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  1. Article ; Online: Profiling Host MicroRNA Responses to Henipavirus Infection.

    Farr, Ryan J / Dahal, Sudeep / Tribolet, Leon / Bean, Andrew G D / Cowled, Christopher / Stewart, Cameron R

    Methods in molecular biology (Clifton, N.J.)

    2023  Volume 2682, Page(s) 261–279

    Abstract: Diseases caused by henipaviruses feature incubation periods of up to 16 days, during which infected animals may show no apparent signs of disease yet be capable of transmitting the virus to humans. This risk has prompted research into host-derived ... ...

    Abstract Diseases caused by henipaviruses feature incubation periods of up to 16 days, during which infected animals may show no apparent signs of disease yet be capable of transmitting the virus to humans. This risk has prompted research into host-derived biomarkers for early disease detection. Here, we describe a methodology for the assaying of host microRNAs (miRs), small non-coding RNAs that show promise as biomarkers for several human diseases and are responsive during early-stage henipavirus infection. In addition to their potential as disease biomarkers, miRNA profiling of henipavirus infections provides insight into cellular and immune pathways associated with disease pathogenesis.
    MeSH term(s) Animals ; Humans ; Henipavirus Infections ; Biological Assay ; MicroRNAs/genetics
    Chemical Substances MicroRNAs
    Language English
    Publishing date 2023-08-22
    Publishing country United States
    Document type Journal Article
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-0716-3283-3_19
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  2. Article ; Online: Detection of SARS-CoV-2 infection by microRNA profiling of the upper respiratory tract.

    Farr, Ryan J / Rootes, Christina L / Stenos, John / Foo, Chwan Hong / Cowled, Christopher / Stewart, Cameron R

    PloS one

    2022  Volume 17, Issue 4, Page(s) e0265670

    Abstract: Host biomarkers are increasingly being considered as tools for improved COVID-19 detection and prognosis. We recently profiled circulating host-encoded microRNA (miRNAs) during SARS-CoV-2 infection, revealing a signature that classified COVID-19 cases ... ...

    Abstract Host biomarkers are increasingly being considered as tools for improved COVID-19 detection and prognosis. We recently profiled circulating host-encoded microRNA (miRNAs) during SARS-CoV-2 infection, revealing a signature that classified COVID-19 cases with 99.9% accuracy. Here we sought to develop a signature suited for clinical application by analyzing specimens collected using minimally invasive procedures. Eight miRNAs displayed altered expression in anterior nasal tissues from COVID-19 patients, with miR-142-3p, a negative regulator of interleukin-6 (IL-6) production, the most strongly upregulated. Supervised machine learning analysis revealed that a three-miRNA signature (miR-30c-2-3p, miR-628-3p and miR-93-5p) independently classifies COVID-19 cases with 100% accuracy. This study further defines the host miRNA response to SARS-CoV-2 infection and identifies candidate biomarkers for improved COVID-19 detection.
    MeSH term(s) Biomarkers ; COVID-19/diagnosis ; Gene Expression Profiling ; Humans ; MicroRNAs/genetics ; MicroRNAs/metabolism ; Respiratory System/metabolism ; SARS-CoV-2/genetics
    Chemical Substances Biomarkers ; MIRN628 microRNA, human ; MicroRNAs
    Language English
    Publishing date 2022-04-05
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2267670-3
    ISSN 1932-6203 ; 1932-6203
    ISSN (online) 1932-6203
    ISSN 1932-6203
    DOI 10.1371/journal.pone.0265670
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  3. Article ; Online: MicroRNA Profiling from Tears as a Potential Non-invasive Method for Early Detection of Diabetic Retinopathy.

    Wong, Wilson K M / Polkamp, Mya / Farr, Ryan J / Kunte, Pooja S / Hardikar, Hrishikesh P / Yajnik, Chittaranjan S / Hardikar, Anandwardhan A / Joglekar, Mugdha V

    Methods in molecular biology (Clifton, N.J.)

    2023  Volume 2678, Page(s) 117–134

    Abstract: Diabetic retinopathy (DR) is a vascular complication of diabetes that can lead to partial or complete loss of vision. Early detection and treatment of DR can prevent blindness. Regular clinical examination is recommended for DR diagnosis; however, it is ... ...

    Abstract Diabetic retinopathy (DR) is a vascular complication of diabetes that can lead to partial or complete loss of vision. Early detection and treatment of DR can prevent blindness. Regular clinical examination is recommended for DR diagnosis; however, it is not always possible or feasible due to limited resources, expertise, time, and infrastructure. Several clinical and molecular biomarkers are proposed for the prediction of DR including microRNAs. MicroRNAs are a class of small non-coding RNAs that are found in biofluids and can be measured using reliable and sensitive methods. The most commonly used biofluid for microRNA profiling is plasma or serum; however, tear fluid (tears) is also demonstrated to contain microRNAs. MicroRNAs isolated from tears present a non-invasive source for DR detection. Different methods of microRNA profiling are available including digital PCR-based methods that can detect up to a single copy of microRNA in the biofluids. Here, we describe microRNA isolation from tears using manual method as well as using a high-throughput automated platform followed by microRNA profiling using digital PCR system.
    MeSH term(s) Humans ; Diabetic Retinopathy/diagnosis ; Diabetic Retinopathy/genetics ; MicroRNAs/genetics ; MicroRNAs/analysis ; Early Diagnosis ; Tears/chemistry ; Biomarkers/analysis ; Diabetes Mellitus
    Chemical Substances MicroRNAs ; Biomarkers
    Language English
    Publishing date 2023-06-16
    Publishing country United States
    Document type Journal Article
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-0716-3255-0_8
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  4. Article ; Online: Neutrophil-Associated Responses to Vibrio cholerae Infection in a Natural Host Model.

    Farr, Dustin / Nag, Dhrubajyoti / Chazin, Walter J / Harrison, Simone / Thummel, Ryan / Luo, Xixia / Raychaudhuri, Saumya / Withey, Jeffrey H

    Infection and immunity

    2022  Volume 90, Issue 3, Page(s) e0046621

    Abstract: Vibrio cholerae, the cause of human cholera, is an aquatic bacterium found in association with a variety of animals in the environment, including many teleost fish species. V. cholerae infection induces a proinflammatory response followed by a ... ...

    Abstract Vibrio cholerae, the cause of human cholera, is an aquatic bacterium found in association with a variety of animals in the environment, including many teleost fish species. V. cholerae infection induces a proinflammatory response followed by a noninflammatory convalescent phase. Neutrophils are integral to this early immune response. However, the relationship between the neutrophil-associated protein calprotectin and V. cholerae has not been investigated, nor have the effects of limiting transition metals on V. cholerae growth. Zebrafish are useful as a natural V. cholerae model as the entire infectious cycle can be recapitulated in the presence of an intact intestinal microbiome and mature immune responses. Here, we demonstrate that zebrafish produce a significant neutrophil, interleukin 8 (IL-8), and calprotectin response following V. cholerae infection. Bacterial growth was completely inhibited by purified calprotectin protein or the chemical chelator
    MeSH term(s) Animals ; Cholera/microbiology ; Leukocyte L1 Antigen Complex ; Neutrophils ; Vibrio cholerae/physiology ; Zebrafish
    Chemical Substances Leukocyte L1 Antigen Complex
    Language English
    Publishing date 2022-01-24
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 218698-6
    ISSN 1098-5522 ; 0019-9567
    ISSN (online) 1098-5522
    ISSN 0019-9567
    DOI 10.1128/iai.00466-21
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    Zs.A 684: Show issues Location:
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  5. Article ; Online: Detection of SARS-CoV-2 infection by microRNA profiling of the upper respiratory tract.

    Ryan J Farr / Christina L Rootes / John Stenos / Chwan Hong Foo / Christopher Cowled / Cameron R Stewart

    PLoS ONE, Vol 17, Iss 4, p e

    2022  Volume 0265670

    Abstract: Host biomarkers are increasingly being considered as tools for improved COVID-19 detection and prognosis. We recently profiled circulating host-encoded microRNA (miRNAs) during SARS-CoV-2 infection, revealing a signature that classified COVID-19 cases ... ...

    Abstract Host biomarkers are increasingly being considered as tools for improved COVID-19 detection and prognosis. We recently profiled circulating host-encoded microRNA (miRNAs) during SARS-CoV-2 infection, revealing a signature that classified COVID-19 cases with 99.9% accuracy. Here we sought to develop a signature suited for clinical application by analyzing specimens collected using minimally invasive procedures. Eight miRNAs displayed altered expression in anterior nasal tissues from COVID-19 patients, with miR-142-3p, a negative regulator of interleukin-6 (IL-6) production, the most strongly upregulated. Supervised machine learning analysis revealed that a three-miRNA signature (miR-30c-2-3p, miR-628-3p and miR-93-5p) independently classifies COVID-19 cases with 100% accuracy. This study further defines the host miRNA response to SARS-CoV-2 infection and identifies candidate biomarkers for improved COVID-19 detection.
    Keywords Medicine ; R ; Science ; Q
    Language English
    Publishing date 2022-01-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  6. Article ; Online: Machine Learning Identifies Cellular and Exosomal MicroRNA Signatures of Lyssavirus Infection in Human Stem Cell-Derived Neurons.

    Farr, Ryan J / Godde, Nathan / Cowled, Christopher / Sundaramoorthy, Vinod / Green, Diane / Stewart, Cameron / Bingham, John / O'Brien, Carmel M / Dearnley, Megan

    Frontiers in cellular and infection microbiology

    2021  Volume 11, Page(s) 783140

    Abstract: Despite being vaccine preventable, rabies (lyssavirus) still has a significant impact on global mortality, disproportionally affecting children under 15 years of age. This neurotropic virus is deft at avoiding the immune system while travelling through ... ...

    Abstract Despite being vaccine preventable, rabies (lyssavirus) still has a significant impact on global mortality, disproportionally affecting children under 15 years of age. This neurotropic virus is deft at avoiding the immune system while travelling through neurons to the brain. Until recently, research efforts into the role of non-coding RNAs in rabies pathogenicity and detection have been hampered by a lack of human
    MeSH term(s) Exosomes ; Humans ; Lyssavirus/genetics ; Machine Learning ; MicroRNAs/genetics ; Neurons ; Stem Cells
    Chemical Substances MIRN-598 microRNA, human ; MIRN138 microRNA, human ; MIRN218 microRNA, human ; MIRN346 microRNA, human ; MIRN7977 microRNA, human ; MicroRNAs
    Language English
    Publishing date 2021-12-24
    Publishing country Switzerland
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2619676-1
    ISSN 2235-2988 ; 2235-2988
    ISSN (online) 2235-2988
    ISSN 2235-2988
    DOI 10.3389/fcimb.2021.783140
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  7. Article ; Online: Contextualizing the Well-being of Asexual Youth: Evidence of Differences in Family, Health, and School Outcomes.

    Simon, Kay A / Hawthorne, Heath M / Clark, Alyssa N / Renley, Benton M / Farr, Rachel H / Eaton, Lisa A / Watson, Ryan J

    Journal of youth and adolescence

    2021  Volume 51, Issue 1, Page(s) 128–140

    Abstract: Despite increasing efforts to better understand sexual and gender minority youth (SGMY), asexual youth remain understudied. This study examines differences in health, family support, and school safety among asexual youth (n = 938) from a national study ... ...

    Abstract Despite increasing efforts to better understand sexual and gender minority youth (SGMY), asexual youth remain understudied. This study examines differences in health, family support, and school safety among asexual youth (n = 938) from a national study of SGMY (N = 17,112) ages 13-17. Compared to non-asexual youth, asexual youth were more likely to identify as transgender and report a disability, and less likely to identify as Black or Hispanic/Latino. Transgender (versus cisgender) asexual youth fared worse on most study outcomes. Cisgender asexual (versus cisgender non-asexual) youth fared worse on all study outcomes. Transgender asexual (versus transgender non-asexual) youth reported lower sexuality-related family support. These findings underscore the role of gender identity in understanding the experiences of asexual youth.
    MeSH term(s) Adolescent ; Female ; Gender Identity ; Humans ; Male ; Schools ; Sexual Behavior ; Sexual and Gender Minorities ; Transgender Persons
    Language English
    Publishing date 2021-09-22
    Publishing country United States
    Document type Journal Article
    ZDB-ID 186743-x
    ISSN 1573-6601 ; 0047-2891
    ISSN (online) 1573-6601
    ISSN 0047-2891
    DOI 10.1007/s10964-021-01500-5
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    In stock of ZB MED Cologne/Königswinter

    Zs.B 3120: Show issues Location:
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    bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
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  8. Article: A pilot of the feasibility and usefulness of an aged obese model for use in stroke research.

    Learoyd, Annastazia E / Calmus, Ryan / Cunningham, Chelsea N / England, Tim J / Farr, Tracy D / Fone, Kevin C F / Kendall, David A / O'Sullivan, Saoirse E / Trueman, Rebecca C

    Wellcome open research

    2021  Volume 6, Page(s) 104

    Abstract: Background: ...

    Abstract Background:
    Language English
    Publishing date 2021-05-10
    Publishing country England
    Document type Journal Article
    ISSN 2398-502X
    ISSN 2398-502X
    DOI 10.12688/wellcomeopenres.16592.1
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  9. Article: MicroRNA Biomarkers for Infectious Diseases: From Basic Research to Biosensing.

    Tribolet, Leon / Kerr, Emily / Cowled, Christopher / Bean, Andrew G D / Stewart, Cameron R / Dearnley, Megan / Farr, Ryan J

    Frontiers in microbiology

    2020  Volume 11, Page(s) 1197

    Abstract: In the pursuit of improved diagnostic tests for infectious diseases, several classes of molecules have been scrutinized as prospective biomarkers. Small (18-22 nucleotide), non-coding RNA transcripts called microRNAs (miRNAs) have emerged as promising ... ...

    Abstract In the pursuit of improved diagnostic tests for infectious diseases, several classes of molecules have been scrutinized as prospective biomarkers. Small (18-22 nucleotide), non-coding RNA transcripts called microRNAs (miRNAs) have emerged as promising candidates with extensive diagnostic potential, due to their role in numerous diseases, previously established methods for quantitation and their stability within biofluids. Despite efforts to identify, characterize and apply miRNA signatures as diagnostic markers in a range of non-infectious diseases, their application in infectious disease has advanced relatively slowly. Here, we outline the benefits that miRNA biomarkers offer to the diagnosis, management, and treatment of infectious diseases. Investigation of these novel biomarkers could advance the use of personalized medicine in infectious disease treatment, which raises important considerations for validating their use as diagnostic or prognostic markers. Finally, we discuss new and emerging miRNA detection platforms, with a focus on rapid, point-of-care testing, to evaluate the benefits and obstacles of miRNA biomarkers for infectious disease.
    Keywords covid19
    Language English
    Publishing date 2020-06-03
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2587354-4
    ISSN 1664-302X
    ISSN 1664-302X
    DOI 10.3389/fmicb.2020.01197
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  10. Article ; Online: Modelling Lyssavirus Infections in Human Stem Cell-Derived Neural Cultures.

    Sundaramoorthy, Vinod / Godde, Nathan / Farr, Ryan J / Green, Diane / Haynes, John M / Bingham, John / O'Brien, Carmel M / Dearnley, Megan

    Viruses

    2020  Volume 12, Issue 4

    Abstract: Rabies is a zoonotic neurological infection caused by lyssavirus that continues to result in devastating loss of human life. Many aspects of rabies pathogenesis in human neurons are not well understood. Lack of appropriate ex-vivo models for studying ... ...

    Abstract Rabies is a zoonotic neurological infection caused by lyssavirus that continues to result in devastating loss of human life. Many aspects of rabies pathogenesis in human neurons are not well understood. Lack of appropriate ex-vivo models for studying rabies infection in human neurons has contributed to this knowledge gap. In this study, we utilize advances in stem cell technology to characterize rabies infection in human stem cell-derived neurons. We show key cellular features of rabies infection in our human neural cultures, including upregulation of inflammatory chemokines, lack of neuronal apoptosis, and axonal transmission of viruses in neuronal networks. In addition, we highlight specific differences in cellular pathogenesis between laboratory-adapted and field strain lyssavirus. This study therefore defines the first stem cell-derived ex-vivo model system to study rabies pathogenesis in human neurons. This new model system demonstrates the potential for enabling an increased understanding of molecular mechanisms in human rabies, which could lead to improved control methods.
    MeSH term(s) Animals ; Apoptosis ; Axons/metabolism ; Axons/virology ; Biomarkers ; Calcium/metabolism ; Cell Survival ; Cells, Cultured ; Chemokines/metabolism ; Cytokines/metabolism ; Host-Pathogen Interactions ; Humans ; Immunohistochemistry ; Lyssavirus/physiology ; Mice ; Molecular Imaging ; Neurons/virology ; Rabies virus/physiology ; Rhabdoviridae Infections/virology ; Stem Cells/cytology ; Stem Cells/metabolism
    Chemical Substances Biomarkers ; Chemokines ; Cytokines ; Calcium (SY7Q814VUP)
    Language English
    Publishing date 2020-03-25
    Publishing country Switzerland
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2516098-9
    ISSN 1999-4915 ; 1999-4915
    ISSN (online) 1999-4915
    ISSN 1999-4915
    DOI 10.3390/v12040359
    Database MEDical Literature Analysis and Retrieval System OnLINE

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