41 research outputs found

    Pan-genome of the nine <i>L</i>. <i>ruminis</i> strains.

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    <p>A flower-plot depicting the gene content in the pan- (4301), core (1234), and accessory (3067) genomes of <i>L</i>. <i>ruminis</i> is shown. The number of strain-specific genes per genome is shown in the flower petals. Names for each <i>L</i>. <i>ruminis</i> strain are indicated. Annotated core and accessory genes are provided in the <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0175541#pone.0175541.s001" target="_blank">S1 Table</a>.</p

    Phylogenetic tree analysis of the <i>L</i>. <i>ruminis</i> genomes.

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    <p>Unrooted phylogenies of the <i>L</i>. <i>ruminis</i> genomes were based on the multiple sequence alignment of core proteins and constructed with the neighbor-joining tree-building algorithm (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0175541#sec002" target="_blank">Materials and Methods</a> for details). Names of the <i>L</i>. <i>ruminis</i> strains from which each genome is derived are shown. Four distinct phyletic clades were identified based on host-gut source (human, bovine, porcine, or equine) and are indicated accordingly.</p

    Size prediction for the <i>L</i>. <i>ruminis</i> pan- and core genomes.

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    <p>New gene numbers in the pan- and core genomes are plotted against the number of added <i>L</i>. <i>ruminis</i> genomes. Each fitted curve was generated using the median values for the number of new genes.</p

    Schematic outline of the putative homolactic and heterolactic fermentative pathways in <i>L</i>. <i>ruminis</i>.

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    <p>Depicted is the glycolytic metabolism that can occur during homolactic fermentation via the Embden-Meyerhof-Parnas (EMP) pathway <b>(A)</b> or heterolactic fermentation via the phosphoketolase pathway (PK) <b>(B)</b>. Included are the various pathway reactions with their precursor metabolites and enzymes. Shown in the insets are the names of the glycolytic enzymes, either numbered (1–11) or alphabetized (a-e) along with the locus tags of their putative genes in the nine <i>L</i>. <i>ruminis</i> genomes. Enzymes that overlap in both pathways are numbered similarly.</p

    Schematic representation of the fumarate reductase-catalyzed reaction.

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    <p>Shown is the reaction catalyzed by fumarate reductase, where the reduction of fumarate to succinate is coupled with the oxidation of menaquinol to menaquinone. Included are the nine locus tags for the putative fumarate reductase gene found present in the <i>L</i>. <i>ruminis</i> core genome.</p

    Structure-based drug discovery to identify SARS-CoV2 spike protein–ACE2 interaction inhibitors

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    After the emergence of the COVID-19 pandemic in late 2019, the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has undergone a dynamic evolution driven by the acquisition of genetic modifications, resulting in several variants that are further classified as variants of interest (VOIs), variants under monitoring (VUM) and variants of concern (VOC) by World Health Organization (WHO). Currently, there are five SARS-CoV-2 VOCs (Alpha, Beta, Delta, Gamma and Omicron), two VOIs (Lambda and Mu) and several other VOIs that have been reported globally. In this study, we report a natural compound, Curcumin, as the potential inhibitor to the interactions between receptor binding domain (RBD(S1)) and human angiotensin-converting enzyme 2 (hACE2) domains and showcased its inhibitory potential for the Delta and Omicron variants through a computational approach by implementing state of the art methods. The study for the first time revealed a higher efficiency of Curcumin, especially for hindering the interaction between RBD(S1) and hACE-2 domains of Delta and Omicron variants as compared to other lead compounds. We investigated that the mutations in the RBD(S1) of VOC especially Delta and Omicron variants affect its structure compared to that of the wild type and other variants and therefore altered its binding to the hACE2 receptor. Molecular docking and molecular dynamics (MD) simulation analyses substantially supported the findings in terms of the stability of the docked complexes. This study offers compelling evidence, warranting a more in-depth exploration into the impact of these alterations on the binding of identified drug molecules with the Spike protein. Further investigation into their potential therapeutic effects in vivo is highly recommended. Communicated by Ramaswamy H. Sarma</p

    Binding of recombinant SpaFED-piliated lactococcal cells to ECM proteins.

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    <p><i>In vitro</i> binding specificities between the normalized (OD600 = 0.5) cultures of recombinant WT (GRS1189) and SpaF pilin-deleted (GRS1126) SpaFED-piliated lactococci (along with GRS71 and GRS1052 cells as controls) and the fibronectin (<b>A</b>), collagen I (<b>B</b>), and collagen IV (<b>C</b>) proteins were evaluated using the procedure described in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0113922#s4" target="_blank">Materials and Methods</a>. Triplicate measurements were made for each of the ECM protein experiments, each of which was performed independently twice. SEM is indicated as error bars. For all ECM proteins tested, differences between the GRS1189 and GRS1226 binding results from pairwise comparisons against the GRS71 data are regarded very significant (<i>P</i>≤0.005).</p

    Stimulation of TLR2-dependent NF-κB activation by recombinant SpaFED-piliated lactococci.

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    <p>The HEK-TLR2 cell line was treated with live (−) or heat-treated (100°C for 10 minutes) (+) normalized cultures of recombinant WT (GRS1189) and SpaF pilin-deleted (GRS1126) SpaFED-piliated lactococci (MOI 100). Levels of TLR2-dependent NF-κB activation were assessed as described in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0113922#s4" target="_blank">Materials and Methods</a>. Testing of the GRS71 and GRS1052 control strains was as well conducted. DMEM cell-culture medium and a TLR2-agonist lipopeptide (Pam3CSK4; 1 ng/ml) served as negative and positive controls, respectively. Quadruplicate measurements were taken for two independent experiments. SEM is shown as error bars. Pairwise differences between the GRS1189 and GRS1226 data (without heat inactivation) are considered very significant (<i>P</i>≤0.005).</p

    Effect of cell-to-cell contacts on TLR2-induced NF-κB activation by recombinant SpaFED-piliated lactococci.

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    <p>Using a Transwell membrane-segregated system, HEK-TLR2 cells were treated with non-partitioned (−) and partitioned (+) normalized cultures of recombinant WT (GRS1189) and SpaF pilin-deleted (GRS1126) SpaFED-piliated lactococci (MOI 100). Monitoring of TLR2-dependent NF-κB activation was carried out as outlined in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0113922#s4" target="_blank">Materials and Methods</a>. Included as controls were GRS71 and GRS1052 cells (MOI 100), DMEM cell-culture medium, and Pam3CSK4 (1 ng/ml). Triplicate measurements were taken for a single experiment. SEM is indicated as error bars.</p

    Stimulation of DC-cytokine production by recombinant SpaFED-piliated lactococci.

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    <p>Human monocyte-derived dendritic cells (moDCs) were treated with normalized cultures of recombinant WT (GRS1189) and SpaF pilin-deleted (GRS1126) SpaFED-piliated lactococci (MOI 50). Stimulated TNF-α (<b>A</b>), IL-12 (<b>B</b>), and IL-10 (<b>C</b>) cytokine production was measured as described in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0113922#s4" target="_blank">Materials and Methods</a>. GRS71 and GRS1052 cells (MOI 50) and DMEM cell-culture medium were included as controls. Measurements were performed in triplicate using moDCs from four new and different donors each time. SEM is shown as error bars. For all tested cytokines, differences in a pairwise comparison between the GRS1189 and GRS1226 data are judged not significant (<i>P</i>≥0.05).</p
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