Slx5/Slx8-dependent ubiquitin hotspots on chromatin contribute to stress tolerance

Chromatin is a highly regulated environment, and protein association with chromatin is often controlled by post-translational modifications and the corresponding enzymatic machinery. Specifically, SUMO-targeted ubiquitin ligases (STUbLs) have emerged as key players in nuclear quality control, genome maintenance, and transcription. However, how STUbLs select specific substrates among myriads of SUMOylated proteins on chromatin remains unclear. Here, we reveal a remarkable co-localization of the budding yeast STUbL Slx5/Slx8 and ubiquitin at seven genomic loci that we term "ubiquitin hotspots". Ubiquitylation at these sites depends on Slx5/Slx8 and protein turnover on the Cdc48 segregase. We identify the transcription factor-like Ymr111c/Euc1 to associate with these sites and to be a critical determinant of ubiquitylation. Euc1 specifically targets Slx5/Slx8 to ubiquitin hotspots via bipartite binding of Slx5 that involves the Slx5 SUMO-interacting motifs and an additional, novel substrate recognition domain. Interestingly, the Euc1-ubiquitin hotspot pathway acts redundantly with chromatin modifiers of the H2A.Z and Rpd3L pathways in specific stress responses. Thus, our data suggest that STUbL-dependent ubiquitin hotspots shape chromatin during stress adaptation

Predictability of Self-Organizing Systems

We study the predictability of large events in self-organizing systems. We focus on a set of models which have been studied as analogs of earthquake faults and fault systems, and apply methods based on techniques which are of current interest in seismology. In all cases we find detectable correlations between precursory smaller events and the large events we aim to forecast. We compare predictions based on different patterns of precursory events and find that for all of the models a new precursor based on the spatial distribution of activity outperforms more traditional measures based on temporal variations in the local activity.Comment: 15 pages, plain.tex with special macros included, 4 figure

The quest for companions to post-common envelope binaries. II. NSVS14256825 and HS0705+6700

We report new mid-eclipse times of the two close binaries NSVS14256825 and HS0705+6700, harboring an sdB primary and a low-mass main-sequence secondary. Both objects display clear variations in the measured orbital period, which can be explained by the action of a third object orbiting the binary. If this interpretation is correct, the third object in NSVS14256825 is a giant planet with a mass of roughly 12 M_Jup. For HS0705+6700, we provide evidence that strengthens the case for the suggested periodic nature of the eclipse time variation and reduces the uncertainties in the parameters of the brown dwarf implied by that model. The derived period is 8.4 yr and the mass is 31 M_Jup, if the orbit is coplanar with the binary. This research is part of the PlanetFinders project, an ongoing collaboration between professional astronomers and student groups at high schools.Comment: Accepted by Astron. and Astrophy

Partitioning of U, Th and K Between Metal, Sulfide and Silicate, Insights into the Volatile-Content of Mercury

During the early stages of the Solar System formation, especially during the T-Tauri phase, the Sun emitted strong solar winds, which are thought to have expelled a portion of the volatile elements from the inner solar system. It is therefore usually believed that the volatile depletion of a planet is correlated with its proximity to the Sun. This trend was supported by the K/Th and K/U ratios of Venus, the Earth, and Mars. Prior to the MESSENGER mission, it was expected that Mercury is the most volatile-depleted planet. However, the Gamma Ray Spectrometer of MESSENGER spacecraft revealed elevated K/U and K/Th ratios for the surface of Mercury, much higher than previous expectations. It is possible that the K/Th and K/U ratios on the surface are not a reliable gauge of the bulk volatile content of Mercury. Mercury is enriched in sulfur and is the most reduced of the terrestrial planets, with oxygen fugacity (fO2) between IW-6.3 and IW-2.6 log units. At these particular compositions, U, Th and K behave differently and can become more siderophile or chalcophile. If significant amounts of U and Th are sequestered in the core, the apparent K/U and K/Th ratios measured on the surface may not represent the volatile budget of the whole planet. An accurate determination of the partitioning of these elements between silicate, metal, and sulfide phases under Mercurian conditions is therefore essential to better constrain Mercury's volatile content and assess planetary formation models

Software Citation Implementation Challenges

The main output of the FORCE11 Software Citation working group (https://www.force11.org/group/software-citation-working-group) was a paper on software citation principles (https://doi.org/10.7717/peerj-cs.86) published in September 2016. This paper laid out a set of six high-level principles for software citation (importance, credit and attribution, unique identification, persistence, accessibility, and specificity) and discussed how they could be used to implement software citation in the scholarly community. In a series of talks and other activities, we have promoted software citation using these increasingly accepted principles. At the time the initial paper was published, we also provided guidance and examples on how to make software citable, though we now realize there are unresolved problems with that guidance. The purpose of this document is to provide an explanation of current issues impacting scholarly attribution of research software, organize updated implementation guidance, and identify where best practices and solutions are still needed

Comparison of Spectra in Unsequenced Species

International audienceWe introduce a new algorithm for the mass spectromet- ric identication of proteins. Experimental spectra obtained by tandem MS/MS are directly compared to theoretical spectra generated from pro- teins of evolutionarily closely related organisms. This work is motivated by the need of a method that allows the identication of proteins of unsequenced species against a database containing proteins of related organisms. The idea is that matching spectra of unknown peptides to very similar MS/MS spectra generated from this database of annotated proteins can lead to annotate unknown proteins. This process is similar to ortholog annotation in protein sequence databases. The difficulty with such an approach is that two similar peptides, even with just one mod- ication (i.e. insertion, deletion or substitution of one or several amino acid(s)) between them, usually generate very dissimilar spectra. In this paper, we present a new dynamic programming based algorithm: Packet- SpectralAlignment. Our algorithm is tolerant to modications and fully exploits two important properties that are usually not considered: the notion of inner symmetry, a relation linking pairs of spectrum peaks, and the notion of packet inside each spectrum to keep related peaks together. Our algorithm, PacketSpectralAlignment is then compared to SpectralAlignment [1] on a dataset of simulated spectra. Our tests show that PacketSpectralAlignment behaves better, in terms of results and execution tim