%0 Journal Article %J Front Genet %D 2023 %T Editorial: Critical assessment of massive data analysis (CAMDA) annual conference 2021. %A Łabaj, Paweł P %A Dopazo, Joaquin %A Xiao, Wenzhong %A Kreil, David P %B Front Genet %V 14 %P 1154398 %8 2023 %G eng %R 10.3389/fgene.2023.1154398 %0 Journal Article %J Epidemiol Infect %D 2023 %T Evaluation of a combined detection of SARS-CoV-2 and its variants using real-time allele-specific PCR strategy: an advantage for clinical practice. %A Chaves-Blanco, Lucía %A de Salazar, Adolfo %A Fuentes, Ana %A Viñuela, Laura %A Perez-Florido, Javier %A Dopazo, Joaquin %A García, Federico %K Alleles %K COVID-19 %K COVID-19 Testing %K Humans %K Real-Time Polymerase Chain Reaction %K SARS-CoV-2 %K Sensitivity and Specificity %X

This study aimed to assess the ability of a real-time reverse transcription polymerase chain reaction (RT-PCR) with multiple targets to detect SARS-CoV-2 and its variants in a single test. Nasopharyngeal specimens were collected from patients in Granada, Spain, between January 2021 and December 2022. Five allele-specific RT-PCR kits were used sequentially, with each kit designed to detect a predominant variant at the time. When the Alpha variant was dominant, the kit included the HV69/70 deletion, E and N genes. When Delta replaced Alpha, the kit incorporated the L452R mutation in addition to E and N genes. When Omicron became dominant, L452R was replaced with the N679K mutation. Before incorporating each variant kit, a comparative analysis was carried out with SARS-CoV-2 whole genome sequencing (WGS). The results demonstrated that RT-PCR with multiple targets can provide rapid and effective detection of SARS-CoV-2 and its variants in a single test. A very high degree of agreement (96.2%) was obtained between the comparison of RT-PCR and WGS. Allele-specific RT-PCR assays make it easier to implement epidemiological surveillance systems for effective public health decision making.

%B Epidemiol Infect %V 151 %P e201 %8 2023 Nov 24 %G eng %R 10.1017/S095026882300184X %0 Journal Article %J Med Clin (Barc) %D 2023 %T Evidence of the association between increased use of direct oral anticoagulants and a reduction in the rate of atrial fibrillation-related stroke and major bleeding at the population level (2012-2019). %A Loucera, Carlos %A Carmona, Rosario %A Bostelmann, Gerrit %A Muñoyerro-Muñiz, Dolores %A Villegas, Román %A Gonzalez-Manzanares, Rafael %A Dopazo, Joaquin %A Anguita, Manuel %X

BACKGROUND: The introduction of direct-acting oral anticoagulants (DOACs) has shown to decrease atrial fibrillation (AF)-related stroke and bleeding rates in clinical studies, but there is no certain evidence about their effects at the population level. Our aim was to assess changes in AF-related stroke and major bleeding rates between 2012 and 2019 in Andalusia (Spain), and the association between DOACs use and events rates at the population level.

METHODS: All patients with an AF diagnosis from 2012 to 2019 were identified using the Andalusian Health Population Base, that provides clinical information on all Andalusian people. Annual ischemic and hemorrhagic stroke, major bleeding rates, and used antithrombotic treatments were determined. Marginal hazard ratios (HR) were calculated for each treatment.

RESULTS: A total of 95,085 patients with an AF diagnosis were identified. Mean age was 76.1±10.2 years (49.7% women). An increase in the use of DOACs was observed throughout the study period in both males and females (p<0.001). The annual rate of ischemic stroke decreased by one third, while that of hemorrhagic stroke and major bleeding decreased 2-3-fold from 2012 to 2019. Marginal HR was lower than 0.50 for DOACs compared to VKA for all ischemic or hemorrhagic events.

CONCLUSIONS: In this contemporary population-based study using clinical and administrative databases in Andalusia, a significant reduction in the incidence of AF-related ischemic and hemorrhagic stroke and major bleeding was observed between 2012 and 2019. The increased use of DOACs seems to be associated with this reduction.

%B Med Clin (Barc) %8 2023 Nov 20 %G eng %R 10.1016/j.medcli.2023.10.008 %0 Journal Article %J Int J Mol Sci %D 2022 %T Endoglin and MMP14 Contribute to Ewing Sarcoma Spreading by Modulation of Cell-Matrix Interactions. %A Puerto-Camacho, Pilar %A Diaz-Martin, Juan %A Olmedo-Pelayo, Joaquín %A Bolado-Carrancio, Alfonso %A Salguero-Aranda, Carmen %A Jordán-Pérez, Carmen %A Esteban-Medina, Marina %A Alamo-Alvarez, Inmaculada %A Delgado-Bellido, Daniel %A Lobo-Selma, Laura %A Dopazo, Joaquin %A Sastre, Ana %A Alonso, Javier %A Grünewald, Thomas G P %A Bernabeu, Carmelo %A Byron, Adam %A Brunton, Valerie G %A Amaral, Ana Teresa %A de Alava, Enrique %K Bone Neoplasms %K Endoglin %K Humans %K Matrix Metalloproteinase 14 %K Proteomics %K Receptors, Growth Factor %K Sarcoma, Ewing %K Signal Transduction %X

Endoglin (ENG) is a mesenchymal stem cell (MSC) marker typically expressed by active endothelium. This transmembrane glycoprotein is shed by matrix metalloproteinase 14 (MMP14). Our previous work demonstrated potent preclinical activity of first-in-class anti-ENG antibody-drug conjugates as a nascent strategy to eradicate Ewing sarcoma (ES), a devastating rare bone/soft tissue cancer with a putative MSC origin. We also defined a correlation between ENG and MMP14 expression in ES. Herein, we show that ENG expression is significantly associated with a dismal prognosis in a large cohort of ES patients. Moreover, both ENG/MMP14 are frequently expressed in primary ES tumors and metastasis. To deepen in their functional relevance in ES, we conducted transcriptomic and proteomic profiling of in vitro ES models that unveiled a key role of ENG and MMP14 in cell mechano-transduction. Migration and adhesion assays confirmed that loss of ENG disrupts actin filament assembly and filopodia formation, with a concomitant effect on cell spreading. Furthermore, we observed that ENG regulates cell-matrix interaction through activation of focal adhesion signaling and protein kinase C expression. In turn, loss of MMP14 contributed to a more adhesive phenotype of ES cells by modulating the transcriptional extracellular matrix dynamics. Overall, these results suggest that ENG and MMP14 exert a significant role in mediating correct spreading machinery of ES cells, impacting the aggressiveness of the disease.

%B Int J Mol Sci %V 23 %8 2022 Aug 04 %G eng %N 15 %R 10.3390/ijms23158657 %0 Journal Article %J F1000Res %D 2020 %T The ELIXIR Human Copy Number Variations Community: building bioinformatics infrastructure for research. %A Salgado, David %A Armean, Irina M %A Baudis, Michael %A Beltran, Sergi %A Capella-Gutíerrez, Salvador %A Carvalho-Silva, Denise %A Dominguez Del Angel, Victoria %A Dopazo, Joaquin %A Furlong, Laura I %A Gao, Bo %A Garcia, Leyla %A Gerloff, Dietlind %A Gut, Ivo %A Gyenesei, Attila %A Habermann, Nina %A Hancock, John M %A Hanauer, Marc %A Hovig, Eivind %A Johansson, Lennart F %A Keane, Thomas %A Korbel, Jan %A Lauer, Katharina B %A Laurie, Steve %A Leskošek, Brane %A Lloyd, David %A Marqués-Bonet, Tomás %A Mei, Hailiang %A Monostory, Katalin %A Piñero, Janet %A Poterlowicz, Krzysztof %A Rath, Ana %A Samarakoon, Pubudu %A Sanz, Ferran %A Saunders, Gary %A Sie, Daoud %A Swertz, Morris A %A Tsukanov, Kirill %A Valencia, Alfonso %A Vidak, Marko %A Yenyxe González, Cristina %A Ylstra, Bauke %A Béroud, Christophe %K Computational Biology %K DNA Copy Number Variations %K High-Throughput Nucleotide Sequencing %K Humans %X

Copy number variations (CNVs) are major causative contributors both in the genesis of genetic diseases and human neoplasias. While "High-Throughput" sequencing technologies are increasingly becoming the primary choice for genomic screening analysis, their ability to efficiently detect CNVs is still heterogeneous and remains to be developed. The aim of this white paper is to provide a guiding framework for the future contributions of ELIXIR's recently established with implications beyond human disease diagnostics and population genomics. This white paper is the direct result of a strategy meeting that took place in September 2018 in Hinxton (UK) and involved representatives of 11 ELIXIR Nodes. The meeting led to the definition of priority objectives and tasks, to address a wide range of CNV-related challenges ranging from detection and interpretation to sharing and training. Here, we provide suggestions on how to align these tasks within the ELIXIR Platforms strategy, and on how to frame the activities of this new ELIXIR Community in the international context.

%B F1000Res %V 9 %8 2020 %G eng %1 https://www.ncbi.nlm.nih.gov/pubmed/34367618?dopt=Abstract %& 1229 %R 10.12688/f1000research.24887.1 %0 Journal Article %J BMC Bioinformatics %D 2019 %T Exploring the druggable space around the Fanconi anemia pathway using machine learning and mechanistic models. %A Esteban-Medina, Marina %A Peña-Chilet, Maria %A Loucera, Carlos %A Dopazo, Joaquin %K Databases, Factual %K Fanconi Anemia %K Genomics %K Humans %K Machine Learning %K Phenotype %K Proteins %K Signal Transduction %X

BACKGROUND: In spite of the abundance of genomic data, predictive models that describe phenotypes as a function of gene expression or mutations are difficult to obtain because they are affected by the curse of dimensionality, given the disbalance between samples and candidate genes. And this is especially dramatic in scenarios in which the availability of samples is difficult, such as the case of rare diseases.

RESULTS: The application of multi-output regression machine learning methodologies to predict the potential effect of external proteins over the signaling circuits that trigger Fanconi anemia related cell functionalities, inferred with a mechanistic model, allowed us to detect over 20 potential therapeutic targets.

CONCLUSIONS: The use of artificial intelligence methods for the prediction of potentially causal relationships between proteins of interest and cell activities related with disease-related phenotypes opens promising avenues for the systematic search of new targets in rare diseases.

%B BMC Bioinformatics %V 20 %P 370 %8 2019 Jul 02 %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/31266445?dopt=Abstract %R 10.1186/s12859-019-2969-0 %0 Journal Article %J Nat Commun %D 2018 %T The effects of death and post-mortem cold ischemia on human tissue transcriptomes. %A Ferreira, Pedro G %A Muñoz-Aguirre, Manuel %A Reverter, Ferran %A Sá Godinho, Caio P %A Sousa, Abel %A Amadoz, Alicia %A Sodaei, Reza %A Hidalgo, Marta R %A Pervouchine, Dmitri %A Carbonell-Caballero, José %A Nurtdinov, Ramil %A Breschi, Alessandra %A Amador, Raziel %A Oliveira, Patrícia %A Cubuk, Cankut %A Curado, João %A Aguet, François %A Oliveira, Carla %A Dopazo, Joaquin %A Sammeth, Michael %A Ardlie, Kristin G %A Guigó, Roderic %K Blood %K Cold Ischemia %K Death %K Female %K gene expression %K Humans %K Models, Biological %K Postmortem Changes %K RNA, Messenger %K Stochastic Processes %K Transcriptome %X

Post-mortem tissues samples are a key resource for investigating patterns of gene expression. However, the processes triggered by death and the post-mortem interval (PMI) can significantly alter physiologically normal RNA levels. We investigate the impact of PMI on gene expression using data from multiple tissues of post-mortem donors obtained from the GTEx project. We find that many genes change expression over relatively short PMIs in a tissue-specific manner, but this potentially confounding effect in a biological analysis can be minimized by taking into account appropriate covariates. By comparing ante- and post-mortem blood samples, we identify the cascade of transcriptional events triggered by death of the organism. These events do not appear to simply reflect stochastic variation resulting from mRNA degradation, but active and ongoing regulation of transcription. Finally, we develop a model to predict the time since death from the analysis of the transcriptome of a few readily accessible tissues.

%B Nat Commun %V 9 %P 490 %8 2018 02 13 %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/29440659?dopt=Abstract %R 10.1038/s41467-017-02772-x %0 Journal Article %J Sci Rep %D 2018 %T Evolution of the Quorum network and the mobilome (plasmids and bacteriophages) in clinical strains of Acinetobacter baumannii during a decade. %A López, M %A Rueda, A %A Florido, J P %A Blasco, L %A Fernández-García, L %A Trastoy, R %A Fernández-Cuenca, F %A Martínez-Martínez, L %A Vila, J %A Pascual, A %A Bou, G %A Tomas, M %K Acinetobacter baumannii %K Acinetobacter Infections %K Bacteriophages %K Cross Infection %K Humans %K Plasmids %K Quorum Sensing %K Retrospective Studies %X

In this study, we compared eighteen clinical strains of A. baumannii belonging to the ST-2 clone and isolated from patients in the same intensive care unit (ICU) in 2000 (9 strains referred to collectively as Ab_GEIH-2000) and 2010 (9 strains referred to collectively as Ab_GEIH-2010), during the GEIH-REIPI project (Umbrella BioProject PRJNA422585). We observed two main molecular differences between the Ab_GEIH-2010 and the Ab_GEIH-2000 collections, acquired over the course of the decade long sampling interval and involving the mobilome: i) a plasmid harbouring genes for bla ß-lactamase and abKA/abkB proteins of a toxin-antitoxin system; and ii) two temperate bacteriophages, Ab105-1ϕ (63 proteins) and Ab105-2ϕ (93 proteins), containing important viral defence proteins. Moreover, all Ab_GEIH-2010 strains contained a Quorum functional network of Quorum Sensing (QS) and Quorum Quenching (QQ) mechanisms, including a new QQ enzyme, AidA, which acts as a bacterial defence mechanism against the exogenous 3-oxo-C12-HSL. Interestingly, the infective capacity of the bacteriophages isolated in this study (Ab105-1ϕ and Ab105-2ϕ) was higher in the Ab_GEIH-2010 strains (carrying a functional Quorum network) than in the Ab_GEIH-2000 strains (carrying a deficient Quorum network), in which the bacteriophages showed little or no infectivity. This is the first study about the evolution of the Quorum network and the mobilome in clinical strains of Acinetobacter baumannii during a decade.

%B Sci Rep %V 8 %P 2523 %8 2018 02 06 %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/29410443?dopt=Abstract %R 10.1038/s41598-018-20847-7 %0 Journal Article %J Nature communications %D 2016 %T Extension of human lncRNA transcripts by RACE coupled with long-read high-throughput sequencing (RACE-Seq). %A Lagarde, Julien %A Uszczynska-Ratajczak, Barbara %A Santoyo-López, Javier %A Gonzalez, Jose Manuel %A Tapanari, Electra %A Mudge, Jonathan M %A Steward, Charles A %A Wilming, Laurens %A Tanzer, Andrea %A Howald, Cédric %A Chrast, Jacqueline %A Vela-Boza, Alicia %A Antonio Rueda %A López-Domingo, Francisco J %A Dopazo, Joaquin %A Reymond, Alexandre %A Guigó, Roderic %A Harrow, Jennifer %X Long non-coding RNAs (lncRNAs) constitute a large, yet mostly uncharacterized fraction of the mammalian transcriptome. Such characterization requires a comprehensive, high-quality annotation of their gene structure and boundaries, which is currently lacking. Here we describe RACE-Seq, an experimental workflow designed to address this based on RACE (rapid amplification of cDNA ends) and long-read RNA sequencing. We apply RACE-Seq to 398 human lncRNA genes in seven tissues, leading to the discovery of 2,556 on-target, novel transcripts. About 60% of the targeted loci are extended in either 5’ or 3’, often reaching genomic hallmarks of gene boundaries. Analysis of the novel transcripts suggests that lncRNAs are as long, have as many exons and undergo as much alternative splicing as protein-coding genes, contrary to current assumptions. Overall, we show that RACE-Seq is an effective tool to annotate an organism’s deep transcriptome, and compares favourably to other targeted sequencing techniques. %B Nature communications %V 7 %P 12339 %8 2016 %G eng %U http://www.nature.com/articles/ncomms12339 %R 10.1038/ncomms12339 %0 Journal Article %J Nature Communications %D 2016 %T Extension of human lncRNA transcripts by RACE coupled with long-read high-throughput sequencing (RACE-Seq) %A Lagarde, Julien %A Uszczynska-Ratajczak, Barbara %A Santoyo-López, Javier %A Gonzalez, Jose Manuel %A Tapanari, Electra %A Mudge, Jonathan M. %A Steward, Charles A. %A Wilming, Laurens %A Tanzer, Andrea %A Howald, Cédric %A Chrast, Jacqueline %A Vela-Boza, Alicia %A Rueda, Antonio %A Lopez-Domingo, Francisco J. %A Dopazo, Joaquin %A Reymond, Alexandre %A Guigó, Roderic %A Harrow, Jennifer %B Nature Communications %V 7 %8 Jan-11-2016 %G eng %U http://www.nature.com/articles/ncomms12339http://www.nature.com/articles/ncomms12339.pdfhttp://www.nature.com/articles/ncomms12339.pdfhttp://www.nature.com/articles/ncomms12339 %N 1 %! Nat Commun %R 10.1038/ncomms12339 %0 Journal Article %J Eur J Neurol %D 2015 %T The EGR2 gene is involved in axonal Charcot-Marie-Tooth disease. %A Sevilla, T %A Sivera, R %A Martínez-Rubio, D %A Lupo, V %A Chumillas, M J %A Calpena, E %A Dopazo, J %A Vílchez, J J %A Palau, F %A Espinós, C %K Adult %K Aged %K Aged, 80 and over %K Axons %K Charcot-Marie-Tooth Disease %K Early Growth Response Protein 2 %K Exome %K Female %K Humans %K Male %K Middle Aged %K mutation %K Pedigree %K Phenotype %K Severity of Illness Index %K Young Adult %X

BACKGROUND AND PURPOSE: A three-generation family affected by axonal Charcot-Marie-Tooth disease (CMT) was investigated with the aim of discovering genetic defects and to further characterize the phenotype.

METHODS: The clinical, nerve conduction studies and muscle magnetic resonance images of the patients were reviewed. A whole exome sequencing was performed and the changes were investigated by genetic studies, in silico analysis and luciferase reporter assays.

RESULTS: A novel c.1226G>A change (p.R409Q) in the EGR2 gene was identified. Patients presented with a typical, late-onset axonal CMT phenotype with variable severity that was confirmed in the ancillary tests. The in silico studies showed that the residue R409 is an evolutionary conserved amino acid. The p.R409Q mutation, which is predicted as probably damaging, would alter the conformation of the protein slightly and would cause a decrease of gene expression.

CONCLUSIONS: This is the first report of an EGR2 mutation presenting as an axonal CMT phenotype with variable severity. This study broadens the phenotype of the EGR2-related neuropathies and suggests that the genetic testing of patients suffering from axonal CMT should include the EGR2 gene.

%B Eur J Neurol %V 22 %P 1548-55 %8 2015 Dec %G eng %N 12 %1 https://www.ncbi.nlm.nih.gov/pubmed/26204789?dopt=Abstract %R 10.1111/ene.12782 %0 Journal Article %J Scientific Reports %D 2015 %T Exome sequencing reveals a high genetic heterogeneity on familial Hirschsprung disease %A Luzón-Toro, Berta %A Gui, Hongsheng %A Ruiz-Ferrer, Macarena %A Sze-Man Tang, Clara %A Fernández, Raquel M. %A Sham, Pak-Chung %A Torroglosa, Ana %A Kwong-Hang Tam, Paul %A Espino-Paisán, Laura %A Cherny, Stacey S. %A Bleda, Marta %A Enguix-Riego, María Del Valle %A Dopazo, Joaquin %A Antiňolo, Guillermo %A Garcia-Barceló, Maria-Mercè %A Borrego, Salud %B Scientific Reports %V 5 %8 Jan-12-2015 %G eng %U http://www.nature.com/articles/srep16473http://www.nature.com/articles/srep16473.pdfhttp://www.nature.com/articles/srep16473.pdfhttp://www.nature.com/articles/srep16473 %N 1 %! Sci Rep %R 10.1038/srep16473 %0 Journal Article %J Scientific reports %D 2015 %T Exome sequencing reveals a high genetic heterogeneity on familial Hirschsprung disease. %A Luzón-Toro, Berta %A Gui, Hongsheng %A Ruiz-Ferrer, Macarena %A Sze-Man Tang, Clara %A Fernández, Raquel M %A Sham, Pak-Chung %A Torroglosa, Ana %A Kwong-Hang Tam, Paul %A Espino-Paisán, Laura %A Cherny, Stacey S %A Bleda, Marta %A Enguix-Riego, María Del Valle %A Joaquín Dopazo %A Antiňolo, Guillermo %A Garcia-Barceló, Maria-Mercè %A Borrego, Salud %K babelomics %K Hirschprung %K NGS %K prioritization %X Hirschsprung disease (HSCR; OMIM 142623) is a developmental disorder characterized by aganglionosis along variable lengths of the distal gastrointestinal tract, which results in intestinal obstruction. Interactions among known HSCR genes and/or unknown disease susceptibility loci lead to variable severity of phenotype. Neither linkage nor genome-wide association studies have efficiently contributed to completely dissect the genetic pathways underlying this complex genetic disorder. We have performed whole exome sequencing of 16 HSCR patients from 8 unrelated families with SOLID platform. Variants shared by affected relatives were validated by Sanger sequencing. We searched for genes recurrently mutated across families. Only variations in the FAT3 gene were significantly enriched in five families. Within-family analysis identified compound heterozygotes for AHNAK and several genes (N = 23) with heterozygous variants that co-segregated with the phenotype. Network and pathway analyses facilitated the discovery of polygenic inheritance involving FAT3, HSCR known genes and their gene partners. Altogether, our approach has facilitated the detection of more than one damaging variant in biologically plausible genes that could jointly contribute to the phenotype. Our data may contribute to the understanding of the complex interactions that occur during enteric nervous system development and the etiopathology of familial HSCR. %B Scientific reports %V 5 %P 16473 %8 2015 %G eng %U http://www.nature.com/articles/srep16473 %R 10.1038/srep16473 %0 Journal Article %J PLoS One %D 2014 %T Exome sequencing reveals novel and recurrent mutations with clinical significance in inherited retinal dystrophies. %A González-del Pozo, María %A Méndez-Vidal, Cristina %A Bravo-Gil, Nereida %A Vela-Boza, Alicia %A Dopazo, Joaquin %A Borrego, Salud %A Antiňolo, Guillermo %K Adolescent %K Adult %K Amino Acid Sequence %K Base Sequence %K Child %K Chromosome Segregation %K DNA Mutational Analysis %K Exome %K Family %K Female %K Humans %K Inheritance Patterns %K Male %K Middle Aged %K Molecular Sequence Data %K mutation %K Pedigree %K Retinal Dystrophies %K Rhodopsin %X

This study aimed to identify the underlying molecular genetic cause in four Spanish families clinically diagnosed of Retinitis Pigmentosa (RP), comprising one autosomal dominant RP (adRP), two autosomal recessive RP (arRP) and one with two possible modes of inheritance: arRP or X-Linked RP (XLRP). We performed whole exome sequencing (WES) using NimbleGen SeqCap EZ Exome V3 sample preparation kit and SOLID 5500xl platform. All variants passing filter criteria were validated by Sanger sequencing to confirm familial segregation and the absence in local control population. This strategy allowed the detection of: (i) one novel heterozygous splice-site deletion in RHO, c.937-2_944del, (ii) one rare homozygous mutation in C2orf71, c.1795T>C; p.Cys599Arg, not previously associated with the disease, (iii) two heterozygous null mutations in ABCA4, c.2041C>T; p.R681* and c.6088C>T; p.R2030*, and (iv) one mutation, c.2405-2406delAG; p.Glu802Glyfs*31 in the ORF15 of RPGR. The molecular findings for RHO and C2orf71 confirmed the initial diagnosis of adRP and arRP, respectively, while patients with the two ABCA4 mutations, both previously associated with Stargardt disease, presented symptoms of RP with early macular involvement. Finally, the X-Linked inheritance was confirmed for the family with the RPGR mutation. This latter finding allowed the inclusion of carrier sisters in our preimplantational genetic diagnosis program.

%B PLoS One %V 9 %P e116176 %8 2014 %G eng %N 12 %1 https://www.ncbi.nlm.nih.gov/pubmed/25544989?dopt=Abstract %R 10.1371/journal.pone.0116176 %0 Journal Article %J Mol Genet Metab %D 2013 %T Exome sequencing identifies a new mutation in SERAC1 in a patient with 3-methylglutaconic aciduria. %A Tort, Frederic %A García-Silva, María Teresa %A Ferrer-Cortès, Xènia %A Navarro-Sastre, Aleix %A Garcia-Villoria, Judith %A Coll, Maria Josep %A Vidal, Enrique %A Jiménez-Almazán, Jorge %A Dopazo, Joaquin %A Briones, Paz %A Elpeleg, Orly %A Ribes, Antonia %K Adolescent %K Adult %K Carboxylic Ester Hydrolases %K Child %K Exome %K Female %K High-Throughput Nucleotide Sequencing %K Humans %K Infant %K Male %K Metabolism, Inborn Errors %K mutation %X

3-Methylglutaconic aciduria (3-MGA-uria) is a heterogeneous group of syndromes characterized by an increased excretion of 3-methylglutaconic and 3-methylglutaric acids. Five types of 3-MGA-uria (I to V) with different clinical presentations have been described. Causative mutations in TAZ, OPA3, DNAJC19, ATP12, ATP5E, and TMEM70 have been identified. After excluding the known genetic causes of 3-MGA-uria we used exome sequencing to investigate a patient with Leigh syndrome and 3-MGA-uria. We identified a homozygous variant in SERAC1 (c.202C>T; p.Arg68*), that generates a premature stop codon at position 68 of SERAC1 protein. Western blot analysis in patient's fibroblasts showed a complete absence of SERAC1 that was consistent with the prediction of a truncated protein and supports the pathogenic role of the mutation. During the course of this project a parallel study identified mutations in SERAC1 as the genetic cause of the disease in 15 patients with MEGDEL syndrome, which was compatible with the clinical and biochemical phenotypes of the patient described here. In addition, our patient developed microcephaly and optic atrophy, two features not previously reported in MEGDEL syndrome. We highlight the usefulness of exome sequencing to reveal the genetic bases of human rare diseases even if only one affected individual is available.

%B Mol Genet Metab %V 110 %P 73-7 %8 2013 Sep-Oct %G eng %N 1-2 %1 https://www.ncbi.nlm.nih.gov/pubmed/23707711?dopt=Abstract %R 10.1016/j.ymgme.2013.04.021 %0 Journal Article %J Evolutionary bioinformatics online %D 2012 %T Evolutionary Genomics of Genes Involved in Olfactory Behavior in the Drosophila melanogaster Species Group. %A Lavagnino, Nicolás %A Serra, François %A Arbiza, Leonardo %A Dopazo, Hernán %A Hasson, Esteban %X Previous comparative genomic studies of genes involved in olfactory behavior in Drosophila focused only on particular gene families such as odorant receptor and/or odorant binding proteins. However, olfactory behavior has a complex genetic architecture that is orchestrated by many interacting genes. In this paper, we present a comparative genomic study of olfactory behavior in Drosophila including an extended set of genes known to affect olfactory behavior. We took advantage of the recent burst of whole genome sequences and the development of powerful statistical tools to analyze genomic data and test evolutionary and functional hypotheses of olfactory genes in the six species of the Drosophila melanogaster species group for which whole genome sequences are available. Our study reveals widespread purifying selection and limited incidence of positive selection on olfactory genes. We show that the pace of evolution of olfactory genes is mostly independent of the life cycle stage, and of the number of life cycle stages, in which they participate in olfaction. However, we detected a relationship between evolutionary rates and the position that the gene products occupy in the olfactory system, genes occupying central positions tend to be more constrained than peripheral genes. Finally, we demonstrate that specialization to one host does not seem to be associated with bursts of adaptive evolution in olfactory genes in D. sechellia and D. erecta, the two specialists species analyzed, but rather different lineages have idiosyncratic evolutionary histories in which both historical and ecological factors have been involved. %B Evolutionary bioinformatics online %V 8 %P 89-104 %8 2012 %G eng %U http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3273929/?tool=pubmed %R 10.4137/EBO.S8484 %0 Journal Article %J International journal of cancer. Journal international du cancer %D 2012 %T Expression profiling shows differential molecular pathways and provides potential new diagnostic biomarkers for colorectal serrated adenocarcinoma. %A Conesa-Zamora, Pablo %A García-Solano, José %A Garcia-Garcia, Francisco %A Del Carmen Turpin, María %A Trujillo-Santos, Javier %A Torres-Moreno, Daniel %A Oviedo-Ramírez, Isabel %A Carbonell-Muñoz, Rosa %A Muñoz-Delgado, Encarnación %A Rodriguez-Braun, Edith %A Ana Conesa %A Pérez-Guillermo, Miguel %X Serrated adenocarcinoma (SAC) is a recently recognized colorectal cancer (CRC) subtype accounting for 7.5-8.7% of CRCs. It has been shown that SAC has a poorer prognosis and has different molecular and immunohistochemical features compared to conventional carcinoma (CC) but, to date, only one previous study has analysed its mRNA expression profile by microarray. Using a different microarray platform, we have studied the molecular signature of 11 SACs and compared it with that of 15 matched CC with the aim of discerning the functions which characterize SAC biology and validating, at the mRNA and protein level, the most differentially expressed genes which were also tested using a validation set of 70 SACs and 70 CCs to assess their diagnostic and prognostic values. Microarray data showed a higher representation of morphogenesis-, hypoxia-, cytoskeleton- and vesicle transport-related functions and also an over-expression of fascin1 (actin-bundling protein associated with invasion) and the antiapoptotic gene hippocalcin in SAC all of which were validated both by qPCR and immunohistochemistry. Fascin1 expression was statistically associated with KRAS mutation with 88.6% sensitivity and 85.7% specificity for SAC diagnosis and the positivity of fascin1 or hippocalcin was highly suggestive of SAC diagnosis (sensitivity=100%). Evaluation of these markers in CRCs showing histological and molecular characteristics of high-level microsatellite instability (MSI-H) also helped to distinguish SACs from MSI-H CRCs. Molecular profiling demonstrates that SAC shows activation of distinct signalling pathways and that immunohistochemical fascin1 and hippocalcin expression can be reliably used for its differentiation from other CRC subtypes. © 2012 Wiley Periodicals, Inc. %B International journal of cancer. Journal international du cancer %8 2012 Jun 14 %G eng %R 10.1002/ijc.27674 %0 Journal Article %J PLoS One %D 2012 %T Extensive translatome remodeling during ER stress response in mammalian cells. %A Ventoso, Iván %A Kochetov, Alex %A Montaner, David %A Dopazo, Joaquin %A Santoyo, Javier %K Animals %K Endoplasmic Reticulum Stress %K Humans %K Jurkat Cells %K Mice %K NIH 3T3 Cells %K Oligonucleotide Array Sequence Analysis %K Protein Biosynthesis %K RNA, Messenger %K Transcription, Genetic %X

In this work we have described the translatome of two mammalian cell lines, NIH3T3 and Jurkat, by scoring the relative polysome association of ∼10,000 mRNA under normal and ER stress conditions. We have found that translation efficiencies of mRNA correlated poorly with transcript abundance, although a general tendency was observed so that the highest translation efficiencies were found in abundant mRNA. Despite the differences found between mouse (NIH3T3) and human (Jurkat) cells, both cell types share a common translatome composed by ∼800-900 mRNA that encode proteins involved in basic cellular functions. Upon stress, an extensive remodeling in translatomes was observed so that translation of ∼50% of mRNA was inhibited in both cell types, this effect being more dramatic for those mRNA that accounted for most of the cell translation. Interestingly, we found two subsets comprising 1000-1500 mRNA whose translation resisted or was induced by stress. Translation arrest resistant class includes many mRNA encoding aminoacyl tRNA synthetases, ATPases and enzymes involved in DNA replication and stress response such as BiP. This class of mRNA is characterized by high translation rates in both control and stress conditions. Translation inducible class includes mRNA whose translation was relieved after stress, showing a high enrichment in early response transcription factors of bZIP and zinc finger C2H2 classes. Unlike yeast, a general coordination between changes in translation and transcription upon stress (potentiation) was not observed in mammalian cells. Among the different features of mRNA analyzed, we found a relevant association of translation efficiency with the presence of upstream ATG in the 5'UTR and with the length of coding sequence of mRNA, and a looser association with other parameters such as the length and the G+C content of 5'UTR. A model for translatome remodeling during the acute phase of stress response in mammalian cells is proposed.

%B PLoS One %V 7 %P e35915 %8 2012 %G eng %N 5 %1 https://www.ncbi.nlm.nih.gov/pubmed/22574127?dopt=Abstract %R 10.1371/journal.pone.0035915 %0 Journal Article %J BMC Med Genomics %D 2011 %T Early peroxisome proliferator-activated receptor gamma regulated genes involved in expansion of pancreatic beta cell mass. %A Vivas, Yurena %A Martinez-Garcia, Cristina %A Izquierdo, Adriana %A Garcia-Garcia, Francisco %A Callejas, Sergio %A Velasco, Ismael %A Campbell, Mark %A Ros, Manuel %A Dopazo, Ana %A Dopazo, Joaquin %A Vidal-Puig, Antonio %A Medina-Gomez, Gema %K Animals %K Cell Proliferation %K Cell Survival %K Cholesterol %K Down-Regulation %K Female %K Gene Expression Regulation %K Gene Knockout Techniques %K Insulin Resistance %K Insulin-Secreting Cells %K Mice %K obesity %K Oxidation-Reduction %K Phosphorylation %K PPAR gamma %K Signal Transduction %K Transcription, Genetic %K Transforming Growth Factor beta %X

BACKGROUND: The progression towards type 2 diabetes depends on the allostatic response of pancreatic beta cells to synthesise and secrete enough insulin to compensate for insulin resistance. The endocrine pancreas is a plastic tissue able to expand or regress in response to the requirements imposed by physiological and pathophysiological states associated to insulin resistance such as pregnancy, obesity or ageing, but the mechanisms mediating beta cell mass expansion in these scenarios are not well defined. We have recently shown that ob/ob mice with genetic ablation of PPARγ2, a mouse model known as the POKO mouse failed to expand its beta cell mass. This phenotype contrasted with the appropriate expansion of the beta cell mass observed in their obese littermate ob/ob mice. Thus, comparison of these models islets particularly at early ages could provide some new insights on early PPARγ dependent transcriptional responses involved in the process of beta cell mass expansion

RESULTS: Here we have investigated PPARγ dependent transcriptional responses occurring during the early stages of beta cell adaptation to insulin resistance in wild type, ob/ob, PPARγ2 KO and POKO mice. We have identified genes known to regulate both the rate of proliferation and the survival signals of beta cells. Moreover we have also identified new pathways induced in ob/ob islets that remained unchanged in POKO islets, suggesting an important role for PPARγ in maintenance/activation of mechanisms essential for the continued function of the beta cell.

CONCLUSIONS: Our data suggest that the expansion of beta cell mass observed in ob/ob islets is associated with the activation of an immune response that fails to occur in POKO islets. We have also indentified other PPARγ dependent differentially regulated pathways including cholesterol biosynthesis, apoptosis through TGF-β signaling and decreased oxidative phosphorylation.

%B BMC Med Genomics %V 4 %P 86 %8 2011 Dec 30 %G eng %1 https://www.ncbi.nlm.nih.gov/pubmed/22208362?dopt=Abstract %R 10.1186/1755-8794-4-86 %0 Journal Article %J Plant physiology %D 2011 %T Early transcriptional defence responses in Arabidopsis cell suspension culture under high light conditions. %A González-Pérez, Sergio %A Gutiérrez, Jorge %A Garcia-Garcia, Francisco %A Osuna, Daniel %A Joaquín Dopazo %A Lorenzo, Oscar %A Revuelta, José L %A Arellano, Juan B %X

The early transcriptional defence responses and ROS production in Arabidopsis cell suspension culture (ACSC), containing functional chloroplasts, were examined at high light (HL). The transcriptional analysis revealed that most of the ROS markers identified among the 449 transcripts with significant differential expression were transcripts specifically up-regulated by singlet oxygen (1O2). On the contrary, minimal correlation was established with transcripts specifically up-regulated by superoxide radical (O2•) or hydrogen peroxide (H2O2). The transcriptional analysis was supported by fluorescence microscopy experiments. The incubation of ACSC with the 1O2 sensor green reagent and 2’,7’-dichlorofluorescein diacetate showed that the 30-min-HL-treated cultures emitted fluorescence that corresponded with the production of 1O2, but not of H2O2. Furthermore, the in vivo photodamage of the D1 protein of photosystem II (PSII) indicated that the photogeneration of 1O2 took place within the PSII reaction centre. Functional enrichment analyses identified transcripts that are key components of the ROS signalling transduction pathway in plants as well as others encoding transcription factors that regulate both ROS scavenging and water deficit stress. A meta-analysis examining the transcriptional profiles of mutants and hormone treatments in Arabidopsis showed a high correlation between ACSC at HL and the flu mutant family of Arabidopsis, a producer of 1O2 in plastids. Intriguingly, a high correlation was also observed with aba1 and max4, two mutants with defects in the biosynthesis pathways of two key (apo)carotenoid-derived plant hormones (i.e. ABA and strigolactones, respectively). ACSC has proven to be a valuable system for studying early transcriptional responses to HL stress.

%B Plant physiology %V 156 %P 1439-56 %8 2011 Apr 29 %G eng %U http://www.plantphysiol.org/content/early/2011/04/29/pp.111.177766.short?keytype=ref&ijkey=ph5B6J2khjnqwzN %0 Journal Article %J Plant Physiol %D 2011 %T Early transcriptional defense responses in Arabidopsis cell suspension culture under high-light conditions. %A González-Pérez, Sergio %A Gutiérrez, Jorge %A Garcia-Garcia, Francisco %A Osuna, Daniel %A Dopazo, Joaquin %A Lorenzo, Oscar %A Revuelta, José L %A Arellano, Juan B %K Arabidopsis %K Blotting, Western %K Cell Culture Techniques %K Cells, Cultured %K Chloroplasts %K Cluster Analysis %K Gene Expression Profiling %K Gene Expression Regulation, Plant %K Hydrogen Peroxide %K Light %K mutation %K Oligonucleotide Array Sequence Analysis %K Photosystem II Protein Complex %K Plant Growth Regulators %K Reproducibility of Results %K Reverse Transcriptase Polymerase Chain Reaction %K RNA, Messenger %K Signal Transduction %K Stress, Physiological %K Transcription, Genetic %X

The early transcriptional defense responses and reactive oxygen species (ROS) production in Arabidopsis (Arabidopsis thaliana) cell suspension culture (ACSC), containing functional chloroplasts, were examined at high light (HL). The transcriptional analysis revealed that most of the ROS markers identified among the 449 transcripts with significant differential expression were transcripts specifically up-regulated by singlet oxygen ((1)O(2)). On the contrary, minimal correlation was established with transcripts specifically up-regulated by superoxide radical or hydrogen peroxide. The transcriptional analysis was supported by fluorescence microscopy experiments. The incubation of ACSC with the (1)O(2) sensor green reagent and 2',7'-dichlorofluorescein diacetate showed that the 30-min-HL-treated cultures emitted fluorescence that corresponded with the production of (1)O(2) but not of hydrogen peroxide. Furthermore, the in vivo photodamage of the D1 protein of photosystem II indicated that the photogeneration of (1)O(2) took place within the photosystem II reaction center. Functional enrichment analyses identified transcripts that are key components of the ROS signaling transduction pathway in plants as well as others encoding transcription factors that regulate both ROS scavenging and water deficit stress. A meta-analysis examining the transcriptional profiles of mutants and hormone treatments in Arabidopsis showed a high correlation between ACSC at HL and the fluorescent mutant family of Arabidopsis, a producer of (1)O(2) in plastids. Intriguingly, a high correlation was also observed with ABA deficient1 and more axillary growth4, two mutants with defects in the biosynthesis pathways of two key (apo)carotenoid-derived plant hormones (i.e. abscisic acid and strigolactones, respectively). ACSC has proven to be a valuable system for studying early transcriptional responses to HL stress.

%B Plant Physiol %V 156 %P 1439-56 %8 2011 Jul %G eng %N 3 %1 https://www.ncbi.nlm.nih.gov/pubmed/21531897?dopt=Abstract %R 10.1104/pp.111.177766 %0 Journal Article %J Brief Bioinform %D 2011 %T Evidence for short-time divergence and long-time conservation of tissue-specific expression after gene duplication. %A Huerta-Cepas, Jaime %A Dopazo, Joaquin %A Huynen, Martijn A %A Gabaldón, Toni %K Animals %K Conserved Sequence %K Evolution, Molecular %K Gene Duplication %K gene expression %K Genome %K Humans %K Mice %K Organ Specificity %X

Gene duplication is one of the main mechanisms by which genomes can acquire novel functions. It has been proposed that the retention of gene duplicates can be associated to processes of tissue expression divergence. These models predict that acquisition of divergent expression patterns should be acquired shortly after the duplication, and that larger divergence in tissue expression would be expected for paralogs, as compared to orthologs of a similar age. Many studies have shown that gene duplicates tend to have divergent expression patterns and that gene family expansions are associated with high levels of tissue specificity. However, the timeframe in which these processes occur have rarely been investigated in detail, particularly in vertebrates, and most analyses do not include direct comparisons of orthologs as a baseline for the expected levels of tissue specificity in absence of duplications. To assess the specific contribution of duplications to expression divergence, we combine here phylogenetic analyses and expression data from human and mouse. In particular, we study differences in spatial expression among human-mouse paralogs, specifically duplicated after the radiation of mammals, and compare them to pairs of orthologs in the same species. Our results show that gene duplication leads to increased levels of tissue specificity and that this tends to occur promptly after the duplication event.

%B Brief Bioinform %V 12 %P 442-8 %8 2011 Sep %G eng %N 5 %1 https://www.ncbi.nlm.nih.gov/pubmed/21515902?dopt=Abstract %R 10.1093/bib/bbr022 %0 Journal Article %J Environmental microbiology %D 2011 %T Evolution of the biosynthesis of di-myo-inositol phosphate, a marker of adaptation to hot marine environments. %A Gonçalves, Luís G %A Borges, Nuno %A Serra, François %A Fernandes, Pedro L %A Dopazo, Hernán %A Santos, Helena %X

The synthesis of di-myo-inositol phosphate (DIP), a common compatible solute in hyperthermophiles, involves the consecutive actions of inositol-1-phosphate cytidylyltransferase (IPCT) and di-myo-inositol phosphate phosphate synthase (DIPPS). In most cases, both activities are present in a single gene product, but separate genes are also found in a few organisms. Genes for IPCT and DIPPS were found in the genomes of 33 organisms, all with thermophilic/hyperthermophilic lifestyles. Phylogeny of IPCT/DIPPS revealed an incongruent topology with 16S RNA phylogeny, thus suggesting horizontal gene transfer. The phylogenetic tree of the DIPPS domain was rooted by using phosphatidylinositol phosphate synthase sequences as out-group. The root locates at the separation of genomes with fused and split genes. We propose that the gene encoding DIPPS was recruited from the biosynthesis of phosphatidylinositol. The last DIP-synthesizing ancestor harboured separated genes for IPCT and DIPPS and this architecture was maintained in a crenarchaeal lineage, and transferred by horizontal gene transfer to hyperthermophilic marine Thermotoga species. It is plausible that the driving force for the assembly of those two genes in the early ancestor is related to the acquired advantage of DIP producers to cope with high temperature. This work corroborates the view that Archaea were the first hyperthermophilic organisms.

%B Environmental microbiology %8 2011 Oct 26 %G eng %R 10.1111/j.1462-2920.2011.02621.x %0 Journal Article %J PLoS computational biology %D 2011 %T An evolutionary trade-off between protein turnover rate and protein aggregation favors a higher aggregation propensity in fast degrading proteins. %A De Baets, Greet %A Reumers, Joke %A Delgado Blanco, Javier %A Dopazo, Joaquin %A Schymkowitz, Joost %A Rousseau, Frederic %X

We previously showed the existence of selective pressure against protein aggregation by the enrichment of aggregation-opposing ’gatekeeper’ residues at strategic places along the sequence of proteins. Here we analyzed the relationship between protein lifetime and protein aggregation by combining experimentally determined turnover rates, expression data, structural data and chaperone interaction data on a set of more than 500 proteins. We find that selective pressure on protein sequences against aggregation is not homogeneous but that short-living proteins on average have a higher aggregation propensity and fewer chaperone interactions than long-living proteins. We also find that short-living proteins are more often associated to deposition diseases. These findings suggest that the efficient degradation of high-turnover proteins is sufficient to preclude aggregation, but also that factors that inhibit proteasomal activity, such as physiological ageing, will primarily affect the aggregation of short-living proteins.

%B PLoS computational biology %V 7 %P e1002090 %8 2011 Jun %G eng %R 10.1371/journal.pcbi.1002090 %0 Journal Article %J BMC Bioinformatics %D 2010 %T ETE: a python Environment for Tree Exploration. %A Huerta-Cepas, Jaime %A Dopazo, Joaquin %A Gabaldón, Toni %K Computational Biology %K Databases, Genetic %K Phylogeny %K Software %X

BACKGROUND: Many bioinformatics analyses, ranging from gene clustering to phylogenetics, produce hierarchical trees as their main result. These are used to represent the relationships among different biological entities, thus facilitating their analysis and interpretation. A number of standalone programs are available that focus on tree visualization or that perform specific analyses on them. However, such applications are rarely suitable for large-scale surveys, in which a higher level of automation is required. Currently, many genome-wide analyses rely on tree-like data representation and hence there is a growing need for scalable tools to handle tree structures at large scale.

RESULTS: Here we present the Environment for Tree Exploration (ETE), a python programming toolkit that assists in the automated manipulation, analysis and visualization of hierarchical trees. ETE libraries provide a broad set of tree handling options as well as specific methods to analyze phylogenetic and clustering trees. Among other features, ETE allows for the independent analysis of tree partitions, has support for the extended newick format, provides an integrated node annotation system and permits to link trees to external data such as multiple sequence alignments or numerical arrays. In addition, ETE implements a number of built-in analytical tools, including phylogeny-based orthology prediction and cluster validation techniques. Finally, ETE's programmable tree drawing engine can be used to automate the graphical rendering of trees with customized node-specific visualizations.

CONCLUSIONS: ETE provides a complete set of methods to manipulate tree data structures that extends current functionality in other bioinformatic toolkits of a more general purpose. ETE is free software and can be downloaded from http://ete.cgenomics.org.

%B BMC Bioinformatics %V 11 %P 24 %8 2010 Jan 13 %G eng %1 https://www.ncbi.nlm.nih.gov/pubmed/20070885?dopt=Abstract %R 10.1186/1471-2105-11-24 %0 Journal Article %J PLoS One %D 2010 %T Exploring the link between germline and somatic genetic alterations in breast carcinogenesis. %A Bonifaci, Núria %A Górski, Bohdan %A Masojć, Bartlomiej %A Wokołorczyk, Dominika %A Jakubowska, Anna %A Dębniak, Tadeusz %A Berenguer, Antoni %A Serra Musach, Jordi %A Brunet, Joan %A Dopazo, Joaquin %A Narod, Steven A %A Lubiński, Jan %A Lázaro, Conxi %A Cybulski, Cezary %A Pujana, Miguel Angel %K Adult %K Bone Morphogenetic Protein Receptors, Type I %K Breast %K Breast Neoplasms %K Calcium-Calmodulin-Dependent Protein Kinases %K Case-Control Studies %K Cyclin-Dependent Kinases %K Disease Progression %K Estrogen Receptor alpha %K Female %K Gene Frequency %K Genetic Predisposition to Disease %K Genome-Wide Association Study %K Genotype %K Germ-Line Mutation %K Humans %K Odds Ratio %K Poland %K Polymorphism, Single Nucleotide %K Protein Serine-Threonine Kinases %K Protein-Tyrosine Kinases %K Receptor Protein-Tyrosine Kinases %K Receptor, EphA3 %K Receptor, EphA7 %K Receptor, EphB1 %K Risk Factors %X

Recent genome-wide association studies (GWASs) have identified candidate genes contributing to cancer risk through low-penetrance mutations. Many of these genes were unexpected and, intriguingly, included well-known players in carcinogenesis at the somatic level. To assess the hypothesis of a germline-somatic link in carcinogenesis, we evaluated the distribution of somatic gene labels within the ordered results of a breast cancer risk GWAS. This analysis suggested frequent influence on risk of genetic variation in loci encoding for "driver kinases" (i.e., kinases encoded by genes that showed higher somatic mutation rates than expected by chance and, therefore, whose deregulation may contribute to cancer development and/or progression). Assessment of these predictions using a population-based case-control study in Poland replicated the association for rs3732568 in EPHB1 (odds ratio (OR) = 0.79; 95% confidence interval (CI): 0.63-0.98; P(trend) = 0.031). Analyses by early age at diagnosis and by estrogen receptor α (ERα) tumor status indicated potential associations for rs6852678 in CDKL2 (OR = 0.32, 95% CI: 0.10-1.00; P(recessive) = 0.044) and rs10878640 in DYRK2 (OR = 2.39, 95% CI: 1.32-4.30; P(dominant) = 0.003), and for rs12765929, rs9836340, rs4707795 in BMPR1A, EPHA3 and EPHA7, respectively (ERα tumor status P(interaction)<0.05). The identification of three novel candidates as EPH receptor genes might indicate a link between perturbed compartmentalization of early neoplastic lesions and breast cancer risk and progression. Together, these data may lay the foundations for replication in additional populations and could potentially increase our knowledge of the underlying molecular mechanisms of breast carcinogenesis.

%B PLoS One %V 5 %P e14078 %8 2010 Nov 22 %G eng %N 11 %1 https://www.ncbi.nlm.nih.gov/pubmed/21124932?dopt=Abstract %R 10.1371/journal.pone.0014078 %0 Book %D 2009 %T Evolución y Adaptación.150 años después del Origen de las Especies %E H. Dopazo %E Navarro, A. %X

Evolución y Adaptación: 150 años después del Origen de las Especies es un homenaje a la figura de Charles Darwin al cumplirse 200 años de su nacimiento y 150 años de la publicación que lo hiciese mundialmente famoso. En esta edición 101 autores convocados por la Sociedad Española de Biología Evolutiva han resumido su trabajo de investigación en 51 artículos. Estos se han agrupado en temáticas que abarcan los problemas de la evolución molecular, el cambio morfológico, la evolución del desarrollo, el origen de las especies y su interacción, la diversidad biológica, la evolución del comportamiento, la paleobiología, la evolución experimental, la evolución cultural y la evolución en la filosofía y la docencia. Muchos de estos trabajos representan décadas de constante investigación en el laboratorio y en el campo. El común denominador de los artículos que contiene este libro es el esfuerzo por transmitir a un público no necesariamente experto la actualidad de las investigaciones que en el campo de la adaptación y la evolución se desarrolla en diferentes laboratorios. Esta obra resume por lo tanto, gran parte de las investigaciones que  en materia de evolución biológica se realiza en España. Esta edición deja constancia entonces del "Hecho de la Evolución", y de la actualidad de teoría evolutiva moderna como cuerpo explicativo del mundo biológico 150 años después del origen de las especies. 

%I Obrapropia. %C Valencia. España %P 510 %G eng %0 Journal Article %J Microbiology %D 2009 %T Exploring the antimicrobial action of a carbon monoxide-releasing compound through whole-genome transcription profiling of Escherichia coli %A Nobre, L. S. %A Fatima Al-Shahrour %A Dopazo, J. %A Saraiva, L. M. %K Bacterial Genes %K Bacterial/genetics %K Biofilms Carbon Monoxide/*metabolism Escherichia coli/*genetics/metabolism Escherichia coli Proteins/genetics/metabolism *Gene Expression Profiling Gene Expression Regulation %K Regulator Genetic Complementation Test Methionine/metabolism Microbial Viability Mutation Oligonucleotide Array Sequence Analysis Organometallic Compounds/*pharmacology Phenotype RNA %X

We recently reported that carbon monoxide (CO) has bactericidal activity. To understand its mode of action we analysed the gene expression changes occurring when Escherichia coli, grown aerobically and anaerobically, is treated with the CO-releasing molecule CORM-2 (tricarbonyldichlororuthenium(II) dimer). Microarray analysis shows that the E. coli CORM-2 response is multifaceted, with a high number of differentially regulated genes spread through several functional categories, namely genes involved in inorganic ion transport and metabolism, regulators, and genes implicated in post-translational modification, such as chaperones. CORM-2 has a higher impact in E. coli cells grown anaerobically, as judged by the repression of genes belonging to eight functional classes which are not seen in the response of aerobically CORM-2-treated cells. The biological relevance of the variations caused by CORM-2 was substantiated by studying the CORM-2 sensitivity of selected E. coli mutants. The results show that the deletion of redox-sensing regulators SoxS and OxyR increased the sensitivity to CORM-2 and suggest that while SoxS plays an important role in protection against CORM-2 under both growth conditions, OxyR seems to participate only in the aerobic CORM-2 response. Under anaerobic conditions, we found that the heat-shock proteins IbpA and IbpB contribute to CORM-2 defence since the deletion of these genes increases the sensitivity of the strain. The induction of several met genes and the hypersensitivity to CORM-2 of the DeltametR, DeltametI and DeltametN mutant strains suggest that CO has effects on the methionine metabolism of E. coli. CORM-2 also affects the transcription of several E. coli biofilm-related genes and increases biofilm formation in E. coli. In particular, the absence of tqsA or bhsA increases the resistance of E. coli to CORM-2, and deletion of tsqA leads to a strain that has lost its capacity to form biofilm upon treatment with CORM-2. In spite of the relatively stable nature of the CO molecule, our results show that CO is able to trigger a significant alteration in the transcriptome of E. coli which necessarily has effects in several key metabolic pathways.

%B Microbiology %V 155 %P 813-24 %G eng %U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=19246752 %0 Journal Article %J Microbiology (Reading) %D 2009 %T Exploring the antimicrobial action of a carbon monoxide-releasing compound through whole-genome transcription profiling of Escherichia coli. %A Nobre, Lígia S %A Al-Shahrour, Fátima %A Dopazo, Joaquin %A Saraiva, Lígia M %K Biofilms %K Carbon Monoxide %K Escherichia coli %K Escherichia coli Proteins %K Gene Expression Profiling %K Gene Expression Regulation, Bacterial %K Genes, Bacterial %K Genes, Regulator %K Genetic Complementation Test %K Methionine %K Microbial Viability %K mutation %K Oligonucleotide Array Sequence Analysis %K Organometallic Compounds %K Phenotype %K RNA, Bacterial %X

We recently reported that carbon monoxide (CO) has bactericidal activity. To understand its mode of action we analysed the gene expression changes occurring when Escherichia coli, grown aerobically and anaerobically, is treated with the CO-releasing molecule CORM-2 (tricarbonyldichlororuthenium(II) dimer). Microarray analysis shows that the E. coli CORM-2 response is multifaceted, with a high number of differentially regulated genes spread through several functional categories, namely genes involved in inorganic ion transport and metabolism, regulators, and genes implicated in post-translational modification, such as chaperones. CORM-2 has a higher impact in E. coli cells grown anaerobically, as judged by the repression of genes belonging to eight functional classes which are not seen in the response of aerobically CORM-2-treated cells. The biological relevance of the variations caused by CORM-2 was substantiated by studying the CORM-2 sensitivity of selected E. coli mutants. The results show that the deletion of redox-sensing regulators SoxS and OxyR increased the sensitivity to CORM-2 and suggest that while SoxS plays an important role in protection against CORM-2 under both growth conditions, OxyR seems to participate only in the aerobic CORM-2 response. Under anaerobic conditions, we found that the heat-shock proteins IbpA and IbpB contribute to CORM-2 defence since the deletion of these genes increases the sensitivity of the strain. The induction of several met genes and the hypersensitivity to CORM-2 of the DeltametR, DeltametI and DeltametN mutant strains suggest that CO has effects on the methionine metabolism of E. coli. CORM-2 also affects the transcription of several E. coli biofilm-related genes and increases biofilm formation in E. coli. In particular, the absence of tqsA or bhsA increases the resistance of E. coli to CORM-2, and deletion of tsqA leads to a strain that has lost its capacity to form biofilm upon treatment with CORM-2. In spite of the relatively stable nature of the CO molecule, our results show that CO is able to trigger a significant alteration in the transcriptome of E. coli which necessarily has effects in several key metabolic pathways.

%B Microbiology (Reading) %V 155 %P 813-824 %8 2009 Mar %G eng %N Pt 3 %1 https://www.ncbi.nlm.nih.gov/pubmed/19246752?dopt=Abstract %R 10.1099/mic.0.023911-0 %0 Journal Article %J Genome Biol %D 2008 %T Evolutionary potentials: structure specific knowledge-based potentials exploiting the evolutionary record of sequence homologs %A Panjkovich, A. %A Melo, F. %A M. A. Marti-Renom %X ABSTRACT: We introduce a new type of knowledge-based potentials for protein structure prediction, called ’evolutionary potentials’, which are derived using a single experimental protein structure and all three-dimensional models of its homologous sequences. The new potentials have been benchmarked against other knowledge-based potentials, resulting in a significant increase in accuracy for model assessment. In contrast to standard knowledge-based potentials, we propose that evolutionary potentials capture key determinants of thermodynamic stability and specific sequence constraints required for fast folding. %B Genome Biol %V 9 %P R68 %G eng %U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18397517 %0 Journal Article %J Methods Mol Biol %D 2008 %T Expression and microarrays. %A Dopazo, Joaquin %A Al-Shahrour, Fátima %K Animals %K Computational Biology %K gene expression %K Gene Expression Profiling %K Humans %K Oligonucleotide Array Sequence Analysis %X

High throughput methodologies have increased by several orders of magnitude the amount of experimental microarray data available. Nevertheless, translating these data into useful biological knowledge remains a challenge. There is a risk of perceiving these methodologies as mere factories that produce never-ending quantities of data if a proper biological interpretation is not provided. Methods of interpreting these data are continuously evolving. Typically, a simple two-step approach has been used, in which genes of interest are first selected based on thresholds for the experimental values, and then enrichment in biologically relevant terms in the annotations of these genes is analyzed in a second step. For various reasons, such methods are quite poor in terms of performance and new procedures inspired by systems biology that directly address sets of functionally related genes are currently under development.

%B Methods Mol Biol %V 453 %P 245-55 %8 2008 %G eng %1 https://www.ncbi.nlm.nih.gov/pubmed/18712307?dopt=Abstract %R 10.1007/978-1-60327-429-6_12 %0 Journal Article %J BMC Genomics %D 2007 %T Evidence for systems-level molecular mechanisms of tumorigenesis. %A Hernández, Pilar %A Huerta-Cepas, Jaime %A Montaner, David %A Al-Shahrour, Fátima %A Valls, Joan %A Gómez, Laia %A Capellà, Gabriel %A Dopazo, Joaquin %A Pujana, Miguel Angel %K Cell Transformation, Neoplastic %K Gene Expression Profiling %K Gene Expression Regulation, Neoplastic %K Humans %K Male %K Models, Biological %K Models, Genetic %K Models, Statistical %K Neoplasm Proteins %K Neoplasms %K Prostatic Neoplasms %K Protein Interaction Mapping %K RNA, Messenger %K Signal Transduction %K Systems biology %X

BACKGROUND: Cancer arises from the consecutive acquisition of genetic alterations. Increasing evidence suggests that as a consequence of these alterations, molecular interactions are reprogrammed in the context of highly connected and regulated cellular networks. Coordinated reprogramming would allow the cell to acquire the capabilities for malignant growth.

RESULTS: Here, we determine the coordinated function of cancer gene products (i.e., proteins encoded by differentially expressed genes in tumors relative to healthy tissue counterparts, hereafter referred to as "CGPs") defined as their topological properties and organization in the interactome network. We show that CGPs are central to information exchange and propagation and that they are specifically organized to promote tumorigenesis. Centrality is identified by both local (degree) and global (betweenness and closeness) measures, and systematically appears in down-regulated CGPs. Up-regulated CGPs do not consistently exhibit centrality, but both types of cancer products determine the overall integrity of the network structure. In addition to centrality, down-regulated CGPs show topological association that correlates with common biological processes and pathways involved in tumorigenesis.

CONCLUSION: Given the current limited coverage of the human interactome, this study proposes that tumorigenesis takes place in a specific and organized way at the molecular systems-level and suggests a model that comprises the precise down-regulation of groups of topologically-associated proteins involved in particular functions, orchestrated with the up-regulation of specific proteins.

%B BMC Genomics %V 8 %P 185 %8 2007 Jun 20 %G eng %1 https://www.ncbi.nlm.nih.gov/pubmed/17584915?dopt=Abstract %R 10.1186/1471-2164-8-185 %0 Journal Article %J BMC Genomics %D 2007 %T Evidence for systems-level molecular mechanisms of tumorigenesis %A Hernandez, P. %A Huerta-Cepas, J. %A Montaner, D. %A Fatima Al-Shahrour %A Valls, J. %A Gomez, L. %A Capella, G. %A Dopazo, J. %A Pujana, M. A. %K *Cell Transformation %K Biological Models %K Genetic Models %K Messenger/metabolism Signal Transduction Systems Biology %K Neoplastic *Gene Expression Profiling *Gene Expression Regulation %K Neoplastic Humans Male Models %K Statistical Neoplasm Proteins/*physiology Neoplasms/etiology/*genetics Prostatic Neoplasms/genetics Protein Interaction Mapping RNA %X BACKGROUND: Cancer arises from the consecutive acquisition of genetic alterations. Increasing evidence suggests that as a consequence of these alterations, molecular interactions are reprogrammed in the context of highly connected and regulated cellular networks. Coordinated reprogramming would allow the cell to acquire the capabilities for malignant growth. RESULTS: Here, we determine the coordinated function of cancer gene products (i.e., proteins encoded by differentially expressed genes in tumors relative to healthy tissue counterparts, hereafter referred to as "CGPs") defined as their topological properties and organization in the interactome network. We show that CGPs are central to information exchange and propagation and that they are specifically organized to promote tumorigenesis. Centrality is identified by both local (degree) and global (betweenness and closeness) measures, and systematically appears in down-regulated CGPs. Up-regulated CGPs do not consistently exhibit centrality, but both types of cancer products determine the overall integrity of the network structure. In addition to centrality, down-regulated CGPs show topological association that correlates with common biological processes and pathways involved in tumorigenesis. CONCLUSION: Given the current limited coverage of the human interactome, this study proposes that tumorigenesis takes place in a specific and organized way at the molecular systems-level and suggests a model that comprises the precise down-regulation of groups of topologically-associated proteins involved in particular functions, orchestrated with the up-regulation of specific proteins. %B BMC Genomics %V 8 %P 185 %G eng %U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17584915 %0 Journal Article %J Cancer Res %D 2006 %T ERCC4 associated with breast cancer risk: a two-stage case-control study using high-throughput genotyping %A Milne, R. L. %A Ribas, G. %A Gonzalez-Neira, A. %A Fagerholm, R. %A Salas, A. %A Gonzalez, E. %A Dopazo, J. %A Nevanlinna, H. %A M. Robledo %A Benitez, J. %K 80 and over Breast Neoplasms/epidemiology/*genetics/pathology Case-Control Studies DNA-Binding Proteins/genetics/*physiology Female Finland/epidemiology Genes %K Adult Aged Aged %K Recessive Genetic Predisposition to Disease Genotype Humans Introns/genetics Linkage Disequilibrium Middle Aged Neoplasm Proteins/genetics/*physiology Neoplasm Staging *Polymorphism %K Single Nucleotide Risk Spain/epidemiology %X The failure of linkage studies to identify further high-penetrance susceptibility genes for breast cancer points to a polygenic model, with more common variants having modest effects on risk, as the most likely candidate. We have carried out a two-stage case-control study in two European populations to identify low-penetrance genes for breast cancer using high-throughput genotyping. Single-nucleotide polymorphisms (SNPs) were selected across preselected cancer-related genes, choosing tagSNPs and functional variants where possible. In stage 1, genotype frequencies for 640 SNPs in 111 genes were compared between 864 breast cancer cases and 845 controls from the Spanish population. In stage 2, candidate SNPs identified in stage 1 (nominal P < 0.01) were tested in a Finnish series of 884 cases and 1,104 controls. Of the 10 candidate SNPs in seven genes identified in stage 1, one (rs744154) on intron 1 of ERCC4, a gene belonging to the nucleotide excision repair pathway, was associated with recessive protection from breast cancer after adjustment for multiple testing in stage 2 (odds ratio, 0.57; Bonferroni-adjusted P = 0.04). After considering potential functional SNPs in the region of high linkage disequilibrium that extends across the entire gene and upstream into the promoter region, we concluded that rs744154 itself could be causal. Although intronic, it is located on the first intron, in a region that is highly conserved across species, and could therefore be functionally important. This study suggests that common intronic variation in ERCC4 is associated with protection from breast cancer. %B Cancer Res %V 66 %P 9420-7 %G eng %U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17018596 %0 Journal Article %J BMC Genomics %D 2006 %T Exploring the reasons for the large density of triplex-forming oligonucleotide target sequences in the human regulatory regions %A Goni, J. R. %A Vaquerizas, J. M. %A Dopazo, J. %A Orozco, M. %K Animals Base Sequence Computational Biology DNA/chemistry/*genetics/*metabolism Genome %K Genetic/genetics Regulatory Sequences %K Human/genetics Humans Mice Nucleic Acid Conformation Nucleotides/genetics Oligonucleotides/chemistry/*genetics/*metabolism Promoter Regions %K Nucleic Acid/*genetics Transcription Factors/metabolism %X BACKGROUND: DNA duplex sequences that can be targets for triplex formation are highly over-represented in the human genome, especially in regulatory regions. RESULTS: Here we studied using bioinformatics tools several properties of triplex target sequences in an attempt to determine those that make these sequences so special in the genome. CONCLUSION: Our results strongly suggest that the unique physical properties of these sequences make them particularly suitable as "separators" between protein-recognition sites in the promoter region. %B BMC Genomics %V 7 %P 63 %G eng %U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16566817 %0 Journal Article %J Evol Bioinform Online %D 2005 %T Evolution of proteins and proteomes: a phylogenetics approach %A Gabaldón, T. %X The study of evolutionary relationships among protein sequences was one of the first applications of bioinformatics. Since then, and accompanying the wealth of biological data produced by genome sequencing and other high-throughput techniques, the use of bioinformatics in general and phylogenetics in particular has been gaining ground in the study of protein and proteome evolution. Nowadays, the use of phylogenetics is instrumental not only to infer the evolutionary relationships among species and their genome sequences, but also to reconstruct ancestral states of proteins and proteomes and hence trace the paths followed by evolution. Here I survey recent progress in the elucidation of mechanisms of protein and proteome evolution in which phylogenetics has played a determinant role. %B Evol Bioinform Online %V 1 %P 51-61 %G eng %U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=19325853 %0 Journal Article %J Clinical cancer research : an official journal of the American Association for Cancer Research %D 2004 %T Expression profiling of T-cell lymphomas differentiates peripheral and lymphoblastic lymphomas and defines survival related genes. %A Martinez-Delgado, Beatriz %A Meléndez, Barbara %A Cuadros, Marta %A Alvarez, Javier %A Castrillo, Jose Maria %A Ruiz De La Parte, Ana %A Mollejo, Manuela %A Bellas, Carmen %A Diaz, Ramon %A Lombardía, Luis %A Fatima Al-Shahrour %A Domínguez, Orlando %A Cascon, Alberto %A Robledo, Mercedes %A Rivas, Carmen %A Benitez, Javier %X

PURPOSE: T-Cell lymphomas constitute heterogeneous and aggressive tumors in which pathogenic alterations remain largely unknown. Expression profiling has demonstrated to be a useful tool for molecular classification of tumors. EXPERIMENTAL DESIGN: Using DNA microarrays (CNIO-OncoChip) containing 6386 cancer-related genes, we established the expression profiling of T-cell lymphomas and compared them to normal lymphocytes and lymph nodes. RESULTS: We found significant differences between the peripheral and lymphoblastic T-cell lymphomas, which include a deregulation of nuclear factor-kappaB signaling pathway. We also identify differentially expressed genes between peripheral T-cell lymphoma tumors and normal T lymphocytes or reactive lymph nodes, which could represent candidate tumor markers of these lymphomas. Additionally, a close relationship between genes associated to survival and those that differentiate among the stages of disease and responses to therapy was found. CONCLUSIONS: Our results reflect the value of gene expression profiling to gain insight about the molecular alterations involved in the pathogenesis of T-cell lymphomas.

%B Clinical cancer research : an official journal of the American Association for Cancer Research %V 10 %P 4971-82 %8 2004 Aug 1 %G eng %U http://clincancerres.aacrjournals.org/content/10/15/4971.long %0 Journal Article %J Nucleic Acids Res %D 2003 %T EVA: Evaluation of protein structure prediction servers %A Koh, I. Y. %A Eyrich, V. A. %A M. A. Marti-Renom %A Przybylski, D. %A Madhusudhan, M. S. %A Eswar, N. %A Grana, O. %A Pazos, F. %A Valencia, A. %A Sali, A. %A Rost, B. %K Automation Databases %K Protein %K Protein Internet *Protein Conformation Protein Folding Protein Structure %K Protein Structural Homology %K Secondary Proteins/chemistry Reproducibility of Results *Sequence Analysis %X EVA (http://cubic.bioc.columbia.edu/eva/) is a web server for evaluation of the accuracy of automated protein structure prediction methods. The evaluation is updated automatically each week, to cope with the large number of existing prediction servers and the constant changes in the prediction methods. EVA currently assesses servers for secondary structure prediction, contact prediction, comparative protein structure modelling and threading/fold recognition. Every day, sequences of newly available protein structures in the Protein Data Bank (PDB) are sent to the servers and their predictions are collected. The predictions are then compared to the experimental structures once a week; the results are published on the EVA web pages. Over time, EVA has accumulated prediction results for a large number of proteins, ranging from hundreds to thousands, depending on the prediction method. This large sample assures that methods are compared reliably. As a result, EVA provides useful information to developers as well as users of prediction methods. %B Nucleic Acids Res %V 31 %P 3311-5 %G eng %U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12824315 %0 Journal Article %J J Biol Chem %D 2003 %T Examining the role of glutamic acid 183 in chloroperoxidase catalysis %A Yi, X. %A A. Conesa %A Punt, P. J. %A Hager, L. P. %K Aspergillus niger/metabolism Catalase/metabolism Catalysis Chloride Peroxidase/*chemistry/*metabolism Chlorine/metabolism Chromatography %K Ion Exchange Circular Dichroism Crystallography %K Polyacrylamide Gel Fungi/enzymology Glutamic Acid/*chemistry Histidine/chemistry/metabolism Hydrogen-Ion Concentration Immunoblotting Isoelectric Focusing Mutation Oxidoreductases/metabolism Plasmids/metabolism %K X-Ray Electrophoresis %X Site-directed mutagenesis has been used to investigate the role of glutamic acid 183 in chloroperoxidase catalysis. Based on the x-ray crystallographic structure of chloroperoxidase, Glu-183 is postulated to function on distal side of the heme prosthetic group as an acid-base catalyst in facilitating the reaction between the peroxidase and hydrogen peroxide with the formation of Compound I. In contrast, the other members of the heme peroxidase family use a histidine residue in this role. Plasmids have now been constructed in which the codon for Glu-183 is replaced with a histidine codon. The mutant recombinant gene has been expressed in Aspergillus niger. An analysis of the produced mutant gene shows that the substitution of Glu-183 with a His residue is detrimental to the chlorination and dismutation activity of chloroperoxidase. The activity is reduced by 85 and 50% of wild type activity, respectively. However, quite unexpectedly, the epoxidation activity of the mutant enzyme is significantly enhanced approximately 2.5-fold. These results show that Glu-183 is important but not essential for the chlorination activity of chloroperoxidase. It is possible that the increased epoxidation of the mutant enzyme is based on an increase in the hydrophobicity of the active site. %B J Biol Chem %V 278 %P 13855-9 %G eng %U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12576477 %0 Journal Article %J Bioinformatics %D 2001 %T EVA: continuous automatic evaluation of protein structure prediction servers %A Eyrich, V. A. %A M. A. Marti-Renom %A Przybylski, D. %A Madhusudhan, M. S. %A Fiser, A. %A Pazos, F. %A Valencia, A. %A Sali, A. %A Rost, B. %K Automation Internet *Protein Conformation Proteins/*analysis *Software %X Evaluation of protein structure prediction methods is difficult and time-consuming. Here, we describe EVA, a web server for assessing protein structure prediction methods, in an automated, continuous and large-scale fashion. Currently, EVA evaluates the performance of a variety of prediction methods available through the internet. Every week, the sequences of the latest experimentally determined protein structures are sent to prediction servers, results are collected, performance is evaluated, and a summary is published on the web. EVA has so far collected data for more than 3000 protein chains. These results may provide valuable insight to both developers and users of prediction methods. AVAILABILITY: http://cubic.bioc.columbia.edu/eva. CONTACT: eva@cubic.bioc.columbia.edu %B Bioinformatics %V 17 %P 1242-3 %G eng %U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11751240 %0 Journal Article %J J Biol Chem %D 2001 %T Expression of the Caldariomyces fumago chloroperoxidase in Aspergillus niger and characterization of the recombinant enzyme %A A. Conesa %A van De Velde, F. %A van Rantwijk, F. %A Sheldon, R. A. %A van den Hondel, C. A. %A Punt, P. J. %K Aspergillus niger/enzymology/genetics Catalysis Chloride Peroxidase/biosynthesis/*genetics Fungal Proteins/biosynthesis/*genetics Recombinant Proteins/biosynthesis/genetics Substrate Specificity %X The Caldariomyces fumago chloroperoxidase was successfully expressed in Aspergillus niger. The recombinant enzyme was produced in the culture medium as an active protein and could be purified by a three-step purification procedure. The catalytic behavior of recombinant chloroperoxidase (rCPO) was studied and compared with that of native CPO. The specific chlorination activity (47 units/nmol) of rCPO and its pH optimum (pH 2.75) were very similar to those of native CPO. rCPO catalyzes the oxidation of various substrates in comparable yields and selectivities to native CPO. Indole was oxidized to 2-oxindole with 99% selectivity and thioanisole to the corresponding R-sulfoxide (enantiomeric excess >98%). Incorporation of (18)O from labeled H(2)18O(2) into the oxidized products was 100% in both cases. %B J Biol Chem %V 276 %P 17635-40 %G eng %U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11278701