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  • 1
    Online Resource
    Online Resource
    Springer Science and Business Media LLC ; 2021
    In:  Synthesis Lectures on Signal Processing Vol. 12, No. 2 ( 2021-07-12), p. 1-409
    In: Synthesis Lectures on Signal Processing, Springer Science and Business Media LLC, Vol. 12, No. 2 ( 2021-07-12), p. 1-409
    Type of Medium: Online Resource
    ISSN: 1932-1236 , 1932-1694
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2021
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  • 2
    In: Journal of Virology, American Society for Microbiology, Vol. 95, No. 13 ( 2021-06-10)
    Abstract: Kaposi’s sarcoma-associated herpesvirus (KSHV) is an important oncogenic virus previously shown to be neurotropic, but studies on neuronal cell infection and pathogenesis are still very limited. Here, we characterized the effects of KSHV infection on neuronal SH-SY5Y cells by the recombinant virus rKSHV.219, which expresses both green fluorescent protein (GFP) and red fluorescent protein (RFP) to reflect the latent and lytic phases of infection. We demonstrated that infected cells have a higher growth rate and that KSHV infection can be sustained. Interestingly, the infected cells can transition spontaneously back and forth between lytic and latent phases of infection, producing progeny viruses but without any adverse effects on cell growth. In addition, transcriptome analysis of viral and cellular genes in latent and lytic cells showed that unlike other infected cell lines, the latently infected cells expressed both latent and most, but not all, of the lytic genes required for infectious virion production. The viral genes uniquely expressed by the lytic cells were mainly involved in the early steps of virus binding. Some of the cellular genes that were deregulated in both latently and lytically infected cells are involved in cell adhesion, cell signal pathways, and tumorigenesis. The downregulated cellular CCDN1, PAX5, and NFASC and upregulated CTGF, BMP4, YAP1, LEF1, and HLA-DRB1 genes were found to be associated with cell adhesion molecules (CAMs), hippo signaling, and cancer. These deregulated genes may be involved in creating an environment that is unique in neuronal cells to sustain cell growth upon KSHV infection and not observed in other infected cell types. IMPORTANCE Our study has provided evidence that neuronal SH-SY5Y cells displayed unique cellular responses upon KSHV infection. Unlike other infected cells, this neuronal cell line displayed a higher growth rate upon infection and can spontaneously transition back and forth between latent and lytic phases of infection. Unlike other latently infected cells, a number of lytic genes were also expressed in the latent phase of infection in addition to the established latent viral genes. They may play a role in deregulating a number of host genes that are involved in cell signaling and tumorigenesis in order to sustain the infection and growth advantages for the cells. Our study has provided novel insights into KSHV infection of neuronal cells and a potential new model for further studies to explore the underlying mechanism in viral and host interactions for neuronal cells and the association of KSHV with neuronal diseases.
    Type of Medium: Online Resource
    ISSN: 0022-538X , 1098-5514
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2021
    detail.hit.zdb_id: 1495529-5
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  • 3
    Online Resource
    Online Resource
    MDPI AG ; 2021
    In:  Entropy Vol. 23, No. 10 ( 2021-10-11), p. 1324-
    In: Entropy, MDPI AG, Vol. 23, No. 10 ( 2021-10-11), p. 1324-
    Abstract: One of the important steps in the annotation of genomes is the identification of regions in the genome which code for proteins. One of the tools used by most annotation approaches is the use of signals extracted from genomic regions that can be used to identify whether the region is a protein coding region. Motivated by the fact that these regions are information bearing structures we propose signals based on measures motivated by the average mutual information for use in this task. We show that these signals can be used to identify coding and noncoding sequences with high accuracy. We also show that these signals are robust across species, phyla, and kingdom and can, therefore, be used in species agnostic genome annotation algorithms for identifying protein coding regions. These in turn could be used for gene identification.
    Type of Medium: Online Resource
    ISSN: 1099-4300
    Language: English
    Publisher: MDPI AG
    Publication Date: 2021
    detail.hit.zdb_id: 2014734-X
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  • 4
    Online Resource
    Online Resource
    Mary Ann Liebert Inc ; 2021
    In:  Neurotrauma Reports Vol. 2, No. 1 ( 2021-12-01), p. 626-638
    In: Neurotrauma Reports, Mary Ann Liebert Inc, Vol. 2, No. 1 ( 2021-12-01), p. 626-638
    Type of Medium: Online Resource
    ISSN: 2689-288X
    Language: English
    Publisher: Mary Ann Liebert Inc
    Publication Date: 2021
    detail.hit.zdb_id: 3044482-2
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  • 5
    Online Resource
    Online Resource
    American Society for Microbiology ; 2020
    In:  Journal of Clinical Microbiology Vol. 58, No. 4 ( 2020-03-25)
    In: Journal of Clinical Microbiology, American Society for Microbiology, Vol. 58, No. 4 ( 2020-03-25)
    Abstract: The highly infectious and zoonotic pathogen Francisella tularensis is the etiologic agent of tularemia, a potentially fatal disease if untreated. Despite the high average nucleotide identity, which is 〉 99.2% for the virulent subspecies and 〉 98% for all four subspecies, including the opportunistic microbe Francisella tularensis subsp. novicida , there are considerable differences in genetic organization. These chromosomal disparities contribute to the substantial differences in virulence observed between the various F. tularensis subspecies and subtypes. The methods currently available to genotype F. tularensis cannot conclusively identify the associated subpopulation without using time-consuming testing or complex scoring matrices. To address this need, we developed both single and multiplex quantitative real-time PCR (qPCR) assays that can accurately detect and identify the hypervirulent F. tularensis subsp. tularensis subtype A.I, the virulent F. tularensis subsp. tularensis subtype A.II, F. tularensis subsp. holarctica (also referred to as type B), and F. tularensis subsp. mediasiatica , as well as opportunistic F. tularensis subsp. novicida from each other and near neighbors, such as Francisella philomiragia , Francisella persica , and Francisella -like endosymbionts found in ticks. These fluorescence-based singleplex and non-matrix scoring multiplex qPCR assays utilize a hydrolysis probe, providing sensitive and specific F. tularensis subspecies and subtype identification in a rapid manner. Furthermore, sequencing of the amplified F. tularensis targets provides clade confirmation and informative strain-specific details. Application of these qPCR- and sequencing-based detection assays will provide an improved capability for molecular typing and clinical diagnostics, as well as facilitate the accurate identification and differentiation of F. tularensis subpopulations during epidemiological investigations of tularemia source outbreaks.
    Type of Medium: Online Resource
    ISSN: 0095-1137 , 1098-660X
    RVK:
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2020
    detail.hit.zdb_id: 1498353-9
    SSG: 12
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