SolRgene: an online database to explore disease resistance genes in tuber-bearing Solanum species

Background The cultivated potato (Solanum tuberosum L.) is an important food crop, but highly susceptible to many pathogens. The major threat to potato production is the Irish famine pathogen Phytophthora infestans, which causes the devastating late blight disease. Potato breeding makes use of germplasm from wild relatives (wild germplasm) to introduce resistances into cultivated potato. The Solanum section Petota comprises tuber-bearing species that are potential donors of new disease resistance genes. The aim of this study was to explore Solanum section Petota for resistance genes and generate a widely accessible resource that is useful for studying and implementing disease resistance in potato. Description The SolRgene database contains data on resistance to P. infestans and presence of R genes and R gene homologues in Solanum section Petota. We have explored Solanum section Petota for resistance to late blight in high throughput disease tests under various laboratory conditions and in field trials. From resistant wild germplasm, segregating populations were generated and assessed for the presence of resistance genes. All these data have been entered into the SolRgene database. To facilitate genetic and resistance gene evolution studies, phylogenetic data of the entire SolRgene collection are included, as well as a tool for generating phylogenetic trees of selected groups of germplasm. Data from resistance gene allele-mining studies are incorporated, which enables detection of R gene homologs in related germplasm. Using these resources, various resistance genes have been detected and some of these have been cloned, whereas others are in the cloning pipeline. All this information is stored in the online SolRgene database, which allows users to query resistance data, sequences, passport data of the accessions, and phylogenic classifications. Conclusion Solanum section Petota forms the basis of the SolRgene database, which contains a collection of resistance data of an unprecedented size and precision. Complemented with R gene sequence data and phylogenetic tools, SolRgene can be considered the primary resource for information on R genes from potato and wild tuber-bearing relatives

The effect of pH on coupled mass transfer and sol-gel reaction in a two-phase system

The coupled mass transfer and chemical reactions of a gel-forming compound in a two-phase system were recently analyzed in detail [Castelijns et al. J. Appl. Phys. 2006, 100, 024916]. In this successive work, the gel-forming chemical tetramethylorthosilicate (TMOS) was dissolved in a mineral oil and placed together with heavy water (D2O) in small cylinders. The transfer of TMOS from the oleic phase to the aqueous phase was monitored through nuclear magnetic resonance (NMR) relaxation time measurements of hydrogen in the oleic phase. The rate of gelation was measured through NMR relaxation time measurements of deuterium in the aqueous phase. The temperature, the initial concentration of TMOS, and the type of buffer in the aqueous phase were varied in the experiments. The mass transfer is driven by the rate of hydrolysis, which increases with temperature. The hydrolysis rate is the lowest at a neutral pH and is the highest at a low pH. In the aqueous phase, a sharp decrease in the transverse relaxation time (T2) of 2H is observed, which is attributed to the gel reaction. The plateau in T2 indicates the gel transition point. The gel rates increase with increasing temperature and increasing concentration, and are the highest at a neutral pH

Ammonium addition inhibits 13C-methane incorporation into methanotroph membrane lipids in a freshwater sediment

To investigate the effect of ammonium addition on the species composition and activity of freshwater methane oxidizing bacteria, intact sediment cores were labeled with (CH4)-C-13 and incubated under ambient and elevated ammonium concentrations. After 7 days, methanotroph activity was assessed by quantifying the isotopic composition of the carbon in membrane lipids. The 16-carbon rather than the 18-carbon methanotroph-specific biomarkers showed a clear enrichment in C-13, suggesting the importance of group I methanotrophs in these sediments. Ammonium addition resulted in a depleted isotopic signal compared to ambient controls, suggesting that high ammonium concentrations inhibit methane incorporation into cellular components. These results compare favorably with studies that showed ammonium inhibition of methane oxidation, and extend these findings by demonstrating the effect of nitrogen fertilization on methanotroph lipid synthesis. [KEYWORDS: methane; freshwater; sediment; ammonium; lipid; stable carbon isotope Methane oxidation; fatty-acid; atmospheric methane; community structure; loosdrecht lakes; peaty sediments; eutrophic lake; bacteria; carbon; nitrification]

Linking flow cytometric cell sorting and compound-specific 13C-analysis to determine population-specific isotopic signatures and growth rates in cyanobacteria-dominated lake plankton

A novel methodology was applied to determine the 13C signatures of natural cyanobacterial and algal populations by combined compound-specific isotope ratio mass spectrometry and pyrolytic methylation-gas chromatography (Py-GC-IRMS) of the fatty acids released from phytoplankton fractions collected using fluorescence-activated cell sorting. Py-GC-IRMS provided direct analysis of the very small samples (<200 ng total C) derived from the cell sorting of individual phototrophic populations, while minimizing the chances on contamination and loss in sample handling. Despite trichome lengths exceeding the diameter of the sort droplets, filamentous cyanobacteria were amenable to population-specific cell sorting. In concert with 13C-CO2 labeling, the combined use of flow cytometric cell sorting and Py-GC-IRMS enabled both the assessment of standing stocks and of population-specific growth rates of the predominant cyanobacterial and algal taxa in Lake Loosdrecht (The Netherlands). Filamentous prochlorophytes, formerly the dominant cyanobacterial taxon in the lake, appeared less abundant in recent years and exhibited growth rates 30%-40% lower than the rates recorded for oscillatorioid populations. Diatom and green algal populations grew at rates 4- to 10-fold higher than filamentous cyanobacteria and are thus important for the lake's carbon budget. This approach offers new possibilities in studying plankton dynamics at a resolution not feasible in the past. [KEYWORDS: cell sorting ; fatty acid profile ; oscillatorioids ; pyrolytic methylation ; specific growth rates ; stable isotope labeling]

Permeability reduction in porous materials by in situ formed silica gel

The effect of in situ formed silica gel on the permeability of a porous material was investigated experimentally. Gelling solutions of tetra-methyl-ortho-silicate (TMOS) and methanol in water were imbibed into dry sandstone plates and cured for several days. The permeability of the untreated sandstone is on the order of 1 µm^2, whereas the intrinsic permeability of the silica alcogel is 5–6 orders of magnitude lower. The method of beam bending was employed to measure concurrently the permeability D and Young’s modulus Ep of cylindrical gel rods, prepared from the TMOS-based sol-gel solutions. Second, the permeabilities and moduli of the treated sandstones were measured. For both types of samples the gel structure was varied by varying the concentration of the TMOS in a solution and the pH of the water used. The parameters D and Ep follow from a detailed analysis of the measured relaxation of the load that is applied to the sample under constant deflection. In case of the gels, the relaxation was interpreted using common expressions for hydrodynamic relaxation and viscoelastic (VE) relaxation. It was found that the permeability of the gels decreases with increasing silica content and that acid-catalyzed gels exhibit a significantly lower permeability than base-catalyzed gels. The modulus Ep increases with increasing silica content and aging time. The relaxation data of the sandstone—treated with gel—exhibited a more complex behavior. The normalized load curves showed hydrodynamic relaxation as well as strong and fast VE relaxation. The relaxation data for the rock samples treated with the lowest concentration gel was fitted successfully with the predictions. For higher concentrations the fit was less accurate, but the permeability estimates were within an order of magnitude. The overall permeability of the treated rock is higher than the intrinsic permeability of the gels; this indicates that the gel does not completely fill the pore space. Nevertheless, the permeability is reduced by a factor 10^4 with respect to untreated sandstone, and therefore the gel adequately blocks the pores