Using Phylogeny to Improve Genome-Wide Distant Homology Recognition

The gap between the number of known protein sequences and structures continues to widen, particularly as a result of sequencing projects for entire genomes. Recently there have been many attempts to generate structural assignments to all genes on sets of completed genomes using fold-recognition methods. We developed a method that detects false positives made by these genome-wide structural assignment experiments by identifying isolated occurrences. The method was tested using two sets of assignments, generated by SUPERFAMILY and PSI-BLAST, on 150 completed genomes. A phylogeny of these genomes was built and a parsimony algorithm was used to identify isolated occurrences by detecting occurrences that cause a gain at leaf level. Isolated occurrences tend to have high e-values, and in both sets of assignments, a sudden increase in isolated occurrences is observed for e-values >10(−8) for SUPERFAMILY and >10(−4) for PSI-BLAST. Conditions to predict false positives are based on these results. Independent tests confirm that the predicted false positives are indeed more likely to be incorrectly assigned. Evaluation of the predicted false positives also showed that the accuracy of profile-based fold-recognition methods might depend on secondary structure content and sequence length. We show that false positives generated by fold-recognition methods can be identified by considering structural occurrence patterns on completed genomes; occurrences that are isolated within the phylogeny tend to be less reliable. The method provides a new independent way to examine the quality of fold assignments and may be used to improve the output of any genome-wide fold assignment method

Seasonal adjustment of daily data with CAMPLET

In the last decade large data sets have become available, both in terms of the number of time series and with higher frequencies (weekly, daily and even higher). All series may suffer from seasonality, which hides other important fluctuations. Therefore time series are typically seasonally adjusted. However, standard seasonal adjustment methods cannot handle series with higher than monthly frequencies. Recently, Abeln et al. (2019) presented CAMPLET, a new seasonal adjustment method, which does not produce revisions when new observations become available. The aim of this paper is to show the attractiveness of CAMPLET for seasonal adjustment of daily time series. We apply CAMPLET to daily data on the gas system in the Netherlands

Interplay between Folding and Assembly of Fibril-Forming Polypeptides.

Polypeptides can self-assemble into hierarchically organized fibrils consisting of a stack of individually folded polypeptides driven together by hydrophobic interaction. Using a coarse grained model, we systematically studied this self-assembly as a function of temperature and hydrophobicity of the residues on the outside of the building block. We find the self-assembly can occur via two different pathways - a random aggregation-folding route, and a templated-folding process - thus indicating a strong coupling between folding and assembly. The simulation results can explain experimental evidence that assembly through stacking of folded building blocks is rarely observed, at the experimental concentrations. The model thus provides a generic picture of hierarchical fibril formation.Comment: Accepted in Physical Review Letter

Which Aortic Valve Can Be Surgically Reconstructed?

Purpose of Review Preservation or repair of the aortic valve has evolved dynamically in the past 20 years. It leads to a high freedom from valve-related complications if an adequate valve durability can be achieved; it may possibly also improve survival. To date, little structured information is available about which valves can be repaired and which should better be replaced. Recent Findings For surgical decision-making, the size of the aortic root is important and the anatomy of the aortic valve must be considered. In the presence of root aneurysm, most tricuspid and bicuspid aortic valves can be preserved. In aortic regurgitation and normal aortic dimensions, the majority of tricuspid and bicuspid aortic valves can be repaired with good long-term durability. In bicuspid aortic valves, the morphologic characteristics must be taken into consideration. Unicuspid and quadricuspid aortic valves can be repaired in selected cases. Generally, cusp calcification is a sign of a poor substrate for repair; the same is true for cusp retraction and cusp destruction due to active endocarditis. They are associated with limited valve durability. Summary Using current concepts, many non-calcified aortic valves can be repaired. Modern imaging, in particular three-dimensional transesophageal echocardiography (TEE), should be able to define repairable aortic valves with a high probability