Plant transposable elements,with an emphasis on grass species

Transposable elements are presents in all known genomes so far, and have the faculty of changing their genomic location and/or number of copies within the genome. They are mobile endogenous genetic elements, with a large variety of structure and transposition mechanism. In crops, they compose the major part of the nucleic DNA, up to 80% in some cereals like maize and wheat. Despite their omnipresence, they are largely unknown and uncharacterized within the Poaceae family. In this review, we describe a possible classification of the elements present in this family, some of their known transposition mechanism, their known activity and possible action in crops, and their possible origin.     

Hop as an interesting source of resveratrol for brewers: optimization of the extraction and quantitative study by liquid chromatography/atmospheric pressure chemical ionization tandem mass spectrometry

Nowadays, hop is used almost exclusively by brewers for bitterness and flavor. Although hop polyphenols have been widely studied in the past decade for their antioxidant activity in the boiling kettle, very little is known about their real impact on health. The discovery of resveratrol in hop pellets highlights the potential health-promoting effect of moderate beer consumption. Here, we have optimized a quantitative extraction procedure for resveratrol in hop pellets. Preliminary removal of hydrophobic bitter compounds with toluene and cyclohexane at room temperature allows 99% trans-resveratrol recovery by ethanol:water (75:25, v/v) solid/liquid extraction at 60 degrees C. Reverse phase liquid chromatography proves an excellent means of separating isomers. In addition, we have compared two mass spectrometry ionization methods-atmospheric pressure chemical ionization (APCI) and electrospray ionization (ESI)-in both the positive and the negative modes. On the basis of standard additions applied with the optimized extraction procedure and reverse phase high-performance liquid chromatography-APCI(+)-tandem mass spectrometry, it appears that Tomahawk hop pellets (T90, harvest 2002) contain 0.5 ppm trans-resveratrol, 2 ppm trans-piceid, no cis-resveratrol, and 0.9 ppm cis-piceid.     

Use of gas chromatography-olfactometry to identify key odorant compounds in dark chocolate. Comparison of samples before and after conching

After vacuum distillation and liquid-liquid extraction, the volatile fractions of dark chocolates were analyzed by gas chromatography-olfactometry and gas chromatography-mass spectrometry. Aroma extract dilution analysis revealed the presence of 33 potent odorants in the neutral/basic fraction. Three of these had a strong chocolate flavor: 2-methylpropanal, 2-methylbutanal, and 3-methylbutanal. Many others were characterized by cocoa/praline-flavored/nutty/coffee notes: 2,3-dimethylpyrazine, trimethylpyrazine, tetramethylpyrazine, 3(or 2),5-dimethyl-2(or 3)-ethylpyrazine, 3,5(or 6)-diethyl-2-methylpyrazine, and furfurylpyrrole. Comparisons carried out before and after conching indicate that although no new key odorant is synthesized during the heating process, levels of 2-phenyl-5-methyl-2-hexenal, Furaneol, and branched pyrazines are significantly increased while most Strecker aldehydes are lost by evaporation.     

Comparative study of methods for DNA preparation from olive oil samples to identify cultivar SSR alleles in commercial oil samples: possible forensic applications

Virgin olive oil is made from diverse cultivars either mixed or single. Those ensure different tastes and typicity, and these may be also enhanced by the region of production of cultivars. The different olive oil labels correspond to their chemical composition and acidity. Labels also may correspond to a protected origin indication, and thus, such oils contain a given composition in cultivars. To verify the main cultivars used at the source of an olive oil sample, our method is based on DNA technology. DNA is present in all olive oil samples and even in refined oil, but the quantity may depend on the oil processing technology and oil conservation conditions. Thus, several supports were used to retain DNA checking different techniques (silica extraction, hydroxyapatite, magnetic beads, and spun column) to prepare DNA from variable amounts of oil. At this stage, it was usable for amplification through PCR technology and especially with the magnetic beads, and further purification processes were checked. Finally, the final method used magnetic beads. DNA is released from beads in a buffer. Once purified, we showed that it did not contain compounds inhibiting PCR amplification using SSR primers. Aliquot dilution fractions of this solution were successfully routinely used through PCR with different SSR primer sets. This enables confident detection of eventual alien alleles in oil samples. First applied to virgin oil samples of known composition, either single cultivars or mixtures of them, the method was verified working on commercial virgin oil samples using bottles bought in supermarkets. Last, we defined a protocol starting from 2 x 40 mL virgin olive oil, and DNA was prepared routinely in about 5 h. It was convenient to genotype together several loci per sample to check whether alleles were in accordance with those of expected cultivars. Thus, forensic applications of our method are expected. However, the method needs further improvement to work on all oil samples.     

Adapting ecotoxicological tests based on earthworm behavior to assess the potential effectiveness of forest soil liming

Two laboratory experiments were carried out to determine the potential effects of lime application on the behavior of earthworms inoculated in an acidified forest soil from Vosges Mountains. Several field soils were studied: (i) a non-limed soil that had received decades of atmospheric acid depositions $({\text{pH}}_{{\text{H}}_2\text{O}}=3.9)$, (ii) an in situ limed soil that had been limed 6 years before at 2.5 t ha^?1 $({\text{pH}}_{{\text{H}}_2\text{O}}=4.2)$ and (iii) in vitro limed soils composed of non-limed soil mixed with several lime amounts in the laboratory corresponding to field rates of 1, 2.5, 5, 10 and 20 t ha^?1. Firstly, we adapted the earthworm avoidance test (ISO, 2006) by using Eisenia fetida as the model organism and Lumbricus castaneus, a local species, to determine earthworm preference between non-limed and limed soils. Secondly, a cast production (CP) study was performed according to Capowiez et al. (2009) with Lumbricus terrestris, in seven different treatments (non-limed soil, in situ limed and five in vitro limed soils with pH from 5 to 6.3). Both species avoided the non-limed soil in favour of in situ and in vitro limed soils for both species. Results of the CP bioassay showed that the bioturbation behavior of L. terrestris significantly increased with the increase of soil pH, following a dose–response curve. However, in the long term (>6 years), the application of lime was insufficient to significantly improve soil conditions for enhancing earthworm activity. In conclusion, we may recommend this kind of earthworm laboratory tests with field soils to assess any changes in soil quality over time due to liming application.     

ULTRASONOGRAPHIC CHARACTERISTICS OF THE ABDOMINAL ESOPHAGUS AND CARDIA IN DOGS

Differential diagnoses for regurgitation and vomiting in dogs include diseases of the gastroesophageal junction. The purpose of this cross‐sectional study was to describe ultrasonographic characteristics of the abdominal esophagus and gastric cardia in normal dogs and dogs with clinical disease involving this region. A total of 126 dogs with no clinical signs of gastrointestinal disease and six dogs with clinical diseases involving the gastroesophageal junction were included. For seven euthanized dogs, ultrasonographic features were also compared with gross pathology and histopathology. Cardial and abdominal esophageal wall thicknesses were measured ultrasonographically for all normal dogs and effects of weight, sex, age, and stomach filling were tested. Five layers could be identified in normal esophageal and cardial walls. The inner esophageal layer was echogenic, corresponding to the cornified mucosa and glandular portion of the submucosa. The cardia was characterized by a thick muscularis, and a transitional zone between echogenic esophageal and hypoechoic gastric mucosal layers. Mean (±SD) cardial wall thicknesses for normal dogs were 7.6 mm (±1.6), 9.7 mm (±1.8), 10.8 mm (±1.6), 13.3 mm (±2.5) for dogs in the <10 kg, 10–19.9 kg, 20–29.9 kg and ≥30 kg weight groups, respectively. Mean (±SD) esophageal wall thicknesses were: 4.1 mm (±0.6), 5.1 mm (±1.3), 5.6 mm (±1), and 6.4 mm (±1.1) for the same weight groups, respectively. Measurements of wall thickness were significantly correlated with dog weight group. Ultrasonography assisted diagnosis in all six clinically affected dogs. Findings supported the use of transabdominal ultrasonography as a diagnostic test for dogs with suspected gastroesophageal disease.     

Antibiotic susceptibility of bacteria isolated from infections in cats and dogs throughout Europe (2002–2009)

A monitoring program of the pre-treatment susceptibility of clinical isolates of bacteria from diseased dogs and cats was active between the years 2002 and 2009. Susceptibility of each isolated strain to a panel of nine antibiotics (amoxicillin/clavulanic acid, ampicillin, penicillin, clindamycin, doxycycline, enrofloxacin, marbofloxacin, trimethoprim and trimethoprim/sulfamethoxazole) was assessed. The Minimum Inhibitory Concentration (MIC) of marbofloxacin was also determined by a standardized microdilution technique following CLSI recommendations. In total, 1857 bacterial strains were collected throughout Europe from cases of otitis, respiratory, urinary and dermatological infections. Although bacterial susceptibility varied for each of the antibiotics within the panel, patterns of susceptibility were similar to those described in the literature for comparable time periods and geographical areas. With a clinical resistance varying from 0 to 14.48% against the isolated strains, marbofloxacin susceptibility was very high and remains an effective antibiotic for the treatment of otitis, urinary, respiratory and dermatological infections in companion animals.