Automated and assisted RNA resonance assignment using NMR chemical shift statistics

The three-dimensional structure determination of RNAs by NMR spectroscopy relies on chemical shift assignment, which still constitutes a bottleneck. In order to develop more efficient assignment strategies, we analysed relationships between sequence and 1H and 13C chemical shifts. Statistics of resonances from regularly Watson-Crick base-paired RNA revealed highly characteristic chemical shift clusters. We developed two approaches using these statistics for chemical shift assignment of double-stranded RNA (dsRNA): a manual approach that yields starting points for resonance assignment and simplifies decision trees and an automated approach based on the recently introduced automated resonance assignment algorithm FLYA. Both strategies require only unlabeled RNAs and three 2D spectra for assigning the H2/C2, H5/C5, H6/C6, H8/C8 and H1′/C1′ chemical shifts. The manual approach proved to be efficient and robust when applied to the experimental data of RNAs with a size between 20 nt and 42 nt. The more advanced automated assignment approach was successfully applied to four stem-loop RNAs and a 42 nt siRNA, assigning 92-100% of the resonances from dsRNA regions correctly. This is the first automated approach for chemical shift assignment of non-exchangeable protons of RNA and their corresponding 13C resonances, which provides an important step toward automated structure determination of RNA

Code of conduct for scientific integrity

The scientific landscape has changed considerably since the Swiss Academies of Arts and Sciences published Integrity in scientific research: Principles and procedures in 2008. Consequently, an expert group was set up with members from the Swiss Academies of Arts and Sciences, the Swiss National Science Foundation, swissuniversities, and Innosuisse to review the changes that have taken place in recent years and to draw up this Code of conduct for scientific integrity. This Code is aimed at everyone involved in the generation, dissemination, and advancement of knowledge within the Swiss higher education system. This includes scientists, institutions, and funding organisations. Institutions and funding organisations have a special role to play in creating and maintaining the conditions in which scientific integrity can thrive. Scientific integrity is based on the observance of fundamental principles and their many different contextual concretisations. These principles guide scien- tists in their research and teaching and help them to deal with the practical, ethical, and intellectual challenges they can expect to encounter. The aim of this code of conduct is to promote appropriate attitudes and to help build a robust culture of scientific integrity that will stand the test of time. Ethical scientific behaviour rests on the basic principles of reliability, honesty, respect, and accountability and supports the concretisations of these basic principles within a specific frame of reference. This Code is intended to be a dynamic document. Its aim is to strengthen scientific integrity in all avenues of research and education, with a particular emphasis on the training and development of young people. Another of its aims is to establish a culture of research integrity in the scientific community, with the Code providing a welcome framework rather than imposing its own set of rules. It promotes common understanding and parity of treatment in dealing with violations of scientific integrity within and between institutions. The Code also considers current developments in the fields of Open Science and social media, and it examines the issue of time limitation from several points of view. In addition, it offers practical recommendations on how to set up an organisation for the protection of scientific integrity and describes the processes involved

Kodex zur wissenschaftlichen Integrität

Im Jahr 2008 haben die Akademien der Wissenschaften Schweiz «Grundsätze und Verfahrensregeln zur wissenschaftlichen Integrität» veröffentlicht. Seitdem hat sich das wissenschaftliche Umfeld erheblich verändert. Um diesen Entwicklungen Rechnung zu tragen, hat eine ExpertInnengruppe mit VertreterInnen der Akademien der Wissenschaften Schweiz, des Schweizerischen Nationalfonds, swissuniversities und Innosuisse einen neuen Kodex zur wissenschaftlichen Integrität erarbeitet. Er basiert auf den Grundprinzipien Verlässlichkeit, Redlichkeit, Respekt und Verantwortung und trägt dazu bei, eine Kultur wissenschaftlicher Integrität nachhaltig zu stärken. Mit dem Kodex soll wissenschaftlich integres Verhalten in allen Aspekten von Forschung und Lehre, insbesondere auch bei der Ausbildung und Förderung des Nachwuchses gestärkt werden. Der Kodex berücksichtigt aktuelle Entwicklungen in den Bereichen Open Science und Social Media und beleuchtet das Thema Verjährung. Wie diese Standards in den eigenen Reglementen verankert und konkret umgesetzt werden, liegt in der Kompetenz der Hochschulen und Förderorganisationen.Akademien der Wissenschaften Schweiz (2021): Kodex für Wissenschaftliche Integrität. go.akademien-schweiz.ch/integrity. http://doi.org/10.5281/zenodo.4707584

Resultado do Edital Nº 47 -CAPES - Programa de Doutorado Sanduíche no Exterior

Here we present measurements of surface tension and viscosity of the bulk glass-forming alloy Pd_(43)Cu_(27)Ni_(10)P_(20) performed during containerless processing under reduced gravity. We applied the oscillating drop method in an electromagnetic levitation facility on board of parabolic flights. The measured viscosity exhibits a pronounced temperature dependence following an Arrhenius law over a temperature range from 1100 K to 1450 K. Together with literature values of viscosity at lower temperatures, the viscosity of Pd_(43)Cu_(27)Ni_(10)P_(20) can be well described by a free volume model. X-ray diffraction analysis on the material retrieved after the parabolic flights confirm the glassy nature after vitrification of the bulk samples and thus the absence of crystallization during processing over a wide temperature range

rbFOX1/MBNL1 competition for CCUG RNA repeats binding contributes to myotonic dystrophy type 1/type 2 differences

Myotonic dystrophy type 1 and type 2 (DM1, DM2) are caused by expansions of CTG and CCTG repeats, respectively. RNAs containing expanded CUG or CCUG repeats interfere with the metabolism of other RNAs through titration of the Muscleblind-like (MBNL) RNA binding proteins. DM2 follows a more favorable clinical course than DM1, suggesting that specific modifiers may modulate DM severity. Here, we report that the rbFOX1 RNA binding protein binds to expanded CCUG RNA repeats, but not to expanded CUG RNA repeats. Interestingly, rbFOX1 competes with MBNL1 for binding to CCUG expanded repeats and overexpression of rbFOX1 partly releases MBNL1 from sequestration within CCUG RNA foci in DM2 muscle cells. Furthermore, expression of rbFOX1 corrects alternative splicing alterations and rescues muscle atrophy, climbing and flying defects caused by expression of expanded CCUG repeats in a Drosophila model of DM2.Peer reviewe

The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases

The SIB Swiss Institute of Bioinformatics (www.isb-sib.ch) provides world-class bioinformatics databases, software tools, services and training to the international life science community in academia and industry. These solutions allow life scientists to turn the exponentially growing amount of data into knowledge. Here, we provide an overview of SIB's resources and competence areas, with a strong focus on curated databases and SIB's most popular and widely used resources. In particular, SIB's Bioinformatics resource portal ExPASy features over 150 resources, including UniProtKB/Swiss-Prot, ENZYME, PROSITE, neXtProt, STRING, UniCarbKB, SugarBindDB, SwissRegulon, EPD, arrayMap, Bgee, SWISS-MODEL Repository, OMA, OrthoDB and other databases, which are briefly described in this article