Novel Proteorhodopsin variants from the Mediterranean and Red Seas

Proteorhodopsins, ubiquitous retinylidene photoactive proton pumps, were recently found in the widespread uncultured SAR86 bacterial group in oceanic surface waters. To survey proteorhodopsin diversity, new degenerate sets of proteorhodopsin primers were designed based on a genomic proteorhodopsin gene sequence originating from an Antarctic fosmid library. New proteorhodopsin variants were identified in Red Sea samples that were most similar to the original green-light absorbing proteorhodopsins found in Monterey Bay California. Unlike green-absorbing proteorhodopsins however, these new variants contained a glutamine residue at position 105, the same site recently shown to control spectral tuning in naturally occurring proteorhodopsins. Different proteorhodopsin variants were also found in the Mediterranean Sea. These proteorhodopsins formed new and distinctive proteorhodopsin groups. Phylogenetic analyses show that some of the new variants were very different from previously characterized proteorhodopsins, and formed the deepest branching groups found so far among marine proteorhodopsins. The existence of these varied proteorhodopsin sequences suggests that this class of proteins has undergone substantial evolution. These variants could represent functionally divergent paralogous genes, derived from the same or similar species, or orthologous proteorhodopsins that are distributed amongst divergent planktonic microbial taxa.     

Statistical analysis and biological interpretation of the flow cytometric heterogeneity observed in bacterial axenic cultures

Histogram comparison and meaningful statistics in flow cytometry is probably the most widely encountered mathematical problem in flow cytometry. Ideally, a test for determining the statistical equality or difference of flow cytometric distributions will identify the significant differences or similarities of the obtained histograms. This situation is of particular interest when flow cytometry is used to study the heterogeneity of axenic bacterial populations. We have statistically measured the heterogeneity of successive cytometric measures, the modifications produced after 20 transfers from the same culture, and the differences between 20 subcultures of identical origin. The heterogeneity of the bacterial populations and the similarity of the obtained 360 histograms were analysed by standard statistical methods. We have studied bacterial axenic cultures in order to detect, quantify and interpret their cytometric heterogeneity, and to assess intrinsic differences and differences produced by laboratory manipulations. We concluded that the standard axenic cultures have a considerable intrinsic cellular and molecular heterogeneity. We suggest that the heterogeneity we have detected basically has two origins: cell size diversity and cell cycle variations.     

Identification of the human salivary cystatin complex by the coupling of high-performance liquid chromatography and ion-trap mass spectrometry

Human salivary cystatins, five major (S, S1, S2, SA, SN) and two minor (C and D), are multifunctional proteins playing a different role in the oral environment. Salivary cystatin SN is able to effectively inhibit lysosomal cathepsins B, C, H and L and cystatin SA inhibits cathepsins C and L in vitro. These activities suggest, particularly for cystatin SN, an important role in the control of proteolytic events in vivo. Differently, cystatins S are involved, together with statherin, in the mineral balance of the tooth. Due to their distinct role, a reliable method for identification and quantification of the different cystatins, as well as of possible truncated and derived forms, could be helpful for the assessment of the status of the oral cavity. To this purpose high-performance liquid chromatography electrospray ionization mass spectrometry (HPLC-ESI MS) was applied to the analysis of human saliva obtained from healthy subjects. All known salivary cystatins, with the exception of cystatin C, were detected. Strong evidence was also obtained for the presence in saliva of post-translational modified isoforms of cystatins, which may be related to donor habits. Cystatin SN and cystatins S, S1 and S2 were well separated by HPLC-ESI MS coupling from other components and thus this approach can be successfully applied to their quantification.     

Coumarin inhibits the growth of carrot (Daucus carota L. cv. Saint Valery) cells in suspension culture

We used a carrot (Daucus carota L. cv. Saint Valery) cell suspension culture as a simplified model system to study the effects of the allelochemical compound coumarin (1,2 benzopyrone) on cell growth and utilisation of exogenous nitrate, ammonium and carbohydrates. Exposure to micromolar levels of coumarin caused severe inhibition of cell growth starting from the second day of culture onwards. At the same time, the presence of 50 mumol/L coumarin caused accumulation of free amino acids and of ammonium in the cultured cells, and stimulated their glutamine synthetase, glutamate dehydrogenase, glucose-6-phosphate dehydrogenase and phosphoenolpyruvate carboxylase activities. Malate dehydrogenase, on the other hand, was inhibited under the same conditions. These effects were interpreted in terms of the stimulation of protein catabolism and/or interference with protein biosynthesis induced by coumarin. This could have led to a series of compensatory changes in the activities of enzymes linking nitrogen and carbon metabolism. Because coumarin seemed to abolish the exponential phase and to accelerate the onset of the stationary phase of cell growth, we hypothesise that such allelochemical compounds may act in nature as an inhibitor of the cell cycle and/or as a senescence-promoting substance.     

The combined use of oral and topical lipophilic antioxidants increases their levels both in sebum and stratum corneum

The concentration of Vitamin E (vit E) and ubiquinone (CoQ10), which together with squalene (SQ), play a key role against external oxidative insult, has been shown to decrease significantly during ageing. The aim of the present study is to inquire the effect of the combined use of topical bio-cosmetics containing natural active principles (including sebum-like lipid fractions, sebum and epidermal lipophilic and hydrophilic antioxidants), and oral antioxidant supplements on the antioxidant content of sebum and stratum corneum. We therefore treated the face and the back of 50 female volunteers aged 21-40, daily for two months, with a base cream containing 0.05% ubiquinone, 0.1% vit E, and 1% squalene. In addition 50 mg of CoQ10 + 50 mg of d-RRR-alpha-tocopheryl acetate + 50 microg of selenium were administered orally to half of the volunteers (Group A). Group B was represented by 25 volunteers who were treated only topically. Every 15 days during treatment the levels of CoQ10, vit E and SQ were verified in sebum, stratum corneum, and plasma. The daily topical application of the cream led to a significant increase, that peaked after 60 days, of the levels of CoQ10, d-RRR-alpha-tocopherol and SQ in the sebum (Group B), without significantly affecting the stratum corneum or plasma concentrations of the redox couple CoQ10H2/CoQ10 and vit E. The concomitant oral admistration of antioxidants produced in Group A a significant increase of the levels of CoQ10H2/CoQ10 and vit E both in plasma and stratum corneum after 15 and 30 days treatment respectively, compared to Group B. However the sebum levels of lipophilic antioxidants and SQ did not show a significant increase. After the treatments, the levels of CoQ10H2/CoQ10, vit E and SQ went back to basal levels within 6-8 days in sebum, 12-16 days in the stratum corneum, and 3-6 days in plasma. Therefore topical application of the antioxidants was able to increase their level in sebum, while the concomitant oral administration also affected the levels of vit E and CoQ10 in the stratum corneum.     

Emission of volatile organic compounds by apple trees under spider mite attack and attraction of predatory mites

Emission rates of volatile organic compounds (VOCs) from Pirus malus L. subsp. mitis (Wallr.) var. Golden Delicious and var. Starking attacked by the phytophagous mite Panonychus ulmi Koch, and their attractiveness to the predatory mites Amblyseius andersoni Chant and Amblyseius californicus McGregor, were studied during three years. A large variability was found in the emission of individual VOCs depending on the infestation, the apple tree variety and the date. There were larger total VOC emission rates and larger total VOC leaf concentrations in apple trees attacked by phytophagous mites, especially in the var. Starking. In infested trees of this variety, there were also more predatory mites. An olfactometer assay showed that predatory mites preferentially chose branches infested by Panonychus ulmi (85% went to infested branches vs 15% to uninfested control branches) indicating that volatiles may be used as cues to find their prey.     

The beta-tubulin gene of Babesia and Theileria parasites is an informative marker for species discrimination

A fragment of the beta-tubulin gene was polymerase chain reaction (PCR) amplified from genomic DNAs of Babesia bovis, Babesia bigemina, Babesia divergens, Babesia major, Babesia caballi, Babesia equi, Babesia microti, Theileria annulata and Theileria sergenti. Single amplification products were obtained for each of these species, but the size of the amplicons varied from 310 to 460 bp. Sequence analysis revealed that this variation is due to the presence of a single intron, which ranged from 20 to 170 bp. The extensive genetic variability at the beta-tubulin locus has been exploited to develop two types of species identification assays. The first assay can be used on samples containing mostly parasite DNA, like those prepared from infected erythrocytes. Following PCR amplification, the species identification is obtained directly from the size of the products (for Babesia species infecting human or horse) or using a simple PCR-restriction fragment length polymorphism (RFLP) protocol (for Babesia species infecting cattle). The second assay can be used on samples prepared from whole blood, that contain both parasite and host DNAs. In this case, due to the strong conservation of the beta-tubulin gene, co-amplification of a gene fragment from the host DNA was observed. A nested PCR assay was developed for the specific amplification of parasite DNA, using a primer designed to span the exon-intron boundary. Direct identification of Babesia species infecting human and horse is again obtained after the electrophoretic separation of the amplification products, while for Babesia and Theileria species infecting cattle, differentiation is based on a nested PCR-RFLP protocol. These methods may be used for the simultaneous identification of horses and cattle carrying multiple parasites by means of a single PCR or using the PCR-RFLP protocol.