LIVIVO - The Search Portal for Life Sciences

zur deutschen Oberfläche wechseln
Advanced search

Search results

Result 1 - 4 of total 4

Search options

  1. Article ; Online: The Easy-to-Use SARS-CoV-2 Assembler for Genome Sequencing: Development Study.

    Rueca, Martina / Giombini, Emanuela / Messina, Francesco / Bartolini, Barbara / Di Caro, Antonino / Capobianchi, Maria Rosaria / Gruber, Cesare Em

    JMIR bioinformatics and biotechnology

    2022  Volume 3, Issue 1, Page(s) e31536

    Abstract: Background: Early sequencing and quick analysis of the SARS-CoV-2 genome have contributed to the understanding of the dynamics of COVID-19 epidemics and in designing countermeasures at a global level.: Objective: Amplicon-based next-generation ... ...

    Abstract Background: Early sequencing and quick analysis of the SARS-CoV-2 genome have contributed to the understanding of the dynamics of COVID-19 epidemics and in designing countermeasures at a global level.
    Objective: Amplicon-based next-generation sequencing (NGS) methods are widely used to sequence the SARS-CoV-2 genome and to identify novel variants that are emerging in rapid succession as well as harboring multiple deletions and amino acid-changing mutations.
    Methods: To facilitate the analysis of NGS sequencing data obtained from amplicon-based sequencing methods, here, we propose an easy-to-use SARS-CoV-2 genome assembler: the Easy-to-use SARS-CoV-2 Assembler (ESCA) pipeline.
    Results: Our results have shown that ESCA could perform high-quality genome assembly from Ion Torrent and Illumina raw data and help the user in easily correct low-coverage regions. Moreover, ESCA includes the possibility of comparing assembled genomes of multisample runs through an easy table format.
    Conclusions: In conclusion, ESCA automatically furnished a variant table output file, fundamental to rapidly recognizing variants of interest. Our pipeline could be a useful method for obtaining a complete, rapid, and accurate analysis even with minimal knowledge in bioinformatics.
    Language English
    Publishing date 2022-03-14
    Publishing country Canada
    Document type Journal Article
    ISSN 2563-3570
    ISSN (online) 2563-3570
    DOI 10.2196/31536
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  2. Article ; Online: ESCA pipeline: Easy-to-use SARS-CoV-2 genome Assembler

    Rueca, Martina / Giombini, Emanuela / Messina, Francesco / Bartolini, Barbara / Di Caro, Antonino / Capobianchi, Maria R. / Gruber, Cesare E.M.

    bioRxiv

    Abstract: Early sequencing and quick analysis of SARS-CoV-2 genome are contributing to un-derstand the dynamics of COVID19 epidemics and to countermeasures design at global level. Amplicon-based NGS methods are widely used to sequence the SARS-CoV-2 genome and to ... ...

    Abstract Early sequencing and quick analysis of SARS-CoV-2 genome are contributing to un-derstand the dynamics of COVID19 epidemics and to countermeasures design at global level. Amplicon-based NGS methods are widely used to sequence the SARS-CoV-2 genome and to identify novel variants that are emerging in rapid succession, harboring multiple deletions and amino acid changing mutations. To facilitate the analysis of NGS sequencing data obtained from amplicon-based sequencing methods, here we propose an easy-to-use SARS-CoV-2 genome Assembler: the ESCA pipeline. Results showed that ESCA can perform high quality genome assembly from IonTor-rent and Illumina raw data, and help the user in easily correct low-coverage regions. Moreover, ESCA includes the possibility to compare assembled genomes of multi sample runs through an easy table format.
    Keywords covid19
    Language English
    Publishing date 2021-05-21
    Publisher Cold Spring Harbor Laboratory
    Document type Article ; Online
    DOI 10.1101/2021.05.21.445156
    Database COVID19

    Full text online

    Kategorien

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  3. Article ; Online: Laboratory management of Crimean-Congo haemorrhagic fever virus infections: perspectives from two European networks.

    Bartolini, Barbara / Gruber, Cesare Em / Koopmans, Marion / Avšič, Tatjana / Bino, Sylvia / Christova, Iva / Grunow, Roland / Hewson, Roger / Korukluoglu, Gulay / Lemos, Cinthia Menel / Mirazimi, Ali / Papa, Anna / Sanchez-Seco, Maria Paz / Sauer, Aisha V / Zeller, Hervè / Nisii, Carla / Capobianchi, Maria Rosaria / Ippolito, Giuseppe / Reusken, Chantal B /
    Di Caro, Antonino

    Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin

    2019  Volume 24, Issue 5

    Abstract: BackgroundCrimean-Congo haemorrhagic fever virus (CCHFV) is considered an emerging infectious disease threat in the European Union. Since 2000, the incidence and geographic range of confirmed CCHF cases have markedly increased, following changes in the ... ...

    Abstract BackgroundCrimean-Congo haemorrhagic fever virus (CCHFV) is considered an emerging infectious disease threat in the European Union. Since 2000, the incidence and geographic range of confirmed CCHF cases have markedly increased, following changes in the distribution of its main vector,
    MeSH term(s) Animals ; Clinical Laboratory Techniques/methods ; Communicable Diseases, Emerging/epidemiology ; DNA, Viral/analysis ; DNA, Viral/genetics ; Disease Outbreaks/prevention & control ; Enzyme-Linked Immunosorbent Assay ; Hemorrhagic Fever Virus, Crimean-Congo/genetics ; Hemorrhagic Fever Virus, Crimean-Congo/immunology ; Hemorrhagic Fever Virus, Crimean-Congo/isolation & purification ; Hemorrhagic Fever, Crimean/diagnosis ; Hemorrhagic Fever, Crimean/epidemiology ; Hemorrhagic Fever, Crimean/transmission ; Hemorrhagic Fever, Crimean/virology ; Humans ; Immunoglobulin G/blood ; Ixodidae ; Laboratories ; Laboratory Proficiency Testing/methods ; Laboratory Proficiency Testing/standards ; Sequence Analysis, RNA ; Ticks/virology
    Chemical Substances DNA, Viral ; Immunoglobulin G
    Language English
    Publishing date 2019-01-31
    Publishing country Sweden
    Document type Journal Article ; Review
    ZDB-ID 1338803-4
    ISSN 1560-7917 ; 1025-496X
    ISSN (online) 1560-7917
    ISSN 1025-496X
    DOI 10.2807/1560-7917.ES.2019.24.5.1800093
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    In stock of ZB MED Cologne/Königswinter

    Zs.A 5066: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (2.OG)
    ab Jg. 2022: Lesesaal (EG)

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

  4. Article: Microarray gene expression profiling of neural tissues in bovine spastic paresis

    Pariset, Lorraine / Bongiorni, Silvia / Bueno, Susana / Gruber, Cesare EM / Prosperini, Gianluca / Chillemi, Giovanni / Bicorgna, Silvia / Gentile, Arcangelo / Valentini, Alessio

    BMC veterinary research. 2013 Dec., v. 9, no. 1

    2013  

    Abstract: BACKGROUND: Bovine Spastic Paresis (BSP) is a neuromuscular disorder which affects both male and female cattle. BSP is characterized by spastic contraction and overextension of the gastrocnemious muscle of one or both limbs and is associated with a ... ...

    Abstract BACKGROUND: Bovine Spastic Paresis (BSP) is a neuromuscular disorder which affects both male and female cattle. BSP is characterized by spastic contraction and overextension of the gastrocnemious muscle of one or both limbs and is associated with a scarce increase in body weight. This disease seems to be caused by an autosomal and recessive gene, with incomplete penetration, although no genes clearly involved with its onset have been so far identified. We employed cDNA microarrays to identify metabolic pathways affected by BSP in Romagnola cattle breed. Investigation of those pathways at the genome level can help to understand this disease. RESULTS: Microarray analysis of control and affected individuals resulted in 268 differentially expressed genes. These genes were subjected to KEGG pathway functional clustering analysis, revealing that they are predominantly involved in Cell Communication, Signalling Molecules and Interaction and Signal Transduction, Diseases and Nervous System classes. Significantly enriched KEGG pathway’s classes for the differentially expressed genes were calculated; interestingly, all those significantly under-expressed in the affected samples are included in Neurodegenerative Diseases. To identify genome locations possibly harbouring gene(s) involved in the disease, the chromosome distribution of the differentially expressed genes was also investigated. CONCLUSIONS: The cDNA microarray we used in this study contains a brain library and, even if carrying an incomplete transcriptome representation, it has proven to be a valuable tool allowing us to add useful and new information to a poorly studied disease. By using this tool, we examined nearly 15000 transcripts and analysed gene pathways affected by the disease. Particularly, our data suggest also a defective glycinergic synaptic transmission in the development of the disease and an alteration of calcium signalling proteins. We provide data to acquire knowledge of a genetic disease for which literature still presents poor results and that could be further and specifically analysed in the next future. Moreover this study, performed in livestock, may also harbour molecular information useful for understanding human diseases.
    Keywords biochemical pathways ; body weight ; brain ; calcium ; cattle ; cattle breeds ; chromosomes ; cluster analysis ; complementary DNA ; disease transmission ; gene expression ; genetic disorders ; human diseases ; microarray technology ; muscles ; nervous system diseases ; paresis ; proteins ; recessive genes ; signal transduction ; synaptic transmission ; transcriptome
    Language English
    Dates of publication 2013-12
    Size p. 687.
    Publishing place Springer-Verlag
    Document type Article
    ISSN 1746-6148
    DOI 10.1186/1746-6148-9-122
    Database NAL-Catalogue (AGRICOLA)

    More links

    Kategorien

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

To top