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Browsing Recerca: articles, congressos, llibres by Subject "Saccharomyces cerevisiae"

Browsing Recerca: articles, congressos, llibres by Subject "Saccharomyces cerevisiae"

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  • A high-throughput approach to profile RNA structure
    Delli Ponti, Riccardo, 1987-; Marti, Stefanie; Armaos, Alexandros, 1989-; Tartaglia, Gian Gaetano (Oxford University Press, 2017)
    Here we introduce the Computational Recognition of Secondary Structure (CROSS) method to calculate the structural profile of an RNA sequence (single- or double-stranded state) at single-nucleotide resolution and without ...
  • A RAGE based strategy for the genome engineering of the human respiratory pathogen mycoplasma pneumoniae
    García Morales, Luis; Ruiz, Estelle; Gourgues, Géraldine; Rideau, Fabien; Piñero-Lambea, Carlos; Lluch-Senar, Maria 1982-; Blanchard, Alain; Lartigue, Carole (American Chemical Society (ACS), 2020)
    Genome engineering of microorganisms has become a standard in microbial biotechnologies. Several efficient tools are available for the genetic manipulation of model bacteria such as Escherichia coli and Bacillus subtilis, ...
  • A systematic screen identifies Saf5 as a link between splicing and transcription in fission yeast
    Borao Arriazu, Sonia, 1993-; Vega, Montserrat; Boronat i Llop, Susanna, 1965-; Hidalgo Hernando, Elena; Hümmer, Stefan; Ayté del Olmo, José (Public Library of Science (PLoS), 2024)
    Splicing is an important step of gene expression regulation in eukaryotes, as there are many mRNA precursors that can be alternatively spliced in different tissues, at different cell cycle phases or under different external ...
  • Abf1 and other general regulatory factors control ribosome biogenesis gene expression in budding yeast
    Bosio, Maria Cristina; Fermi, Beatrice; Spagnoli, Gloria; Levati, Elisabetta; Rubbi, Liudmilla; Ferrari, Roberto; Pellegrini, Matteo; Dieci, Giorgio (Oxford University Press, 2017)
    Ribosome biogenesis in Saccharomyces cerevisiae involves a regulon of >200 genes (Ribi genes) coordinately regulated in response to nutrient availability and cellular growth rate. Two cis-acting elements called PAC and ...
  • Adaptation of S. cerevisiae to fermented food environments reveals remarkable genome plasticity and the footprints of domestication
    Legras, Jean-Luc; Galeote, Virginie; Bigey, Frédéric; Camarasa, Carole; Marsit, Souhir; Nidelet, Thibault; Sanchez, Isabelle; Couloux, Arnaud; Guy, Julie; Franco-Duarte, Ricardo; Marcet Houben, Marina; Gabaldón Estevan, Juan Antonio, 1973-; Schuller, Dorit; Sampaio, José Paulo; Dequin, Sylvie (Oxford University Press, 2018)
    The budding yeast Saccharomyces cerevisiae can be found in the wild and is also frequently associated with human activities. Despite recent insights into the phylogeny of this species, much is still unknown about how ...
  • An experimental assay of the interactions of amino acids from orthologous sequences shaping a complex fitness landscape
    Pokusaeva, Victoria O.; Usmanova, Dinara R.; Putintseva, Ekaterina V.; Espinar, Lorena; Sarkisyan, Karen S.; Mishin, Alexander S.; Bogatyreva, Natalya S.; Ivankov, Dmitry N.; Akopyan, Arseniy V.; Avvakumov, Sergey Ya; Povolotskaya, Inna, 1986-; Filion, Guillaume; Carey, Lucas, 1980-; Kondrashov, Fyodor A., 1979- (Public Library of Science (PLoS), 2019)
    Characterizing the fitness landscape, a representation of fitness for a large set of genotypes, is key to understanding how genetic information is interpreted to create functional organisms. Here we determined the ...
  • Cell cycle transcriptomics of Capsaspora provides insights into the evolution of cyclin-CDK machinery
    Pérez-Posada, Alberto, 1993-; Dudin, Omaya; Ocaña Pallarès, Eduard, 1991-; Ruiz Trillo, Iñaki; Ondracka, Andrej (Public Library of Science (PLoS), 2020)
    Progression through the cell cycle in eukaryotes is regulated on multiple levels. The main driver of the cell cycle progression is the periodic activity of cyclin-dependent kinase (CDK) complexes. In parallel, transcription ...
  • Comparison of Xrn1 and Rat1 5' → 3' exoribonucleases in budding yeast supports the specific role of Xrn1 in cotranslational mRNA decay
    Pérez Ortín, José E.; Jordán Pla, Antonio; Zang, Yujie; Moreno García, Jorge; Bassot, Claudio; Barba Aliaga, Marina; Campos Mata, Leire de, 1991-; Choder, Mordechai; Díez Antón, Juana, 1962-; Piazza, Ilaria; Pelechano, Vicent; García Martínez, José (Wiley, 2024)
    The yeast Saccharomyces cerevisiae and most eukaryotes carry two 5' → 3' exoribonuclease paralogs. In yeast, they are called Xrn1, which shuttles between the nucleus and the cytoplasm, and executes major cytoplasmic messenger ...
  • CReasPy-Cloning: a method for simultaneous cloning and engineering of megabase-sized genomes in yeast using the CRISPR-Cas9 system.
    Ruiz, Estelle; Talenton, Vincent; Dubrana, Marie-Pierre; Guesdon, Gabrielle; Lluch-Senar, Maria 1982-; Salin, Franck; Sirand-Pugnet, Pascal; Arfi, Yonathan; Lartigue, Carole (American Chemical Society (ACS), 2019)
    Over the past decade, a new strategy was developed to bypass the difficulties to genetically engineer some microbial species by transferring (or "cloning") their genome into another organism that is amenable to efficient ...
  • Evolution of the SH3 domain specificity landscape in yeasts
    Verschueren, Erik; Spiess, Matthias; Gkourtsa, Areti; Avula, Teja; Landgraf, Christiane; Tapia Mancilla, Victor; Huber, Aline; Volkmer, Rudolf; Winsor, Barbara; Serrano Pubull, Luis, 1982-; Hochstenbach, Frans; Distel, Ben (Public Library of Science (PLoS), 2015)
    To explore the conservation of Src homology 3 (SH3) domain-mediated networks in evolution, we compared the specificity landscape of these domains among four yeast species, Saccharomyces cerevisiae, Ashbya gossypii, Candida ...
  • Improvement of biochemical methods of polyP quantification
    Bru, Samuel; Jiménez, Javier; Canadell, David; Ariño, Joaquín; Clotet Erra, Josep (Shared Science Publishers, 2017)
    Polyphosphate (polyP) is an abundant and physiologically important biomolecule for virtually any living cell. Therefore, determination of changes in cellular content of polyP is crucial for its functional characterization. ...
  • A mathematical model of rna3 recruitment in the replication cycle of brome mosaic virus
    Huffman, Tori; Link, Kathryn; Nardini, John; Poag, Laura; Flores, Kevin; Banks, H. Thomas; Blasco Moreno, Bernat, 1986-; Jungfleisch, Jennifer, 1986-; Díez Antón, Juana, 1962- (Academic Publications, 2014)
    Positive-strand RNA viruses, such as the brome mosaic virus (BMV) and hepatitis C virus, utilize a replication cycle which involves the recruitment of RNA genomes from the cellular translation machinery to the viral ...
  • Metabolite profiling studies in Saccharomyces cerevisiae: an assisting tool to prioritize host targets for antiviral drug screening.
    Schneider, Konstantin; Krömer, Jens Olaf; Wittmann, Christoph; Alves-Rodrigues, Isabel; Meyerhans, Andreas; Díez Antón, Juana, 1962-; Heinzle, Elmar (BioMed Central, 2009)
    Background The cellular proteins Pat1p, Lsm1p, and Dhh1p are required for the replication of some positive-strand viruses and therefore are potential targets for new antiviral drugs. To prioritize host targets for antiviral ...
  • Nonlinear fitness consequences of variation in expression level of a eukaryotic gene
    Rest, Joshua S.; Morales, Christopher M.; Waldron, John B.; Opulente, Dana A.; Fisher, Julius; Moon, Seungjae; Bullaughey, Kevin; Carey, Lucas, 1980-; Dedousis, Demitri (University of Chicago Press, 2013)
    Levels of gene expression show considerable variation in eukaryotes, but no fine-scale maps have been made of the fitness consequences of such variation in controlled genetic backgrounds and environments. To address this, ...
  • RNA secondary structure mediates alternative 3'ss selection in Saccharomyces cerevisiae
    Plass Pórtulas, Mireya, 1982-; Codony Servat, Carles; Ferreira, Pedro G.; Vilardell, Josep; Eyras Jiménez, Eduardo (Cold Spring Harbor Laboratory Press (CSHL Press) -- RNA, 2012)
    Alternative splicing is the mechanism by which different combinations of exons in the pre-mRNA give rise to distinct mature mRNAs. This process is mediated by splicing factors that bind the pre-mRNA and affect the recognition ...
  • Structural constraints revealed in consistent nucleosome positions in the genome of S. cerevisiae
    Nikolaou, Christoforos; Althammer, Sonja Daniela; Beato, Miguel; Guigó Serra, Roderic (BioMed Central, 2010)
    BACKGROUND: Recent advances in the field of high-throughput genomics have rendered possible the performance of genome-scale studies to define the nucleosomal landscapes of eukaryote genomes. Such analyses are aimed towards ...
  • The HOG pathway dictates the short-term translational response after hyperosmotic shock
    Warringer, Jonas; Hult, Malin; Regot Rodríguez de Mier, Sergi; Posas Garriga, Francesc; Sunnerhagen, Per (American Society for Cell Biology, 2010)
    Cellular responses to environmental changes occur on different levels. We investigated the translational response of yeast cells after mild hyperosmotic shock by isolating mRNA associated with multiple ribosomes (polysomes) ...
  • Topoisomerase II regulates yeast genes with singular chromatin architectures
    Nikolaou, Christoforos; Bermúdez, Ignacio; Manichanh, Chaysavanh; García Martínez, José; Guigó Serra, Roderic; Pérez Ortín, José E.; Roca, Joaquim (Oxford University Press, 2013)
    Eukaryotic topoisomerase II (topo II) is the essential decatenase of newly replicated chromosomes and the main relaxase of nucleosomal DNA. Apart from these general tasks, topo II participates in more specialized functions. ...
  • Yeast Cip1 is activated by environmental stress to inhibit Cdk1–G1 cyclins via Mcm1 and Msn2/4
    Chang, Ya-Lan; Tseng, Shun-Fu; Huang, Yu-Ching; Shen, Zih-Jie; Hsu, Pang-Hung; Hsieh, Meng-Hsun; Yang, Chia-Wei; Tognetti, Silvia; Canal de Torres, Berta, 1988-; Subirana, Laia; Wang, Chien-Wei; Chen, Hsiao-Tan; Lin, Chi-Ying; Posas Garriga, Francesc; Teng, Shu-Chun (Nature Publishing Group, 2017)
    Upon environmental changes, proliferating cells delay cell cycle to prevent further damage accumulation. Yeast Cip1 is a Cdk1 and Cln2-associated protein. However, the function and regulation of Cip1 are still poorly ...

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