Pushing Structural Information into the Yeast Interactome by High-Throughput Protein Docking Experiments

The last several years have seen the consolidation of high-throughput proteomics initiatives to identify and characterize protein interactions and macromolecular complexes in model organisms. In particular, more that 10,000 high-confidence protein-protein interactions have been described between the roughly 6,000 proteins encoded in the budding yeast genome (Saccharomyces cerevisiae). However, unfortunately, high-resolution three-dimensional structures are only available for less than one hundred of these interacting pairs. Here, we expand this structural information on yeast protein interactions by running the first-ever high-throughput docking experiment with some of the best state-of-the-art methodologies, according to our benchmarks. To increase the coverage of the interaction space, we also explore the possibility of using homology models of varying quality in the docking experiments, instead of experimental structures, and assess how it would affect the global performance of the methods. In total, we have applied the docking procedure to 217 experimental structures and 1,023 homology models, providing putative structural models for over 3,000 protein-protein interactions in the yeast interactome. Finally, we analyze in detail the structural models obtained for the interaction between SAM1-anthranilate synthase complex and the MET30-RNA polymerase III to illustrate how our predictions can be straightforwardly used by the scientific community. The results of our experiment will be integrated into the general 3D-Repertoire pipeline, a European initiative to solve the structures of as many as possible protein complexes in yeast at the best possible resolution. All docking results are available at http://gatealoy.pcb.ub.es/HT_docking/

Effect of linguistic framing and information provision on attitudes towards induced seismicity and seismicity regulation

Shale gas is an expanding energy source worldwide, yet ‘fracking’ remains controversial. Amongst public concerns is induced seismicity (tremors). The UK had the most stringent induced seismicity regulations in the world, prior to instating a moratorium on shale gas development. The Government cited induced seismicity as the key rationale for its November 2019 English moratorium. Yet, little is known about how the public perceives induced seismicity, whether they support regulatory change, or how framing and information provision affect perceptions. Across three waves of a longitudinal experimental UK survey (N = 2777; 1858; 1439), we tested whether framing of induced seismicity influences support for changing regulations. The surveys compared (1) quantitative versus qualitative framings, (2) information provision about regulatory limits in other countries and (3) seismicity from other industries, and (4) framing a seismic event as an ‘earthquake’ or something else. We find low support for changing current policy, and that framing and information provision made little difference to this. The one strong influence on perceptions of seismic events came from the type of activity causing the event; shale gas extraction clearly led to the most negative reactions. We discuss implications for future UK policy on shale gas and geothermal energy in an evolving energy landscape

Residues coevolution guides the systematic identification of alternative functional conformations in proteins

We present here a new approach for the systematic identification of functionally relevant conformations in proteins. Our fully automated pipeline, based on discrete molecular dynamics enriched with coevolutionary information, is able to capture alternative conformational states in 76% of the proteins studied, providing key atomic details for understanding their function and mechanism of action. We also demonstrate that, given its sampling speed, our method is well suited to explore structural transitions in a high-throughput manner, and can be used to determine functional conformational transitions at the entire proteome level

Spin-orbital Jahn-Teller bipolarons

Polarons and spin-orbit (SO) coupling are distinct quantum effects that play a critical role in charge transport and spin-orbitronics. Polarons originate from strong electron-phonon interaction and are ubiquitous in polarizable materials featuring electron localization, in particular $\mathrm{3d}$ transition metal oxides (TMOs). On the other hand, the relativistic coupling between the spin and orbital angular momentum is notable in lattices with heavy atoms and develops in $\mathrm{5d}$ TMOs, where electrons are spatially delocalized. Here we combine ab initio calculations and magnetic measurements to show that these two seemingly mutually exclusive interactions are entangled in the electron-doped SO-coupled Mott insulator $\mathrm{Ba_2Na_{1-x}Ca_xOsO_6}$ ($0< x < 1$), unveiling the formation of spin-orbital bipolarons. Polaron charge trapping, favoured by the Jahn-Teller lattice activity, converts the Os $\mathrm{5d^1}$ spin-orbital $\mathrm{J_{eff}=3/2}$ levels, characteristic of the parent compound $\mathrm{Ba_2NaOsO_6}$ (BNOO), into a bipolaron $\mathrm{5d^2}$ $\mathrm{J_{eff}=2}$ manifold, leading to the coexistence of different J-effective states in a single-phase material. The gradual increase of bipolarons with increasing doping creates robust in-gap states that prevents the transition to a metal phase even at ultrahigh doping, thus preserving the Mott gap across the entire doping range from $\mathrm{d^1}$ BNOO to $\mathrm{d^2}$ $\mathrm{Ba_2CaOsO_6}$ (BCOO)

Functional and Structural Analysis of C-Terminal BRCA1 Missense Variants

Germline inactivating mutations in BRCA1 and BRCA2 genes are responsible for Hereditary Breast and Ovarian Cancer Syndrome (HBOCS). Genetic testing of these genes is available, although approximately 15% of tests identify variants of uncertain significance (VUS). Classification of these variants into pathogenic or non-pathogenic type is an important challenge in genetic diagnosis and counseling. The aim of the present study is to functionally assess a set of 7 missense VUS (Q1409L, S1473P, E1586G, R1589H, Y1703S, W1718L and G1770V) located in the C-terminal region of BRCA1 by combining in silico prediction tools and structural analysis with a transcription activation (TA) assay. The in silico prediction programs gave discrepant results making its interpretation difficult. Structural analysis of the three variants located in the BRCT domains (Y1703S, W1718L and G1770V) reveals significant alterations of BRCT structure. The TA assay shows that variants Y1703S, W1718L and G1770V dramatically compromise the transcriptional activity of BRCA1, while variants Q1409L, S1473P, E1586G and R1589H behave like wild-type BRCA1. In conclusion, our results suggest that variants Y1703S, W1718L and G1770V can be classified as likely pathogenic BRCA1 mutations

Sustainability of Long-term Care: Puzzling Tasks Ahead for Policy-Makers

Background: The sustainability of long-term care (LTC) is a prominent policy priority in many Western countries. LTC is one of the most pressing fiscal issues for the growing population of elderly people in the European Union (EU) Member States. Country recommendations regarding LTC are prominent under the EU’s European Semester. Methods: This paper examines challenges related to the financial- and organizational sustainability of LTC systems in the EU. We combined a targeted literature review and a descriptive selected country analysis of: (1) public- and private funding; (2) informal care and externalities; and (3) the possible role of technology in increasing productivity. Countries were selected via purposive sampling to establish a cohort of country cases covering the spectrum of differences in LTC systems: public spending, private funding, informal care use, informal care support, and cash benefits. Results: The aging of the population, the increasing gap between availability of informal care and demand for LTC, substantial market failures of private funding for LTC, and fiscal imbalances in some countries, have led to structural reforms and enduring pressures for LTC policy-makers across the EU. Our exploration of national policies illustrates different solutions that attempt to promote fairness while stimulating efficient delivery of services. Important steps must be taken to address the sustainability of LTC. First, countries should look deeper into the possibilities of complementing public- and private funding, as well as at addressing market failures of private funding. Second, informal care externalities with spill-over into neighboring policy areas, the labor force, and formal LTC workers, should be properly addressed. Thirdly, innovations in LTC services should be stimulated to increase productivity through technology and process innovations, and to reduce costs. Conclusion: The analysis shows why it is difficult for EU Member State governments to meet all their goals for sustainable LTC, given the demographic- and fiscal circumstances, and the complexities of LTC systems. It also shows the usefulness to learn from policy design and implementation of LTC policy in other countries, within and outside the EU. Researchers can contribute by studying conditions, under which the strategies explored might deliver solutions for policy-maker

Sustainability of Long-term Care: Puzzling Tasks Ahead for Policy-Makers

Abstract Background: The sustainability of long-term care (LTC) is a prominent policy priority in many Western countries. LTC is one of the most pressing fiscal issues for the growing population of elderly people in the European Union (EU) Member States. Country recommendations regarding LTC are prominent under the EU&apos;s European Semester. Methods: This paper examines challenges related to the financial-and organizational sustainability of LTC systems in the EU. We combined a targeted literature review and a descriptive selected country analysis of: (1) public-and private funding; (2) informal care and externalities; and (3) the possible role of technology in increasing productivity. Countries were selected via purposive sampling to establish a cohort of country cases covering the spectrum of differences in LTC systems: public spending, private funding, informal care use, informal care support, and cash benefits. Results: The aging of the population, the increasing gap between availability of informal care and demand for LTC, substantial market failures of private funding for LTC, and fiscal imbalances in some countries, have led to structural reforms and enduring pressures for LTC policy-makers across the EU. Our exploration of national policies illustrates different solutions that attempt to promote fairness while stimulating efficient delivery of services. Important steps must be taken to address the sustainability of LTC. First, countries should look deeper into the possibilities of complementing public-and private funding, as well as at addressing market failures of private funding. Second, informal care externalities with spill-over into neighboring policy areas, the labor force, and formal LTC workers, should be properly addressed. Thirdly, innovations in LTC services should be stimulated to increase productivity through technology and process innovations, and to reduce costs. Conclusion: The analysis shows why it is difficult for EU Member State governments to meet all their goals for sustainable LTC, given the demographic-and fiscal circumstances, and the complexities of LTC systems. It also shows the usefulness to learn from policy design and implementation of LTC policy in other countries, within and outside the EU. Researchers can contribute by studying conditions, under which the strategies explored might deliver solutions for policy-makers

Scientific Potential of Einstein Telescope

Einstein gravitational-wave Telescope (ET) is a design study funded by the European Commission to explore the technological challenges of and scientific benefits from building a third generation gravitational wave detector. The three-year study, which concluded earlier this year, has formulated the conceptual design of an observatory that can support the implementation of new technology for the next two to three decades. The goal of this talk is to introduce the audience to the overall aims and objectives of the project and to enumerate ET's potential to influence our understanding of fundamental physics, astrophysics and cosmology.Comment: Conforms to conference proceedings, several author names correcte

Scientific Objectives of Einstein Telescope

The advanced interferometer network will herald a new era in observational astronomy. There is a very strong science case to go beyond the advanced detector network and build detectors that operate in a frequency range from 1 Hz-10 kHz, with sensitivity a factor ten better in amplitude. Such detectors will be able to probe a range of topics in nuclear physics, astronomy, cosmology and fundamental physics, providing insights into many unsolved problems in these areas.Comment: 18 pages, 4 figures, Plenary talk given at Amaldi Meeting, July 201

Early and extensive CD55 loss from red blood cells supports a causal role in malarial anaemia

BACKGROUND\ud \ud Levels of complement regulatory proteins (CrP) on the surface of red blood cells (RBC) decrease during severe malarial anaemia and as part of cell ageing process. It remains unclear whether CrP changes seen during malaria contribute to the development of anaemia, or result from an altered RBC age distribution due to suppressive effects of malaria on erythropoiesis.\ud \ud METHODS\ud \ud A cross sectional study was conducted in the north-east coast of Tanzania to investigate whether the changes in glycosylphosphatidylinositol (GPI)-anchored complement regulatory proteins (CD55 and CD59) contributes to malaria anaemia. Blood samples were collected from a cohort of children under intensive surveillance for Plasmodium falciparum parasitaemia and illness. Levels of CD55 and CD59 were measured by flow cytometer and compared between anaemic (8.08 g/dl) and non- anaemic children (11.42 g/dl).\ud \ud RESULTS\ud \ud Levels of CD55 and CD59 decreased with increased RBC age. CD55 levels were lower in anaemic children and the difference was seen in RBC of all ages. Levels of CD59 were lower in anaemic children, but these differences were not significant. CD55, but not CD59, levels correlated positively with the level of haemoglobin in anaemic children.\ud \ud CONCLUSION\ud \ud The extent of CD55 loss from RBC of all ages early in the course of malarial anaemia and the correlation of CD55 with haemoglobin levels support the hypothesis that CD55 may play a causal role in this disorder