• ER-associated degradation: protein quality control and beyond

  Ruggiano, Annamaria, 1985-; Foresti, Ombretta; Carvalho, Pedro C. (Rockefeller University Press, 2014)

  Even with the assistance of many cellular factors, a significant fraction of newly synthesized proteins ends up misfolded. Cells evolved protein quality control systems to ensure that these potentially toxic species are ...
• Long-term asymmetrical acceleration of protein evolution after gene duplication

  Pich Roselló, Oriol, 1992-; Kondrashov, Fyodor A., 1979- (Oxford University Press, 2014)

  Rapid divergence of gene copies after duplication is thought to determine the fate of the copies and evolution of novel protein functions. However, data on how long the gene copies continue to experience an elevated rate ...
• eQTL-Detect: nextflow-based pipeline for eQTL detection in modular format with sharable and parallelizable scripts

  Chitneedi, Praveen Krishna; Hadlich, Frieder; Moreira, Gabriel C. M.; Espinosa-Carrasco, José; Li, Changxi; Plastow, Graham; Fischer, Daniel; Charlier, Carole; Rocha, Dominique; Chamberlain, Amanda J.; Kuehn, Christa (Oxford University Press, 2024)

  Bioinformatic pipelines are becoming increasingly complex with the ever-accumulating amount of Next-generation sequencing (NGS) data. Their orchestration is difficult with a simple Bash script, but bioinformatics workflow ...
• The dual-specificity kinase DYRK1A interacts with the Hepatitis B virus genome and regulates the production of viral RNA

  Pastor, Florentin; Charles, Emilie; Di Vona, Chiara, 1981-; Chapelle, Maëlys; Rivoire, Michel; Passot, Guillaume; Chabot, Benoit; Luna, Susana de la; Lucifora, Julie; Durantel, David; Salvetti, Anna (Public Library of Science (PLoS), 2024)

  The genome of Hepatitis B virus (HBV) persists in infected hepatocytes as a nuclear episome (cccDNA) that is responsible for the transcription of viral genes and viral rebound, following antiviral treatment arrest in ...
• Clinical and molecular characterization of steatotic liver disease in the setting of immune-mediated inflammatory diseases

  García Nieto, Enrique; Esteve-Codina, Anna; Gut, Marta; Arias-Loste, María Teresa (Elsevier, 2024)

  Background & aims: Growing evidence suggests an increased prevalence of metabolic dysfunction-associated steatotic liver disease (MASLD) in the context of immune-mediated inflammatory diseases (IMIDs). We aimed to clinically ...
• Rare variant analyses in 51,256 type 2 diabetes cases and 370,487 controls reveal the pathogenicity spectrum of monogenic diabetes genes

  Huerta-Chagoya, Alicia; Bonàs-Guarch, Silvia; Mollandin, Fanny; Mercader, Josep M. (Nature Research, 2024)

  Type 2 diabetes (T2D) genome-wide association studies (GWASs) often overlook rare variants as a result of previous imputation panels' limitations and scarce whole-genome sequencing (WGS) data. We used TOPMed imputation and ...
• Enlarged brain perivascular spaces correlate with blood plasma osmolality in the healthy population: A longitudinal study

  Morozova, Alexandra; Španiel, Filip; Škoch, Antonín; Brabec, Marek; Zolotarov, Grygoriy; Musil, Vladimir; Zach, Petr (Elsevier, 2024)

  Enlarged perivascular spaces (EPVS) are increasingly recognized as an MRI detectable feature of neuroinflammatory processes and age-related neurodegenerative changes. Understanding perivascular characteristics in healthy ...
• The genetic architecture of protein interaction affinity and specificity

  Bendel, Alexandra M.; Faure, Andre J.; Klein, Dominique; Shimada, Kenji; Lyautey, Romane; Schiffelholz, Nicole; Kempf, Georg; Cavadini, Simone; Lehner, Ben, 1978-; Diss, Guillaume (Nature Research, 2024)

  The encoding and evolution of specificity and affinity in protein-protein interactions is poorly understood. Here, we address this question by quantifying how all mutations in one protein, JUN, alter binding to all other ...
• Theoretical assessment of indistinguishable peptides in mass spectrometry-based proteomics

  Elhamraoui, Zahra; Borràs, Eva; Wilhelm, Mathias; Sabidó Aguadé, Eduard, 1981- (American Chemical Society (ACS), 2024)

  Mass-spectrometry-based proteomics has advanced with the integration of experimental and predicted spectral libraries, which have significantly improved peptide identification in complex search spaces. However, challenges ...
• Regulation of Cx36 trafficking through the early secretory pathway by COPII cargo receptors and Grasp55

  Tetenborg, Stephan; Ariakia, Fatemeh; Martinez Soler, Elizabeth; Shihabeddin, Eyad; Cebrian Lazart, Ignacio; Miller, Adam C.; O'Brien, John T. (Springer, 2024)

  Gap junctions formed by the major neuronal connexin Cx36 function as electrical synapses in the nervous system and provide unique functions such as synchronizing neuron activities or supporting network oscillations. Although ...
• A research data management (RDM) community for ELIXIR

  D'Anna, Flora; D'Altri, Teresa, 1984-; Andrabi, Munazah (F1000Research, 2024)

  Research data management (RDM) is central to the implementation of the FAIR (Findable Accessible, Interoperable, Reusable) and Open Science principles. Recognising the importance of RDM, ELIXIR Platforms and Nodes have ...
• The senescence-associated secretory phenotype induces cellular plasticity and tissue regeneration

  Ritschka, Birgit,1985-; Storer, Mekayla, 1981-; Mas Malavila, Alba; Heinzmann, Florian; Ortells Campos, Mª Carmen, 1984-; Morton, Jennifer P.; Sansom, Owen J.; Zender, Lars; Keyes, William M., 1973- (Cold Spring Harbor Laboratory Press (CSHL Press), 2017)

  Senescence is a form of cell cycle arrest induced by stress such as DNA damage and oncogenes. However, while arrested, senescent cells secrete a variety of proteins collectively known as the senescence-associated secretory ...
• Selenoprotein gene nomenclature

  Gladyshev, Vadim N.; Guigó Serra, Roderic; Zhang, Yan (American Society for Biochemistry and Molecular Biology (ASBMB), 2016)

  The human genome contains 25 genes coding for selenocysteine-containing proteins (selenoproteins). These proteins are involved in a variety of functions, most notably redox homeostasis. Selenoprotein enzymes with known ...
• C/EBPα induces highly efficient macrophage transdifferentiation of B lymphoma and leukemia cell lines and impairs their tumorigenicity

  Rapino, Francesca, 1982-; Robles, Eloy F.; Richter-Larrea, Jose A.; Kallin, Eric M.; Martinez-Climent, Jose A.; Graf, T. (Thomas) (Cell Press, 2013)

  Earlier work demonstrated that the transcription factor C/EBPα can convert immature and mature murine B lineage cells into functional macrophages. Testing >20 human lymphoma and leukemia B cell lines, we found that most ...
• Genetic diversity and population structure of rice varieties cultivated in temperate regions

  Reig-Valiente, Juan L.; Viruel, Juan; Sales, Ester; Marqués, Luis; Terol, Javier; Gut, Marta; Derdak, Sophia; Talón, Manuel; Domingo, Concha (Springer Open, 2016)

  Background. After its domestication, rice cultivation expanded from tropical regions towards northern latitudes with temperate climate in a progressive process to overcome limiting photoperiod and temperature conditions. ...
• Fasting shapes chromatin architecture through an mTOR/RNA Pol I axis

  Al-Refaie, Nada; Padovani, Francesco; Hornung, Johanna; Pudelko, Lorenz; Binando, Francesca; Carmen Fabregat, Andrea del; Zhao, Qiuxia; Towbin, Benjamin D.; Sarinay Cenik, Elif; Stroustrup, Nicholas; Padeken, Jan; Schmoller, Kurt M.; Cabianca, Daphne S. (Nature Research, 2024)

  Chromatin architecture is a fundamental mediator of genome function. Fasting is a major environmental cue across the animal kingdom, yet how it impacts three-dimensional (3D) genome organization is unknown. Here we show ...
• The genetic architecture of protein stability

  Faure, Andre J.; Martí Aranda, Aina; Hidalgo-Carcedo, Cristina; Beltran, Antoni; Schmiedel, Jörn M.; Lehner, Ben, 1978- (Nature Research, 2024)

  There are more ways to synthesize a 100-amino acid (aa) protein (20100) than there are atoms in the universe. Only a very small fraction of such a vast sequence space can ever be experimentally or computationally surveyed. ...
• High-resolution kinetics and cellular determinants of SARS-CoV-2 antibody response over two years after COVID-19 vaccination

  Rubio, Rocío; Macià, Dídac; Barrios, Diana; Vidal, Marta; Jiménez, Alfons; Molinos-Albert, Luis M.; Díaz, Natalia; Canyelles, Mar; Lara Escandell, Maria; Planchais, Cyril; Santamaria, Pere; Carolis, Carlo; Izquierdo, Luis; Aguilar, Ruth; Moncunill, Gemma; Dobaño, Carlota (Elsevier, 2024)

  Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) studies usually rely on cross-sectional data of large cohorts but limited repeated samples, overlooking significant inter-individual antibody kinetic differences. ...
• Surface conversion of the dynamics of bacteria escaping chemorepellents

  Braham, Asma; Lemelle, Laurence; Ducasse, Romain; Toukabri, Houyem; Mottin, Eleonore; Fabrèges, Benoit; Calvez, Vincent; Place, Christophe (Springer, 2024)

  Flagellar swimming hydrodynamics confers a recognized advantage for attachment on solid surfaces. Whether this motility further enables the following environmental cues was experimentally explored. Motile E. coli (OD ~ ...
• Reactive oxygen species activate the Drosophila TNF receptor Wengen for damage-induced regeneration

  Esteban-Collado, José; Fernández Mañas, Mar; Fernández-Moreno, Manuel; Maeso, Ignacio; Corominas Guiu, Montserrat; Serras Rigalt, Florenci (EMBO Press, 2024)

  Tumor necrosis factor receptors (TNFRs) control pleiotropic pro-inflammatory functions that range from apoptosis to cell survival. The ability to trigger a particular function will depend on the upstream cues, association ...

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