypic and pedigree data. We have developed a programmatic workflow to reanalyse genome-phenome data. It uses the RD-Connect GPAP's Application Programming Interface (API) and relies on the big-data technologies upon which the system is built. We have applied the workflow to prioritise rare known pathogenic variants from 4411 undiagnosed cases. The queries returned an average of 1.45 variants per case, which first were evaluated in bulk by a panel of disease experts and afterwards specifically by the submitter of each case. A total of 120 index cases (21.2% of prioritised cases, 2.7% of all exome/genome-negative samples) have already been solved, with others being under investigation. The implementation of solutions as the one described here provide the technical framework to enable periodic case-level data re-evaluation in clinical settings, as recommended by the American College of Medical Genetics

Selective synthesis of 1-O-Alkyl(poly)glycerol Ethers by catalytic reductive alkylation of carboxylic acids with a recyclable catalytic system

International audience(Poly)glycerol monoethers were synthesized in good yield and selectivity by the catalytic reductive alkylation of glycerol, diglycerol, and triglycerol with readily available, cheap and/or bio-sourced carboxylic acids. The reaction was catalyzed by 1 mol % of Pd/C under 50 bar H(2) using an acid ion-exchange resin as a recyclable cocatalyst. The catalytic system was recycled several times, and a mechanism is proposed for this transformation

Reductive N-methylation of amines with calcium hydride and Pd/C catalyst

International audienceThe methylation of amines by paraformaldehyde in the presence of calcium hydride as a source of hydrogen and palladium on charcoal as catalyst was studied. Depending on the quantity of paraformaldehyde, monomethylated and dimethylated amines were selectively and efficiently prepared in one pot with good yields

The soil quality concept as a framework to assess management practices in vulnerable agroecosystems : a case study in Mediterranean vineyards

Land management aiming to sustain ecosystem services is an important issue, especially in biodiversity hot spots such as found in Mediterranean areas. In Mediterranean areas, viticulture is an important land use. Vineyards are frequently found on inherently poor soils and are submitted to intensive management practices, which threaten soil functioning and associated ecosystem services. To encourage winegrowers and stakeholders to be reflective and adapt their vineyard practices, we evaluated the effects of three soil management practices (inter row plant cover duration, weeding and fertilization strategies) on soil functioning in 146 commercial plots distributed in Southern France, by a complementary set of biological and physico-chemical indicators. We used the concept of soil dynamic quality to evaluate some soil management practices on soil functioning. The influence of inherent soil properties derived from pedogenesis on soil dynamic indicator response was accounted for by considering the response of soil indicators for three soil groups differing in their stoniness and Ca carbonate content. The three soil management practices systematically influenced some nematode-based indicators, whereas other indicators were ascribable to a specific soil type or practice. We demonstrated that the potential of soil management practices to enhance soil functioning is restricted by soil type. In particular for calcareous soils, the soil functioning is very stable limiting effects of soil management practices. The presence of a cover crop, even temporary, in the inter row, is the only practice which benefits soil functioning whatever the soil type whereas organic fertilization and chemical weeding exhibit contrasting results on soil functioning

Evolved thermostable transketolase for the valorization of vegetable oils.

International audienc

N2O and CH4 emissions from soils under conventional and no-till management practices in Goiania (Cerrados, Brazil)

Nitrous oxide (N2O) and methane (CH4) are important greenhouse gases (GHG) produced respectively by the naturally occurring microbial processes of incomplete denitrification or nitrification and methanogenesis. Tillage practices and climate affect the release of GHGs. No tillage (DMC) systems may increase CO2-C fixation in soil but also N2O and CH4 emissions. The aim of this article is to question whether the positive effect of a DMC system observed on carbon storage for the topsoil layer in Cerrado soils is offset or not by the N2O and/or CH4 emissions. Two 5-year-old systems, tillage (disc on the first 15 cm called offset: OFF) and a direct-sowing mulch-based crop system (DMC) with an additional cover crop were studied during a cropping cycle. N2O and CH4 fluxes are determined using a closed-chamber, N2O and CO2 concentrations are measured at 3 depths (10-, 20- and 30 cm). No significant difference between treatments was observed for both gases (for emissions and concentrations). Soil NO contents increase from surface to depth (30 cm) and range from 300 ppbv to 3 ppm for both treatments. Total annual estimated emissions of N2O range from 31 to 35 g N2O-N ha(-1) year(-1) for DMC and OFF respectively which is low and corresponds only to 0.03% of he total N-fertilizer applied. Monthly means N2O emissions were strongly correlated to monthly means of N2O content at 10 cm depth (R-2 = -0.66) and seem to increase exponentially with monthly mean Water Filled Pore Space WFPS (0-10 cm layer) (R-2 = 0.33). CH4 fluxes were very low as well: both treatment act as source of CH4 (245 and 403 g CH4-C ha(-1) year(-1) for DMC and OFF respectively. On a CO-C equivalent basis these results correspond to 4.1 and 4.7 kg CO2-C ha(-1) year(-1) for NO and to 1.9 and 3.1 kg CO2-C ha(-1) year(-1) for CH4 for DMC and OFF respectively. As a result, the carbon sequestration balance taking into account the CO2, CH4 and N2O on a CO2-C equivalent basis is in favour of DMC treatment considering that this treatment increases carbon storage originated from CO-C for the topsoil (0-10 cm) layer (350 kg C ha(-1) year(-1)) in comparison with OFF treatment

Cropping systems, carbon sequestration and erosion in Brazil, a review

Soils represent a large carbon pool, approximately 1500 Gt, which is equivalent to almost three times the quantity stored in terrestrial biomass and twice the amount stored in the atmosphere. Any modification of land use or land management can induce variations in soil carbon stocks, even in agricultural systems that are perceived to be in a steady state. Tillage practices often induce soil aerobic conditions that are favourable to microbial activity and may lead to a degradation of soil structure. As a result, mineralisation of soil organic matter increases in the long term. The adoption of no-tillage systems and the maintenance of a permanent vegetation cover using Direct seeding Mulch-based Cropping system or DMC, may increase carbon levels in the topsoil. In Brazil, no-tillage practices (mainly DMC), were introduced approximately 30 years ago in the south in the Parana state, primarily as a means of reducing erosion. Subsequently, research has begun to study the management of the crop waste products and their effects on soil fertility, either in terms of phosphorus management, as a means of controlling soil acidity, or determining how manures can be applied in a more localised manner. The spread of no-till in Brazil has involved a large amount of extension work. The area under no-tillage is still increasing in the centre and north of the country and currently occupies ca. 20 million hectares, covering a diversity of environmental conditions, cropping systems and management practices. Most studies of Brazilian soils give rates of carbon storage in the top 40 cm of the soil of 0.4 to 1.7 t C ha(-1) per year, with the highest rates in the Cerrado region. However, caution must be taken when analysing DMC systems in terms of carbon sequestration. Comparisons should include changes in trace gas fluxes and should not be limited to a consideration of carbon storage in the soil alone if the full implications for global warming are to be assessed