First-generation transgenic plants and statistics

The statistical analyses of populations of first-generation transgenic plants are commonly based on mean and variance and generally require a test of normality. Since in many cases the assumptions of normality are not met, analyses can result in erroneous conclusions. Transformation of data to normality, the use of other distributions, or distribution-free statistical tests should then be used to obtain valid conclusions from these populations.     

Lactate dehydrogenase (LDH) gene duplication during chordate evolution: the cDNA sequence of the LDH of the tunicate Styela plicata

L-Lactate dehydrogenase (L-LDH, E.C. 1.1.1.27) is encoded by two or three loci in all vertebrates examined, with the exception of lampreys, which have a single LDH locus. Biochemical characterizations of LDH proteins have suggested that a gene duplication early in vertebrate evolution gave rise to Ldh-A and Ldh-B and that an additional locus, Ldh-C arose in a number of lineages more recently. Although some phylogenetic studies of LDH protein sequences have supported this pattern of gene duplication, others have contradicted it. In particular, a number of studies have suggested that Ldh-C represents the earliest divergence among vertebrate LDHs and that it may have diverged from the other loci well before the origin of vertebrates. Such hypotheses make explicit statements about the relationship of vertebrate and invertebrate LDHs, but to date, no closely related invertebrate LDH sequences have been available for comparison. We have attempted to provide further data on the timing of gene duplications leading to multiple vertebrate LDHs by determining the cDNA sequence of the LDH of the tunicate Styela plicata. Phylogenetic analyses of this and other LDH sequences provide strong support for the duplications giving rise to multiple vertebrate LDHs having occurred after vertebrates diverged from tunicates. The timing of these LDH duplications is consistent with data from a number of other gene families suggesting widespread gene duplication near the origin of vertebrates. With respect to the relationships among vertebrate LDHs, our data are not consistent with previous claims that Ldh-C represented the earliest divergence. However, the precise relationships among some of the main lineages of vertebrate LDHs were not resolved in our analyses.      

Identification of agronomically important QTL in tetraploid potato cultivars using a marker–trait association analysis

Key message

Nineteen tuber quality traits in potato were phenotyped in 205 cultivars and 299 breeder clones. Association analysis using 3364 AFLP loci and 653 SSR-alleles identified QTL for these traits.

Abstract

Two association mapping panels were analysed for marker–trait associations to identify quantitative trait loci (QTL). The first panel comprised 205 historical and contemporary tetraploid potato cultivars that were phenotyped in field trials at two locations with two replicates (the academic panel). The second panel consisted of 299 potato cultivars and included recent breeds obtained from five Dutch potato breeding companies and reference cultivars (the industrial panel). Phenotypic data for the second panel were collected during subsequent clonal selection generations at the individual breeding companies. QTL were identified for 19 agro-morphological and quality traits. Two association mapping models were used: a baseline model without, and a more advanced model with correction for population structure and genetic relatedness. Correction for population structure and genetic relatedness was performed with a kinship matrix estimated from marker information. The detected QTL partly not only confirmed previous studies, e.g. for tuber shape and frying colour, but also new QTL were found like for after baking darkening and enzymatic browning. Pleiotropic effects could be discerned for several QTL.     

Phosphorus in the sediment of the Loosdrecht lakes and its implications for lake restoration perspectives

In 1984 the external phosphorus load of the shallow eutrophic Loosdrecht lakes was reduced from 3.3 to 1.0 mg m^–2 d^–1. The effect of phosphorus release from the sediment on lake restoration was investigated. Diffusive release under aerobic conditions (20 °C) decreased from 1 mg m^–2 d^–1 in 1984 to 0.3 mg m^–2 d^–1 in 1990. The generation of inorganic phosphorus due to mineralization during summer equals 3 mg m^–2 d^–1, which is much higher than the measured rate of diffusive release. Despite that, the phosphorus release is hardly stimulated by anaerobic conditions, which indicates that only a small amount of phosphorus is adsorbed by ferric iron in the top sediment layer. This apparent discrepancy is probably caused by the uptake of inorganic phosphorus uptake during resuspension and the loss of inorganic phosphorus with downward seepage.The estimated removal of phosphorus due to downward seepage of 0.8 mg m^–2 d^–1 agrees well with the average phosphorus retention in the lake. This indicates that sediment burial and diagenesis are unimportant mechanisms for withdrawing phosphorus from the nutrient cycle.Between 1982 and 1991 the total phosphorus content of the upper 2 cm of the sediment decreased from 0.94 to 0.60 g kg^–1 DW. At present, about 20% of total phosphorus in this layer is potentially bioavailable, but largely incorporated in easily degradable organic matter. This pool is much smaller in deeper layers. Based on the estimated and measured rates and pool sizes, the annual average phosphorus cycle in the lakes was modelled to evaluate the effects of various restoration measures. The main predictions of the model are: 1) further reduction of the external load may cause a gradual decrease of the total phosphorus concentration in the lake water; 2) dredging and iron addition, without reduction of the external load, may give a rapid improvement followed by a slow return to the present situation; and 3) reduction of the external load, combined with a cut off of downward seepage will not improve the water quality.     

Isolation and characterization of mutants impaired in the selective degradation of peroxisomes in the yeast Hansenula polymorpha.

We have isolated a collection of peroxisome degradation-deficient (Pdd-) mutants of the yeast Hansenula polymorpha which are impaired in the selective autophagy of alcohol oxidase-containing peroxisomes. Two genes, designated PDD1 and PDD2, have been identified by complementation and linkage analyses. In both mutant strains, the glucose-induced proteolytic turnover of peroxisomes is fully prevented. The pdd1 and pdd2 mutant phenotypes were caused by recessive monogenic mutations. Mutations mapped in the PDD1 gene appeared to affect the initial step of peroxisome degradation, namely, sequestration of the organelle to be degraded by membrane multilayers. Thus, Pdd1p may be involved in the initial signalling events which determine which peroxisome will be degraded. The product of the PDD2 gene appeared to be essential for mediating the second step in selective peroxisome degradation, namely, fusion and subsequent uptake of the sequestered organelles into the vacuole. pdd1 and pdd2 mutations showed genetic interactions which suggested that the corresponding gene products may physically or functionally interact with each other.     

Chromatographic analysis of the enantiomers of ifosfamide and some of its metabolites in plasma and urine

The enantiomers of the cytostatic drug ifosfamide and the two metabolites 2- and 3-dechloroethylifosfamide were isolated from plasma and urine by liquid-liquid extraction with ethyl acetate, resolved on a Chirasil- -val gas chromatographic column and detected by a nitrogen-phosphorus-selective flame ionisation detector. Resolution of the racemic compounds for identification purposes was also accomplished with high-performance liquid chromatography on a chiral column. The validated gas chromatographic method was suitable to determine the total concentrations and the enantiomeric composition of ifosfamide and its dechloroethylated metabolites in plasma and urine samples from treated patients. Some metabolic preferences in the metabolism of ifosfamide were found.