Highlights d Cities possess a consistent ''core'' set of non-human microbes d Urban microbiomes echo important features of cities and city-life d Antimicrobial resistance genes are widespread in cities d Cities contain many novel bacterial and viral species

The usage made of protein surfaces by nucleic acids still remains largely unknown, due to the lack of available structural data and the inherent complexity associated to protein surface deformability and evolution. In this work, we present a method that contributes to decipher such complexity by predicting protein-DNA interfaces and characterizing their properties. It relies on three biologically and physically meaningful descriptors, namely evolutionary conservation, physico-chemical properties and surface geometry. We carefully assessed its performance on several hundreds of protein structures. We achieve a higher sensitivity compared to state-of-the-art methods, and similar precision. Importantly, we show that our method is able to unravel 'hidden' binding sites by applying it to unbound protein structures and to proteins binding to DNA via multiple sites and in different conformations. It is implemented as a fully automated tool, JET 2 DNA , freely accessible at: http://www.lcqb.upmc.fr/JET2DNA. We also provide a new reference dataset of 187 protein-DNA complex structures, representative of all types of protein-DNA interactions, along with a subset of associated unbound structures: http://www.lcqb.upmc.fr/PDNAbenchmarks.

Interactions between proteins and nucleic acids are at the heart of many essential biological processes. Despite increasing structural information about how these interactions may take place, our understanding of the usage made of protein surfaces by nucleic acids is still very limited. This is in part due to the inherent complexity associated to protein surface deformability and evolution. In this work, we present a method that contributes to decipher such complexity by predicting protein-DNA interfaces and characterizing their properties. It relies on three biologically and physically meaningful descriptors, namely evolutionary conservation, physico-chemical properties and surface geometry. We carefully assessed its performance on several hundreds of protein structures and compared it to several machinelearning state-of-the-art methods. Our approach achieves a higher sensitivity compared to the other methods, with a similar precision. Importantly, we show that it is able to unravel 'hidden' binding sites by applying it to unbound protein structures and to proteins binding to DNA via multiple sites and in different conformations. It is also applicable to the detection of RNA-binding sites, without significant loss of performance. This confirms that DNA and RNA-binding sites share similar properties. Our method is implemented as a fully automated tool, JET 2 DNA , freely accessible at: http://www.lcqb.upmc.fr/JET2DNA. We also provide a new dataset of 187 protein-DNA complex structures, along with a subset of 82 associated unbound structures. The set represents the largest body of high-resolution crystallographic structures of protein-DNA complexes, use biological protein assemblies as DNA-binding units, and covers all major types of protein-DNA interactions.

Background One of the contributing factors to ocular surface health is a stable precorneal tear film. Considering the increasing interest in rabbits as pets and the limited literature available on domestic rabbit tearing, the aim of this study was to establish normative data for examination of the tear film in domestic rabbits. Results The study included 75 client-owned domestic Holland Lop rabbits (150 eyes). The following examinations were performed in each eye: Schirmer tear test-1, tear osmometry, interferometry, tear meniscus height measurement and meibography (quantifying meibomian gland loss as a percentage). The resulting median (95% central range) values were 10.0 (5.0–17.3) mm/min for the Schirmer tear test-1, 345.0 (280.5–376.1) mOsm/L for tear osmolarity, grade 2 (1–4) of interferometry, 0.28 (0.20–0.47) mm for tear meniscus height and 0.0 (0.0–67.6) % meibomian gland loss. A significant association was found between tear osmolarity and age, with an estimated decrease of − 4.0 mOsm/L with each additional year of age (p < 0.001). The distributions of interferometry grades were significantly different between males and females (p < 0.001), with grade 1 and grade 2 being the most frequent in females and males, respectively. A weak negative correlation was also observed between interferometry grade and the percentage of meibomian gland loss (r = − 0.22, p = 0.006). Conclusions This is an original study that documents extensive tear film parameters in healthy Holland Lop rabbits. The results can be used as normative data for the examination of the tear film in this lagomorph breed.

Physical interactions between proteins are central to all biological processes. Yet, the current knowledge of who interacts with whom in the cell and in what manner relies on partial, noisy, and highly heterogeneous data. Thus, there is a need for methods comprehensively describing and organizing such data. LEVELNET is a versatile and interactive tool for visualizing, exploring, and comparing protein–protein interaction (PPI) networks inferred from different types of evidence. LEVELNET helps to break down the complexity of PPI networks by representing them as multi‐layered graphs and by facilitating the direct comparison of their subnetworks toward biological interpretation. It focuses primarily on the protein chains whose 3D structures are available in the Protein Data Bank. We showcase some potential applications, such as investigating the structural evidence supporting PPIs associated to specific biological processes, assessing the co‐localization of interaction partners, comparing the PPI networks obtained through computational experiments versus homology transfer, and creating PPI benchmarks with desired properties.