Article
Biochemical Research Methods
Eva Maria Trinidad, Enrique Vidal, Esther Coronado, Anna Esteve-Codina, Victoria Castel, Adela Canete, Marta Gut, Simon Heath, Jaime Font de Mora
Summary: Analysis of tumor cell-free DNA methylome has great potential for cancer subtyping and prognosis, but is often hindered by low quality and yield of cfDNA. This study demonstrates the feasibility of using very low-input cfDNA for whole-methylome and copy-number profiling studies through enzymatic conversion of unmethylated cysteines. The findings support the use of liquid biopsy and EM-seq to assess cfDNA methylation in cancer patients, particularly in rare cancers with limited liquid biopsy volume due to ethical regulations in pediatric patients.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Plant Sciences
Jose A. Abelenda, Noemi Trabanco, Ivan del Olmo, Jenifer Pozas, Maria del Mar Martin-Trillo, Jessica Gomez-Garrido, Anna Esteve-Codina, Monica Pernas, Jose A. Jarillo, Manuel Pineiro
Summary: The flowering response of oilseed rape (OSR) to high ambient temperature is diverse, with one variety exhibiting opposite behavior. BnaFTA2 plays a key role in temperature-dependent flowering initiation in OSR, and additional molecular mechanisms are involved in its repression under high ambient temperature. The presence of H3K4me3 in BnaFTA2 is reduced at high temperature, suggesting a role for this active chromatin marker in the flowering response of OSR to warming.
PLANT CELL AND ENVIRONMENT
(2023)
Article
Microbiology
Asier Ramos-Pardo, Rocio Castro-Alvarez, Guillermo Quindos, Elena Eraso, Elena Sevillano, Vladimir R. Kaberdin
Summary: This study aimed to investigate the impact of external pH, substrate nature, and strain origin on the production of protease, lipase, and hemolysin in Candida albicans. The pH value had a significant effect on the detection of protease and lipase, while the activity of hemolysin was not affected by pH. Additionally, the anatomical origin of the isolates was found to be associated with the detected activities.
Article
Biotechnology & Applied Microbiology
Xavier Coves, Marc Bravo, Pol Huedo, Oscar Conchillo-Sole, Andromeda-Celeste Gomez, Anna Esteve-Codina, Marc Dabad, Marta Gut, Xavier Daura, Daniel Yero, Isidre Gibert
Summary: The quorum sensing system in Stenotrophomonas maltophilia controls various virulence-related phenotypes and may serve as a potential target for controlling pathogenicity mechanisms.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2023)
Article
Biology
David G. Valcarce, Marta F. Riesco, Leyre Cuesta-Martin, Anna Esteve-Codina, Juan Manuel Martinez-Vazquez, Vanesa Robles
Summary: Chronic stress has negative effects on behavior, reproductive parameters, and progeny in zebrafish. It induces anxiety-like behavior, overexpression of endoplasmic reticulum stress-related genes in the brain, and compromised sperm motility. Additionally, chronic stress alters the molecular status and development of progeny.
Article
Developmental Biology
Marina Ramiro-Pareta, Claudia Muller-Sanchez, Rosa Portella-Fortuny, Carolina Soler-Botija, Alejo Torres-Cano, Anna Esteve-Codina, Antoni Bayes-Genis, Manuel Reina, Francesc X. Soriano, Eloi Montanez, Ofelia M. Martinez-Estrada
Summary: Wt1 is crucial for epicardium development and is also expressed in coronary endothelial cells. Deletion of Wt1 in coronary endothelial cells disrupted the development of coronary blood vessels and myocardium. The deletion of Wt1 had a major impact on the molecular signature of coronary endothelial cells and affected the expression of genes involved in the proliferation, migration, and differentiation of these cells.
Article
Neurosciences
Erin A. Greguske, Alberto F. Maroto, Mireia Borrajo, Aida Palou, Marta Gut, Anna Esteve-Codina, Alejandro Barrallo-Gimeno, Jordi Llorens
Summary: The vestibular ganglion contains primary sensory neurons that respond to stress or loss of hair cells, and their survival and functional competence are important for repairing or regenerating the hair cells. In this study, exposure to ototoxicant IDPN caused reversible detachment and synaptic uncoupling between hair cells and ganglion neurons. Gene expression analysis revealed downregulation of synapse-related terms and genes involved in neuronal activity and growth. Decreased expression of BDNF mRNA and other identified genes further supported the hypothesis that decreased input from hair cells triggers these expression changes.
NEUROBIOLOGY OF DISEASE
(2023)
Article
Multidisciplinary Sciences
Yron Joseph Yabut Manaig, Lourdes Criado-Mesas, Anna Esteve-Codina, Emilio Marmol-Sanchez, Anna Castello, Armand Sanchez, Josep M. M. Folch
Summary: The n-6/n-3 PUFA ratio in pig skeletal muscle affects the transcriptome expression related to muscle growth and immune pathways, as well as adipogenesis and immune response. Predicted miRNA-to-mRNA regulatory networks are involved in lipid metabolism, obesity, muscle growth, and protein degradation. The n-6/n-3 PUFA ratio differences revealed genes, miRNAs, and enriched pathways involved in lipid metabolism, cell proliferation, and inflammation.
Article
Plant Sciences
Irene Cobo-Simon, Jessica Gomez-Garrido, Anna Esteve-Codina, Marc Dabad, Tyler Alioto, Julin N. Maloof, Belen Mendez-Cea, Jose Ignacio Seco, Juan Carlos Linares, Francisco Javier Gallego
Summary: This study investigated the drought response mechanisms and genomic basis of the threatened conifer Cedrus atlantica. The results showed that C. atlantica adapts to drought stress by regulating stomatal closure and photosynthetic activity. However, drought-sensitive individuals failed in metabolism and photosynthesis regulation, as well as in limiting the production of secondary metabolites. Furthermore, genomic differences were found between drought-resilient and sensitive seedlings and between different locations, mainly related to transposable elements.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Geriatrics & Gerontology
Judith Canto-Santos, Laura Valls-Roca, Ester Tobias, Francesc Josep Garcia-Garcia, Mariona Guitart-Mampel, Anna Esteve-Codina, Beatriz Martin-Mur, Mercedes Casado, Rafael Artuch, Estel Solsona-Vilarrasa, Jose Carlos Fernandez-Checa, Carmen Garcia-Ruiz, Carles Rentero, Carlos Enrich, Pedro J. J. Moreno-Lozano, Jose Cesar Milisenda, Francesc Cardellach, Josep M. M. Grau-Junyent, Gloria Garrabou
Summary: In this study, molecular disturbances were found in fibroblast samples from IBM patients, including abnormal gene expression related to inflammation, mitochondria, and cell cycle regulation, as well as functional changes in inflammatory, autophagy, mitochondrial, and metabolic processes. These findings contribute to a better understanding of the pathogenesis of IBM and provide insights for the identification of new biomarkers and therapeutic strategies.
JOURNAL OF CACHEXIA SARCOPENIA AND MUSCLE
(2023)
Article
Endocrinology & Metabolism
Sebastian Zagmutt, Paula Mera, Ismael Gonzalez-Garcia, Kevin Ibeas, Maria del Mar Romero, Arnaud Obri, Beatriz Martin, Anna Esteve-Codina, M. Carmen Soler-Vazquez, Marianela Bastias-Perez, Laia Canes, Elisabeth Auge, Carme Pelegri, Jordi Vilaplana, Xavier Ariza, Jordi Garcia, Jose Martinez-Gonzalez, Nuria Casals, Miguel Lopez, Richard Palmiter, Elisenda Sanz, Albert Quintana, Laura Herrero, Dolors Serra
Summary: Fatty acid metabolism and CPT1A in AgRP neurons play a key role in the maintenance of whole-body fluid and energy balance. This study reveals marked sex differences in fatty acid metabolism and CPT1A expression in AgRP neurons.
BIOLOGY OF SEX DIFFERENCES
(2023)
Article
Immunology
Angela Quintana, Enrique Javier Arenas, Cristina Bernado, Jose Fernandez Navarro, Jonatan Gonzalez, Anna Esteve-Codina, Teresa Moline, Merce Marti, Giuseppe Curigliano, Peter Schmid, Vicente Peg, Joaquin Arribas, Javier Cortes
Summary: The heterogeneity of immune infiltration in breast cancer is an important research area. This study found that the heterogeneity of TILs is related to the presence of immune infiltration, rather than patient characteristics.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Microbiology
Oleg N. Murashko, Kun-Hai Yeh, Chen-Hsin Albert Yu, Vladimir R. Kaberdin, Sue Lin-Chao
Summary: This study demonstrates that fluoride can impact gene expression posttranscriptionally by slowing down RNA degradation, thereby enhancing RNA stability and steady-state mRNA levels in E. coli.
MICROBIOLOGY SPECTRUM
(2023)
Article
Biology
Mie Kobayashi-Ishihara, Katarina Frazao Smutna, Florencia E. Alonso, Jordi Argilaguet, Anna Esteve-Codina, Kerstin Geiger, Meritxell Genesca, Judith Grau-Exposito, Clara Duran-Castells, Selina Rogenmoser, Rene Boettcher, Jennifer Jungfleisch, Baldomero Oliva, Javier P. Martinez, Manqing Li, Michael David, Makoto Yamagishi, Marta Ruiz-Riol, Christian Brander, Yasuko Tsunetsugu-Yokota, Maria J. Buzon, Juana Diez, Andreas Meyerhans
Summary: In cell lines and HIV-1 patient PBMCs, the Schlafen 12 protein (SLFN12) is shown to be an HIV-1 restriction factor that inhibits HIV-1 replication and virus reactivation. SLFN12 establishes a post-transcriptional block in HIV-1-infected cells, dependent on the HIV-1 codon usage and its RNase active sites. SLFN12 expression in PBMCs of HIV-1-infected individuals correlates with viral loads.
COMMUNICATIONS BIOLOGY
(2023)
Article
Biochemical Research Methods
Eva Maria Trinidad, Enrique Vidal, Esther Coronado, Anna Esteve-Codina, Victoria Castel, Adela Cafiete, Marta Gut, Simon Heath, Jaime Font De Mora
Summary: Enzymatic methyl-seq (EM-seq) can be used for low-input liquid biopsy to preserve DNA integrity, allowing for comprehensive methylome and copy-number profiling analysis of tumor cell-free DNA (cfDNA). We developed a model for accurate prediction of genomic subtyping and prognosis. Comparison with in situ cohorts using different techniques and sample origins demonstrated the comparability of cfDNA methylation information. Our findings support the use of EM-seq for assessing the methylome of cancer patients, particularly those with rare cancers like neuroblastomas where liquid biopsy volume is limited by ethical regulations in pediatric patients.
BRIEFINGS IN BIOINFORMATICS
(2023)