Journal: Frontiers in physiology

Article Title: Gut microbiota depletion minimally affects the daily voluntary wheel running activity and food anticipatory activity in female and male C57BL/6J mice.

doi: 10.3389/fphys.2023.1299474

Figure Lengend Snippet: FIGURE 1 The experimental procedure for microbiota depletion and feeding schedule. The days of beginning of ad libitum feeding (ALI, ALII), timed restricted feeding (TRF), food deprivation (FD) and collection of cecum and feces are indicated with the arrows.

Article Snippet: Extracted fecal DNA samples were shipped to Transnetyx Microbiome (Cordova, TN) for library preparation and whole-genome sequencing.

Techniques:

Journal: Frontiers in physiology

Article Title: Gut microbiota depletion minimally affects the daily voluntary wheel running activity and food anticipatory activity in female and male C57BL/6J mice.

doi: 10.3389/fphys.2023.1299474

Figure Lengend Snippet: FIGURE 5 Relative abundances of microbiota taxa from control and antibiotic-treated mice. Plot representing bacterial load in control (A) and antibiotics- treated (B) mice. Antibiotics depleted majority of gut microbiota. The “Mouse proportion” represents the number of reads that map to the One Codex database mouse genome divided by the total number of reads, while the “Bacterial proportion” represents the number of reads that map to bacteria at the taxonomic rank divided by the total number of reads. The “Other” category includes any reads classified as non-bacterial microorganisms. Taxonomic analysis showing gut microbiota population shifts at Family level. Relative abundance of top 15 families of microbial taxa in control (C), and antibiotics-treated (D) are shown. Lachnospiraceae (indicated as green) was present in all control mice but depleted in antibiotics treated mice. Erysipelotrichaceae was not detected in both control and antibiotics-treated mice. Top 15 orders and genus were shown in Supplementary Figure S5A–D. The number in the brackets represents NCBI taxonomic ID.

Article Snippet: Extracted fecal DNA samples were shipped to Transnetyx Microbiome (Cordova, TN) for library preparation and whole-genome sequencing.

Techniques: Control, Bacteria

Journal: Virus research

Article Title: Paracrinal regulation of neutrophil functions by coronaviral infection in iPSC-derived alveolar type II epithelial cells.

doi: 10.1016/j.virusres.2024.199391

Figure Lengend Snippet: Fig. 5. Identification of cytokines secreted by infected iAECIIs and their effect on HL-60 cells. (A) Cytokine array analysis showing the levels of the indicated cy tokines in the medium conditioned by iAECIIs infected with HCoV-229E for 24 or 48 h (24 hpi and 48 hpi). Ctrl – uninfected control. Right panel: cytokine label legend. (B) Western blot analysis of the expression of IL-8 and ICAM-1 in HCoV-229E-infected iAECIIs. (C) Transwell migration assay showing the migration capacity of HL-60 neutrophils in response to a medium conditioned by iAECIIs infected with HCoV-229E for 48 h (48 hpi) in the absence or presence of an IL-8-neutralizing antibody (IL-8 nAb). Ctrl – uninfected control conditioned medium. Data shown as means with SD error bars, n = 3, *p < 0.005, (ANOVA). (D) Representative fluorescence microscopy images of adherent HL-60 neutrophils after incubation with infected iAECIIs in the absence or presence of an ICAM-1-neutralizing antibody (ICAM-1 nAb). Ctrl – uninfected control. (E) Cell count of adherent HL-60 neutrophils. Mean values are shown with SD error bars, n = 3, *p < 0.005.

Article Snippet: Cytokines in the conditioned medium were detected using the Human Cytokine Array Kit (#ARY005B; R&D Systems), and the test strips were moistened and activated according to the manufacturer’s user manual.

Techniques: Infection, Control, Western Blot, Expressing, Transwell Migration Assay, Migration, Fluorescence, Microscopy, Incubation, Cell Counting

Journal: Virus research

Article Title: Paracrinal regulation of neutrophil functions by coronaviral infection in iPSC-derived alveolar type II epithelial cells.

doi: 10.1016/j.virusres.2024.199391

Figure Lengend Snippet: Fig. 6. RNA-seq analysis identifies upstream cytokine pathways in the immune responses by neutrophils. (A and B) Cytoscape ClueGO networks of upregulated genes by infection of iAECIIs with HCoV-229E (A) or triggered by infected HCoV-229 conditioned medium in HL-60 cells (B). (C and D) Bubble plots showing the most enriched GO-BP terms among the genes upregulated by the infection of iAECIIs with HCoV-229E (C) or the genes upregulated in HL-60 cells by cultivation in the infected HCoV-229-conditioned medium (D). (E and F) Hierarchical clustering heatmaps showing the signatures of genes differentially regulated in infected iAECIIs (E) and conditioned medium-stimulated HL-60 cells (F). (G and H) X2K network analysis showing the kinases and transcription factors predicted to regulate differentially expressed genes in infected iAECIIs (G) and conditioned medium-stimulated HL-60 cells (H).

Article Snippet: Cytokines in the conditioned medium were detected using the Human Cytokine Array Kit (#ARY005B; R&D Systems), and the test strips were moistened and activated according to the manufacturer’s user manual.

Techniques: RNA Sequencing, Infection