Reproducibility testing of RAPD,AFLP and SSR markers in plants by a network of European laboratories

A number of PCR-based techniques can be used to detect polymorphisms in plants. For their wide-scale usage in germplasm characterisation and breeding it is important that these marker technologies can be exchanged between laboratories, which in turn requires that they can be standardised to yield reproducible results, so that direct collation and comparison of the data are possible. This article describes a network experiment involving several European laboratories, in which the reproducibility of three popular molecular marker techniques was examined: random-amplified fragment length polymorphism (RAPD), amplified fragment length polymorphism (AFLP) and sequence-tagged microsatellites (SSR). For each technique, an optimal system was chosen, which had been standardised and routinely used by one laboratory. This system (genetic screening package) was distributed to different participating laboratories in the network and the results obtained compared with those of the original sender. Different experiences were gained in this exchange experiment with the different techniques. RAPDs proved difficult to reproduce. For AFLPs, a single-band difference was observed in one track, whilst SSR alleles were amplified by all laboratories, but small differences in their sizing were obtained.     

Why Publishing Everything Is More Effective than Selective Publishing of Statistically Significant Results

Background

De Winter and Happee [1] examined whether science based on selective publishing of significant results may be effective in accurate estimation of population effects, and whether this is even more effective than a science in which all results are published (i.e., a science without publication bias). Based on their simulation study they concluded that “selective publishing yields a more accurate meta-analytic estimation of the true effect than publishing everything, (and that) publishing nonreplicable results while placing null results in the file drawer can be beneficial for the scientific collective” (p.4).

Methods and Findings

Using their scenario with a small to medium population effect size, we show that publishing everything is more effective for the scientific collective than selective publishing of significant results. Additionally, we examined a scenario with a null effect, which provides a more dramatic illustration of the superiority of publishing everything over selective publishing.

Conclusion

Publishing everything is more effective than only reporting significant outcomes.     

Progress in Arabidopsis genome sequencing and functional genomics

Arabidopsis thaliana has a relatively small genome of approximately 130 Mb containing about 10% repetitive DNA. Genome sequencing studies reveal a gene-rich genome, predicted to contain approximately 25000 genes spaced on average every 4.5 kb. Between 10 to 20% of the predicted genes occur as clusters of related genes, indicating that local sequence duplication and subsequent divergence generates a significant proportion of gene families. In addition to gene families, repetitive sequences comprise individual and small clusters of two to three retroelements and other classes of smaller repeats. The clustering of highly repetitive elements is a striking feature of the A. thaliana genome emerging from sequence and other analyses.     

High-resolution electron microscopy and electron tomography: resolution versus precision

The performance of high-resolution electron microscopy and electron tomography is usually discussed in terms of two-point resolution, expressing the possibility of perceiving separately two image points of an object. However, the concept resolution obtains another meaning if one uses prior knowledge about the object and the imaging procedure in the form of a parametric model describing the expectations of the observations. The unknown parameters, such as the positions of the components in an object, can be measured quantitatively by fitting this model to the observations. Due to the statistical nature of the experiment, the resulting solutions for the positions of the components and therefore for the distance between the components will never be exact. An alternative to resolution is then the precision with which the distance can be measured. In the present paper, it is shown that the precision depends on the size of the components, the distance between the components, the resolution of the instrument, and the number of electron counts. For electron tomography, it also depends on the orientation of the object with respect to the rotation axis.     

Excessive production of ammonium from nitrate by some methanol-assimilating yeast strains

Summary Some strains ofCandida boidinii excrete ammonium when grown in nitrate methanol medium under conditions of oxygen limitation but not in wellaerated cultures or under anaerobic conditions. With other carbon sources ammonium excretion is observed only in the late exponential and in the stationary growth phase. Ammonium excretion by methanol-grown cultures approximately equals assimilatory nitrate reduction. The share of total nitrate reduction in the electron transport of methanol-grown cultures is about 18%. Increase in cell yield of oxygen-limited cultures due to nitrate addition was not observed. Nitrate reduction byC. boidinii appears to be not of the true dissimilatory type. Nor is it restricted to the assimilatory type: it is not inhibited or repressed by ammonium and the ammonium excretion occurs in quantities too large to be attributed to amino acid degradation.