Analysis of Biological Features Associated with Meiotic Recombination Hot and Cold Spots in Saccharomyces cerevisiae

Meiotic recombination is not distributed uniformly throughout the genome. There are regions of high and low recombination rates called hot and cold spots, respectively. The recombination rate parallels the frequency of DNA double-strand breaks (DSBs) that initiate meiotic recombination. The aim is to identify biological features associated with DSB frequency. We constructed vectors representing various chromatin and sequence-based features for 1179 DSB hot spots and 1028 DSB cold spots. Using a feature selection approach, we have identified five features that distinguish hot from cold spots in Saccharomyces cerevisiae with high accuracy, namely the histone marks H3K4me3, H3K14ac, H3K36me3, and H3K79me3; and GC content. Previous studies have associated H3K4me3, H3K36me3, and GC content with areas of mitotic recombination. H3K14ac and H3K79me3 are novel predictions and thus represent good candidates for further experimental study. We also show nucleosome occupancy maps produced using next generation sequencing exhibit a bias at DSB hot spots and this bias is strong enough to obscure biologically relevant information. A computational approach using feature selection can productively be used to identify promising biological associations. H3K14ac and H3K79me3 are novel predictions of chromatin marks associated with meiotic DSBs. Next generation sequencing can exhibit a bias that is strong enough to lead to incorrect conclusions. Care must be taken when interpreting high throughput sequencing data where systematic biases have been documented

Luminescence dating, uncertainties and age range

Luminescence ages have an uncertainty of at least 4–5 %, mainly due to systematic errors in both dose rate (conversion factors) and equivalent dose (source calibration) estimation. In most cases, the uncertainty will be higher, due to random errors (e.g., spread in equivalent doses) or uncertainty in assumptions (e.g., water content fluctuations, burial history). Dating is possible for a wide age range of a few decades to about half a million years, although uncertainties are usually relatively large toward the extremes of this range

Measuring sedimentation in tidal marshes:a review on methods and their applicability in biogeomorphological studies

<p>It is increasingly recognised that interactions between geomorphological and biotic processes control the functioning of many ecosystem types as described e.g. by the ecological theory of ecosystem engineering. Consequently, the need for specific bio-geomorphological research methods is growing recently. Much research on bio-geomorphological processes is done in coastal marshes. These areas provide clear examples of ecosystem engineering as well as other bio-geomorphological processes: Marsh vegetation slows down tidal currents and hence stimulates the process of sedimentation, while vice versa, the sedimentation controls ecological processes like vegetation succession. This review is meant to give insights in the various available methods to measure sedimentation, with special attention to their suitability to quantify bio-geomorphological interactions. The choice of method used to measure sedimentation is important to obtain the correct parameters to understand the biogeomorphology of tidal salt marshes. This review, therefore, aims to be a tool for decision making regarding the processes to be measured and the methods to be used. We, subdivide the methods into those measuring suspended sediment concentration (A), sediment deposition (B), accretion (C) and surface-elevation change (D). With this review, we would like to further encourage interdisciplinary studies in the fields of ecology and geomorphology.</p>