The genome of the diatom Thalassiosira pseudonana: ecology, evolution, and metabolism

Diatoms are unicellular algae with plastids acquired by secondary endosymbiosis. They are responsible for approximately 20% of global carbon fixation. We report the 34 million-base pair draft nuclear genome of the marine diatom Thalassiosira pseudonana and its 129 thousand-base pair plastid and 44 thousand-base pair mitochondrial genomes. Sequence and optical restriction mapping revealed 24 diploid nuclear chromosomes. We identified novel genes for silicic acid transport and formation of silica-based cell walls, high-affinity iron uptake, biosynthetic enzymes for several types of polyunsaturated fatty acids, use of a range of nitrogenous compounds, and a complete urea cycle, all attributes that allow diatoms to prosper in aquatic environments.     

Effect of dextransucrase cellobiose acceptor products on the growth of human gut bacteria

The selective fermentation by human gut bacteria of gluco-oligosaccharides obtained from the reaction between the glucosyl group of sucrose and cellobiose, catalyzed by dextransucrases (DSR) from Leuconostoc mesenteroides , has been evaluated. Oligosaccharides were fractionated according to their molecular weight, and their effect on the growth of different bacterial groups was studied. To determine the structure (position and configuration of glycosidic linkages)-function relationship, their properties were compared to those of DSR maltose acceptor products (DSRMal) and of recognized prebiotic carbohydrates (fructo-oligosaccharides, FOS). Cellobiose acceptor products (DSRCel) showed bifidogenic properties similar to those of FOS. However, no significant differences related to molecular weight or isomeric configurations were found for DSRCel and DSRMal products.     

The paradox of the conservation of an endangered fish species in a Mediterranean region under agricultural intensification

We studied the relative value of natural habitats, river and coastal wetlands, and artificial habitats, irrigation canal and ponds, for the conservation of an endangered fish, Iberian toothcarp, in its southernmost area of distribution, characterised by agricultural intensification. Our results show that the bulk of the population of the Iberian toothcarp is concentrated in irrigation ponds. Natural habitats sustained null or impoverished subpopulations, and individuals showed signs of low metabolic activity. This coincided with the relatively high habitat quality observed in ponds, particularly those with submerged aquatic vegetation, in contrast with the chronic eutrophication of the coastal lagoons. In spite of a generalised aggressive management in the irrigation system, featured by periodic vegetation clearance, desiccation and biocide treatment, the subpopulation of the Iberian toothcarp thrives in it probably thanks to adequate water quality and to an active path dynamics maintained by connectivity through the canal. Agro-environmental measures are discussed for the improvement of this species conservation in natural and artificial habitats.     

Influence of disaccharide structure on prebiotic selectivity in vitro

To obtain structure-function information of a range of carbohydrates, which are available only in very small quantities, an in vitro fermentation method using 7 mg of carbohydrate, 0.7 mL of basal medium, and 1% (w/v) of fecal bacteria was validated against a pH-controlled batch culture with 150 mL of basal medium and 1.5 g of test carbohydrate. This method was used to determine the influence of different glycosidic linkages and monosaccharide compositions of disaccharides on the selectivity of microbial fermentation. A prebiotic index (PI) was calculated for each disaccharide. Generally, disaccharides with linkages of 1-2, 1-4, and 1-6 generated a high PI score, with kojibiose and sophorose showing the greatest values (21.62 and 18.63, respectively). Apart from 6alpha-mannobiose, mannose-containing disaccharides gave a low PI due to low numbers of bifidobacteria and lactobacilli and an increase in bacteroides. The structure-function information obtained in this study may lead to a predictive understanding of how specific structures are fermented by the human gut microflora.     

2-Furoylmethyl amino acids and hydroxymethylfurfural as indicators of honey quality

Determination of changes in 2-furoylmethyl amino acids and hydroxymethylfurfural during the storage of four honey samples at 25 and 35 degrees C during 12 months was achieved to assess the potential use of both parameters, singly or in combination, as quality indicators. 2-Furoylmethyl amino acids increased during storage at both temperatures, whereas hydroxymethylfurfural only presented slight variations during storage at 25 degrees C but increased noticeably at 35 degrees C. The study of 2-furoylmethyl amino acids in 49 commercial honeys revealed that 2-furoylmethyl lysine (furosine) was present in all samples, whereas 2-furoylmethyl derivatives of arginine, GABA, and proline were only present in seven samples. Hydroxymethylfurfural can be considered as a good indicator of heat treatments applied to honey samples, whereas 2-furoylmethyl amino acids can be used as suitable markers of the storage period. The use of both parameters can be useful to detect adulteration with invert syrups, excessive heat treatments, or prolonged storage of honey samples.     

Detecting interaction(s) and assessing the impact of component subsets in a chemical mixture using fixed-ratio mixture ray designs

An important environmental and regulatory issue is the protection of human health from potential adverse effects of cumulative exposure to multiple chemicals. Earlier literature suggested restricting inference to specific fixed-ratio rays of interest. Based on appropriate definitions of additivity, single chemical data are used to predict the relationship among the chemicals under the zero-interaction case. Parametric comparisons between the additivity model and the model fit along the fixed-ratio ray(s) are used to detect departure from additivity. Collection of data along reduced fixed-ratio rays, where subsets of chemicals of interest are removed from the mixture and the remaining compounds are at the same relative ratios as considered in the full ray, allow researchers to make inference about the effect of the removed chemicals. Methods for fitting simultaneous confidence bands about the difference between the best fitting model and the model predicted under additivity are developed to identify regions along the rays where significant interactions occur. This general approach is termed the “single chemicals required” (SCR) method of analysis. A second approach, termed “single chemicals not required” (SCNR) method of analysis, is based on underlying assumptions about the parameterization of the response surface. Under general assumptions, polynomial terms for models fit along fixed-ratio rays are associated with interaction terms. Consideration is given to the case where only data along the mixture rays are available. Tests of hypotheses, which consider interactions due to subsets of chemicals, are also developed.     

Triterpenoid saponins from the shells of Argania spinosa seeds

Two new oleanene saponins were isolated from the MeOH extract of the shell of Argania spinosa.They possess protobassic acid and 16alpha-protobassic acid as aglycons. The disaccharide moiety linked to C-3 of the aglycon is made up of two glucose units; the pentasaccharide moiety linked to C-28 is made up of arabinose, xylose, and three rhamnose units. Their structures were elucidated by 1D and 2D NMR experiments including (1)H-(1)H (DQF-COSY, 1D TOCSY, and 2D HOHAHA) and (1)H-(13)C (HSQC and HMBC) spectroscopy along with mass spectrometry.     

Fermentation of white wines in the presence of wood chips of American and French oak

Must obtained from Airén grapes was fermented in the presence of wood chips (4 and 7 g/L) of either French oak (from Vosges, central France, and Allier zones) or American oak. Fermentation yields were higher than in the control fermentations carried out in the absence of wood, and production of volatile substances during fermentation (alcohols, esters, and acetates) was also higher. The volatile substances that leached out of the wood were analyzed by GC-MS-SIR. The results showed that their concentrations depended on the type and amount of the oak; some of these substances were consumed in part by the yeasts during fermentation. A taste panel favorably assessed the wines produced by fermentation in the presence of oak chips, which retained part of the must original fruity aroma.     

Ozone Biomonitoring with Bel-W3 Tobacco Plants in the City of Valencia (Spain)

A biomonitoring study using the ozone-sensitive bioindicator plant Nicotiana tabacum cv. Bel-W3 was conducted in the city of Valencia (eastern Spain) and surrounding areas in 2002. Plants were exposed to ambient air at seven sites, including four traffic-exposed urban sites, a large urban garden and a suburban and a rural station, for six consecutive 2-week periods using highly standardised methods. Foliar injury was registered at all stations in at least one of the exposure periods. The urban stations submitted to intense traffic showed lower ozone injury than the less traffic-exposed stations. Strong changes in the intensity of ozone injury were observed for the different exposure periods. Leaf injury was significantly related to both mean ozone values (24 and 12 h means) and cumulative exposure indices (AOT20, AOT40). However, correlation strength was moderate (r _s?=?0.39 to 0.58), suggesting that the plant response to ozone was modified by environmental factors. The use of sensitive bioindicators like tobacco Bel-W3 in cities provides complementary information to that of continuously operating air quality monitors, as the impact of ambient ozone levels is directly measured.     

Ultrasensitive detection of genetically modified maize DNA by capillary gel electrophoresis with laser-induced fluorescence using different fluorescent intercalating dyes

In this work, four different fluorescent intercalating dyes are compared for the ultrasensitive CGE-LIF detection of DNA from transgenic maize in flours. The fluorescent intercalating dyes compared are YOPRO-1, SYBR-Green-I, Ethidium bromide (EthBr), and EnhanCE. For all the four dyes optimum concentrations are established, and efficient separations of DNA fragments ranging in size from 80 to 1000 bp are obtained. The comparative study demonstrates that SYBR-Green-I and YOPRO-1 provide better limits of detection (LODs) than EnhanCE or EthBr (i.e., LODs are, respectively, 700, 1000, 11300, and 97400 zmol, calculated for a 200-bp DNA fragment). Separations using YOPRO-1 are faster than those using SYBR-Green-I (30 min vs 47 min for the analysis of the 80-1000 bp DNA fragments). Also, separations using YOPRO-1 are more efficient than those using SYBR-Green-I (e.g., 2.4 x 10(6) plates/m vs 1.6 x 10(6) plates/m, respectively, calculated for the 200-bp fragment). Also, buffer depletion and cost per analysis are worse with SYBR-Green-I than with YOPRO-1. Therefore, YOPRO-1 was selected as the preferred intercalating dye. Using this fluorescent compound, analysis time reproducibility for the CGE-LIF separation of the DNA fragments is determined to be better than 1.7% (% RSD, n = 10) within the same day, and better than 1.9% (% RSD, n = 30) for three different days. Moreover, the fluorescence signal obtained using this dye is shown to vary linearly with the DNA concentration in the range studied, i.e., 1-500 ng/microL. It is demonstrated that by using this method 0.01% of transgenic maize can be detected in flour by direct injection of the PCR-amplified sample.