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  1. Article ; Online: Differential Correlation of Transcriptome Data Reveals Gene Pairs and Pathways Involved in Treatment of

    Fleming, Damarius S / Liu, Fang / Li, Robert W

    Molecules (Basel, Switzerland)

    2023  Volume 28, Issue 21

    Abstract: This study is part of the work investigating bioactive fruit enzymes as sustainable alternatives to parasite anthelmintics that can help reverse the trend of lost efficacy. The study looked to define biological and molecular interactions that demonstrate ...

    Abstract This study is part of the work investigating bioactive fruit enzymes as sustainable alternatives to parasite anthelmintics that can help reverse the trend of lost efficacy. The study looked to define biological and molecular interactions that demonstrate the ability of the pomegranate extract punicalagin against intracellular parasites. The study compared transcriptomic reads of two distinct conditions. Condition A was treated with punicalagin (PA) and challenged with
    MeSH term(s) Mice ; Animals ; Transcriptome ; Citrobacter rodentium ; Hydrolyzable Tannins/pharmacology ; Antioxidants/analysis
    Chemical Substances punicalagin (65995-63-3) ; Hydrolyzable Tannins ; Antioxidants
    Language English
    Publishing date 2023-10-31
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 1413402-0
    ISSN 1420-3049 ; 1431-5165 ; 1420-3049
    ISSN (online) 1420-3049
    ISSN 1431-5165 ; 1420-3049
    DOI 10.3390/molecules28217369
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.MO 81: Show issues

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  2. Article ; Online: Differential Correlation of Transcriptome Data Reveals Gene Pairs and Pathways Involved in Treatment of Citrobacter rodentium Infection with Bioactive Punicalagin

    Damarius S. Fleming / Fang Liu / Robert W. Li

    Molecules, Vol 28, Iss 21, p

    2023  Volume 7369

    Abstract: This study is part of the work investigating bioactive fruit enzymes as sustainable alternatives to parasite anthelmintics that can help reverse the trend of lost efficacy. The study looked to define biological and molecular interactions that demonstrate ...

    Abstract This study is part of the work investigating bioactive fruit enzymes as sustainable alternatives to parasite anthelmintics that can help reverse the trend of lost efficacy. The study looked to define biological and molecular interactions that demonstrate the ability of the pomegranate extract punicalagin against intracellular parasites. The study compared transcriptomic reads of two distinct conditions. Condition A was treated with punicalagin (PA) and challenged with Citrobacter rodentium , while condition B (CM) consisted of a group that was challenged and given mock treatment of PBS. To understand the effect of punicalagin on transcriptomic changes between conditions, a differential correlation analysis was conducted. The analysis examined the regulatory connections of genes expressed between different treatment conditions by statistically querying the relationship between correlated gene pairs and modules in differing conditions. The results indicated that punicalagin treatment had strong positive correlations with the over-enriched gene ontology (GO) terms related to oxidoreductase activity and lipid metabolism. However, the GO terms for immune and cytokine responses were strongly correlated with no punicalagin treatment. The results matched previous studies that showed punicalagin to have potent antioxidant and antiparasitic effects when used to treat parasitic infections in mice and livestock. Overall, the results indicated that punicalagin enhanced the effect of tissue-resident genes.
    Keywords parasite ; citrobacter ; bioactive compound ; differential correlation ; Organic chemistry ; QD241-441
    Subject code 572
    Language English
    Publishing date 2023-10-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article: The contribution of BvgR, RisA, and RisS to global gene regulation, intracellular cyclic-di-GMP levels, motility, and biofilm formation in

    Nicholson, Tracy L / Waack, Ursula / Fleming, Damarius S / Chen, Qing / Miller, Laura C / Merkel, Tod J / Stibitz, Scott

    Frontiers in microbiology

    2024  Volume 15, Page(s) 1305097

    Abstract: Bordetella ... ...

    Abstract Bordetella bronchiseptica
    Language English
    Publishing date 2024-03-07
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2587354-4
    ISSN 1664-302X
    ISSN 1664-302X
    DOI 10.3389/fmicb.2024.1305097
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  4. Article: Differentially Expressed MiRNAs and tRNA Genes Affect Host Homeostasis During Highly Pathogenic Porcine Reproductive and Respiratory Syndrome Virus Infections in Young Pigs.

    Fleming, Damarius S / Miller, Laura C

    Frontiers in genetics

    2019  Volume 10, Page(s) 691

    Abstract: Background: ...

    Abstract Background:
    Language English
    Publishing date 2019-08-02
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2606823-0
    ISSN 1664-8021
    ISSN 1664-8021
    DOI 10.3389/fgene.2019.00691
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Transcriptomic Analysis of Liver Indicates Novel Vaccine to Porcine Reproductive and Respiratory Virus Promotes Homeostasis in T-Cell and Inflammatory Immune Responses Compared to a Commercial Vaccine in Pigs

    Damarius S. Fleming / Laura C. Miller / Jiuyi Li / Albert Van Geelen / Yongming Sang

    Frontiers in Veterinary Science, Vol

    2022  Volume 9

    Abstract: ... in the U.S. annually. The challenge with combating PRRSV is a combination of the effect of an extraordinary ...

    Abstract One of the largest impediments for commercial swine production is the presence of Porcine Reproductive and Respiratory Syndrome Virus (PRRSV), a devastating RNA viral infection that is responsible for over $1 billion in loss in the U.S. annually. The challenge with combating PRRSV is a combination of the effect of an extraordinary rate of mutation, the ability to infect macrophages, and subversion of host immune response through a series of actions leading to both immunomodulation and immune evasion. Currently there are a handful of commercial vaccines on the market that have been shown to be effective against homologous infections, but struggle against heterologous or mixed strain infections. However, vaccination is the current best strategy for combating PRRSV, making research into new vaccine technology key. To address these issues with PRRSV and host antiviral functions a novel modified-live vaccine (MLV) able to stimulate known antiviral interferons was created and examined for its ability to potentiate effective immunity and better protection. Here, we examine gene expression in the liver of pigs vaccinated with our novel vaccine, given the liver's large role in antiviral responses and vaccine metabolism. Our study indicated that pigs administered the novel vaccine experience homeostatic gene expression consistent with less inflammation and T-cell depletion risk than pigs administered the commercial vaccine.
    Keywords Porcine Reproductive and Respiratory Syndrome Virus ; liver ; vaccine ; transcriptome ; immunity ; Veterinary medicine ; SF600-1100
    Subject code 570
    Language English
    Publishing date 2022-03-01T00:00:00Z
    Publisher Frontiers Media S.A.
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  6. Article: Transcriptomic Analysis of Liver Indicates Novel Vaccine to Porcine Reproductive and Respiratory Virus Promotes Homeostasis in T-Cell and Inflammatory Immune Responses Compared to a Commercial Vaccine in Pigs.

    Fleming, Damarius S / Miller, Laura C / Li, Jiuyi / Van Geelen, Albert / Sang, Yongming

    Frontiers in veterinary science

    2022  Volume 9, Page(s) 791034

    Abstract: ... in the U.S. annually. The challenge with combating PRRSV is a combination of the effect of an extraordinary ...

    Abstract One of the largest impediments for commercial swine production is the presence of Porcine Reproductive and Respiratory Syndrome Virus (PRRSV), a devastating RNA viral infection that is responsible for over $1 billion in loss in the U.S. annually. The challenge with combating PRRSV is a combination of the effect of an extraordinary rate of mutation, the ability to infect macrophages, and subversion of host immune response through a series of actions leading to both immunomodulation and immune evasion. Currently there are a handful of commercial vaccines on the market that have been shown to be effective against homologous infections, but struggle against heterologous or mixed strain infections. However, vaccination is the current best strategy for combating PRRSV, making research into new vaccine technology key. To address these issues with PRRSV and host antiviral functions a novel modified-live vaccine (MLV) able to stimulate known antiviral interferons was created and examined for its ability to potentiate effective immunity and better protection. Here, we examine gene expression in the liver of pigs vaccinated with our novel vaccine, given the liver's large role in antiviral responses and vaccine metabolism. Our study indicated that pigs administered the novel vaccine experience homeostatic gene expression consistent with less inflammation and T-cell depletion risk than pigs administered the commercial vaccine.
    Language English
    Publishing date 2022-03-24
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2834243-4
    ISSN 2297-1769
    ISSN 2297-1769
    DOI 10.3389/fvets.2022.791034
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article: Comparison of the Transcriptome Response within the Swine Tracheobronchial Lymphnode Following Infection with PRRSV, PCV-2 or IAV-S.

    Miller, Laura C / Fleming, Damarius S / Lager, Kelly M

    Pathogens (Basel, Switzerland)

    2020  Volume 9, Issue 2

    Abstract: ... with either porcine reproductive and respiratory syndrome virus (PRRSV), porcine circovirus type 2 (PCV-2), or swine influenza A virus (IAV-S) infections ... by PRRSV, PCV-2, IAV-S, or sham inoculation. Total RNA was pooled for each group and time-point (1, 3, 6 ... S and PCV-2 viral infections followed a clinical course in the pigs typical ...

    Abstract Porcine reproductive and respiratory syndrome virus (PRRSV) is a major respiratory pathogen of swine that has become extremely costly to the swine industry worldwide, often causing losses in production and animal life due to their ease of spread. However, the intracellular changes that occur in pigs following viral respiratory infections are still scantily understood for PRRSV, as well as other viral respiratory infections. The aim of this study was to acquire a better understanding of the PRRS disease by comparing gene expression changes that occur in tracheobronchial lymph nodes (TBLN) of pigs infected with either porcine reproductive and respiratory syndrome virus (PRRSV), porcine circovirus type 2 (PCV-2), or swine influenza A virus (IAV-S) infections. The study identified and compared gene expression changes in the TBLN of 80 pigs following infection by PRRSV, PCV-2, IAV-S, or sham inoculation. Total RNA was pooled for each group and time-point (1, 3, 6, and 14 dpi) to make 16 libraries-analyses are by Digital Gene Expression Tag Profiling (DGETP). The data underwent standard filtering to generate a list of sequence tag raw counts that were then analyzed using multidimensional and differential expression statistical tests. The results showed that PRRSV, IAV-S and PCV-2 viral infections followed a clinical course in the pigs typical of experimental infection of young pigs with these viruses. Gene expression results echoed this course, as well as uncovered genes related to intersecting and unique host immune responses to the three viruses. By testing and observing the host response to other respiratory viruses, our study has elucidated similarities and differences that can assist in the development of vaccines and therapeutics that shorten or prevent a chronic PRRSV infection.
    Language English
    Publishing date 2020-02-05
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2695572-6
    ISSN 2076-0817
    ISSN 2076-0817
    DOI 10.3390/pathogens9020099
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  8. Article ; Online: Identification of small non-coding RNA classes expressed in swine whole blood during HP-PRRSV infection.

    Fleming, Damarius S / Miller, Laura C

    Virology

    2018  Volume 517, Page(s) 56–61

    Abstract: It has been established that reduced susceptibility to porcine reproductive and respiratory syndrome virus (PRRSV) has a genetic component. This genetic component may take the form of small non-coding RNAs (sncRNA), which are molecules that function as ... ...

    Abstract It has been established that reduced susceptibility to porcine reproductive and respiratory syndrome virus (PRRSV) has a genetic component. This genetic component may take the form of small non-coding RNAs (sncRNA), which are molecules that function as regulators of gene expression. Various sncRNAs have emerged as having an important role in the immune system in humans. The study uses transcriptomic read counts to profile the type and quantity of both well and lesser characterized sncRNAs, such as microRNAs and small nucleolar RNAs to identify and quantify the classes of sncRNA expressed in whole blood between healthy and highly pathogenic PRRSV-infected pigs. Our results returned evidence on nine classes of sncRNA, four of which were consistently statistically significantly different based on Fisher's Exact Test, that can be detected and possibly interrogated for their effect on host dysregulation during PRRSV infections.
    MeSH term(s) Animals ; Gene Expression Regulation, Viral/physiology ; Porcine Reproductive and Respiratory Syndrome/blood ; Porcine Reproductive and Respiratory Syndrome/virology ; Porcine respiratory and reproductive syndrome virus/genetics ; RNA, Small Untranslated/blood ; RNA, Viral/genetics ; Swine/blood
    Chemical Substances RNA, Small Untranslated ; RNA, Viral
    Language English
    Publishing date 2018
    Publishing country United States
    Document type Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 200425-2
    ISSN 1096-0341 ; 0042-6822
    ISSN (online) 1096-0341
    ISSN 0042-6822
    DOI 10.1016/j.virol.2018.01.027
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Ud II Zs.172: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
    ab Jg. 2022: Lesesaal (EG)

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  9. Article ; Online: Comparison of the Transcriptome Response within the Swine Tracheobronchial Lymphnode Following Infection with PRRSV, PCV-2 or IAV-S.

    Laura C. Miller / Damarius S. Fleming / Kelly M. Lager

    Pathogens, Vol 9, Iss 2, p

    2020  Volume 99

    Abstract: ... with either porcine reproductive and respiratory syndrome virus (PRRSV), porcine circovirus type 2 (PCV-2), or swine influenza A virus (IAV-S) infections ... by PRRSV, PCV-2, IAV-S, or sham inoculation. Total RNA was pooled for each group and time-point (1, 3, 6 ... S and PCV-2 viral infections followed a clinical course in the pigs typical ...

    Abstract Porcine reproductive and respiratory syndrome virus (PRRSV) is a major respiratory pathogen of swine that has become extremely costly to the swine industry worldwide, often causing losses in production and animal life due to their ease of spread. However, the intracellular changes that occur in pigs following viral respiratory infections are still scantily understood for PRRSV, as well as other viral respiratory infections. The aim of this study was to acquire a better understanding of the PRRS disease by comparing gene expression changes that occur in tracheobronchial lymph nodes (TBLN) of pigs infected with either porcine reproductive and respiratory syndrome virus (PRRSV), porcine circovirus type 2 (PCV-2), or swine influenza A virus (IAV-S) infections. The study identified and compared gene expression changes in the TBLN of 80 pigs following infection by PRRSV, PCV-2, IAV-S, or sham inoculation. Total RNA was pooled for each group and time-point (1, 3, 6, and 14 dpi) to make 16 libraries—analyses are by Digital Gene Expression Tag Profiling (DGETP). The data underwent standard filtering to generate a list of sequence tag raw counts that were then analyzed using multidimensional and differential expression statistical tests. The results showed that PRRSV, IAV-S and PCV-2 viral infections followed a clinical course in the pigs typical of experimental infection of young pigs with these viruses. Gene expression results echoed this course, as well as uncovered genes related to intersecting and unique host immune responses to the three viruses. By testing and observing the host response to other respiratory viruses, our study has elucidated similarities and differences that can assist in the development of vaccines and therapeutics that shorten or prevent a chronic PRRSV infection.
    Keywords prrsv ; pcv-2 ; iav-s ; lymph node ; immune response ; differential expression ; Medicine ; R
    Subject code 570
    Language English
    Publishing date 2020-02-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  10. Article: Leading edge analysis of transcriptomic changes during pseudorabies virus infection.

    Fleming, Damarius S / Miller, Laura C

    Genomics data

    2016  Volume 10, Page(s) 104–106

    Abstract: Eight RNA samples taken from the tracheobronchial lymph nodes (TBLN) of pigs that were either infected or non-infected with a feral isolate of porcine pseudorabies virus (PRV) were used to investigate changes in gene expression related to the pathogen. ... ...

    Abstract Eight RNA samples taken from the tracheobronchial lymph nodes (TBLN) of pigs that were either infected or non-infected with a feral isolate of porcine pseudorabies virus (PRV) were used to investigate changes in gene expression related to the pathogen. The RNA was processed into fastq files for each library prior to being analyzed using Illumina Digital Gene Expression Tag Profiling sequences (DGETP) which were used as the downstream measure of differential expression. Analyzed tags consisted of 21 base pair sequences taken from time points 1, 3, 6, and 14 days' post infection (dpi) that generated 1,927,547 unique tag sequences. Tag sequences were analyzed for differential transcript expression and gene set enrichment analysis (GSEA) to uncover transcriptomic changes related to PRV pathology progression. In conjunction with the DGETP and GSEA, the study also incorporated use of leading edge analysis to help link the TBLN transcriptome data to clinical progression of PRV at each of the sampled time points. The purpose of this manuscript is to provide useful background on applying the leading edge analysis to GSEA and expression data to help identify genes considered to be of high biological interest. The data in the form of fastq files has been uploaded to the NCBI Gene Expression Omnibus (GEO) (GSE74473) database.
    Language English
    Publishing date 2016-09-30
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2751131-5
    ISSN 2213-5960
    ISSN 2213-5960
    DOI 10.1016/j.gdata.2016.09.014
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