Strand-switching mechanism of Pif1 helicase induced by its collision with a G-quadruplex embedded in dsDNA

G-rich sequences found at multiple sites throughout all genomes may form secondary structures called G-quadruplexes (G4), which act as roadblocks for molecular motors. Among the enzymes thought to process these structures, the Pif1 DNA helicase is considered as an archetypical G4-resolvase and its absence has been linked to G4-related genomic instabilities in yeast. Here we developed a single-molecule assay to observe Pif1 opening a DNA duplex and resolving the G4 in real time. In support of former enzymological studies, we show that the helicase reduces the lifetime of G4 from hours to seconds. However, we observe that in presence of a G4, Pif1 exhibits a strong strand switching behavior, which can lead to Pif1 escaping G4 resolution, depending on the structural context surrounding the substrate. This behavior is also detected in presence of other roadblocks (LNA or RNA). We propose that the efficiency of Pif1 to remove a roadblock (G4 or other) is affected by its strand switching behavior and depends on the context surrounding the obstacle. We discuss how this switching behavior may explain several aspects of Pif1 substrate preference and affect its activity as a G4 resolvase in vivo.

KiSSim: Predicting off-targets from structural similarities in the kinome

Protein kinases are among the most important drug targets because their dysregulation can cause cancer, inflammatory, and degenerative diseases. Developing selective inhibitors is challenging due to the highly conserved binding sites across the roughly 500 human kinases. Thus, detecting subtle similarities on a structural level can help to explain and predict off-targets among the kinase family. Here, we present the kinase-focused and subpocket-enhanced KiSSim fingerprint (Kinase Structural Similarity). The fingerprint builds on the KLIFS pocket definition, composed of 85 residues aligned across all available protein kinase structures, which enables residue-by-residue comparison without a computationally expensive alignment. The residues' physicochemical and spatial properties are encoded within their structural context including key subpockets at the hinge region, the DFG motif, and the front pocket. Since structure was found to contain information complementary to sequence, we used the fingerprint to calculate all-against-all similarities within the structurally covered kinome. Thereby, we could identify off-targets that are unexpected if solely considering the sequence-based kinome tree grouping; for example, Erlobinib’s known kinase off-targets SLK and LOK show high similarities to the key target EGFR (TK group) though belonging to the STE group. KiSSim reflects profiling data better or at least as well as other approaches such as KLIFS pocket sequence identity, KLIFS interaction fingerprints (IFPs), or SiteAlign. To rationalize observed (dis)similarities, the fingerprint values can be visualized in 3D by coloring structures with residue and feature resolution. We believe that the KiSSim fingerprint is a valuable addition to the kinase research toolbox to guide off-target and polypharmacology prediction. The method is distributed as an open-source Python package on GitHub and as conda package: https://github.com/volkamerlab/kissim

Melanoma Immunotherapy and Precision Medicine in the Era of Tumor Micro-Tissue Engineering: Where Are We Now and Where Are We Going?

Malignant melanoma still remains a cancer with very poor survival rates, although it is at the forefront of personalized medicine. Most patients show partial responses and disease progressed due to adaptative resistance mechanisms, preventing long-lasting clinical benefits to the current treatments. The response to therapies can be shaped by not only taking into account cancer cell heterogeneity and plasticity, but also by its structural context as well as the cellular component of the tumor microenvironment (TME). Here, we review the recent development in the field of immunotherapy and target-based therapy and how, in the era of tumor micro-tissue engineering, ex-vivo assays could help to enhance our melanoma biology knowledge in its complexity, translating it in the development of successful therapeutic strategies, as well as in the prediction of therapeutic benefits.

The structure of natively iodinated bovine thyroglobulin

Thyroglobulin is a homodimeric glycoprotein that is essential for the generation of thyroid hormones in vertebrates. Upon secretion into the lumen of follicles in the thyroid gland, tyrosine residues within the protein become iodinated to produce monoiodotyrosine (MIT) and diiodotyrosine (DIT). A subset of evolutionarily conserved pairs of DIT (and MIT) residues can then engage in oxidative coupling reactions that yield either thyroxine (T4; produced from coupling of a DIT `acceptor' with a DIT `donor') or triiodothyronine (T3; produced from coupling of a DIT acceptor with an MIT donor). Although multiple iodotyrosine residues have been identified as potential donors and acceptors, the specificity and structural context of the pairings (i.e. which donor is paired with which acceptor) have remained unclear. Here, single-particle cryogenic electron microscopy (cryoEM) was used to generate a high-resolution reconstruction of bovine thyroglobulin (2.3 Å resolution in the core region and 2.6 Å overall), allowing the structural characterization of two post-reaction acceptor–donor pairs as well as tyrosine residues modified as MIT and DIT. A substantial spatial separation between donor Tyr149 and acceptor Tyr24 was observed, suggesting that for thyroxine synthesis significant peptide motion is required for coupling at the evolutionarily conserved thyroglobulin amino-terminus.

The Concept of Hybridity in Journalism Studies

This paper considers the use of the concept of hybridity in journalism studies, arguing that the concept of hybridity has served an important role in reorienting the field in the face of important processes of social change, but that as a “sensitizing concept” in the sense that Herbert Blumer used the term, it requires critical reflection and more careful specification of its various uses. In the first sections, we map three principal contexts in which the concept has been invoked: one focusing on new media and the blurring of professional boundaries it produces; one focusing on global flows of journalism culture, and a third which treats hybridity not as a novel but as quotidian and rooted in the structural context of the practice of journalism in general. The second part of the paper focuses on issues and challenges in the use of the concept of hybridity. We consider the tendency for hybridity to become a catch-all phrase that substitutes for more specific analysis, and the problem of treating novel phenomena as derivative forms of familiar ones. We then move to critique “presentism” in the discussion of hybridity and the distortions that result from drawing dichotomies between hybrid and “pure” forms, making the argument for taking seriously the idea that hybridity is universal. In the final section, we propose the idea of the hybridity cycle as a way of thinking about stability and change in journalism studies.

Understanding Sexual Agency. Implications for Sexual Health Programming

Debates on human agency, especially female and sexual agency, have permeated the social scientific literature and health educational practice for multiple decades now. This article provides a review of recent agency debates illustrating how criticisms of traditional conceptions of (sexual) agency have led to a notable diversification of the concept. A comprehensive, inclusive description of sexual agency is proposed, focusing on the navigation of goals and desires in the wider structural context, and acknowledging the many forms sexual agency may take. We argue there is no simple relation between sexual agency and sexual health. Next, we describe the implications of such an understanding of sexual agency for Comprehensive Sexuality Education (CSE) and for sexual health and rights (SHR) programming more generally. We put forward validation of agentic variety, gender transformative approaches, meaningful youth participation, and multicomponent strategies as essential in building young peoples’ sexual agency and their role as agents of wider societal change. We also show that these essential conditions, wherever they have been studied, are far from being realized. With this review and connected recommendations, we hope to set the stage for ongoing, well-focused research and development in the area.

Plurality of Analytic Levels and Temporalities in the Study of the Relationship with the Homeland : The Example of the Seasonal Migratory Circuit Connecting the Bouches‑du‑Rhône Region to the Maghreb

In this article I show how, on the field of seasonal migration between the Maghreb and the Bouches‑du‑Rhône, the evolution of the links maintainedwith the “homeland,” the territory and social network in the country of origin and the meaning that migrants themselves give to this relationship can be understood through the intersection of a plurality of analytic levels and temporalities: the political and socio‑economic structural context of the host and origin country; the possibilities provided by migrants’ network; the individual and family strategies of the latter. Sur le terrain des migrations saisonnières entre le Maghreb et les Bouches‑du‑Rhône, j’étudie l’évolution des liens entretenus avec « la patrie », leterritoire et le réseau social d’origine et le sens que les migrants donnent eux‑mêmes à cette relation, une évolution que j’aborde à travers le croisement d’une pluralité de temporalités et d’échelles d’observations : le contexte structurel politique, socio‑économique du pays d’accueil et d’origine ; les possibilités données par le réseau des migrants ; les stratégies individuelles et familiales de ces derniers.