Genomics of wine yeast: functional analysis of new and variable genes

Projecte de recerca elaborat a partir d’una estada a l’Institut National de la Recherche Agronomique, França, entre 2007 i 2009. Saccharomyces cerevisiae ha estat el llevat utilitzat durant mil.lenis en l'elaboració de vins. Tot i així, es té poc coneixement sobre les pressions de selecció que han actuat en la modelització del genoma dels llevats vínics. S’ha seqüenciat el genoma d'una soca vínica comercial, EC1118, obtenint 31 supercontigs que cobreixen el 97% del genoma de la soca de referència, S288c. S’ha trobat que el genoma de la soca vínica es diferencia bàsicament en la possessió de 3 regions úniques que contenen 34 gens implicats en funcions claus per al procés fermentatiu. A banda, s’han dut a terme estudis de filogènia i synteny (ordre dels gens) que mostren que una d'aquestes tres regions és pròxima a una espècie relacionada amb el gènere Saccharomyces, mentre que les altres dos regions tenen un origen no-Saccharomyces. S’ha identificat mitjançant PCR i seqüenciació a Zygosaccharomyces bailii, una espècie contaminant de les fermentacions víniques, com a espècie donadora d'una de les dues regions. Les hibridacions naturals entre soques de diferents espècies dins del grup Saccharomyces sensu stricto ja han estat descrites. El treball és el primer que presenta hibridacions entre espècies Saccharomyces i no-Saccharomyces (Z. bailii, en aquest cas). També s’assenyala que les noves regions es troben freqüent i diferencialment presents entre els clades de S. cerevisiae, trobant-se de manera gairebé exclusiva en el grup de les soques víniques, suggerint que es tracta d'una adquisició recent de transferència gènica. En general, les dades demostren que el genoma de les soques víniques pateix una constant remodelació mitjançant l'adquisició de gens exògens. Els resultats suggereixen que aquests processos estan afavorits per la proximitat ecològica i estan implicats en l'adaptació molecular de les soques víniques a les condicions d'elevada concentració en sucres, poc nitrogen i elevades concentracions en etanol.

Thermodynamics and log–contrast analysis in fluid geochemistry

There are two principal chemical concepts that are important for studying the naturalenvironment. The first one is thermodynamics, which describes whether a system is atequilibrium or can spontaneously change by chemical reactions. The second main conceptis how fast chemical reactions (kinetics or rate of chemical change) take place wheneverthey start. In this work we examine a natural system in which both thermodynamics andkinetic factors are important in determining the abundance of NH+4 , NO−2 and NO−3 insuperficial waters. Samples were collected in the Arno Basin (Tuscany, Italy), a system inwhich natural and antrophic effects both contribute to highly modify the chemical compositionof water. Thermodynamical modelling based on the reduction-oxidation reactionsinvolving the passage NH+4 -& NO−2 -& NO−3 in equilibrium conditions has allowed todetermine the Eh redox potential values able to characterise the state of each sample and,consequently, of the fluid environment from which it was drawn. Just as pH expressesthe concentration of H+ in solution, redox potential is used to express the tendency of anenvironment to receive or supply electrons. In this context, oxic environments, as thoseof river systems, are said to have a high redox potential because O2 is available as anelectron acceptor.Principles of thermodynamics and chemical kinetics allow to obtain a model that oftendoes not completely describe the reality of natural systems. Chemical reactions may indeedfail to achieve equilibrium because the products escape from the site of the rectionor because reactions involving the trasformation are very slow, so that non-equilibriumconditions exist for long periods. Moreover, reaction rates can be sensitive to poorly understoodcatalytic effects or to surface effects, while variables as concentration (a largenumber of chemical species can coexist and interact concurrently), temperature and pressurecan have large gradients in natural systems. By taking into account this, data of 91water samples have been modelled by using statistical methodologies for compositionaldata. The application of log–contrast analysis has allowed to obtain statistical parametersto be correlated with the calculated Eh values. In this way, natural conditions in whichchemical equilibrium is hypothesised, as well as underlying fast reactions, are comparedwith those described by a stochastic approach

Urea nitrogen, creatinine, and uric acid levels in postmortem serum, vitreous humor, and pericardial fluid.

Urea nitrogen, creatinine, and uric acid are relatively stable in postmortem serum and may, therefore, be used for diagnostic purposes when chronic kidney disease and end-stage renal failure are investigated as causes of death. Nevertheless, uncertainties remain in defining the best alternative to postmortem serum for the identification and assessment of significantly decreased kidney function. In this study, we investigated urea nitrogen, creatinine, and uric acid levels in postmortem serum, pericardial fluid, and vitreous humor in a series of medico-legal cases (500 autopsies) with various causes of death. No postmortem interval-related differences were observed in any of the investigated fluids for any analyzed parameter, confirming the biochemical stability of all compounds after death. Data analysis failed to reveal statistically significant differences between postmortem serum and pericardial fluid urea nitrogen, creatinine, and uric acid concentrations. Conversely, statistically significant differences were observed in all analyzed biomarkers between postmortem serum and vitreous humor levels, with lower concentrations of all markers measured in vitreous. The results of this study suggest that, in order to estimate as accurately as possible blood analyte concentrations at the time of death, pericardial fluid should be preferred to vitreous humor.

A combined analysis of the short-term effects of photochemical air pollutants on mortality within the EMECAM project.

In recent years, some epidemiologic studies have attributed adverse effects of air pollutants on health not only to particles and sulfur dioxide but also to photochemical air pollutants (nitrogen dioxide and ozone). The effects are usually small, leading to some inconsistencies in the results of the studies. Furthermore, the different methodologic approaches of the studies used has made it difficult to derive generic conclusions. We provide here a quantitative summary of the short-term effects of photochemical air pollutants on mortality in seven Spanish cities involved in the EMECAM project, using generalized additive models from analyses of single and multiple pollutants. Nitrogen dioxide and ozone data were provided by seven EMECAM cities (Barcelona, Gijón, Huelva, Madrid, Oviedo, Seville, and Valencia). Mortality indicators included daily total mortality from all causes excluding external causes, daily cardiovascular mortality, and daily respiratory mortality. Individual estimates, obtained from city-specific generalized additive Poisson autoregressive models, were combined by means of fixed effects models and, if significant heterogeneity among local estimates was found, also by random effects models. Significant positive associations were found between daily mortality (all causes and cardiovascular) and NO(2), once the rest of air pollutants were taken into account. A 10 microg/m(3) increase in the 24-hr average 1-day NO(2)level was associated with an increase in the daily number of deaths of 0.43% [95% confidence interval (CI), -0.003-0.86%] for all causes excluding external. In the case of significant relationships, relative risks for cause-specific mortality were nearly twice as much as that for total mortality for all the photochemical pollutants. Ozone was independently related only to cardiovascular daily mortality. No independent statistically significant relationship between photochemical air pollutants and respiratory mortality was found. The results in this study suggest that, given the present levels of photochemical pollutants, people living in Spanish cities are exposed to health risks derived from air pollution.

Nitrogen fractions in the microbial biomass in soils of southern Brazil

The reaction of nitrogen compounds with ninhydrin can be used as an indicator of cytoplasmic materials released from microbial cells killed by fumigation. Total-N, ninhydrin-reactive-N (NR-N), ammonium-N (A-N), and α-amino-N in the microbial biomass of soils from the State of Rio Grande do Sul, Brazil, were determined, in 1996, in 0.5 mol L-1 K2SO4 extracts of fumigated and non-fumigated soils. Total-N varied from 20.3 to 104.4 mg kg-1 and the ninhydrin-reactive-N corresponded, in average, to 27% of this. The ninhydrin-reactive-N was made up of 67% ammonium-N and 33% aminoacids with the amino group at the α-carbon position. It was concluded that colorimetric analysis of NR-N and A-N may be used as a direct measure of microbial N in soil. This simple and rapid procedure is adequate for routine analyses.

Relationships between grain yield and accumulation of biomass, nitrogen and phosphorus in common bean cultivars

Shoot biomass is considered a relevant component for crop yield, but relationships between biological productivity and grain yield in legume crops are usually difficult to establish. Two field experiments were carried out to investigate the relationships between grain yield, biomass production and N and P accumulation at reproductive stages of common bean (Phaseolus vulgaris) cultivars. Nine and 18 cultivars were grown on 16 m² plots in 1998 and 1999, respectively, with four replications. Crop biomass was sampled at four growth stages (flowering R6, pod setting R7, beginning of pod filling R8, and mid-pod filling R8.5), grain yield was measured at maturity, and N and P concentrations were determined in plant tissues. In both years, bean cultivars differed in grain yield, in root mass at R6 and R7 stages, and in shoot mass at R6 and R8.5, whereas at R7 and R8 differences in shoot mass were significant in 1998 only. In both years, grain yield did not correlate with shoot mass at R6 and R7 and with root mass at R6. Grain yield correlated with shoot mass at R8 in 1999 but not in 1998, with shoot mass at R8.5 and with root mass at R7 in both years. Path coefficient analysis indicated that shoot mass at R8.5 had a direct effect on grain yield in both years, that root mass at R7 had a direct effect on grain yield in 1998, and that in 1999 the amounts of N and P in shoots at R8.5 had indirect effects on grain yield via shoot mass at R8.5. A combined analysis of both experiments revealed that biomass accumulation, N and P in shoots at R6 and R7 as well as root mass at R6 were similar in both years. In 1998 however bean accumulated more root mass at R7 and more biomass and N and P in shoots at R8 and R8.5, resulting in a 57 % higher grain yield in 1998. This indicates that grain yield of different common bean cultivars is not intrinsically associated with vegetative vigor at flowering and that mechanisms during pod filling can strongly influence the final crop yield. The establishment of a profuse root system during pod setting, associated with the continuous N and P acquisition during early pod filling, seems to be relevant for higher grain yields of common bean.

Monitoring nitrogen nutrition in cotton

Both N excess and deficiency may affect cotton yield and quality. It would therefore be useful to base the N management fertilization on the monitoring of the nutritional status. This study investigated the correlations among the following determination methods of the N nutritional status of cotton (Gossypium hirsutum L., var. Latifolia): chlorophyll readings (SPAD-502®, Minolta), specific-ion nitrate meter (Nitrate Meter C-141, Horiba-Cardy®), and laboratory analysis (conventional foliar diagnosis). Samples were taken weekly from two weeks before flowering to the fifth week after the first flower. The experiment was conducted on the Fazenda Santa Tereza, Itapeva, State of São Paulo, Brazil. The crop was fertilized with 40 kg ha-1 N at planting and 0, 30, 60, 90, and 120 kg ha-1 of side-dressed N. The range of leaf N contents reported as adequate for samples taken 80-90 days after plant emergence (traditional foliar diagnosis) may be used as reference from the beginning of flowering when the plant is not stressed. Specific-ion nitrate meter readings can be used as a nutritional indicator of cotton nutrition from one week after pinhead until the third week of flowering. In this case, plants are well-nourished when readings exceed 8,000 mg L-1 NO3-. The chlorophyll meter can also be used to estimate the nutritional status of cotton from the third week of flowering. In this case the readings should be above 48 in well-nourished plants.

Characterization of soil chemical properties of strawberry fields using principal component analysis

One of the largest strawberry-producing municipalities of Rio Grande do Sul (RS) is Turuçu, in the South of the State. The strawberry production system adopted by farmers is similar to that used in other regions in Brazil and in the world. The main difference is related to the soil management, which can change the soil chemical properties during the strawberry cycle. This study had the objective of assessing the spatial and temporal distribution of soil fertility parameters using principal component analysis (PCA). Soil sampling was based on topography, dividing the field in three thirds: upper, middle and lower. From each of these thirds, five soil samples were randomly collected in the 0-0.20 m layer, to form a composite sample for each third. Four samples were taken during the strawberry cycle and the following properties were determined: soil organic matter (OM), soil total nitrogen (N), available phosphorus (P) and potassium (K), exchangeable calcium (Ca) and magnesium (Mg), soil pH (pH), cation exchange capacity (CEC) at pH 7.0, soil base (V%) and soil aluminum saturation(m%). No spatial variation was observed for any of the studied soil fertility parameters in the strawberry fields and temporal variation was only detected for available K. Phosphorus and K contents were always high or very high from the beginning of the strawberry cycle, while pH values ranged from very low to very high. Principal component analysis allowed the clustering of all strawberry fields based on variables related to soil acidity and organic matter content.

Physical properties of a Red-Yellow Latosol and productivity of a signalgrass pasture fertilized with increasing nitrogen doses

The physical properties and fertility of the soil are important factors in the formation and establishment of pasture. Changes in physical properties affect the movement of water, air, nutrients and roots, which, in turn, affect the productivity and longevity of pastures. The objective of this study was to evaluate the physical properties of the soil and the dry matter yield of a pasture with signalgrass cv. Basilisk (Brachiaria decumbens cv. Basilisk), fertilized with increasing nitrogen doses (N), on a dystrophic Red-Yellow Latosol. The experiment was conducted on the Fazenda Rio Manso of the Universidade Federal dos Vales do Jequitinhonha e Mucuri, in Couto de Magalhães de Minas, State of Minas Gerais, Brazil. To evaluate the annual forage yield, a split plot scheme in a randomized block design with four replications was used, with N doses (0, 50, 100, 150, and 200 kg/ha/year) in the plots and growing seasons (first and second) in the subplots. For soil evaluation, a split plot scheme was used with N doses (0, 25, 50, 75 and 100 kg/ha/cut) in the plots and three sampling times (prior to the experiment, at the end of the first growing season and at the end of the second growing season) in the subplots in a randomized block design with four replications. This analysis was performed separately at two soil depths (0-3 and 10-13 cm). Forage samples were analyzed for the annual dry matter yield (DMY), and soil samples were analyzed for pre-consolidation pressure (σp), initial soil bulk density (Bd), total pore volume (TPV) and void index (Vd). Higher nitrogen doses increased the dry matter yield of signalgrass pasture and the pre-consolidation pressure of the soil. The total pore volume and void index decreased, and the initial soil bulk density increased, though without promoting soil compaction.

Efficiency of nitrogen fertilizer applied at corn sowing in contrasting growing seasons in Paraguay

In order to select soil management practices that increase the nitrogen-use efficiency (NUE) in agro-ecosystems, the different indices of agronomic fertilizer efficiency must be evaluated under varied weather conditions. This study assessed the NUE indices in no-till corn in southern Paraguay. Nitrogen fertilizer rates from 0 to 180 kg ha-1 were applied in a single application at corn sowing and the crop response investigated in two growing seasons (2010 and 2011). The experimental design was a randomized block with three replications. Based on the data of grain yield, dry matter, and N uptake, the following fertilizer indices were assessed: agronomic N-use efficiency (ANE), apparent N recovery efficiency (NRE), N physiological efficiency (NPE), partial factor productivity (PFP), and partial nutrient balance (PNB). The weather conditions varied largely during the experimental period; the rainfall distribution was favorable for crop growth in the first season and unfavorable in the second. The PFP and ANE indices, as expected, decreased with increasing N fertilizer rates. A general analysis of the N fertilizer indices in the first season showed that the maximum rate (180 kg ha-1) obtained the highest corn yield and also optimized the efficiency of NPE, NRE and ANE. In the second season, under water stress, the most efficient N fertilizer rate (60 kg ha-1) was three times lower than in the first season, indicating a strong influence of weather conditions on NUE. Considering that weather instability is typical for southern Paraguay, anticipated full N fertilization at corn sowing is not recommended due the temporal variability of the optimum N fertilizer rate needed to achieve high ANE.

Greenhouse Gas and Nitrogen Fertilizer Scenarios for U.S. Agriculture and Global Biofuels, June 2011

This analysis uses the 2011 FAPRI-CARD (Food and Agricultural Policy Research Institute–Center for Agricultural and Rural Development) baseline to evaluate the impact of four alternative scenarios on U.S. and world agricultural markets, as well as on world fertilizer use and world agricultural greenhouse gas emissions. A key assumption in the 2011 baseline is that ethanol support policies disappear in 2012. The baseline also assumes that existing biofuel mandates remain in place and are binding. Two of the scenarios are adverse supply shocks, the first being a 10% increase in the price of nitrogen fertilizer in the United States, and the second, a reversion of cropland into forestland. The third scenario examines how lower energy prices would impact world agriculture. The fourth scenario reintroduces biofuel tax credits and duties. Given that the baseline excludes these policies, the fourth scenario is an attempt to understand the impact of these policies under the market conditions that prevail in early 2011. A key to understanding the results of this fourth scenario is that in the absence of tax credits and duties, the mandate drives biofuel use. Therefore, when the tax credits and duties are reintroduced, the impacts are relatively small. In general, the results show that the entire international commodity market system is remarkably robust with respect to policy changes in one country or in one sector. The policy implication is that domestic policy changes implemented by a large agricultural producer like the United States can have fairly significant impacts on the aggregate world commodity markets. A second point that emerges from the results is that the law of unintended consequences is at work in world agriculture. For example, a U.S. nitrogen tax that might presumably be motivated for environmental benefit results in an increase in world greenhouse gas emissions. A similar situation occurs in the afforestation scenario in which crop production shifts from high-yielding land in the United States to low-yielding land and probably native vegetation in the rest of the world, resulting in an unintended increase in global greenhouse gas emissions.

LEAF TOTAL NITROGEN CONCENTRATION AS AN INDICATOR OF NITROGEN STATUS FOR PLANTLETS AND YOUNG PLANTS OF EUCALYPTUS CLONES

The use of leaf total nitrogen concentration as an indicator for nutritional diagnosis has some limitations. The objective of this study was to determine the reliability of total N concentration as an indicator of N status for eucalyptus clones, and to compare it with alternative indicators. A greenhouse experiment was carried out in a randomized complete block design in a 2 × 6 factorial arrangement with plantlets of two eucalyptus clones (140 days old) and six levels of N in the nutrient solution. In addition, a field experiment was carried out in a completely randomized design in a 2 × 2 × 2 × 3 factorial arrangement, consisting of two seasons, two regions, two young clones (approximately two years old), and three positions of crown leaf sampling. The field areas (regions) had contrasting soil physical and chemical properties, and their soil contents for total N, NH+4-N, and NO−3-N were determined in five soil layers, up to a depth of 1.0 m. We evaluated the following indicators of plant N status in roots and leaves: contents of total N, NH+4-N, NO−3-N, and chlorophyll; N/P ratio; and chlorophyll meter readings on the leaves. Ammonium (root) and NO−3-N (root and leaf) efficiently predicted N requirements for eucalyptus plantlets in the greenhouse. Similarly, leaf N/P, chlorophyll values, and chlorophyll meter readings provided good results in the greenhouse. However, leaf N/P did not reflect the soil N status, and the use of the chlorophyll meter could not be generalized for different genotypes. Leaf total N concentration is not an ideal indicator, but it and the chlorophyll levels best represent the soil N status for young eucalyptus clones under field conditions.

Critical values of nitrogen indices in tomato plants grown in soil and nutrient solution determined by different statistical procedures

The objective of this study was to establish critical values of the N indices, namely soil-plant analysis development (SPAD), petiole sap N-NO3 and organic N in the tomato leaf adjacent to the first cluster (LAC), under soil and nutrient solution conditions, determined by different statistical approaches. Two experiments were conducted in randomized complete block design with four repli-cations. Tomato plants were grown in soil, in 3 L pot, with five N rates (0, 100, 200, 400 and 800 mg kg-1) and in solution at N rates of 0, 4, 8, 12 and 16 mmol L-1. Experiments in nutrient solution and soil were finished at thirty seven and forty two days after transplanting, respectively. At those times, SPAD index and petiole sap N-NO3 were evaluated in the LAC. Then, plants were harvested, separated in leaves and stem, dried at 70ºC, ground and weighted. The organic N was determined in LAC dry matter. Three statistical procedures were used to calculate critical N values. There were accentuated discrepancies for critical values of N indices obtained with plants grown in soil and nutrient solution as well as for different statistical procedures. Critical values of nitrogen indices at all situations are presented.

Meta-analysis identifies multiple loci associated with kidney function-related traits in east Asian populations.

Chronic kidney disease (CKD), impairment of kidney function, is a serious public health problem, and the assessment of genetic factors influencing kidney function has substantial clinical relevance. Here, we report a meta-analysis of genome-wide association studies for kidney function-related traits, including 71,149 east Asian individuals from 18 studies in 11 population-, hospital- or family-based cohorts, conducted as part of the Asian Genetic Epidemiology Network (AGEN). Our meta-analysis identified 17 loci newly associated with kidney function-related traits, including the concentrations of blood urea nitrogen, uric acid and serum creatinine and estimated glomerular filtration rate based on serum creatinine levels (eGFRcrea) (P < 5.0 × 10(-8)). We further examined these loci with in silico replication in individuals of European ancestry from the KidneyGen, CKDGen and GUGC consortia, including a combined total of ∼110,347 individuals. We identify pleiotropic associations among these loci with kidney function-related traits and risk of CKD. These findings provide new insights into the genetics of kidney function.

A simple gas chromatography method for the analysis of monoethanolamine in air

A simple method determining airborne monoethanolamine has been developed. Monoethanolamine determination has traditionally been difficult due to analytical separation problems. Even in recent sophisticated methods, this difficulty remains as the major issue often resulting in time-consuming sample preparations. Impregnated glass fiber filters were used for sampling. Desorption of monoethanolamine was followed by capillary GC analysis and nitrogen phosphorous selective detection. Separation was achieved using a specific column for monoethanolamines (35% diphenyl and 65% dimethyl polysiloxane). The internal standard was quinoline. Derivatization steps were not needed. The calibration range was 0.5-80 μg/mL with a good correlation (R(2) = 0.996). Averaged overall precisions and accuracies were 4.8% and -7.8% for intraday (n = 30), and 10.5% and -5.9% for interday (n = 72). Mean recovery from spiked filters was 92.8% for the intraday variation, and 94.1% for the interday variation. Monoethanolamine on stored spiked filters was stable for at least 4 weeks at 5°C. This newly developed method was used among professional cleaners and air concentrations (n = 4) were 0.42 and 0.17 mg/m(3) for personal and 0.23 and 0.43 mg/m(3) for stationary measurements. The monoethanolamine air concentration method described here was simple, sensitive, and convenient both in terms of sampling and analytical analysis.