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11 p, 4.1 MB |
The evolution of hematopoietic cells under cancer therapy
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Pich, Oriol (Institut de Recerca Biomèdica) ;
Cortes-Bullich, A. (Institut d'Investigació Biomèdica Sant Pau) ;
Muiños, Ferran (Institut de Recerca Biomèdica) ;
Pratcorona, Marta (Institut d'Investigació Biomèdica Sant Pau) ;
Gonzalez-Perez, A. (Universitat Pompeu Fabra) ;
Lopez-Bigas, N. (Institució Catalana de Recerca i Estudis Avançats)
Chemotherapies may increase mutagenesis of healthy cells and change the selective pressures in tissues, thus influencing their evolution. However, their contributions to the mutation burden and clonal expansions of healthy somatic tissues are not clear. [...]
2021 -  10.1038/s41467-021-24858-3
Nature communications, Vol. 12 Núm. 1 (january 2021) , p. 4803
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12 p, 3.8 MB |
Modular Evolution and Population Variability of Oikopleura dioica Metallothioneins
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Calatayud, Sara (Universitat de Barcelona. Departament de Genètica, Microbiologia i Estadística) ;
García-Risco, Mario (Universitat Autònoma de Barcelona. Departament de Química) ;
Capdevila Vidal, Mercè (Universitat Autònoma de Barcelona. Departament de Química) ;
Cañestro, Cristian (Universitat de Barcelona. Departament de Genètica, Microbiologia i Estadística) ;
Palacios Bonilla, Òscar (Universitat Autònoma de Barcelona. Departament de Química) ;
Albalat, Ricard (Universitat de Barcelona. Departament de Genètica, Microbiologia i Estadística)
Chordate Oikopleura dioica probably is the fastest evolving metazoan reported so far, and thereby, a suitable system in which to explore the limits of evolutionary processes. For this reason, and in order to gain new insights on the evolution of protein modularity, we have investigated the organization, function and evolution of multi-modular metallothionein (MT) proteins in O. [...]
2021 - 10.3389/fcell.2021.702688
Frontiers in Cell and Developmental Biology, Vol. 9 (July 2021) , art. 702688
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14 p, 4.5 MB |
Lineage-level divergence of copepod glycerol transporters and the emergence of isoform-specific trafficking regulation
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Catalán García, Marc (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Chauvigné, François (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Stavang, Jon Anders (University of Bergen. Bergen High Technology Centre Department of Biological Sciences) ;
Nilsen, Frank (University of Bergen. Bergen High Technology Centre Department of Biological Sciences) ;
Cerdà, Joan (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Finn, Roderick Nigel (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí")
Transmembrane conductance of small uncharged solutes such as glycerol typically occurs through aquaglyceroporins (Glps), which are commonly encoded by multiple genes in metazoan organisms. To date, however, little is known concerning the evolution of Glps in Crustacea or what forces might underly such apparent gene redundancy. [...]
2021 - 10.1038/s42003-021-01921-9
Communications Biology, Vol. 4 (May 2021) , art. 643
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11 p, 1.4 MB |
Computational prediction of protein aggregation : advances in proteomics, conformation-specific algorithms and biotechnological applications
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Santos, Jaime (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Pujols Pujol, Jordi (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Pallarès i Goitiz, Irantzu (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Iglesias, Valentin (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Ventura, Salvador (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí")
Protein aggregation is a widespread phenomenon that stems from the establishment of non-native intermolecular contacts resulting in protein precipitation. Despite its deleterious impact on fitness, protein aggregation is a generic property of polypeptide chains, indissociable from protein structure and function. [...]
2020 - 10.1016/j.csbj.2020.05.026
Computational and Structural Biotechnology Journal, Vol. 18 (June 2020) , p. 1403-1413
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13 p, 561.5 KB |
Gene fusions derived by transcriptional readthrough are driven by segmental duplication in human
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McCartney, Ann M. (Dublin City University. Bioinformatics and Molecular Evolution Group) ;
Hyland, Edel M. (Queens University Belfast. Institute for Global Food Security) ;
Cormican, Paul (Animal and Grassland Research and Innovation Centre (Irlanda)) ;
Moran, Raymond J. (Dublin City University. Bioinformatics and Molecular Evolution Group) ;
Webb, Andrew E. (Dublin City University. Bioinformatics and Molecular Evolution Group) ;
Lee, Kate D. (Massey University (New Zealand)) ;
Hernandez Rodriguez, Jessica (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Prado-Martinez, Javier (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Creevey, Christopher J. (Aberystwyth University. Institute of Biological, Environmental and Rural Sciences) ;
Aspden, Julie L. (University of Leeds. School of Molecular and Cellular Biology) ;
McInerney, James O. (University of Nottingham. School of Life Sciences) ;
Marques-Bonet, Tomas 1975- (Institut Català de Paleontologia Miquel Crusafont) ;
O'Connell, Mary J. (University of Nottingham. School of Life Sciences)
Gene fusion occurs when two or more individual genes with independent open reading frames becoming juxtaposed under the same open reading frame creating a new fused gene. A small number of gene fusions described in detail have been associated with novel functions, for example, the hominid-specific PIPSL gene, TNFSF12, and the TWE-PRIL gene family. [...]
2019 - 10.1093/gbe/evz163
Genome biology and evolution, Vol. 11, Issue 9 (September 2019) , p. 2678-2690
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16 p, 3.2 MB |
Bioinformatics and moonlighting proteins
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Hernández, Sergio (Universitat Autònoma de Barcelona. Departament de Bioquímica i de Biologia Molecular) ;
Franco Serrano, Luis (Universitat de Barcelona. Departament de Bioquímica i Biologia Molecular) ;
Calvo, Alejandra (Universidad de la República Regional Norte-Salto. Laboratorio de Inmunología) ;
Ferragut, Gabriela (Universidad de la República Regional Norte-Salto. Laboratorio de Inmunología) ;
Hermoso, Antoni (Universitat de Barcelona. Departament de Bioquímica i Biologia Molecular) ;
Amela Abellan, Isaac (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Gómez, Antonio (Institut d'Investigació Biomèdica de Bellvitge) ;
Querol Murillo, Enrique (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Cedano Rodríguez, Juan Antonio (Universidad de la República Regional Norte-Salto. Laboratorio de Inmunología)
Multitasking or moonlighting is the capability of some proteins to execute two or more biochemical functions. Usually, moonlighting proteins are experimentally revealed by serendipity. For this reason, it would be helpful that Bioinformatics could predict this multifunctionality, especially because of the large amounts of sequences from genome projects. [...]
2015 - 10.3389/fbioe.2015.00090
Frontiers in Bioengineering and Biotechnology, Vol. 3 (June 2015) , art. 90
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11 p, 3.1 MB |
GPCRtm : An amino acid substitution matrix for the transmembrane region of class A G Protein-Coupled Receptors
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Rios Azuara, Santiago (Universitat Autònoma de Barcelona. Laboratori de Medicina Computacional) ;
Fernandez, Marta F. (Universitat Autònoma de Barcelona. Laboratori de Medicina Computacional) ;
Caltabiano, Gianluigi 1978- (Universitat Autònoma de Barcelona. Laboratori de Medicina Computacional) ;
Campillo Grau, María Mercedes (Universitat Autònoma de Barcelona. Laboratori de Medicina Computacional) ;
Pardo Carrasco, Leonardo (Universitat Autònoma de Barcelona. Laboratori de Medicina Computacional) ;
Gonzalez, Angel (Universitat Autònoma de Barcelona. Laboratori de Medicina Computacional)
Protein sequence alignments and database search methods use standard scoring matrices calculated from amino acid substitution frequencies in general sets of proteins. These general-purpose matrices are not optimal to align accurately sequences with marked compositional biases, such as hydrophobic transmembrane regions found in membrane proteins. [...]
2015 - 10.1186/s12859-015-0639-4
BMC bioinformatics, Vol. 16 (July 2015) , art. 2016
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