A Note on the Analysis of the Two-Period Crossover Design When the Period-Treatment Interaction is Significant

In the analysis of a two-period crossover study Grizzle (1965) suggests that, if a preliminary test for a period by treatment interaction (residual effect, carryover effect) is significant at the 10 % level, the direct effects of the treatments should be compared by performing a t-test on the data from the first period only. In this note it is shown that under Grizzle's model the comparison of the direct treatment effects is equivalent to a Behrens-Fisher problem. Depending on one's viewpoint–Bayesian, fiducial, or sampling theory–different solutions are possible. The solutions are illustrated using three well-known data sets.     

Meiotic recombination mirrors patterns of germline replication in mice and humans

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The absence of crossovers on chromosome 4 in Drosophila melanogaster: Imperfection or interesting exception?

Drosophila melanogaster chromosome 4 is an anomaly because of its small size, chromatin structure, and most notably its lack of crossing over during meiosis. Earlier ideas about the absence of crossovers on 4 hypothesize that these unique characteristics function to prevent crossovers. Here, we explore hypotheses about the absence of crossovers on 4, how these have been addressed, and new insights into the mechanism behind this suppression. We review recently published results that indicate that global crossover patterning, in particular the centromere effect, make a major contribution to the prevention of crossovers on 4.     

Distinct histone modifications define initiation and repair of meiotic recombination in the mouse

Little is known about the factors determining the location and activity of the rapidly evolving meiotic crossover hotspots that shape genome diversity. Here, we show that several histone modifications are enriched at the active mouse Psmb9 hotspot, and we distinguish those marks that precede from those that follow hotspot recombinational activity. H3K4Me3, H3K4Me2 and H3K9Ac are specifically enriched in the chromatids that carry an active initiation site, and in the absence of DNA double-strand breaks (DSBs) in Spo11^−/− mice. We thus propose that these marks are part of the substrate for recombination initiation at the Psmb9 hotspot. In contrast, hyperacetylation of H4 is increased as a consequence of DSB formation, as shown by its dependency on Spo11 and by the enrichment detected on both recombining chromatids. In addition, the comparison with another hotspot, Hlx1, strongly suggests that H3K4Me3 and H4 hyperacetylation are common features of DSB formation and repair, respectively. Altogether, the chromatin signatures of the Psmb9 and Hlx1 hotspots provide a basis for understanding the distribution of meiotic recombination.     

On the Role of Baseline Measurements for Crossover Designs under the Self and Mixed Carryover Effects Model

Summary .  It is well known that optimal designs are strongly model dependent. In this article, we apply the Lagrange multiplier approach to the optimal design problem, using a recently proposed model for carryover effects. Generally, crossover designs are not recommended when carryover effects are present and when the primary goal is to obtain an unbiased estimate of the treatment effect. In some cases, baseline measurements are believed to improve design efficiency. This article examines the impact of baselines on optimal designs using two different assumptions about carryover effects during baseline periods and employing a nontraditional crossover design model. As anticipated, baseline observations improve design efficiency considerably for two-period designs, which use the data in the first period only to obtain unbiased estimates of treatment effects, while the improvement is rather modest for three- or four-period designs. Further, we find little additional benefits for measuring baselines at each treatment period as compared to measuring baselines only in the first period. Although our study of baselines did not change the results on optimal designs that are reported in the literature, the problem of strong model dependency problem is generally recognized. The advantage of using multiperiod designs is rather evident, as we found that extending two-period designs to three- or four-period designs significantly reduced variability in estimating the direct treatment effect contrast.     

High-throughput measuring of meiotic recombination rates in barley pollen nuclei using Crystal Digital PCRTM

Breeding exploits novel allelic combinations assured by meiotic recombination. Barley (Hordeum vulgare) single pollen nucleus genotyping enables measurement of meiotic recombination rates in gametes before fertilization without the need for segregating populations. However, so far, established methods rely on whole-genome amplification of every single pollen nucleus due to their limited DNA content, thus restricting the number of analyzed samples. In this study, high-throughput measurements of meiotic recombination rates in barley pollen nuclei without whole-genome amplification were performed through a Crystal Digital PCR^TM-based genotyping assay. Meiotic recombination rates within two centromeric and two distal chromosomal intervals were measured in hybrid plants by genotyping a total of >42 000 individual pollen nuclei (up to 4900 nuclei analyzed per plant). Determined recombination frequencies in pollen nuclei were similar to frequencies in segregating populations. We improved the efficiency of the genotyping by pretreating the pollen nuclei with a thermostable restriction enzyme. Additional opportunities for a higher sample throughput and a further increase of the genotyping efficiency are presented and discussed. Taken together, single barley pollen nucleus genotyping based on Crystal Digital PCR^TM enables reliable, rapid and high-throughput meiotic recombination measurements within defined chromosomal intervals of intraspecific hybrid plants. The successful encapsulation of nuclei from a range of species with different nuclear and genome sizes suggests that the proposed method is broadly applicable to genotyping single nuclei.     

Ultrastructural studies on the centrosome-attracting body: Electron-dense matrix and its role in unequal cleavages in ascidian embryos

In ascidian embryos, three successive unequal cleavages occur at the posterior pole, generating a specific cleavage pattern. A recently reported novel structure designated the centrosome-attracting body (CAB) has been suggested to play essential roles in the unequal cleavages attracting centrosomes and the nucleus towards the posterior pole. To examine the morphological features of the CAB, the ultrastructure of the CAB of two ascidian species, Halocynthia roretzi and Ciona intestinalis was observed by transmission electron microscopy. Detailed observations clarified that the electron-dense matrix (EDM) was a CAB-specific component that was commonly observed in the CAB of both species but was not found in other areas of the embryo. Further observations of the CAB in various staged embryos revealed that the ultrastructure was quite stable, with no difference between points of a cell cycle or between each stage from the 8- to 64-cell stage when unequal cleavage occurred. Observations of extracted embryos implied that the EDM was the extraction-resistant component of the CAB and was tightly anchored to the plasma membrane. It has been proposed that the EDM functions as a physical attachment site at the cell cortex for microtubules emanating from centrosomes and provides a scaffold for the centrosome-attracting machinery. Interestingly, the ultrastructure of the CAB resembled germ plasm reported in other animals, raising the possibility that the CAB-containing posterior-most blastomeres are germline precursors.