A holistic approach to reduce negative impacts of hydropeaking

Hydropeaking is a common phenomenon of water courses that are affected by peak energy production of hydro power plants. It may cause severe impacts on the biodiversity of a stream. In fact, due to hydropeaking fishes, macroinvertebrates and aquatic plants undergo a major stress and frequently they are not able to survive these frequent water level fluctuations. In this paper a case study is presented where several mitigation measures for an affected river are evaluated. Abiotic indicators representing the hydropeaking phenomenon and responsible for an impaired biodiversity are calculated and compared. Furthermore a cost-benefit analysis of the mitigation measures is carried out allowing to define the measures to be realized. Facing the challenge of a holistic approach the study is embedded in a project with public participation of all concerned stakeholders addressing also the need of flood protection and ecologically sound river restoration

Potential of poly(styrene-co-divinylbenzene) monolithic columns for the LC-MS analysis of protein digests

Two polystyrene-based capillary monolithic columns of different length (50 and 250 mm) were used to evaluate the effects of column length on gradient separation of protein digests. A tryptic digest of a 9-protein mixture was used as a test sample. Peak capacities were determined from selected extracted ion chromatograms, and tandem mass spectrometry data were used for database matching using the MASCOT search engine. Peak capacities and protein identification scores were higher for the long column with all gradients. Peak capacities appear to approach a plateau for longer gradient times; maximum peak capacity was estimated to be 294 for the short column and 370 for the long column. Analyses with similar gradient slope produced a ratio of the peak capacities of 3.36 for the long and the short column, which is slightly higher than the expected value of the square root of the column length ratio. The use of a longer monolith improves peptide separation, as reflected by higher peak capacity, and also increases protein identification, as observed from higher identification scores and a larger number of identified peptides. Attention has also been paid to the peak production rate (PPR, peak capacity per unit time). For short analysis times, the short column produces a higher PPR, while for analysis times longer than 40 min, the PPR of the 250-mm column is higher

Genotyping of SNPs in a polyploid genome by pyrosequencing (TM)

Single-nucleotide polymorphisms (SNPs) are the most frequent DNA sequence variations, and they have become increasingly popular markers for association studies. Allelic discrimination of the mostly binary SNPs has been reported for diploid species, mainly the human, but not for polyploid genomes such as the agriculturally important crops. In the present study, we analyzed the applicability of pyrosequencing to genotyping SNPs in tetraploid potatoes. Out of 94 polymorphic loci tested, 76 (81%) proved to be amenable to allelic discrimination by pyrosequencing. An additional locus could be genotyped by the addition of an ssDNA binding protein to the pyrosequencing reaction. Of the remaining 17 loci, two failed because of the presence of paralogs in the genome, while, in the other cases, se F-annealing of the primer or template at the low reaction temperature (28degreesC) employed in pyrosequencing rendered allelic discrimination impossible. The quantitative precision of pyrosequencing was found to be similar to that of conventional dideoxy sequencing and single-nucleotide primer extension. Except for some sequence specific limitations, pyrosequencing appears to be an appropriate method for genotying SNPs in polyploid species because it is possible to distinguish not only between homo- and heterozygosity but also between the different heterazygous states

Genotyping of SNPs in a polyploid genome by pyrosequencing (TM)

Single-nucleotide polymorphisms (SNPs) are the most frequent DNA sequence variations, and they have become increasingly popular markers for association studies. Allelic discrimination of the mostly binary SNPs has been reported for diploid species, mainly the human, but not for polyploid genomes such as the agriculturally important crops. In the present study, we analyzed the applicability of pyrosequencing to genotyping SNPs in tetraploid potatoes. Out of 94 polymorphic loci tested, 76 (81%) proved to be amenable to allelic discrimination by pyrosequencing. An additional locus could be genotyped by the addition of an ssDNA binding protein to the pyrosequencing reaction. Of the remaining 17 loci, two failed because of the presence of paralogs in the genome, while, in the other cases, se F-annealing of the primer or template at the low reaction temperature (28degreesC) employed in pyrosequencing rendered allelic discrimination impossible. The quantitative precision of pyrosequencing was found to be similar to that of conventional dideoxy sequencing and single-nucleotide primer extension. Except for some sequence specific limitations, pyrosequencing appears to be an appropriate method for genotying SNPs in polyploid species because it is possible to distinguish not only between homo- and heterozygosity but also between the different heterazygous states