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  1. Article ; Online: Understanding virus-host interactions in tissues.

    Speranza, Emily

    Nature microbiology

    2023  Volume 8, Issue 8, Page(s) 1397–1407

    Abstract: Although virus-host interactions are usually studied in a single cell type using in vitro assays in immortalized cell lines or isolated cell populations, it is important to remember that what is happening inside one infected cell does not translate to ... ...

    Abstract Although virus-host interactions are usually studied in a single cell type using in vitro assays in immortalized cell lines or isolated cell populations, it is important to remember that what is happening inside one infected cell does not translate to understanding how an infected cell behaves in a tissue, organ or whole organism. Infections occur in complex tissue environments, which contain a host of factors that can alter the course of the infection, including immune cells, non-immune cells and extracellular-matrix components. These factors affect how the host responds to the virus and form the basis of the protective response. To understand virus infection, tools are needed that can profile the tissue environment. This Review highlights methods to study virus-host interactions in the infection microenvironment.
    MeSH term(s) Humans ; Host Microbial Interactions ; Viruses ; Virus Diseases ; Cell Line
    Language English
    Publishing date 2023-07-24
    Publishing country England
    Document type Journal Article ; Review ; Research Support, Non-U.S. Gov't
    ISSN 2058-5276
    ISSN (online) 2058-5276
    DOI 10.1038/s41564-023-01434-7
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Children primed and ready for SARS-CoV-2.

    Speranza, Emily

    Nature microbiology

    2021  Volume 6, Issue 11, Page(s) 1337–1338

    MeSH term(s) COVID-19/immunology ; Child ; Humans ; Immunity, Innate ; RNA-Seq ; Ribonucleoproteins, Small Cytoplasmic ; SARS-CoV-2 ; Severity of Illness Index
    Chemical Substances Ribonucleoproteins, Small Cytoplasmic
    Language English
    Publishing date 2021-10-20
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Intramural
    ISSN 2058-5276
    ISSN (online) 2058-5276
    DOI 10.1038/s41564-021-00984-y
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article: Preservation of scRNA-Seq Libraries Using Existing Inactivation Protocols.

    Sturdevant, Gail L / Meade-White, Kimberly D / Best, Sonja M / Speranza, Emily

    Pathogens (Basel, Switzerland)

    2024  Volume 13, Issue 2

    Abstract: Single-cell RNA sequencing has soared in popularity in recent years. The ability to deeply profile the states of individual cells during the course of disease or infection has helped to expand our knowledge of coordinated responses. However, significant ... ...

    Abstract Single-cell RNA sequencing has soared in popularity in recent years. The ability to deeply profile the states of individual cells during the course of disease or infection has helped to expand our knowledge of coordinated responses. However, significant challenges arise when performing this analysis in high containment settings such as biosafety level 3 (BSL-3), BSL-3+ and BSL-4. Working in containment is necessary for many important pathogens, such as Ebola virus, Marburg virus, Lassa virus, Nipah and Hendra viruses. Since standard operating procedures (SOPs) for inactivation are extensive and may compromise sample integrity, we tested whether the removal of single-cell sequencing libraries from containment laboratories using existing inactivation protocols for nucleic acid extraction (Trizol, RLT buffer, or AVL buffer) was feasible. We have demonstrated that the inactivation does not affect sample quality and can work with existing methods for inactivation.
    Language English
    Publishing date 2024-02-13
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2695572-6
    ISSN 2076-0817
    ISSN 2076-0817
    DOI 10.3390/pathogens13020167
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article: Spatial Patterning Analysis of Cellular Ensembles (SPACE) enables statistically robust discovery of complex spatial organization at the cell and tissue level.

    Schrom, Edward C / McCaffrey, Erin F / Radtke, Andrea J / Speranza, Emily / Arakkal, Leanne / Thakur, Nishant / Grant, Spencer / Germain, Ronald N

    bioRxiv : the preprint server for biology

    2023  

    Abstract: Spatial patterns of cells and other entities drive both physiologic and pathologic processes within tissues. While many imaging and transcriptomic methods document tissue organization, discerning these patterns is challenging, especially when they ... ...

    Abstract Spatial patterns of cells and other entities drive both physiologic and pathologic processes within tissues. While many imaging and transcriptomic methods document tissue organization, discerning these patterns is challenging, especially when they involve multiple entities in complex arrangements. To address this challenge, we present Spatial Patterning Analysis of Cellular Ensembles (SPACE), an R package for analysis of high-plex tissue images generated using any collection modality. Unlike existing platforms, SPACE detects context-dependent associations, quantitative gradients and orientations, and other organizational complexities. Via a robust information theoretic framework, SPACE explores all possible ensembles - single entities, pairs, triplets, and so on - and ranks the strongest patterns of tissue organization. Using lymph node images for which ground truth has been defined, we validate SPACE and demonstrate its advantages. We then use SPACE to reanalyze a public dataset of human tuberculosis granulomas, verifying known patterns and discovering new patterns with possible insights into disease progression.
    Language English
    Publishing date 2023-12-10
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.12.08.570837
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article: Host Transcriptional Response to Ebola Virus Infection.

    Speranza, Emily / Connor, John H

    Vaccines

    2017  Volume 5, Issue 3

    Abstract: Ebola virus disease (EVD) is a serious illness that causes severe disease in humans and non-human primates (NHPs) and has mortality rates up to 90%. EVD is caused by ... ...

    Abstract Ebola virus disease (EVD) is a serious illness that causes severe disease in humans and non-human primates (NHPs) and has mortality rates up to 90%. EVD is caused by the
    Language English
    Publishing date 2017-09-20
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2703319-3
    ISSN 2076-393X
    ISSN 2076-393X
    DOI 10.3390/vaccines5030030
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Host Transcriptional Response to Ebola Virus Infection

    Emily Speranza / John H Connor

    Vaccines, Vol 5, Iss 3, p

    2017  Volume 30

    Abstract: Ebola virus disease (EVD) is a serious illness that causes severe disease in humans and non-human primates (NHPs) and has mortality rates up to 90%. EVD is caused by the Ebolavirus and currently there are no licensed therapeutics or vaccines to treat EVD. ...

    Abstract Ebola virus disease (EVD) is a serious illness that causes severe disease in humans and non-human primates (NHPs) and has mortality rates up to 90%. EVD is caused by the Ebolavirus and currently there are no licensed therapeutics or vaccines to treat EVD. Due to its high mortality rates and potential as a bioterrorist weapon, a better understanding of the disease is of high priority. Multiparametric analysis techniques allow for a more complete understanding of a disease and the host response. Analysis of RNA species present in a sample can lead to a greater understanding of activation or suppression of different states of the immune response. Transcriptomic analyses such as microarrays and RNA-Sequencing (RNA-Seq) have been important tools to better understand the global gene expression response to EVD. In this review, we outline the current knowledge gained by transcriptomic analysis of EVD.
    Keywords Ebola virus disease ; host response ; transcriptomic ; RNA-Seq ; microarray ; immune response ; Medicine ; R
    Language English
    Publishing date 2017-09-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Article ; Online: Author Correction: Commensal-driven immune zonation of the liver promotes host defence.

    Gola, Anita / Dorrington, Michael G / Speranza, Emily / Sala, Claudia / Shih, Rochelle M / Radtke, Andrea J / Wong, Harikesh S / Baptista, Antonio P / Hernandez, Jonathan M / Castellani, Gastone / Fraser, Iain D C / Germain, Ronald N

    Nature

    2022  Volume 611, Issue 7935, Page(s) E7

    Language English
    Publishing date 2022-10-24
    Publishing country England
    Document type Published Erratum
    ZDB-ID 120714-3
    ISSN 1476-4687 ; 0028-0836
    ISSN (online) 1476-4687
    ISSN 0028-0836
    DOI 10.1038/s41586-022-05462-x
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 26: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)
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    Zs.MO 244: Show issues

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  8. Article ; Online: Pulmonary infection induces persistent, pathogen-specific lipidomic changes influencing trained immunity.

    Roberts, Lydia M / Schwarz, Benjamin / Speranza, Emily / Leighton, Ian / Wehrly, Tara / Best, Sonja / Bosio, Catharine M

    iScience

    2021  Volume 24, Issue 9, Page(s) 103025

    Abstract: Resolution of infection results in development of trained innate immunity which is typically beneficial for defense against unrelated secondary infection. Epigenetic changes including modification of histones via binding of various polar metabolites ... ...

    Abstract Resolution of infection results in development of trained innate immunity which is typically beneficial for defense against unrelated secondary infection. Epigenetic changes including modification of histones via binding of various polar metabolites underlie the establishment of trained innate immunity. Therefore, host metabolism and this response are intimately linked. However, little is known regarding the influence of lipids on the development and function of trained immunity. Utilizing two models of pulmonary bacterial infection combined with multi-omic approaches, we identified persistent, pathogen-specific changes to the lung lipidome that correlated with differences in the trained immune response against a third unrelated pathogen. Further, we establish the specific cellular populations in the lung that contribute to this altered lipidome. Together these results expand our understanding of the pulmonary trained innate immune response and the contributions of host lipids in informing that response.
    Language English
    Publishing date 2021-08-24
    Publishing country United States
    Document type Journal Article
    ISSN 2589-0042
    ISSN (online) 2589-0042
    DOI 10.1016/j.isci.2021.103025
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Pulmonary infection induces persistent, pathogen-specific lipidomic changes influencing trained immunity

    Lydia M. Roberts / Benjamin Schwarz / Emily Speranza / Ian Leighton / Tara Wehrly / Sonja Best / Catharine M. Bosio

    iScience, Vol 24, Iss 9, Pp 103025- (2021)

    2021  

    Abstract: Summary: Resolution of infection results in development of trained innate immunity which is typically beneficial for defense against unrelated secondary infection. Epigenetic changes including modification of histones via binding of various polar ... ...

    Abstract Summary: Resolution of infection results in development of trained innate immunity which is typically beneficial for defense against unrelated secondary infection. Epigenetic changes including modification of histones via binding of various polar metabolites underlie the establishment of trained innate immunity. Therefore, host metabolism and this response are intimately linked. However, little is known regarding the influence of lipids on the development and function of trained immunity. Utilizing two models of pulmonary bacterial infection combined with multi-omic approaches, we identified persistent, pathogen-specific changes to the lung lipidome that correlated with differences in the trained immune response against a third unrelated pathogen. Further, we establish the specific cellular populations in the lung that contribute to this altered lipidome. Together these results expand our understanding of the pulmonary trained innate immune response and the contributions of host lipids in informing that response.
    Keywords Biological sciences ; Immunity ; Genomics ; Lipidomics ; Science ; Q
    Language English
    Publishing date 2021-09-01T00:00:00Z
    Publisher Elsevier
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

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  10. Article ; Online: Author Correction: Commensal-driven immune zonation of the liver promotes host defence.

    Gola, Anita / Dorrington, Michael G / Speranza, Emily / Sala, Claudia / Shih, Rochelle M / Radtke, Andrea J / Wong, Harikesh S / Baptista, Antonio P / Hernandez, Jonathan M / Castellani, Gastone / Fraser, Iain D C / Germain, Ronald N

    Nature

    2021  Volume 597, Issue 7874, Page(s) E1

    Abstract: A Correction to this paper has been published: https://doi.org/10.1038/s41586-021-03346-0. ...

    Abstract A Correction to this paper has been published: https://doi.org/10.1038/s41586-021-03346-0.
    Language English
    Publishing date 2021-08-09
    Publishing country England
    Document type Published Erratum
    ZDB-ID 120714-3
    ISSN 1476-4687 ; 0028-0836
    ISSN (online) 1476-4687
    ISSN 0028-0836
    DOI 10.1038/s41586-021-03346-0
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 26: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)
    Zs.MG 9: Show issues
    Zs.MO 244: Show issues

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