Successful amplification of rice chloroplast microsatellites from century-old grass samples from the park grass experiment

We report the successful amplification of microsatellite markers for the chloroplast genome from century-old samples of 2 grasses growing in the Park Grass Experiment (PGE):Anthoxanthum ordoratum andFestuca rubra. This opens the possibility of establishing a long-term genetic time series for the PGE, which began in 1856 and is believed to be the oldest ecological experiment in existence. Although the plant samples used were not originally prepared or stored with molecular analysis in mind, the hexadecyltrimethylammonium bromide (CTAB) method of DNA extraction was successfully used. Obtained DNA was degraded but could be amplified by means of PCR. It produced bands around the expected size for chloroplast microsatellite primers derived from rice. When sequenced, bands showed good homology with sequences from rice chloroplast genomes listed in GenBank (accession No X15901).     

Voltammetric behavior of 4',7-dimethoxy-3'-isoflavone sulfonic sodium and its enhancement determination in the presence of surfactant

Voltammetric behavior of 4',7-dimethoxy-3'-isoflavone sulfonic sodium (DISS) was studied by linear sweep voltammetry and cyclic voltammetry. DISS caused two waves between pH 8.0 and 12.0. Above pH 8.0, the peak current of first wave Pc1 of DISS was enhanced in the presence of cetyltrimethylammonium bromide (CTAB). Based on this, a novel method for the determination of DISS was proposed. In Britton-Robinson buffer solution (pH 11.7) containing 9.4 x 10(-6)mol L(-1) CTAB, the peak potential of first wave Pc1 of DISS was -1.59 V (vs standard saturated calomel electrode) and its first-order derivative peak current was proportional to the concentration of DISS in the range 5.0 x 10(-8)-6.0 x 10(-7)mol L(-1) (r=0.998). The detection limit was 1 x 10(-8)mol L(-1), which was 10 times lower than that of the corresponding reduction wave. The method was applied to the determination of DISS in synthetic samples.     

Long-term effective population sizes, temporal stability of genetic composition and potential for local adaptation in anadromous brown trout (Salmo trutta) populations

We examined the long-term temporal (1910s to 1990s) genetic variation at eight microsatellite DNA loci in brown trout (Salmo trutta L) collected from five anadromous populations in Denmark to assess the long-term stability of genetic composition and to estimate effective population sizes (Ne). Contemporary and historical samples consisted of tissue and archived scales, respectively. Pairwise thetaST estimates, a hierarchical analysis of molecular variance (amova) and multidimensional scaling analysis of pairwise genetic distances between samples revealed much closer genetic relationships among temporal samples from the same populations than among samples from different populations. Estimates of Ne, using a likelihood-based implementation of the temporal method, revealed Ne >or= 500 in two of three populations for which we have historical data. A third population in a small (3 km) river showed Ne >or= 300. Assuming a stepping-stone model of gene flow we considered the relative roles of gene flow, random genetic drift and selection to assess the possibilities for local adaptation. The requirements for local adaptation were fulfilled, but only adaptations resulting from strong selection were expected to occur at the level of individual populations. Adaptations resulting from weak selection were more likely to occur on a regional basis, i.e. encompassing several populations. Ne appears to have declined recently in at least one of the studied populations, and the documented recent declines of many other anadromous brown trout populations may affect the persistence of local adaptation.     

A likelihood approach for quantitative-trait-locus mapping with selected pedigrees

Selective sampling is a cost-effective design for mapping quantitative trait loci (QTLs). A unified framework, which naturally combines two complementary sources of linkage information in the data, is proposed for the mapping of QTLs using selected pedigrees. Score statistics for detecting linkage are introduced for single-locus models (univariate or bivariate phenotypes) and two-locus epistasis models. A computer implementation of the methods for single-locus univariate-phenotype models is provided for nuclear families with arbitrary number of sibs and is freely available.     

Micell-mediated extraction for the spectrophotometric determination of nitrite in water and biological samples based on its reaction with p-nitroaniline in the presence of diphenylamine

A cloud point extraction process using the nonionic surfactant Triton X-100 to extract nitrite from aqueous solution was investigated. The method is based on the color reaction of nitrite with p-nitroaniline in the presence of diphenylamine in acid media and micell-mediated extraction of an azo product. The optimal extraction and reaction conditions (e.g., acid concentration, reagent concentration, effect of time) were studied, and the analytical characteristics of the method (e.g., limit of detection, linear range, molar absorptivity, preconcentration, and improvement factors) were obtained. Linearity was obeyed in the range of 2-40 ng ml(-1) of nitrite ion. The detection limit of the method is 0.87 ng ml(-1) of nitrite ion. The interference effect of some anions and cations was also tested. The method was applied to the determination of nitrite in tap water, waste water, and human urine samples.     

Measuring residual solvents in pharmaceutical samples using fast gas chromatography techniques

Residual process solvents in pharmaceutical samples are monitored using gas chromatography (GC) with either flame ionization detection (FID) or mass spectrometry. Based on good manufacturing practices, measuring residual solvents is mandatory for the release testing of all active pharmaceutical ingredients and is routinely performed on samples of process intermediates. General GC methods have been developed to monitor solvents routinely used in the drug synthesis process. It is now possible to take advantage of GC equipment with faster temperature ramping capabilities, in combination with shorter capillary GC columns, to achieve a considerable gain in efficiency and a reduction in analysis turnaround time. In this paper, the development and implementation of fast GC methods for residual solvents testing will be discussed. Continued efforts to improve the efficiency of gas chromatography using existing technologies such as, the ThermoOrion Flash GC will also be discussed.     

Polymerase Chain Reaction in Detection of Gymnodinium mikimotoi and Alexandrium minutum in Field Samples from Southwest India

Polymerase chain reaction (PCR) primers were constructed for the detection of two toxic dinoflagellate species, Gymnodinium mikimotoi and Alexandrium minutum. The primers amplified a product of expected size from cultured cells of G. mikimotoi and A. minutum. The species-specific primers targeting G. mikimotoi did not yield any product with a wide range of other cultured algae used as negative controls. Primers designed for A. minutum were species-group-specific since it PCR yielded a product from the closely related species A. ostenfeldii and A. andersonii, but not from other species of this genus tested. The confirmation of PCR products was performed by digestion of the products with restriction enzymes. Sensitivity analyses of the primers on DNA template from cultured cells was positive by PCR at a DNA template concentration of 1.5 × 10⁻⁴ ng/μl (0.3 cells/L) for A. minutum, and at a DNA concentration of 2.5 × 10⁻² ng/μl (697 cells/L) for G. mikimotoi. The PCR method for detection of G. mikimotoi and A. minutum was applied on field samples collected with a plankton net. Gymnodinium mikimotoi could be detected in 11 field samples by microscopy, and all these field samples were positive by PCR. The cell counts of G. mikimotoi in simultaneously collected water samples ranged from 306 to 2077/L. Alexandrium minutum could be detected by microscopy in 3 different field samples. The cell counts in water samples collected at the same time as the net samples ranged from 115 to 1115 cells/L. Alexandrium minutum was detected by PCR in these field samples, with the exception of the sample displaying the lowest cell count (115 cells/L). Plankton samples that were negative by microscopy for any of the two target species were also negative by PCR. All the PCR products from field samples were confirmed by restriction enzyme digestion. The application of PCR-based detection of harmful algal bloom species for aquaculture and monitoring purposes in natural field samples is discussed. Received April 4, 2000; accepted September 25, 2000.     

Millimeter wave power density in aqueous biological samples

Power density distribution inside a water sample placed between two parallel lossy dielectric plates (Polystyrene) was calculated using Fresnel equations for the frequency range of 42.25-53.57 GHz. Due to the multiple internal reflections from the sample boundaries, the distribution of the power density within the thin sample is more uniform than that within a semi-infinite medium. The power density in a sample depends on the thicknesses of the sample and the adjacent dielectric plates. For the given frequency range the sample thickness optimal for power density uniformity varies between 0.28 and 0.33 mm. The front plate has a significant effect on the magnitude of the power density within the sample but little effect on the power density distribution. The thicker the rear plate, the greater is the non uniformity of the power density distribution within the sample. Based on the calculated data, we determined the dimension of an exposure chamber providing the optimal power density distribution uniformity for mm-wave irradiation.     

Simultaneous quantification of 12 different nucleotides and nucleosides released from renal epithelium and in human urine samples using ion-pair reversed-phase HPLC

Nucleotides and nucleosides are not only involved in cellular metabolism but also act extracellularly via P1 and P2 receptors, to elicit a wide variety of physiological and pathophysiological responses through paracrine and autocrine signalling pathways. For the first time, we have used an ion-pair reversed-phase high-performance liquid chromatography ultraviolet (UV)-coupled method to rapidly and simultaneously quantify 12 different nucleotides and nucleosides (adenosine triphosphate, adenosine diphosphate, adenosine monophosphate, adenosine, uridine triphosphate, uridine diphosphate, uridine monophosphate, uridine, guanosine triphosphate, guanosine diphosphate, guanosine monophosphate, guanosine): (1) released from a mouse renal cell line (M1 cortical collecting duct) and (2) in human biological samples (i.e., urine). To facilitate analysis of urine samples, a solid-phase extraction step was incorporated (overall recovery rate ≥ 98 %). All samples were analyzed following injection (100 μl) into a Synergi Polar-RP 80 Å (250 × 4.6 mm) reversed-phase column with a particle size of 10 μm, protected with a guard column. A gradient elution profile was run with a mobile phase (phosphate buffer plus ion-pairing agent tetrabutylammonium hydrogen sulfate; pH 6) in 2–30 % acetonitrile (v/v) for 35 min (including equilibration time) at 1 ml min⁻¹ flow rate. Eluted compounds were detected by UV absorbance at 254 nm and quantified using standard curves for nucleotide and nucleoside mixtures of known concentration. Following validation (specificity, linearity, limits of detection and quantitation, system precision, accuracy, and intermediate precision parameters), this protocol was successfully and reproducibly used to quantify picomolar to nanomolar concentrations of nucleosides and nucleotides in isotonic and hypotonic cell buffers that transiently bathed M1 cells, and urine samples from normal subjects and overactive bladder patients.

Electronic supplementary material

The online version of this article (doi:10.1007/s11302-012-9321-8) contains supplementary material, which is available to authorized users.     

Microelectronic-sensing assay to detect presence of Verotoxins in human faecal samples

Aims: To develop a novel Vero cell assay that implements a real‐time cell electronic sensing (RT‐CES) system for the determination of the presence of verotoxin‐producing Escherichia coli (VTEC). The assay overcomes the major drawbacks in conventional Vero cell assay, for example, labour‐intensive and time‐consuming. Methods and Results: Cells were grown onto the surfaces of microelectronic sensors that are integrated into the bottom surfaces of the microtiter plate. Cellular viability was monitored in real‐time and quantified based on changes in the sensor’s electrical impedance. For cell viability measurement, the data generated on the RT‐CES system correlated well with those obtained by the Vero cell assay for Verotoxins. To assess cytotoxicity, test cells growing on microelectronic sensors were treated with either supernatant from pure cultures, or stool samples. The specific neutralizing antibodies of VT1 and VT2 were used to identify specific toxins in the samples. Conclusions: The RT‐CES assay provides a sensitive measurement comparable to conventional crystal violet assay. The assay has been successfully and specifically used to identify VTEC in human faecal samples. Significance and Impact of the Study: The RT‐CES assay significantly shortens the testing time from 48 to 72 h required by the crystal violet assay to only 15 h with automated operation.