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  1. AU=Delgado-Chaves Fernando M AU=Delgado-Chaves Fernando M
  2. AU="Castresana, Mónica"
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  1. Artikel: Data of transcriptional effects of the merbarone-mediated inhibition of TOP2

    Delgado-Chaves, Fernando M. / Martínez-García, Pedro Manuel / Herrero-Ruiz, Andrés / Gómez-Vela, Francisco / Divina, Federico / Jimeno-González, Silvia / Cortés-Ledesma, Felipe

    Data in Brief. 2022 Oct., v. 44

    2022  

    Abstract: Type II DNA topoisomerases relax topological stress by transiently gating DNA passage in a controlled cut-and-reseal mechanism that affects both DNA strands. Therefore, they are essential to overcome topological problems associated with DNA metabolism. ... ...

    Abstract Type II DNA topoisomerases relax topological stress by transiently gating DNA passage in a controlled cut-and-reseal mechanism that affects both DNA strands. Therefore, they are essential to overcome topological problems associated with DNA metabolism. Their aberrant activity results in the generation of DNA double-strand breaks, which can seriously compromise cell survival and genome integrity. Here, we profile the transcriptome of human-telomerase-immortalized retinal pigment epithelial 1 (RPE-1) cells when treated with merbarone, a drug that catalytically inhibits type II DNA topoisomerases. We performed RNA-Seq after 4 and 8 h of merbarone treatment and compared transcriptional profiles versus untreated samples. We report raw sequencing data together with lists of gene counts and differentially expressed genes.
    Schlagwörter DNA ; cell viability ; drugs ; epithelium ; gene expression regulation ; genes ; metabolism ; sequence analysis ; topology ; transcription (genetics) ; transcriptome
    Sprache Englisch
    Erscheinungsverlauf 2022-10
    Erscheinungsort Elsevier Inc.
    Dokumenttyp Artikel
    ZDB-ID 2786545-9
    ISSN 2352-3409
    ISSN 2352-3409
    DOI 10.1016/j.dib.2022.108499
    Datenquelle NAL Katalog (AGRICOLA)

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  2. Artikel ; Online: Data of transcriptional effects of the merbarone-mediated inhibition of TOP2.

    Delgado-Chaves, Fernando M / Martínez-García, Pedro Manuel / Herrero-Ruiz, Andrés / Gómez-Vela, Francisco / Divina, Federico / Jimeno-González, Silvia / Cortés-Ledesma, Felipe

    Data in brief

    2022  Band 44, Seite(n) 108499

    Abstract: Type II DNA topoisomerases relax topological stress by transiently gating DNA passage in a controlled cut-and-reseal mechanism that affects both DNA strands. Therefore, they are essential to overcome topological problems associated with DNA metabolism. ... ...

    Abstract Type II DNA topoisomerases relax topological stress by transiently gating DNA passage in a controlled cut-and-reseal mechanism that affects both DNA strands. Therefore, they are essential to overcome topological problems associated with DNA metabolism. Their aberrant activity results in the generation of DNA double-strand breaks, which can seriously compromise cell survival and genome integrity. Here, we profile the transcriptome of human-telomerase-immortalized retinal pigment epithelial 1 (RPE-1) cells when treated with merbarone, a drug that catalytically inhibits type II DNA topoisomerases. We performed RNA-Seq after 4 and 8 h of merbarone treatment and compared transcriptional profiles versus untreated samples. We report raw sequencing data together with lists of gene counts and differentially expressed genes.
    Sprache Englisch
    Erscheinungsdatum 2022-08-01
    Erscheinungsland Netherlands
    Dokumenttyp Journal Article
    ZDB-ID 2786545-9
    ISSN 2352-3409 ; 2352-3409
    ISSN (online) 2352-3409
    ISSN 2352-3409
    DOI 10.1016/j.dib.2022.108499
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  3. Artikel ; Online: Computational Analysis of the Global Effects of

    Delgado-Chaves, Fernando M / Gómez-Vela, Francisco / Divina, Federico / García-Torres, Miguel / Rodriguez-Baena, Domingo S

    Genes

    2020  Band 11, Heft 7

    Abstract: Gene networks have arisen as a promising tool in the comprehensive modeling and analysis of complex diseases. Particularly in viral infections, the understanding of the host-pathogen mechanisms, and the immune response to these, is considered a major ... ...

    Abstract Gene networks have arisen as a promising tool in the comprehensive modeling and analysis of complex diseases. Particularly in viral infections, the understanding of the host-pathogen mechanisms, and the immune response to these, is considered a major goal for the rational design of appropriate therapies. For this reason, the use of gene networks may well encourage therapy-associated research in the context of the coronavirus pandemic, orchestrating experimental scrutiny and reducing costs. In this work, gene co-expression networks were reconstructed from RNA-Seq expression data with the aim of analyzing the time-resolved effects of gene
    Mesh-Begriff(e) Animals ; Antigens, Surface/genetics ; Antigens, Surface/immunology ; Computational Biology/methods ; Coronavirus Infections/genetics ; Coronavirus Infections/immunology ; GPI-Linked Proteins/genetics ; GPI-Linked Proteins/immunology ; Gene Expression Regulation ; Gene Regulatory Networks ; Host-Pathogen Interactions/genetics ; Host-Pathogen Interactions/immunology ; Mice, Knockout ; Murine hepatitis virus
    Chemische Substanzen Antigens, Surface ; GPI-Linked Proteins ; Ly6e protein, mouse
    Schlagwörter covid19
    Sprache Englisch
    Erscheinungsdatum 2020-07-21
    Erscheinungsland Switzerland
    Dokumenttyp Journal Article
    ZDB-ID 2527218-4
    ISSN 2073-4425 ; 2073-4425
    ISSN (online) 2073-4425
    ISSN 2073-4425
    DOI 10.3390/genes11070831
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  4. Artikel ; Online: Computational Inference of Gene Co-Expression Networks for the identification of Lung Carcinoma Biomarkers: An Ensemble Approach.

    Delgado-Chaves, Fernando M / Gómez-Vela, Francisco / García-Torres, Miguel / Divina, Federico / Vázquez Noguera, José Luis

    Genes

    2019  Band 10, Heft 12

    Abstract: ... biomarkers, genes N C K A P 1 L and D M D are highlighted due to their implications in a considerable portion ...

    Abstract Gene Networks (GN), have emerged as an useful tool in recent years for the analysis of different diseases in the field of biomedicine. In particular, GNs have been widely applied for the study and analysis of different types of cancer. In this context, Lung carcinoma is among the most common cancer types and its short life expectancy is partly due to late diagnosis. For this reason, lung cancer biomarkers that can be easily measured are highly demanded in biomedical research. In this work, we present an application of gene co-expression networks in the modelling of lung cancer gene regulatory networks, which ultimately served to the discovery of new biomarkers. For this, a robust GN inference was performed from microarray data concomitantly using three different co-expression measures. Results identified a major cluster of genes involved in SRP-dependent co-translational protein target to membrane, as well as a set of 28 genes that were exclusively found in networks generated from cancer samples. Amongst potential biomarkers, genes N C K A P 1 L and D M D are highlighted due to their implications in a considerable portion of lung and bronchus primary carcinomas. These findings demonstrate the potential of GN reconstruction in the rational prediction of biomarkers.
    Mesh-Begriff(e) Algorithms ; Biomarkers, Tumor/genetics ; Computational Biology ; Dystrophin/genetics ; Gene Expression ; Gene Regulatory Networks ; Humans ; Lung/metabolism ; Lung Neoplasms/genetics ; Membrane Proteins/genetics ; Mutation ; Smoking/genetics
    Chemische Substanzen Biomarkers, Tumor ; DMD protein, human ; Dystrophin ; Membrane Proteins ; NCKAP1L protein, human (144351-15-5)
    Sprache Englisch
    Erscheinungsdatum 2019-11-22
    Erscheinungsland Switzerland
    Dokumenttyp Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2527218-4
    ISSN 2073-4425 ; 2073-4425
    ISSN (online) 2073-4425
    ISSN 2073-4425
    DOI 10.3390/genes10120962
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  5. Artikel ; Online: Data of transcriptional effects of the merbarone-mediated inhibition of TOP2

    Fernando M. Delgado-Chaves / Pedro Manuel Martínez-García / Andrés Herrero-Ruiz / Francisco Gómez-Vela / Federico Divina / Silvia Jimeno-González / Felipe Cortés-Ledesma

    Data in Brief, Vol 44, Iss , Pp 108499- (2022)

    2022  

    Abstract: Type II DNA topoisomerases relax topological stress by transiently gating DNA passage in a controlled cut-and-reseal mechanism that affects both DNA strands. Therefore, they are essential to overcome topological problems associated with DNA metabolism. ... ...

    Abstract Type II DNA topoisomerases relax topological stress by transiently gating DNA passage in a controlled cut-and-reseal mechanism that affects both DNA strands. Therefore, they are essential to overcome topological problems associated with DNA metabolism. Their aberrant activity results in the generation of DNA double-strand breaks, which can seriously compromise cell survival and genome integrity. Here, we profile the transcriptome of human-telomerase-immortalized retinal pigment epithelial 1 (RPE-1) cells when treated with merbarone, a drug that catalytically inhibits type II DNA topoisomerases. We performed RNA-Seq after 4 and 8 h of merbarone treatment and compared transcriptional profiles versus untreated samples. We report raw sequencing data together with lists of gene counts and differentially expressed genes.
    Schlagwörter Topoisomerase inhibition ; Differential gene expression ; DNA supercoiling ; Merbarone ; RNA-Seq ; Computer applications to medicine. Medical informatics ; R858-859.7 ; Science (General) ; Q1-390
    Thema/Rubrik (Code) 612
    Sprache Englisch
    Erscheinungsdatum 2022-10-01T00:00:00Z
    Verlag Elsevier
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  6. Artikel ; Online: Computational Analysis of the Global Effects of Ly6E in the Immune Response to Coronavirus Infection Using Gene Networks

    Fernando M. Delgado-Chaves / Francisco Gómez-Vela / Federico Divina / Miguel García-Torres / Domingo S. Rodriguez-Baena

    Genes, Vol 11, Iss 831, p

    2020  Band 831

    Abstract: Gene networks have arisen as a promising tool in the comprehensive modeling and analysis of complex diseases. Particularly in viral infections, the understanding of the host-pathogen mechanisms, and the immune response to these, is considered a major ... ...

    Abstract Gene networks have arisen as a promising tool in the comprehensive modeling and analysis of complex diseases. Particularly in viral infections, the understanding of the host-pathogen mechanisms, and the immune response to these, is considered a major goal for the rational design of appropriate therapies. For this reason, the use of gene networks may well encourage therapy-associated research in the context of the coronavirus pandemic, orchestrating experimental scrutiny and reducing costs. In this work, gene co-expression networks were reconstructed from RNA-Seq expression data with the aim of analyzing the time-resolved effects of gene Ly6E in the immune response against the coronavirus responsible for murine hepatitis (MHV). Through the integration of differential expression analyses and reconstructed networks exploration, significant differences in the immune response to virus were observed in Ly6E <math display="inline"> <semantics> <msup> <mrow></mrow> <mrow> <mi>Δ</mi> <mi>H</mi> <mi>S</mi> <mi>C</mi> </mrow> </msup> </semantics> </math> compared to wild type animals. Results show that Ly6E ablation at hematopoietic stem cells (HSCs) leads to a progressive impaired immune response in both liver and spleen. Specifically, depletion of the normal leukocyte mediated immunity and chemokine signaling is observed in the liver of Ly6E <math display="inline"> <semantics> <msup> <mrow></mrow> <mrow> <mi>Δ</mi> <mi>H</mi> <mi>S</mi> <mi>C</mi> </mrow> </msup> </semantics> </math> mice. On the other hand, the immune response in the spleen, which seemed to be mediated by an intense chromatin activity in the normal situation, is replaced by ECM remodeling in Ly6E <math display="inline"> <semantics> <msup> <mrow></mrow> <mrow> <mi>Δ</mi> <mi>H</mi> ...
    Schlagwörter gene co-expression network ; murine coronavirus ; viral infection ; immune response ; data mining ; systems biology ; Genetics ; QH426-470
    Thema/Rubrik (Code) 570
    Sprache Englisch
    Erscheinungsdatum 2020-07-01T00:00:00Z
    Verlag MDPI AG
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  7. Artikel: Computational Analysis of the Global Effects of Ly6E in the Immune Response to Coronavirus Infection Using Gene Networks

    Delgado-Chaves, Fernando M / Gómez-Vela, Francisco / Divina, Federico / García-Torres, Miguel / Rodriguez-Baena, Domingo S

    Abstract: Gene networks have arisen as a promising tool in the comprehensive modeling and analysis of complex diseases. Particularly in viral infections, the understanding of the host-pathogen mechanisms, and the immune response to these, is considered a major ... ...

    Abstract Gene networks have arisen as a promising tool in the comprehensive modeling and analysis of complex diseases. Particularly in viral infections, the understanding of the host-pathogen mechanisms, and the immune response to these, is considered a major goal for the rational design of appropriate therapies. For this reason, the use of gene networks may well encourage therapy-associated research in the context of the coronavirus pandemic, orchestrating experimental scrutiny and reducing costs. In this work, gene co-expression networks were reconstructed from RNA-Seq expression data with the aim of analyzing the time-resolved effects of gene Ly6E in the immune response against the coronavirus responsible for murine hepatitis (MHV). Through the integration of differential expression analyses and reconstructed networks exploration, significant differences in the immune response to virus were observed in Ly6E Δ H S C compared to wild type animals. Results show that Ly6E ablation at hematopoietic stem cells (HSCs) leads to a progressive impaired immune response in both liver and spleen. Specifically, depletion of the normal leukocyte mediated immunity and chemokine signaling is observed in the liver of Ly6E Δ H S C mice. On the other hand, the immune response in the spleen, which seemed to be mediated by an intense chromatin activity in the normal situation, is replaced by ECM remodeling in Ly6E Δ H S C mice. These findings, which require further experimental characterization, could be extrapolated to other coronaviruses and motivate the efforts towards novel antiviral approaches.
    Schlagwörter covid19
    Verlag WHO
    Dokumenttyp Artikel
    Anmerkung WHO #Covidence: #670190
    Datenquelle COVID19

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  8. Artikel ; Online: Role of a cryptic tRNA gene operon in survival under translational stress.

    Santamaría-Gómez, Javier / Rubio, Miguel Ángel / López-Igual, Rocío / Romero-Losada, Ana B / Delgado-Chaves, Fernando M / Bru-Martínez, Roque / Romero-Campero, Francisco J / Herrero, Antonia / Ibba, Michael / Ochoa de Alda, Jesús A G / Luque, Ignacio

    Nucleic acids research

    2021  Band 49, Heft 15, Seite(n) 8757–8776

    Abstract: As compared to eukaryotes, bacteria have a reduced tRNA gene set encoding between 30 and 220 tRNAs. Although in most bacterial phyla tRNA genes are dispersed in the genome, many species from distinct phyla also show genes forming arrays. Here, we show ... ...

    Abstract As compared to eukaryotes, bacteria have a reduced tRNA gene set encoding between 30 and 220 tRNAs. Although in most bacterial phyla tRNA genes are dispersed in the genome, many species from distinct phyla also show genes forming arrays. Here, we show that two types of arrays with distinct evolutionary origins exist. This work focuses on long tRNA gene arrays (L-arrays) that encompass up to 43 genes, which disseminate by horizontal gene transfer and contribute supernumerary tRNA genes to the host. Although in the few cases previously studied these arrays were reported to be poorly transcribed, here we show that the L-array of the model cyanobacterium Anabaena sp. PCC 7120, encoding 23 functional tRNAs, is largely induced upon impairment of the translation machinery. The cellular response to this challenge involves a global reprogramming of the transcriptome in two phases. tRNAs encoded in the array are induced in the second phase of the response, directly contributing to cell survival. Results presented here show that in some bacteria the tRNA gene set may be partitioned between a housekeeping subset, which constantly sustains translation, and an inducible subset that is generally silent but can provide functionality under particular conditions.
    Mesh-Begriff(e) Anabaena/genetics ; Anti-Bacterial Agents/pharmacology ; Gene Expression Regulation, Bacterial ; Genes, Bacterial ; Genome, Bacterial ; Microbial Viability/genetics ; Operon ; Protein Biosynthesis ; RNA, Transfer/genetics ; RNA, Transfer/metabolism ; Regulatory Sequences, Nucleic Acid ; Stress, Physiological/genetics
    Chemische Substanzen Anti-Bacterial Agents ; RNA, Transfer (9014-25-9)
    Sprache Englisch
    Erscheinungsdatum 2021-08-11
    Erscheinungsland England
    Dokumenttyp Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 186809-3
    ISSN 1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
    ISSN (online) 1362-4962 ; 1362-4954
    ISSN 0301-5610 ; 0305-1048
    DOI 10.1093/nar/gkab661
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  9. Artikel ; Online: Ensemble and Greedy Approach for the Reconstruction of Large Gene Co-Expression Networks

    Francisco Gómez-Vela / Fernando M. Delgado-Chaves / Domingo S. Rodríguez-Baena / Miguel García-Torres / Federico Divina

    Entropy, Vol 21, Iss 12, p

    2019  Band 1139

    Abstract: Gene networks have become a powerful tool in the comprehensive analysis of gene expression. Due to the increasing amount of available data, computational methods for networks generation must deal with the so-called curse of dimensionality in the quest ... ...

    Abstract Gene networks have become a powerful tool in the comprehensive analysis of gene expression. Due to the increasing amount of available data, computational methods for networks generation must deal with the so-called curse of dimensionality in the quest for the reliability of the obtained results. In this context, ensemble strategies have significantly improved the precision of results by combining different measures or methods. On the other hand, structure optimization techniques are also important in the reduction of the size of the networks, not only improving their topology but also keeping a positive prediction ratio. In this work, we present Ensemble and Greedy networks (EnGNet), a novel two-step method for gene networks inference. First, EnGNet uses an ensemble strategy for co-expression networks generation. Second, a greedy algorithm optimizes both the size and the topological features of the network. Not only do achieved results show that this method is able to obtain reliable networks, but also that it significantly improves topological features. Moreover, the usefulness of the method is proven by an application to a human dataset on post-traumatic stress disorder, revealing an innate immunity-mediated response to this pathology. These results are indicative of the method’s potential in the field of biomarkers discovery and characterization.
    Schlagwörter gene networks ; scale-free networks ; ensemble networks ; graph theory ; computational biology ; mutual information networks ; biomarkers discovery ; Science ; Q ; Astrophysics ; QB460-466 ; Physics ; QC1-999
    Thema/Rubrik (Code) 000
    Sprache Englisch
    Erscheinungsdatum 2019-11-01T00:00:00Z
    Verlag MDPI AG
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  10. Artikel ; Online: Improved blood culture workflow in the time to detection of microorganisms placing incubators systems outside of microbiology laboratory.

    Orellana, M Angeles / Chaves, Fernando / Delgado, Rafael

    Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology

    2020  Band 51, Heft 3, Seite(n) 1103–1108

    Abstract: ... with one BACT/ALERT 3D module located in the microbiology laboratory (ML) (access 8 a.m. to 10 p.m.) and ... with BACT/ALERT VIRTUO. During the 8:00 a.m. to 10:00 p.m. shift, the average ETs were 3.54 ± 5.06 vs 1.59 ... reduction of time during the 10:00 p.m. to 8:00 a.m. shift, where the average ET was 10.52 ± 5.23 vs 1.00 ...

    Abstract Purpose: We analyzed the workflow of the blood culture procedure with one blood culture incubator in the microbiology laboratory, in comparison with the workflow with the incubators systems placing outside, and in a microbiology laboratory without 24-h staffing.
    Methods: We assessed the elapsed time (ET) and time-to-result (TTR) in the two laboratory workflows during 1 month period in consecutive years. First period with one BACT/ALERT 3D module located in the microbiology laboratory (ML) (access 8 a.m. to 10 p.m.) and second period with three BACT/ALERT VIRTUO modules (one located in ML and two in the core sample laboratory, access 24 h).
    Results: The mean ET with BACT/ALERT 3D was 7.09 ± 6.15 h and 1.32 ± 3.14 h with BACT/ALERT VIRTUO. During the 8:00 a.m. to 10:00 p.m. shift, the average ETs were 3.54 ± 5.06 vs 1.59 ± 1.29 h for the two time periods, respectively. Since the automated loading of bottles on the BACT/ALERT VIRTUO allows processing of blood cultures during the night shift, there was a significant reduction of time during the 10:00 p.m. to 8:00 a.m. shift, where the average ET was 10.52 ± 5.23 vs 1.00 ± 4.40 h, respectively. The percentage of positivity in the first period was 9.03% and 11.18% in the second (p = 0.0003). The average TTR in the first period was 24.78 ± 15.9 h and 16.85 ± 14.13 h in the second (p < 0.0001).
    Conclusions: Easy 24-h access to blood culture incubators resulted in significant improvement in the workflow of blood culture, decreasing ET, and therefore decreasing the time to positivity and the efficiency of recovery.
    Mesh-Begriff(e) Bacteria/genetics ; Bacteria/growth & development ; Bacteria/isolation & purification ; Bacteriological Techniques/instrumentation ; Bacteriological Techniques/methods ; Blood Culture/instrumentation ; Blood Culture/methods ; Humans ; Incubators ; Laboratories ; Time Factors ; Workflow
    Sprache Englisch
    Erscheinungsdatum 2020-05-18
    Erscheinungsland Brazil
    Dokumenttyp Journal Article
    ZDB-ID 2017175-4
    ISSN 1678-4405 ; 1517-8382
    ISSN (online) 1678-4405
    ISSN 1517-8382
    DOI 10.1007/s42770-020-00298-x
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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