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Article ; Online: ceRNA analysis of SARS-CoV-2.

Arancio, Walter

2020 Volume 166, Issue 1, Page(s) 271–274

Abstract: Viral RNAs can perturb the miRNA regulatory network, competing with host RNAs as part of their infective process. An in silico competing endogenous RNA (ceRNA) analysis has been carried on SARS-CoV-2. The results suggest that, in humans, the decrease of ... ...

Abstract	Viral RNAs can perturb the miRNA regulatory network, competing with host RNAs as part of their infective process. An in silico competing endogenous RNA (ceRNA) analysis has been carried on SARS-CoV-2. The results suggest that, in humans, the decrease of microRNA activity caused by viral RNAs can lead to a perturbation of vesicle trafficking and the inflammatory response, in particular by enhancing KLF10 activity. The results suggest also that, during the study of the mechanics of viral infections, it could be of general interest to investigate the competition of viral RNA with cellular transcripts for shared microRNAs.
MeSH term(s)	A549 Cells ; COVID-19/pathology ; Cell Line, Tumor ; Early Growth Response Transcription Factors/genetics ; Early Growth Response Transcription Factors/metabolism ; Gene Regulatory Networks/genetics ; Humans ; Kruppel-Like Transcription Factors/genetics ; Kruppel-Like Transcription Factors/metabolism ; MicroRNAs/genetics ; RNA, Messenger/genetics ; RNA, Viral/genetics ; SARS-CoV-2/genetics
Chemical Substances	Early Growth Response Transcription Factors ; KLF10 protein, human ; Kruppel-Like Transcription Factors ; MicroRNAs ; RNA, Messenger ; RNA, Viral
Keywords	covid19
Language	English
Publishing date	2020-11-17
Publishing country	Austria
Document type	Journal Article
ZDB-ID	7491-3
ISSN	1432-8798 ; 0304-8608
ISSN (online)	1432-8798
ISSN	0304-8608
DOI	10.1007/s00705-020-04856-4
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Article: ceRNA analysis of SARS-CoV-2

Arancio, Walter

Archives of virology. 2021 Jan., v. 166, no. 1

2021

Abstract	Viral RNAs can perturb the miRNA regulatory network, competing with host RNAs as part of their infective process. An in silico competing endogenous RNA (ceRNA) analysis has been carried on SARS-CoV-2. The results suggest that, in humans, the decrease of microRNA activity caused by viral RNAs can lead to a perturbation of vesicle trafficking and the inflammatory response, in particular by enhancing KLF10 activity. The results suggest also that, during the study of the mechanics of viral infections, it could be of general interest to investigate the competition of viral RNA with cellular transcripts for shared microRNAs.
Keywords	computer simulation ; humans ; inflammation ; lead ; mechanics ; microRNA ; physiological transport ; virology
Language	English
Dates of publication	2021-01
Size	p. 271-274.
Publishing place	Springer Vienna
Document type	Article
Note	NAL-light
ZDB-ID	7491-3
ISSN	1432-8798 ; 0304-8608
ISSN (online)	1432-8798
ISSN	0304-8608
DOI	10.1007/s00705-020-04856-4
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Progerin expression induces a significant downregulation of transcription from human repetitive sequences in iPSC-derived dopaminergic neurons.

Arancio, Walter

GeroScience

2019 Volume 41, Issue 1, Page(s) 39–49

Abstract: Repetitive DNA sequences represent about half of the human genome. They have a central role in human biology, especially neurobiology, but are notoriously difficult to study. The purpose of this study was to quantify the transcription from repetitive ... ...

Abstract	Repetitive DNA sequences represent about half of the human genome. They have a central role in human biology, especially neurobiology, but are notoriously difficult to study. The purpose of this study was to quantify the transcription from repetitive sequences in a progerin-expressing cellular model of neuronal aging. Progerin is a nuclear protein causative of the Hutchinson-Gilford progeria syndrome that is also incrementally expressed during the normal aging process. A dedicated pipeline of analysis allowed to quantify transcripts containing repetitive sequences from RNAseq datasets oblivious of their genomic localization, tolerating a sufficient degree of mutational noise, all with low computational requirements. The pipeline has been applied to a published panel of RNAseq datasets derived from a well-established and well-described cellular model of aging of dopaminergic neurons. Progerin expression strongly downregulated the transcription from all the classes of repetitive sequences: satellites, long and short interspersed nuclear elements, human endogenous retroviruses, and DNA transposon. The Alu element represented by far the principal source of transcript originating either from repetitive sequences or from canonical coding genes; it was expressed on average at 192,493.5 reads per kilobase million (RPKM) (SE = 21,081.3) in the control neurons and dropped to 43,760.1 RPKM (SE = 5315.0) in the progerin-expressing neurons, being significant downregulated (p = 0.0005). The results highlighted a global perturbation of transcripts derived from repetitive sequences in a cellular model of aging and provided a direct link between progerin expression and alteration of transcription from human repetitive elements.
MeSH term(s)	Aging/genetics ; Alu Elements/genetics ; Cellular Senescence/genetics ; Dopaminergic Neurons/physiology ; Down-Regulation/genetics ; Fibroblasts/physiology ; Humans ; Induced Pluripotent Stem Cells/physiology ; Lamin Type A/genetics ; Progeria/genetics ; Retroelements/genetics ; Transcription, Genetic/genetics
Chemical Substances	Lamin Type A ; Retroelements ; prelamin A
Language	English
Publishing date	2019-01-08
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2886586-8
ISSN	2509-2723 ; 2509-2715
ISSN (online)	2509-2723
ISSN	2509-2715
DOI	10.1007/s11357-018-00050-2
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Article: ceRNA analysis of SARS-CoV-2

Arancio, Walter

Arch. virol

Abstract	Viral RNAs can perturb the miRNA regulatory network, competing with host RNAs as part of their infective process. An in silico competing endogenous RNA (ceRNA) analysis has been carried on SARS-CoV-2. The results suggest that, in humans, the decrease of microRNA activity caused by viral RNAs can lead to a perturbation of vesicle trafficking and the inflammatory response, in particular by enhancing KLF10 activity. The results suggest also that, during the study of the mechanics of viral infections, it could be of general interest to investigate the competition of viral RNA with cellular transcripts for shared microRNAs.
Keywords	covid19
Publisher	WHO
Document type	Article
Note	WHO #Covidence: #928484
Database	COVID19

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Article ; Online: Repetitive Sequence Transcription in Breast Cancer.

Arancio, Walter / Coronnello, Claudia

Cells

2022 Volume 11, Issue 16

Abstract: Repetitive sequences represent about half of the human genome. They are actively transcribed and play a role during development and in epigenetic regulation. The altered activity of repetitive sequences can lead to genomic instability and they can ... ...

Abstract	Repetitive sequences represent about half of the human genome. They are actively transcribed and play a role during development and in epigenetic regulation. The altered activity of repetitive sequences can lead to genomic instability and they can contribute to the establishment or the progression of degenerative diseases and cancer transformation. In this work, we analyzed the expression profiles of DNA repetitive sequences in the breast cancer specimens of the HMUCC cohort. Satellite expression is generally upregulated in breast cancers, with specific families upregulated per histotype: in HER2-enriched cancers, they are the human satellite II (HSATII), in luminal A and B, they are part of the ALR family and in triple-negative, they are part of SAR and GSAT families, together with a perturbation in the transcription from endogenous retroviruses and their LTR sequences. We report that the background expression of repetitive sequences in healthy tissues of cancer patients differs from the tissues of non-cancerous controls. To conclude, peculiar patterns of expression of repetitive sequences are reported in each specimen, especially in the case of transcripts arising from satellite repeats.
MeSH term(s)	Breast Neoplasms/genetics ; Endogenous Retroviruses/genetics ; Epigenesis, Genetic ; Female ; Genome, Human ; Humans ; Repetitive Sequences, Nucleic Acid/genetics
Language	English
Publishing date	2022-08-14
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2661518-6
ISSN	2073-4409 ; 2073-4409
ISSN (online)	2073-4409
ISSN	2073-4409
DOI	10.3390/cells11162522
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Article ; Online: MBS: a genome browser annotation track for high-confident microRNA binding sites in whole human transcriptome.

Arancio, Walter / Sciaraffa, Nicolina / Coronnello, Claudia

Database : the journal of biological databases and curation

2023 Volume 2023

Abstract: MicroRNAs (miRNAs) are small non-coding ribonucleic acids (RNAs) that play a role in many regulatory pathways in eukaryotes. They usually exert their functions by binding mature messenger RNAs. The prediction of the binding targets of the endogenous ... ...

Abstract	MicroRNAs (miRNAs) are small non-coding ribonucleic acids (RNAs) that play a role in many regulatory pathways in eukaryotes. They usually exert their functions by binding mature messenger RNAs. The prediction of the binding targets of the endogenous miRNAs is crucial to unravel the processes they are involved in. In this work, we performed an extensive miRNA binding sites (MBS) prediction over all the annotated transcript sequences and made them available through an UCSC track. MBS annotation track allows to study and visualize the human miRNA binding sites transcriptome-wide in a genome browser, together with any other available information the user is interested in. In the creation of the database that underlies the MBS track, three consolidated algorithms of miRNA binding prediction have been used: PITA, miRanda and TargetScan, and information about the binding sites predicted by all of them has been collected. MBS track displays high-confident miRNA binding sites for the whole length of each human transcript, both coding and non-coding ones. Each annotation can redirect to a web page with the details of the miRNA binding and the involved transcripts. MBS can be easily applied to retrieve specific information such as the effects of alternative splicing on miRNA binding or when a specific miRNA binds an exon-exon junction in the mature RNA. Overall, MBS will be of great help for studying and visualizing, in a user-friendly mode, the predicted miRNA binding sites on all the transcripts arising from a gene or a region of interest. Database URL https://datasharingada.fondazionerimed.com:8080/MBS.
MeSH term(s)	Humans ; Transcriptome/genetics ; MicroRNAs/genetics ; MicroRNAs/metabolism ; Algorithms ; Genome ; Binding Sites
Chemical Substances	MicroRNAs
Language	English
Publishing date	2023-04-28
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2496706-3
ISSN	1758-0463 ; 1758-0463
ISSN (online)	1758-0463
ISSN	1758-0463
DOI	10.1093/database/baad015
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Article ; Online: Repetitive sequences in aging.

Arancio, Walter / Coronnello, Claudia

Aging

2021 Volume 13, Issue 8, Page(s) 10816–10817

MeSH term(s)	Aging/genetics ; Aging/immunology ; Cellular Senescence/genetics ; Cellular Senescence/immunology ; CpG Islands/genetics ; DNA Methylation/immunology ; Epigenesis, Genetic/immunology ; Genomic Instability/immunology ; Humans ; Interferon Type I/genetics ; Interferon Type I/metabolism ; Progeria/genetics ; Progeria/immunology ; Repetitive Sequences, Nucleic Acid ; Signal Transduction/genetics ; Signal Transduction/immunology
Chemical Substances	Interferon Type I
Language	English
Publishing date	2021-04-24
Publishing country	United States
Document type	Editorial
ISSN	1945-4589
ISSN (online)	1945-4589
DOI	10.18632/aging.203020
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Article ; Online: A bioinformatics analysis of Lamin-A regulatory network: a perspective on epigenetic involvement in Hutchinson-Gilford progeria syndrome.

Arancio, Walter

Rejuvenation research

2012 Volume 15, Issue 2, Page(s) 123–127

Abstract: Hutchinson-Gilford progeria syndrome (HGPS) is a rare human genetic disease that leads to premature aging. HGPS is caused by mutation in the Lamin-A (LMNA) gene that leads, in affected young individuals, to the accumulation of the progerin protein, ... ...

Abstract	Hutchinson-Gilford progeria syndrome (HGPS) is a rare human genetic disease that leads to premature aging. HGPS is caused by mutation in the Lamin-A (LMNA) gene that leads, in affected young individuals, to the accumulation of the progerin protein, usually present only in aging differentiated cells. Bioinformatics analyses of the network of interactions of the LMNA gene and transcripts are presented. The LMNA gene network has been analyzed using the BioGRID database (http://thebiogrid.org/) and related analysis tools such as Osprey (http://biodata.mshri.on.ca/osprey/servlet/Index) and GeneMANIA ( http://genemania.org/). The network of interaction of LMNA transcripts has been further analyzed following the competing endogenous (ceRNA) hypotheses (RNA cross-talk via microRNAs [miRNAs]) and using the miRWalk database and tools (www.ma.uni-heidelberg.de/apps/zmf/mirwalk/). These analyses suggest particular relevance of epigenetic modifiers (via acetylase complexes and specifically HTATIP histone acetylase) and adenosine triphosphate (ATP)-dependent chromatin remodelers (via pBAF, BAF, and SWI/SNF complexes).
MeSH term(s)	Adenosine Triphosphate/metabolism ; Aging ; Chromatin/metabolism ; Computational Biology/methods ; Databases, Genetic ; Epigenesis, Genetic ; Gene Regulatory Networks ; Humans ; Lamin Type A/metabolism ; Male ; Models, Biological ; Models, Genetic ; Progeria/genetics ; Progeria/metabolism ; Prostatic Neoplasms/metabolism ; Software
Chemical Substances	Chromatin ; Lamin Type A ; Adenosine Triphosphate (8L70Q75FXE)
Language	English
Publishing date	2012-04
Publishing country	United States
Document type	Journal Article
ZDB-ID	2150779-X
ISSN	1557-8577 ; 1549-1684
ISSN (online)	1557-8577
ISSN	1549-1684
DOI	10.1089/rej.2011.1250
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Article: An extended catalogue of ncRNAs in Streptomyces coelicolor reporting abundant tmRNA, RNase-P RNA and RNA fragments derived from pre-ribosomal RNA leader sequences

Arancio, Walter / Genovese, Swonild I / Benfante, Viviana / Gallo, Giuseppe / Coronnello, Claudia

Archives of microbiology. 2022 Sept., v. 204, no. 9

2022

Abstract: Streptomyces coelicolor is a model organism for studying streptomycetes. This genus possesses relevant medical and economical roles, because it produces many biologically active metabolites of pharmaceutical interest, including the majority of ... ...

Abstract	Streptomyces coelicolor is a model organism for studying streptomycetes. This genus possesses relevant medical and economical roles, because it produces many biologically active metabolites of pharmaceutical interest, including the majority of commercialized antibiotics. In this bioinformatic study, the transcriptome of S. coelicolor has been analyzed to identify novel RNA species and quantify the expression of both annotated and novel transcripts in solid and liquid growth medium cultures at different times. The major characteristics disclosed in this study are: (i) the diffuse antisense transcription; (ii) the great abundance of transfer-messenger RNAs (tmRNA); (iii) the abundance of rnpB transcripts, paramount for the RNase-P complex; and (iv) the presence of abundant fragments derived from pre-ribosomal RNA leader sequences of unknown biological function. Overall, this study extends the catalogue of ncRNAs in S. coelicolor and suggests an important role of non-coding transcription in the regulation of biologically active molecule production.
Keywords	RNA ; Streptomyces coelicolor ; bioactive compounds ; bioinformatics ; commercialization ; culture media ; liquids ; metabolites ; microbiology ; transcriptome
Language	English
Dates of publication	2022-09
Size	p. 582.
Publishing place	Springer Berlin Heidelberg
Document type	Article
ZDB-ID	124824-8
ISSN	1432-072X ; 0302-8933
ISSN (online)	1432-072X
ISSN	0302-8933
DOI	10.1007/s00203-022-03203-2
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: A multivariate statistical test for differential expression analysis.

Tumminello, Michele / Bertolazzi, Giorgio / Sottile, Gianluca / Sciaraffa, Nicolina / Arancio, Walter / Coronnello, Claudia

Scientific reports

2022 Volume 12, Issue 1, Page(s) 8265

Abstract: Statistical tests of differential expression usually suffer from two problems. Firstly, their statistical power is often limited when applied to small and skewed data sets. Secondly, gene expression data are usually discretized by applying arbitrary ... ...

Abstract	Statistical tests of differential expression usually suffer from two problems. Firstly, their statistical power is often limited when applied to small and skewed data sets. Secondly, gene expression data are usually discretized by applying arbitrary criteria to limit the number of false positives. In this work, a new statistical test obtained from a convolution of multivariate hypergeometric distributions, the Hy-test, is proposed to address these issues. Hy-test has been carried out on transcriptomic data from breast and kidney cancer tissues, and it has been compared with other differential expression analysis methods. Hy-test allows implicit discretization of the expression profiles and is more selective in retrieving both differential expressed genes and terms of Gene Ontology. Hy-test can be adopted together with other tests to retrieve information that would remain hidden otherwise, e.g., terms of (1) cell cycle deregulation for breast cancer and (2) "programmed cell death" for kidney cancer.
MeSH term(s)	Breast Neoplasms/genetics ; Female ; Gene Expression Profiling/methods ; Gene Ontology ; Humans ; Kidney Neoplasms/genetics ; Models, Statistical
Language	English
Publishing date	2022-05-18
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-022-12246-w
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