bluuebunny/crossref_metadata_2025 huggingface dataset:
Meta-analysis of (single-cell method) benchmarks reveals the need for extensibility and interoperability
Authors: Sonrel Anthony , Luetge Almut , Soneson Charlotte , Mallona Izaskun , Germain Pierre-Luc , Knyazev Sergey , Gilis Jeroen , Gerber Reto , Seurinck Ruth , Paul Dominique , Sonder Emanuel , Crowell Helena L. , Fanaswala Imran , Al-Ajami Ahmad , Heidari Elyas , Schmeing Stephan , Milosavljevic Stefan , Saeys Yvan , Mangul Serghei , Robinson Mark D.
Published: September 2022

Computational methods represent the lifeblood of modern molecular biology. Benchmarking is important for all methods, but with a focus here on computational methods, benchmarking is critical to dissect important steps of analysis pipelines, formally assess performance across common situations as well as edge cases, and ultimately guide users on what tools to use. Benchmarking can also be important for community building and advancing methods in a principled way. We conducted a meta-analysis of recent single-cell benchmarks to summarize the scope, extensibility, neutrality, as well as technical features and whether best practices in open data and reproducible research were followed. The results highlight that while benchmarks often make code available and are in principle reproducible, they remain difficult to extend, for example, as new methods and new ways to assess methods emerge. In addition, embracing containerization and workflow systems would enhance reusability of intermediate benchmarking results, thus also driving wider adoption.
Anticodon-like loop-mediated dimerization in the crystal structures of HDV-like CPEB3 ribozymes
Authors: Przytula-Mally Anna Ilaria , Engilberge Sylvain , Johannsen Silke , Olieric Vincent , Masquida Benoît , Sigel Roland K.O.
Published: September 2022

Cytoplasmic polyadenylation element-binding (CPEB) proteins are involved in many cellular processes, including cell division, synaptic plasticity, learning, and memory. A highly conserved, short mammalian ribozyme has been found within the second intron of the CPEB3 gene. Based on its cleavage mechanism and structural features, this ribozyme belongs to the hepatitis delta virus (HDV)-like ribozyme family. Here, we present the first crystallographic structures of human and chimpanzee CPEB3 ribozymes, both confirming the general topology of the HDV ribozyme with two parallel coaxial helical stacks. However, the residues involved in forming the P1.1 mini-helix, which is an integral part of the characteristic nested double pseudoknot involving P1, P2, and P3, instead participate in a seven nucleotides loop with a conformation similar to the one from the anticodon (AC) loop of tRNAs when interacting with the mRNA codon. The conformation of the loop supports the formation of a four-base pair helix by interacting with the AC-like loop from a symmetry-related ribozyme leading to ribozyme dimer formation. The present crystal structures link for the first time the sequence specificities of the CPEB3 and the HDV (genomic and antigenomic) ribozymes to their different structural features. This work corroborates the hypothesis made by Szostak that HDV ribozymes may have evolved from the CPEB3 ribozyme.