e coli  (ATCC)


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    ATCC e coli
    E Coli, supplied by ATCC, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    e coli escherichia coli migula castellani  (ATCC)


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    ATCC e coli escherichia coli migula castellani
    (A) Heatmap of top marker genes for the decidual HLA-DR low and HLA-DR high subsets, classical and non-classical blood monocytes. Each column is a bin of a fixed number of cells and each row represents a gene. A subset of genes within each cluster is annotated. High and low expression are represented as red and blue, respectively. (B) Violin plots comparing expression of gene markers within decidual macrophage subsets. (C) Surface expression of HLA-DR and CD11c measured by flow cytometry. (D) Brightfield and fluorescence profiles of macrophage subsets captured using imaging flow cytometry. (E) Median Fluorescence Intensities (MFI) of macrophage surface markers on decidual macrophage subsets (n = 7/group). (F) Frequencies of TREM2+ FOLR2+ (n = 5/group) and CD163+ (n = 7/group) within decidual macrophages. (G) Phospho p65 signal in blood monocytes and decidual macrophage subsets (n = 3/group) by flow cytometry. Error bars represent the mean and standard error of the mean (SEM). (H) Comparison of baseline secreted cytokine profiles (median) of sorted decidual macrophage subsets (n = 4/group) and blood monocytes (n = 2). * and # represent significant differences relative to blood monocytes between HLA-DR low and HLA-DR high macrophages, respectively. (I) Responses to overnight lipopolysaccharide (LPS) stimulation of total decidual leukocytes (n = 8/group). Error bars represent the mean and standard error of the mean (SEM). (J) MFI of intracellular cellROX (n = 7/group). (K) Percentage of <t>E.</t> <t>coli</t> pHrodo+ (n = 8/group) in decidual macrophages. (L) Oxygen consumption rate and extracellular acidification rates of decidual macrophages (n = 6/group). ****p < 0.0001, **p < 0.01, *p < 0.05, and #p<0.1.
    E Coli Escherichia Coli Migula Castellani, supplied by ATCC, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    1) Product Images from "Multimodal profiling of term human decidua demonstrates immune adaptations with pregravid obesity"

    Article Title: Multimodal profiling of term human decidua demonstrates immune adaptations with pregravid obesity

    Journal: Cell reports

    doi: 10.1016/j.celrep.2023.112769

    (A) Heatmap of top marker genes for the decidual HLA-DR low and HLA-DR high subsets, classical and non-classical blood monocytes. Each column is a bin of a fixed number of cells and each row represents a gene. A subset of genes within each cluster is annotated. High and low expression are represented as red and blue, respectively. (B) Violin plots comparing expression of gene markers within decidual macrophage subsets. (C) Surface expression of HLA-DR and CD11c measured by flow cytometry. (D) Brightfield and fluorescence profiles of macrophage subsets captured using imaging flow cytometry. (E) Median Fluorescence Intensities (MFI) of macrophage surface markers on decidual macrophage subsets (n = 7/group). (F) Frequencies of TREM2+ FOLR2+ (n = 5/group) and CD163+ (n = 7/group) within decidual macrophages. (G) Phospho p65 signal in blood monocytes and decidual macrophage subsets (n = 3/group) by flow cytometry. Error bars represent the mean and standard error of the mean (SEM). (H) Comparison of baseline secreted cytokine profiles (median) of sorted decidual macrophage subsets (n = 4/group) and blood monocytes (n = 2). * and # represent significant differences relative to blood monocytes between HLA-DR low and HLA-DR high macrophages, respectively. (I) Responses to overnight lipopolysaccharide (LPS) stimulation of total decidual leukocytes (n = 8/group). Error bars represent the mean and standard error of the mean (SEM). (J) MFI of intracellular cellROX (n = 7/group). (K) Percentage of E. coli pHrodo+ (n = 8/group) in decidual macrophages. (L) Oxygen consumption rate and extracellular acidification rates of decidual macrophages (n = 6/group). ****p < 0.0001, **p < 0.01, *p < 0.05, and #p<0.1.
    Figure Legend Snippet: (A) Heatmap of top marker genes for the decidual HLA-DR low and HLA-DR high subsets, classical and non-classical blood monocytes. Each column is a bin of a fixed number of cells and each row represents a gene. A subset of genes within each cluster is annotated. High and low expression are represented as red and blue, respectively. (B) Violin plots comparing expression of gene markers within decidual macrophage subsets. (C) Surface expression of HLA-DR and CD11c measured by flow cytometry. (D) Brightfield and fluorescence profiles of macrophage subsets captured using imaging flow cytometry. (E) Median Fluorescence Intensities (MFI) of macrophage surface markers on decidual macrophage subsets (n = 7/group). (F) Frequencies of TREM2+ FOLR2+ (n = 5/group) and CD163+ (n = 7/group) within decidual macrophages. (G) Phospho p65 signal in blood monocytes and decidual macrophage subsets (n = 3/group) by flow cytometry. Error bars represent the mean and standard error of the mean (SEM). (H) Comparison of baseline secreted cytokine profiles (median) of sorted decidual macrophage subsets (n = 4/group) and blood monocytes (n = 2). * and # represent significant differences relative to blood monocytes between HLA-DR low and HLA-DR high macrophages, respectively. (I) Responses to overnight lipopolysaccharide (LPS) stimulation of total decidual leukocytes (n = 8/group). Error bars represent the mean and standard error of the mean (SEM). (J) MFI of intracellular cellROX (n = 7/group). (K) Percentage of E. coli pHrodo+ (n = 8/group) in decidual macrophages. (L) Oxygen consumption rate and extracellular acidification rates of decidual macrophages (n = 6/group). ****p < 0.0001, **p < 0.01, *p < 0.05, and #p<0.1.

    Techniques Used: Marker, Expressing, Flow Cytometry, Fluorescence, Imaging, Comparison

    (A and B) Dot plots comparing (A) lymphocyte and (B) macrophage proportions within CD45+ decidual cells in lean pregnant women (n = 6 for Tregs, 32 for rest) and those with obesity (n = 6 for Tregs, 31 for rest). (C) Gating strategy and dot plots comparing frequencies of S100A9+ cells within HLA-DR high macrophages (n = 5/group). Error bars represent the mean and standard error of the mean (SEM). (D) Stacked bar graph comparing frequencies of decidual leukocytes within total cells sequenced in each group (within CD45+ cells). (E) Stacked bar comparing HLA-DR high macrophage cluster within total CD45+ cells. (F and G) Gene Ontology (GO) terms of genes that are up- (F) and downregulated (G) with pregravid obesity within HLA-DR high macrophages predicted by Metascape. Only differentially expressed genes with a Log 2 fold change cutoff of 0.4 were analyzed. (H) Violin plots compared normalized transcripts of select genes that are significantly up- (left) or downregulated (right) with obesity. (I) Dot plots comparing frequencies of TREM1+ cells or cytokine expressing cells within HLA-DR high macrophages (n = 5/group). Error bars represent the mean and standard error of the mean (SEM). (J) Violin plots comparing secreted factors at baseline by FACS sorted HLA-DR high macrophages (n = 3/group). (K) Experimental design for measuring ex vivo macrophage responses to E. coli or bacterial TLRs. (L) Bar graphs comparing cytokine-producing cells TNFα+IL-6+ (left) and TNFα+IL-6+IL1β+ (right) following stimulation with bacterial TLRs and E. coli (n = 6/group). Error bars represent the mean and standard error of the mean (SEM). ****p < 0.0001, ***p < 0.001, **p < 0.01, *p < 0.05.
    Figure Legend Snippet: (A and B) Dot plots comparing (A) lymphocyte and (B) macrophage proportions within CD45+ decidual cells in lean pregnant women (n = 6 for Tregs, 32 for rest) and those with obesity (n = 6 for Tregs, 31 for rest). (C) Gating strategy and dot plots comparing frequencies of S100A9+ cells within HLA-DR high macrophages (n = 5/group). Error bars represent the mean and standard error of the mean (SEM). (D) Stacked bar graph comparing frequencies of decidual leukocytes within total cells sequenced in each group (within CD45+ cells). (E) Stacked bar comparing HLA-DR high macrophage cluster within total CD45+ cells. (F and G) Gene Ontology (GO) terms of genes that are up- (F) and downregulated (G) with pregravid obesity within HLA-DR high macrophages predicted by Metascape. Only differentially expressed genes with a Log 2 fold change cutoff of 0.4 were analyzed. (H) Violin plots compared normalized transcripts of select genes that are significantly up- (left) or downregulated (right) with obesity. (I) Dot plots comparing frequencies of TREM1+ cells or cytokine expressing cells within HLA-DR high macrophages (n = 5/group). Error bars represent the mean and standard error of the mean (SEM). (J) Violin plots comparing secreted factors at baseline by FACS sorted HLA-DR high macrophages (n = 3/group). (K) Experimental design for measuring ex vivo macrophage responses to E. coli or bacterial TLRs. (L) Bar graphs comparing cytokine-producing cells TNFα+IL-6+ (left) and TNFα+IL-6+IL1β+ (right) following stimulation with bacterial TLRs and E. coli (n = 6/group). Error bars represent the mean and standard error of the mean (SEM). ****p < 0.0001, ***p < 0.001, **p < 0.01, *p < 0.05.

    Techniques Used: Expressing, Ex Vivo

    KEY RESOURCES TABLE
    Figure Legend Snippet: KEY RESOURCES TABLE

    Techniques Used: Luminex, Recombinant, Lysis, Staining, Translocation Assay, Flow Cytometry, Sequencing, Software

    e coli escherichia coli migula castellani  (ATCC)


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    ATCC e coli escherichia coli migula castellani
    E Coli Escherichia Coli Migula Castellani, supplied by ATCC, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    e coli  (ATCC)


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    ATCC e coli
    E Coli, supplied by ATCC, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    e coli escherichia coli migula castellani  (ATCC)


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    ATCC e coli escherichia coli migula castellani
    E Coli Escherichia Coli Migula Castellani, supplied by ATCC, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    e coli escherichia coli migula castellani  (ATCC)


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    ATCC e coli escherichia coli migula castellani
    ( A ) Experimental design for in vitro bacterial and viral stimulation. Purified monocytes were cultured in the presence/absence of <t>E.</t> <t>coli</t> or RSV for 16 hr. Cell pellets were used for bulk RNA-Seq analyses and supernatants were used for Luminex analyses of secreted cytokines and chemokines. ( B ) Bubble plot of key secreted factors significantly different following E. coli infection. The size of the bubble represents the quantity of the secreted analyte (log-transformed) whereas color represents statistical significance relative to no stimulation controls. Statistically significant analytes between lean and obese groups are highlighted with # - p<0.05. ( C ) Venn diagram (right) and corresponding functional enrichment (left) of genes upregulated with E. coli infection in lean and obese groups (Green denotes common DEG, blue DEG unique to lean group, and yellow DEG unique to the obese group) using metascape. The length of the bar indicates the number of genes in each gene ontology (GO) term. Color represents the statistical significance of each GO term. ( D ) Heatmap comparing fold changes of the genes upregulated in both groups (77 genes) that mapped to GO terms ‘myeloid cell differentiation’, ‘inflammatory response to antigenic stimulus’, ‘leukocyte apoptotic process’, ‘regulation of leukocyte activity’, ‘cytokine activity’, and ‘positive regulation of protein phosphorylation’. ( E ) Heatmap comparing normalized transcript counts (blue – low to red – high) of genes exclusively upregulated in the lean group following E. coli infection. ( F ) Experimental design for measuring ex vivo phagocytosis by cord blood monocytes. ( G ) Bar graph depicting colorimetric readout of phagocytosed E. coli particles by UCB monocyte. * or /#- p<0.05, #### - p<0.0001.
    E Coli Escherichia Coli Migula Castellani, supplied by ATCC, used in various techniques. Bioz Stars score: 93/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    1) Product Images from "Maternal obesity blunts antimicrobial responses in fetal monocytes"

    Article Title: Maternal obesity blunts antimicrobial responses in fetal monocytes

    Journal: eLife

    doi: 10.7554/eLife.81320

    ( A ) Experimental design for in vitro bacterial and viral stimulation. Purified monocytes were cultured in the presence/absence of E. coli or RSV for 16 hr. Cell pellets were used for bulk RNA-Seq analyses and supernatants were used for Luminex analyses of secreted cytokines and chemokines. ( B ) Bubble plot of key secreted factors significantly different following E. coli infection. The size of the bubble represents the quantity of the secreted analyte (log-transformed) whereas color represents statistical significance relative to no stimulation controls. Statistically significant analytes between lean and obese groups are highlighted with # - p<0.05. ( C ) Venn diagram (right) and corresponding functional enrichment (left) of genes upregulated with E. coli infection in lean and obese groups (Green denotes common DEG, blue DEG unique to lean group, and yellow DEG unique to the obese group) using metascape. The length of the bar indicates the number of genes in each gene ontology (GO) term. Color represents the statistical significance of each GO term. ( D ) Heatmap comparing fold changes of the genes upregulated in both groups (77 genes) that mapped to GO terms ‘myeloid cell differentiation’, ‘inflammatory response to antigenic stimulus’, ‘leukocyte apoptotic process’, ‘regulation of leukocyte activity’, ‘cytokine activity’, and ‘positive regulation of protein phosphorylation’. ( E ) Heatmap comparing normalized transcript counts (blue – low to red – high) of genes exclusively upregulated in the lean group following E. coli infection. ( F ) Experimental design for measuring ex vivo phagocytosis by cord blood monocytes. ( G ) Bar graph depicting colorimetric readout of phagocytosed E. coli particles by UCB monocyte. * or /#- p<0.05, #### - p<0.0001.
    Figure Legend Snippet: ( A ) Experimental design for in vitro bacterial and viral stimulation. Purified monocytes were cultured in the presence/absence of E. coli or RSV for 16 hr. Cell pellets were used for bulk RNA-Seq analyses and supernatants were used for Luminex analyses of secreted cytokines and chemokines. ( B ) Bubble plot of key secreted factors significantly different following E. coli infection. The size of the bubble represents the quantity of the secreted analyte (log-transformed) whereas color represents statistical significance relative to no stimulation controls. Statistically significant analytes between lean and obese groups are highlighted with # - p<0.05. ( C ) Venn diagram (right) and corresponding functional enrichment (left) of genes upregulated with E. coli infection in lean and obese groups (Green denotes common DEG, blue DEG unique to lean group, and yellow DEG unique to the obese group) using metascape. The length of the bar indicates the number of genes in each gene ontology (GO) term. Color represents the statistical significance of each GO term. ( D ) Heatmap comparing fold changes of the genes upregulated in both groups (77 genes) that mapped to GO terms ‘myeloid cell differentiation’, ‘inflammatory response to antigenic stimulus’, ‘leukocyte apoptotic process’, ‘regulation of leukocyte activity’, ‘cytokine activity’, and ‘positive regulation of protein phosphorylation’. ( E ) Heatmap comparing normalized transcript counts (blue – low to red – high) of genes exclusively upregulated in the lean group following E. coli infection. ( F ) Experimental design for measuring ex vivo phagocytosis by cord blood monocytes. ( G ) Bar graph depicting colorimetric readout of phagocytosed E. coli particles by UCB monocyte. * or /#- p<0.05, #### - p<0.0001.

    Techniques Used: In Vitro, Purification, Cell Culture, RNA Sequencing Assay, Luminex, Infection, Transformation Assay, Functional Assay, Cell Differentiation, Activity Assay, Ex Vivo

    ( A ) Bar graph representing the number of upregulated (red) or downregulated (blue) differentially expressed genes (DEG) in each group. ( B ) Venn diagram representing the number of downregulated DEG following E. coli stimulation in each group. ( C ) Functional enrichment of downregulated DEG detected in both groups (top, green), or exclusively in the lean (middle, blue) and obese (bottom, orange) groups. ( D ) Violin plots comparing fold changes of DEGs downregulated following E. coli stimulation and involved in antigen presentation.
    Figure Legend Snippet: ( A ) Bar graph representing the number of upregulated (red) or downregulated (blue) differentially expressed genes (DEG) in each group. ( B ) Venn diagram representing the number of downregulated DEG following E. coli stimulation in each group. ( C ) Functional enrichment of downregulated DEG detected in both groups (top, green), or exclusively in the lean (middle, blue) and obese (bottom, orange) groups. ( D ) Violin plots comparing fold changes of DEGs downregulated following E. coli stimulation and involved in antigen presentation.

    Techniques Used: Functional Assay

    ( A ) Bar graph representing the number of upregulated (red) or downregulated (blue) DEG in each group. ( B ) Heatmap of upregulated genes involved in interferon signaling pathway. ( C ) Surface protein levels of interferon receptor 1 (IFNAR1) represented as the fraction of positive cells (top) or median fluorescent intensity (bottom). *- p<0.05, ***- p<0.001. ( D ) Venn diagram representing the number of downregulated DEG following RSV stimulation. ( E ) Functional enrichment of downregulated DEG detected in both groups (top, green), or exclusively in the lean group (top, blue) and obese group (bottom, orange). ( F ) Four-way venn comparing overall gene expression (both up- and down-regulated genes) changes following E. coli and RSV infections. ( G ) Five way functional enrichment of unique DEG and the 79 DEG induced in all groups induced following in vitro infection with E. coli and RSV.
    Figure Legend Snippet: ( A ) Bar graph representing the number of upregulated (red) or downregulated (blue) DEG in each group. ( B ) Heatmap of upregulated genes involved in interferon signaling pathway. ( C ) Surface protein levels of interferon receptor 1 (IFNAR1) represented as the fraction of positive cells (top) or median fluorescent intensity (bottom). *- p<0.05, ***- p<0.001. ( D ) Venn diagram representing the number of downregulated DEG following RSV stimulation. ( E ) Functional enrichment of downregulated DEG detected in both groups (top, green), or exclusively in the lean group (top, blue) and obese group (bottom, orange). ( F ) Four-way venn comparing overall gene expression (both up- and down-regulated genes) changes following E. coli and RSV infections. ( G ) Five way functional enrichment of unique DEG and the 79 DEG induced in all groups induced following in vitro infection with E. coli and RSV.

    Techniques Used: Functional Assay, Expressing, In Vitro, Infection

    ( A ) Dot plots comparing median fluorescence intensity (MFI) ± SEM of phosphorylated signaling molecules downstream of TLR4 sensing (n=5/group). *- p<0.05, **- p<0.01. ( B ) Representative brightfield and fluorescent images of stimulated and unstimulated UCB monocytes profiled using imagine flow cytometry (n=3–4/group). NF-kB (p50–AF488) and nucleus (7-AAD) are shown in green and red respectively. Surface stains for CD14 and HLA-DR are shown in aqua and fuchsia respectively. Overlay of NF-kB and nuclei stain was used to determine translocation within CD14 + HLA-DR+monocytes. Bar graph comparing percentage translocated cells following LPS stimulation in lean and obese groups. ( C ) Bar graph comparing changes in trimethyl modification on H3K9 residues following LPS stimulation (relative to no stimulation controls) detected using flow cytometry. ( D ) Graph representing the kinetics of ECAR of stimulated monocytes following glucose injection and blockade of glycolysis. ( E ) Bar graph comparing DAR frequencies in each group following LPS stimulation. ( F ) Heatmap demonstrating overall accessibility differences following LPS stimulation around the promoter. ( G ) Over-represented transcription factors identified from motif analysis of DARs more open in lean compared to obese groups following LPS stimulation. X-axis represented percentage of peaks with motifs identified and color represents p-value on log10 scale ( H ) Pileups of key inflammatory loci post LPS stimulation ( I ) Four-way Venn of genes accessible (ATAC-Seq) exclusively in the lean group post LPS stimulation with genes exclusively upregulated (RNA-Seq) in the lean group following LPS, E. coli and RSV infection. Select overlapping genes are highlighted. ( J ) UMAP of single nuclei ATAC-Seq of LPS stimulated and sorted monocytes. ( K ) Feature plots demonstrating a cluster of activated monocytes (cluster 1). Color intensity represents fragments mapping to open chromatin regions. ( L ) Proportions of monocytes within each group mapping to activated monocyte cluster. ( M ) Pileups of inflammatory loci in activated monocytes with/without LPS stimulation. * - p<0.05; ** - p<0.01.
    Figure Legend Snippet: ( A ) Dot plots comparing median fluorescence intensity (MFI) ± SEM of phosphorylated signaling molecules downstream of TLR4 sensing (n=5/group). *- p<0.05, **- p<0.01. ( B ) Representative brightfield and fluorescent images of stimulated and unstimulated UCB monocytes profiled using imagine flow cytometry (n=3–4/group). NF-kB (p50–AF488) and nucleus (7-AAD) are shown in green and red respectively. Surface stains for CD14 and HLA-DR are shown in aqua and fuchsia respectively. Overlay of NF-kB and nuclei stain was used to determine translocation within CD14 + HLA-DR+monocytes. Bar graph comparing percentage translocated cells following LPS stimulation in lean and obese groups. ( C ) Bar graph comparing changes in trimethyl modification on H3K9 residues following LPS stimulation (relative to no stimulation controls) detected using flow cytometry. ( D ) Graph representing the kinetics of ECAR of stimulated monocytes following glucose injection and blockade of glycolysis. ( E ) Bar graph comparing DAR frequencies in each group following LPS stimulation. ( F ) Heatmap demonstrating overall accessibility differences following LPS stimulation around the promoter. ( G ) Over-represented transcription factors identified from motif analysis of DARs more open in lean compared to obese groups following LPS stimulation. X-axis represented percentage of peaks with motifs identified and color represents p-value on log10 scale ( H ) Pileups of key inflammatory loci post LPS stimulation ( I ) Four-way Venn of genes accessible (ATAC-Seq) exclusively in the lean group post LPS stimulation with genes exclusively upregulated (RNA-Seq) in the lean group following LPS, E. coli and RSV infection. Select overlapping genes are highlighted. ( J ) UMAP of single nuclei ATAC-Seq of LPS stimulated and sorted monocytes. ( K ) Feature plots demonstrating a cluster of activated monocytes (cluster 1). Color intensity represents fragments mapping to open chromatin regions. ( L ) Proportions of monocytes within each group mapping to activated monocyte cluster. ( M ) Pileups of inflammatory loci in activated monocytes with/without LPS stimulation. * - p<0.05; ** - p<0.01.

    Techniques Used: Fluorescence, Flow Cytometry, Staining, Translocation Assay, Modification, Injection, RNA Sequencing Assay, Infection

    ( A ) NHP model of maternal diet-induced obesity. Fetal (GD130) PBMC, ileal leukocytes, and spleenocytes were obtained from rhesus macaque born to dams on a control chow diet (n=3) and western-style diet (n=4). Fetal macrophages from ileal lamina propria lymphocytes and splenocytes were FACS-sorted and cultured overnight with E. coli . Supernatants were collected and cytokines/chemokines were measured using Luminex. ( B ) Bar graph representing the frequency (mean and ± SEM) of responding fetal monocytes to LPS in PBMC isolated from GD130 fetal circulation measured by intracellular cytokine staining. ( C ) Frequencies of CD14 + HLA-DR+macrophages within live total ileal leukocytes (top) or live CD3-CD20- leukocytes (bottom) ( D–E ) Median fluorescence intensity (MFI) of ( D ) M1-associated HLA-DR and ( E ) M2-associated CD209 and CD206 within live macrophage population in ileum (top) and spleen (bottom). ( F–G ) Bubble plots comparing significantly different cytokine/chemokine levels in response to E. coli stimulation in ( F ) gut (ileum) and ( G ) splenic macrophages. Statistical differences between chow and WSD groups are highlighted. *-p<0.05.
    Figure Legend Snippet: ( A ) NHP model of maternal diet-induced obesity. Fetal (GD130) PBMC, ileal leukocytes, and spleenocytes were obtained from rhesus macaque born to dams on a control chow diet (n=3) and western-style diet (n=4). Fetal macrophages from ileal lamina propria lymphocytes and splenocytes were FACS-sorted and cultured overnight with E. coli . Supernatants were collected and cytokines/chemokines were measured using Luminex. ( B ) Bar graph representing the frequency (mean and ± SEM) of responding fetal monocytes to LPS in PBMC isolated from GD130 fetal circulation measured by intracellular cytokine staining. ( C ) Frequencies of CD14 + HLA-DR+macrophages within live total ileal leukocytes (top) or live CD3-CD20- leukocytes (bottom) ( D–E ) Median fluorescence intensity (MFI) of ( D ) M1-associated HLA-DR and ( E ) M2-associated CD209 and CD206 within live macrophage population in ileum (top) and spleen (bottom). ( F–G ) Bubble plots comparing significantly different cytokine/chemokine levels in response to E. coli stimulation in ( F ) gut (ileum) and ( G ) splenic macrophages. Statistical differences between chow and WSD groups are highlighted. *-p<0.05.

    Techniques Used: Western Blot, Cell Culture, Luminex, Isolation, Staining, Fluorescence

    e coli o157 h7 atcc35150  (ATCC)


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    ATCC e coli o157 h7 atcc35150
    E Coli O157 H7 Atcc35150, supplied by ATCC, used in various techniques. Bioz Stars score: 96/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    e coli  (ATCC)


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    ATCC e coli
    E Coli, supplied by ATCC, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    e coli atcc 11229  (ATCC)


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    ATCC e coli atcc 11229
    E Coli Atcc 11229, supplied by ATCC, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    e coli atcc 11775 t  (ATCC)


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    ATCC e coli atcc 11775 t
    The neighbour-joining phylogenetic tree based on 16S rRNA gene sequences of isolated <t>E.</t> <t>coli</t> / E. fergusonii strains from patients with IBD or IC patients and healthy controls (HCs). The numbers at the nodes indicate the percentage of 1000 bootstrap replicates, and Escherichia hermannii CIP 103176 T was used an outgroup. The accession numbers of retrieved 16S rRNA gene sequences are given in parentheses. Strains names with colour codes (red = IBD; green = IC; and blue = HCs).
    E Coli Atcc 11775 T, supplied by ATCC, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Images

    1) Product Images from "Differentiation of Escherichia fergusonii and Escherichia coli Isolated from Patients with Inflammatory Bowel Disease/Ischemic Colitis and Their Antimicrobial Susceptibility Patterns"

    Article Title: Differentiation of Escherichia fergusonii and Escherichia coli Isolated from Patients with Inflammatory Bowel Disease/Ischemic Colitis and Their Antimicrobial Susceptibility Patterns

    Journal: Antibiotics

    doi: 10.3390/antibiotics12010154

    The neighbour-joining phylogenetic tree based on 16S rRNA gene sequences of isolated E. coli / E. fergusonii strains from patients with IBD or IC patients and healthy controls (HCs). The numbers at the nodes indicate the percentage of 1000 bootstrap replicates, and Escherichia hermannii CIP 103176 T was used an outgroup. The accession numbers of retrieved 16S rRNA gene sequences are given in parentheses. Strains names with colour codes (red = IBD; green = IC; and blue = HCs).
    Figure Legend Snippet: The neighbour-joining phylogenetic tree based on 16S rRNA gene sequences of isolated E. coli / E. fergusonii strains from patients with IBD or IC patients and healthy controls (HCs). The numbers at the nodes indicate the percentage of 1000 bootstrap replicates, and Escherichia hermannii CIP 103176 T was used an outgroup. The accession numbers of retrieved 16S rRNA gene sequences are given in parentheses. Strains names with colour codes (red = IBD; green = IC; and blue = HCs).

    Techniques Used: Isolation

    The neighbour-joining phylogenetic tree based on 16S rRNA gene sequences of isolated E. coli / E. fergusonii strains from patients with IBD or IC. The numbers at the nodes indicate the percentage of 1000 bootstrap replicates. Escherichia hermannii CIP 103176T was used an outgroup. The accession numbers of retrieved 16S rRNA gene sequences are given in parentheses. Strain names in red and blue represent IBD (red = CD; and blue = UC), and green represents IC.
    Figure Legend Snippet: The neighbour-joining phylogenetic tree based on 16S rRNA gene sequences of isolated E. coli / E. fergusonii strains from patients with IBD or IC. The numbers at the nodes indicate the percentage of 1000 bootstrap replicates. Escherichia hermannii CIP 103176T was used an outgroup. The accession numbers of retrieved 16S rRNA gene sequences are given in parentheses. Strain names in red and blue represent IBD (red = CD; and blue = UC), and green represents IC.

    Techniques Used: Isolation

    The neighbour-joining phylogenetic tree based on 583-bp adk gene sequences of isolated E. coli strains from patients with IBD or IC. The numbers at the nodes indicate the percentage of 400 bootstrap replicates. Routltella planticola KpH165 was used an outgroup. Strain names in red and blue represent IBD (red = CD; and blue = UC), and green represents IC. The accession numbers are provided in parentheses whose adk gene sequences were retrieved from whole genome sequences.
    Figure Legend Snippet: The neighbour-joining phylogenetic tree based on 583-bp adk gene sequences of isolated E. coli strains from patients with IBD or IC. The numbers at the nodes indicate the percentage of 400 bootstrap replicates. Routltella planticola KpH165 was used an outgroup. Strain names in red and blue represent IBD (red = CD; and blue = UC), and green represents IC. The accession numbers are provided in parentheses whose adk gene sequences were retrieved from whole genome sequences.

    Techniques Used: Isolation

    Differentiating adk gene nucleotides of E. coli against E. fergusonii strains.
    Figure Legend Snippet: Differentiating adk gene nucleotides of E. coli against E. fergusonii strains.

    Techniques Used: Sequencing

    e coli o157 h7 atcc 51659  (ATCC)


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    Structured Review

    ATCC e coli o157 h7 atcc 51659
    Overview of selected records reporting antibacterial activity of polyphenols sourced from date kernel extracts.
    E Coli O157 H7 Atcc 51659, supplied by ATCC, used in various techniques. Bioz Stars score: 93/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Images

    1) Product Images from "A systematic review of antibacterial activity of polyphenolic extract from date palm ( Phoenix dactylifera L.) kernel"

    Article Title: A systematic review of antibacterial activity of polyphenolic extract from date palm ( Phoenix dactylifera L.) kernel

    Journal: Frontiers in Pharmacology

    doi: 10.3389/fphar.2022.1043548

    Overview of selected records reporting antibacterial activity of polyphenols sourced from date kernel extracts.
    Figure Legend Snippet: Overview of selected records reporting antibacterial activity of polyphenols sourced from date kernel extracts.

    Techniques Used: Activity Assay

    (A) Boxplot of pooled median ± range of zone of inhibition (ZOI) results reported in included studies against four pathogens gram positive: S. aureus , B. subtilis and gram negative: E. Coli , P. aeruginosa (values in parentheses indicate number of studies). (B) Boxplot of pooled median ± range of minimum inhibitory concentration (MIC) results reported against S. aureus and E. Coli in included studies (values in parentheses indicate number of studies).
    Figure Legend Snippet: (A) Boxplot of pooled median ± range of zone of inhibition (ZOI) results reported in included studies against four pathogens gram positive: S. aureus , B. subtilis and gram negative: E. Coli , P. aeruginosa (values in parentheses indicate number of studies). (B) Boxplot of pooled median ± range of minimum inhibitory concentration (MIC) results reported against S. aureus and E. Coli in included studies (values in parentheses indicate number of studies).

    Techniques Used: Inhibition, Concentration Assay

    (A) Boxplot of pooled median ± range of minimum inhibitory concentration (MIC) results reported against S. aureus in included studies (values in parentheses indicate number of studies). *Gallic acid was isolated from the date seed extract and used for the test. (B) Boxplot of pooled median ± range of minimum inhibitory concentration (MIC) results reported E. coli in included studies (values in parentheses indicate number of studies). *Gallic acid was isolated from the date seed extract and used for the test. (C) Boxplot of pooled median ± range of minimum bactericidal concentration (MBC) results reported against S. aureus and E. coli in included studies (values in parentheses indicate number of studies).
    Figure Legend Snippet: (A) Boxplot of pooled median ± range of minimum inhibitory concentration (MIC) results reported against S. aureus in included studies (values in parentheses indicate number of studies). *Gallic acid was isolated from the date seed extract and used for the test. (B) Boxplot of pooled median ± range of minimum inhibitory concentration (MIC) results reported E. coli in included studies (values in parentheses indicate number of studies). *Gallic acid was isolated from the date seed extract and used for the test. (C) Boxplot of pooled median ± range of minimum bactericidal concentration (MBC) results reported against S. aureus and E. coli in included studies (values in parentheses indicate number of studies).

    Techniques Used: Concentration Assay, Isolation

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    ATCC e coli
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    ATCC e coli escherichia coli migula castellani
    (A) Heatmap of top marker genes for the decidual HLA-DR low and HLA-DR high subsets, classical and non-classical blood monocytes. Each column is a bin of a fixed number of cells and each row represents a gene. A subset of genes within each cluster is annotated. High and low expression are represented as red and blue, respectively. (B) Violin plots comparing expression of gene markers within decidual macrophage subsets. (C) Surface expression of HLA-DR and CD11c measured by flow cytometry. (D) Brightfield and fluorescence profiles of macrophage subsets captured using imaging flow cytometry. (E) Median Fluorescence Intensities (MFI) of macrophage surface markers on decidual macrophage subsets (n = 7/group). (F) Frequencies of TREM2+ FOLR2+ (n = 5/group) and CD163+ (n = 7/group) within decidual macrophages. (G) Phospho p65 signal in blood monocytes and decidual macrophage subsets (n = 3/group) by flow cytometry. Error bars represent the mean and standard error of the mean (SEM). (H) Comparison of baseline secreted cytokine profiles (median) of sorted decidual macrophage subsets (n = 4/group) and blood monocytes (n = 2). * and # represent significant differences relative to blood monocytes between HLA-DR low and HLA-DR high macrophages, respectively. (I) Responses to overnight lipopolysaccharide (LPS) stimulation of total decidual leukocytes (n = 8/group). Error bars represent the mean and standard error of the mean (SEM). (J) MFI of intracellular cellROX (n = 7/group). (K) Percentage of <t>E.</t> <t>coli</t> pHrodo+ (n = 8/group) in decidual macrophages. (L) Oxygen consumption rate and extracellular acidification rates of decidual macrophages (n = 6/group). ****p < 0.0001, **p < 0.01, *p < 0.05, and #p<0.1.
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    96
    ATCC e coli o157 h7 atcc35150
    (A) Heatmap of top marker genes for the decidual HLA-DR low and HLA-DR high subsets, classical and non-classical blood monocytes. Each column is a bin of a fixed number of cells and each row represents a gene. A subset of genes within each cluster is annotated. High and low expression are represented as red and blue, respectively. (B) Violin plots comparing expression of gene markers within decidual macrophage subsets. (C) Surface expression of HLA-DR and CD11c measured by flow cytometry. (D) Brightfield and fluorescence profiles of macrophage subsets captured using imaging flow cytometry. (E) Median Fluorescence Intensities (MFI) of macrophage surface markers on decidual macrophage subsets (n = 7/group). (F) Frequencies of TREM2+ FOLR2+ (n = 5/group) and CD163+ (n = 7/group) within decidual macrophages. (G) Phospho p65 signal in blood monocytes and decidual macrophage subsets (n = 3/group) by flow cytometry. Error bars represent the mean and standard error of the mean (SEM). (H) Comparison of baseline secreted cytokine profiles (median) of sorted decidual macrophage subsets (n = 4/group) and blood monocytes (n = 2). * and # represent significant differences relative to blood monocytes between HLA-DR low and HLA-DR high macrophages, respectively. (I) Responses to overnight lipopolysaccharide (LPS) stimulation of total decidual leukocytes (n = 8/group). Error bars represent the mean and standard error of the mean (SEM). (J) MFI of intracellular cellROX (n = 7/group). (K) Percentage of <t>E.</t> <t>coli</t> pHrodo+ (n = 8/group) in decidual macrophages. (L) Oxygen consumption rate and extracellular acidification rates of decidual macrophages (n = 6/group). ****p < 0.0001, **p < 0.01, *p < 0.05, and #p<0.1.
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    ATCC e coli atcc 11229
    (A) Heatmap of top marker genes for the decidual HLA-DR low and HLA-DR high subsets, classical and non-classical blood monocytes. Each column is a bin of a fixed number of cells and each row represents a gene. A subset of genes within each cluster is annotated. High and low expression are represented as red and blue, respectively. (B) Violin plots comparing expression of gene markers within decidual macrophage subsets. (C) Surface expression of HLA-DR and CD11c measured by flow cytometry. (D) Brightfield and fluorescence profiles of macrophage subsets captured using imaging flow cytometry. (E) Median Fluorescence Intensities (MFI) of macrophage surface markers on decidual macrophage subsets (n = 7/group). (F) Frequencies of TREM2+ FOLR2+ (n = 5/group) and CD163+ (n = 7/group) within decidual macrophages. (G) Phospho p65 signal in blood monocytes and decidual macrophage subsets (n = 3/group) by flow cytometry. Error bars represent the mean and standard error of the mean (SEM). (H) Comparison of baseline secreted cytokine profiles (median) of sorted decidual macrophage subsets (n = 4/group) and blood monocytes (n = 2). * and # represent significant differences relative to blood monocytes between HLA-DR low and HLA-DR high macrophages, respectively. (I) Responses to overnight lipopolysaccharide (LPS) stimulation of total decidual leukocytes (n = 8/group). Error bars represent the mean and standard error of the mean (SEM). (J) MFI of intracellular cellROX (n = 7/group). (K) Percentage of <t>E.</t> <t>coli</t> pHrodo+ (n = 8/group) in decidual macrophages. (L) Oxygen consumption rate and extracellular acidification rates of decidual macrophages (n = 6/group). ****p < 0.0001, **p < 0.01, *p < 0.05, and #p<0.1.
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    ATCC e coli atcc 11775 t
    The neighbour-joining phylogenetic tree based on 16S rRNA gene sequences of isolated <t>E.</t> <t>coli</t> / E. fergusonii strains from patients with IBD or IC patients and healthy controls (HCs). The numbers at the nodes indicate the percentage of 1000 bootstrap replicates, and Escherichia hermannii CIP 103176 T was used an outgroup. The accession numbers of retrieved 16S rRNA gene sequences are given in parentheses. Strains names with colour codes (red = IBD; green = IC; and blue = HCs).
    E Coli Atcc 11775 T, supplied by ATCC, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    ATCC e coli o157 h7 atcc 51659
    Overview of selected records reporting antibacterial activity of polyphenols sourced from date kernel extracts.
    E Coli O157 H7 Atcc 51659, supplied by ATCC, used in various techniques. Bioz Stars score: 93/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Image Search Results


    (A) Heatmap of top marker genes for the decidual HLA-DR low and HLA-DR high subsets, classical and non-classical blood monocytes. Each column is a bin of a fixed number of cells and each row represents a gene. A subset of genes within each cluster is annotated. High and low expression are represented as red and blue, respectively. (B) Violin plots comparing expression of gene markers within decidual macrophage subsets. (C) Surface expression of HLA-DR and CD11c measured by flow cytometry. (D) Brightfield and fluorescence profiles of macrophage subsets captured using imaging flow cytometry. (E) Median Fluorescence Intensities (MFI) of macrophage surface markers on decidual macrophage subsets (n = 7/group). (F) Frequencies of TREM2+ FOLR2+ (n = 5/group) and CD163+ (n = 7/group) within decidual macrophages. (G) Phospho p65 signal in blood monocytes and decidual macrophage subsets (n = 3/group) by flow cytometry. Error bars represent the mean and standard error of the mean (SEM). (H) Comparison of baseline secreted cytokine profiles (median) of sorted decidual macrophage subsets (n = 4/group) and blood monocytes (n = 2). * and # represent significant differences relative to blood monocytes between HLA-DR low and HLA-DR high macrophages, respectively. (I) Responses to overnight lipopolysaccharide (LPS) stimulation of total decidual leukocytes (n = 8/group). Error bars represent the mean and standard error of the mean (SEM). (J) MFI of intracellular cellROX (n = 7/group). (K) Percentage of E. coli pHrodo+ (n = 8/group) in decidual macrophages. (L) Oxygen consumption rate and extracellular acidification rates of decidual macrophages (n = 6/group). ****p < 0.0001, **p < 0.01, *p < 0.05, and #p<0.1.

    Journal: Cell reports

    Article Title: Multimodal profiling of term human decidua demonstrates immune adaptations with pregravid obesity

    doi: 10.1016/j.celrep.2023.112769

    Figure Lengend Snippet: (A) Heatmap of top marker genes for the decidual HLA-DR low and HLA-DR high subsets, classical and non-classical blood monocytes. Each column is a bin of a fixed number of cells and each row represents a gene. A subset of genes within each cluster is annotated. High and low expression are represented as red and blue, respectively. (B) Violin plots comparing expression of gene markers within decidual macrophage subsets. (C) Surface expression of HLA-DR and CD11c measured by flow cytometry. (D) Brightfield and fluorescence profiles of macrophage subsets captured using imaging flow cytometry. (E) Median Fluorescence Intensities (MFI) of macrophage surface markers on decidual macrophage subsets (n = 7/group). (F) Frequencies of TREM2+ FOLR2+ (n = 5/group) and CD163+ (n = 7/group) within decidual macrophages. (G) Phospho p65 signal in blood monocytes and decidual macrophage subsets (n = 3/group) by flow cytometry. Error bars represent the mean and standard error of the mean (SEM). (H) Comparison of baseline secreted cytokine profiles (median) of sorted decidual macrophage subsets (n = 4/group) and blood monocytes (n = 2). * and # represent significant differences relative to blood monocytes between HLA-DR low and HLA-DR high macrophages, respectively. (I) Responses to overnight lipopolysaccharide (LPS) stimulation of total decidual leukocytes (n = 8/group). Error bars represent the mean and standard error of the mean (SEM). (J) MFI of intracellular cellROX (n = 7/group). (K) Percentage of E. coli pHrodo+ (n = 8/group) in decidual macrophages. (L) Oxygen consumption rate and extracellular acidification rates of decidual macrophages (n = 6/group). ****p < 0.0001, **p < 0.01, *p < 0.05, and #p<0.1.

    Article Snippet: To measure cytokine responses of decidua macrophages, 10 6 thawed cells were stimulated for 6h at 37°C in RPMI supplemented with 10% FBS in the presence or absence of bacterial TLR cocktail containing 1 μg/mL LPS (TLR4 ligand, E.coli 055:B5; Invivogen, San Diego, CA), 2 μg/mL Pam3CSK4 (TLR1/2 agonist, Invivogen), and 1 μg/mL FSL-1 (TLR2/6 agonist, Sigma, St. Louis, MO), or 6 X 10 5 cfu/mL E. coli (Escherichia coli (Migula) Castellani and Chalmers ATCC 11775).

    Techniques: Marker, Expressing, Flow Cytometry, Fluorescence, Imaging, Comparison

    (A and B) Dot plots comparing (A) lymphocyte and (B) macrophage proportions within CD45+ decidual cells in lean pregnant women (n = 6 for Tregs, 32 for rest) and those with obesity (n = 6 for Tregs, 31 for rest). (C) Gating strategy and dot plots comparing frequencies of S100A9+ cells within HLA-DR high macrophages (n = 5/group). Error bars represent the mean and standard error of the mean (SEM). (D) Stacked bar graph comparing frequencies of decidual leukocytes within total cells sequenced in each group (within CD45+ cells). (E) Stacked bar comparing HLA-DR high macrophage cluster within total CD45+ cells. (F and G) Gene Ontology (GO) terms of genes that are up- (F) and downregulated (G) with pregravid obesity within HLA-DR high macrophages predicted by Metascape. Only differentially expressed genes with a Log 2 fold change cutoff of 0.4 were analyzed. (H) Violin plots compared normalized transcripts of select genes that are significantly up- (left) or downregulated (right) with obesity. (I) Dot plots comparing frequencies of TREM1+ cells or cytokine expressing cells within HLA-DR high macrophages (n = 5/group). Error bars represent the mean and standard error of the mean (SEM). (J) Violin plots comparing secreted factors at baseline by FACS sorted HLA-DR high macrophages (n = 3/group). (K) Experimental design for measuring ex vivo macrophage responses to E. coli or bacterial TLRs. (L) Bar graphs comparing cytokine-producing cells TNFα+IL-6+ (left) and TNFα+IL-6+IL1β+ (right) following stimulation with bacterial TLRs and E. coli (n = 6/group). Error bars represent the mean and standard error of the mean (SEM). ****p < 0.0001, ***p < 0.001, **p < 0.01, *p < 0.05.

    Journal: Cell reports

    Article Title: Multimodal profiling of term human decidua demonstrates immune adaptations with pregravid obesity

    doi: 10.1016/j.celrep.2023.112769

    Figure Lengend Snippet: (A and B) Dot plots comparing (A) lymphocyte and (B) macrophage proportions within CD45+ decidual cells in lean pregnant women (n = 6 for Tregs, 32 for rest) and those with obesity (n = 6 for Tregs, 31 for rest). (C) Gating strategy and dot plots comparing frequencies of S100A9+ cells within HLA-DR high macrophages (n = 5/group). Error bars represent the mean and standard error of the mean (SEM). (D) Stacked bar graph comparing frequencies of decidual leukocytes within total cells sequenced in each group (within CD45+ cells). (E) Stacked bar comparing HLA-DR high macrophage cluster within total CD45+ cells. (F and G) Gene Ontology (GO) terms of genes that are up- (F) and downregulated (G) with pregravid obesity within HLA-DR high macrophages predicted by Metascape. Only differentially expressed genes with a Log 2 fold change cutoff of 0.4 were analyzed. (H) Violin plots compared normalized transcripts of select genes that are significantly up- (left) or downregulated (right) with obesity. (I) Dot plots comparing frequencies of TREM1+ cells or cytokine expressing cells within HLA-DR high macrophages (n = 5/group). Error bars represent the mean and standard error of the mean (SEM). (J) Violin plots comparing secreted factors at baseline by FACS sorted HLA-DR high macrophages (n = 3/group). (K) Experimental design for measuring ex vivo macrophage responses to E. coli or bacterial TLRs. (L) Bar graphs comparing cytokine-producing cells TNFα+IL-6+ (left) and TNFα+IL-6+IL1β+ (right) following stimulation with bacterial TLRs and E. coli (n = 6/group). Error bars represent the mean and standard error of the mean (SEM). ****p < 0.0001, ***p < 0.001, **p < 0.01, *p < 0.05.

    Article Snippet: To measure cytokine responses of decidua macrophages, 10 6 thawed cells were stimulated for 6h at 37°C in RPMI supplemented with 10% FBS in the presence or absence of bacterial TLR cocktail containing 1 μg/mL LPS (TLR4 ligand, E.coli 055:B5; Invivogen, San Diego, CA), 2 μg/mL Pam3CSK4 (TLR1/2 agonist, Invivogen), and 1 μg/mL FSL-1 (TLR2/6 agonist, Sigma, St. Louis, MO), or 6 X 10 5 cfu/mL E. coli (Escherichia coli (Migula) Castellani and Chalmers ATCC 11775).

    Techniques: Expressing, Ex Vivo

    KEY RESOURCES TABLE

    Journal: Cell reports

    Article Title: Multimodal profiling of term human decidua demonstrates immune adaptations with pregravid obesity

    doi: 10.1016/j.celrep.2023.112769

    Figure Lengend Snippet: KEY RESOURCES TABLE

    Article Snippet: To measure cytokine responses of decidua macrophages, 10 6 thawed cells were stimulated for 6h at 37°C in RPMI supplemented with 10% FBS in the presence or absence of bacterial TLR cocktail containing 1 μg/mL LPS (TLR4 ligand, E.coli 055:B5; Invivogen, San Diego, CA), 2 μg/mL Pam3CSK4 (TLR1/2 agonist, Invivogen), and 1 μg/mL FSL-1 (TLR2/6 agonist, Sigma, St. Louis, MO), or 6 X 10 5 cfu/mL E. coli (Escherichia coli (Migula) Castellani and Chalmers ATCC 11775).

    Techniques: Luminex, Recombinant, Lysis, Staining, Translocation Assay, Flow Cytometry, Sequencing, Software

    The neighbour-joining phylogenetic tree based on 16S rRNA gene sequences of isolated E. coli / E. fergusonii strains from patients with IBD or IC patients and healthy controls (HCs). The numbers at the nodes indicate the percentage of 1000 bootstrap replicates, and Escherichia hermannii CIP 103176 T was used an outgroup. The accession numbers of retrieved 16S rRNA gene sequences are given in parentheses. Strains names with colour codes (red = IBD; green = IC; and blue = HCs).

    Journal: Antibiotics

    Article Title: Differentiation of Escherichia fergusonii and Escherichia coli Isolated from Patients with Inflammatory Bowel Disease/Ischemic Colitis and Their Antimicrobial Susceptibility Patterns

    doi: 10.3390/antibiotics12010154

    Figure Lengend Snippet: The neighbour-joining phylogenetic tree based on 16S rRNA gene sequences of isolated E. coli / E. fergusonii strains from patients with IBD or IC patients and healthy controls (HCs). The numbers at the nodes indicate the percentage of 1000 bootstrap replicates, and Escherichia hermannii CIP 103176 T was used an outgroup. The accession numbers of retrieved 16S rRNA gene sequences are given in parentheses. Strains names with colour codes (red = IBD; green = IC; and blue = HCs).

    Article Snippet: We extracted 645 bp adk gene sequences of type species and representatives of E. coli and E. fergusonii species, including E. coli ATCC 11775 T (CP033092), E. coli O157:H7 (BA000007), E. coli K12 (U00096), E. fergusonii ATCC 35469 T (CU928158), and E. fergusonii RHB19-C05 (CP057657), from respective whole genome sequences and aligned all the adk gene sequences of 83 isolates with adk gene sequences from E. coli KCTC 2441 T , E. coli 25922, and E. fergusonii KCTC 22525 T using a multalign interface server [ ].

    Techniques: Isolation

    The neighbour-joining phylogenetic tree based on 16S rRNA gene sequences of isolated E. coli / E. fergusonii strains from patients with IBD or IC. The numbers at the nodes indicate the percentage of 1000 bootstrap replicates. Escherichia hermannii CIP 103176T was used an outgroup. The accession numbers of retrieved 16S rRNA gene sequences are given in parentheses. Strain names in red and blue represent IBD (red = CD; and blue = UC), and green represents IC.

    Journal: Antibiotics

    Article Title: Differentiation of Escherichia fergusonii and Escherichia coli Isolated from Patients with Inflammatory Bowel Disease/Ischemic Colitis and Their Antimicrobial Susceptibility Patterns

    doi: 10.3390/antibiotics12010154

    Figure Lengend Snippet: The neighbour-joining phylogenetic tree based on 16S rRNA gene sequences of isolated E. coli / E. fergusonii strains from patients with IBD or IC. The numbers at the nodes indicate the percentage of 1000 bootstrap replicates. Escherichia hermannii CIP 103176T was used an outgroup. The accession numbers of retrieved 16S rRNA gene sequences are given in parentheses. Strain names in red and blue represent IBD (red = CD; and blue = UC), and green represents IC.

    Article Snippet: We extracted 645 bp adk gene sequences of type species and representatives of E. coli and E. fergusonii species, including E. coli ATCC 11775 T (CP033092), E. coli O157:H7 (BA000007), E. coli K12 (U00096), E. fergusonii ATCC 35469 T (CU928158), and E. fergusonii RHB19-C05 (CP057657), from respective whole genome sequences and aligned all the adk gene sequences of 83 isolates with adk gene sequences from E. coli KCTC 2441 T , E. coli 25922, and E. fergusonii KCTC 22525 T using a multalign interface server [ ].

    Techniques: Isolation

    The neighbour-joining phylogenetic tree based on 583-bp adk gene sequences of isolated E. coli strains from patients with IBD or IC. The numbers at the nodes indicate the percentage of 400 bootstrap replicates. Routltella planticola KpH165 was used an outgroup. Strain names in red and blue represent IBD (red = CD; and blue = UC), and green represents IC. The accession numbers are provided in parentheses whose adk gene sequences were retrieved from whole genome sequences.

    Journal: Antibiotics

    Article Title: Differentiation of Escherichia fergusonii and Escherichia coli Isolated from Patients with Inflammatory Bowel Disease/Ischemic Colitis and Their Antimicrobial Susceptibility Patterns

    doi: 10.3390/antibiotics12010154

    Figure Lengend Snippet: The neighbour-joining phylogenetic tree based on 583-bp adk gene sequences of isolated E. coli strains from patients with IBD or IC. The numbers at the nodes indicate the percentage of 400 bootstrap replicates. Routltella planticola KpH165 was used an outgroup. Strain names in red and blue represent IBD (red = CD; and blue = UC), and green represents IC. The accession numbers are provided in parentheses whose adk gene sequences were retrieved from whole genome sequences.

    Article Snippet: We extracted 645 bp adk gene sequences of type species and representatives of E. coli and E. fergusonii species, including E. coli ATCC 11775 T (CP033092), E. coli O157:H7 (BA000007), E. coli K12 (U00096), E. fergusonii ATCC 35469 T (CU928158), and E. fergusonii RHB19-C05 (CP057657), from respective whole genome sequences and aligned all the adk gene sequences of 83 isolates with adk gene sequences from E. coli KCTC 2441 T , E. coli 25922, and E. fergusonii KCTC 22525 T using a multalign interface server [ ].

    Techniques: Isolation

    Differentiating adk gene nucleotides of E. coli against E. fergusonii strains.

    Journal: Antibiotics

    Article Title: Differentiation of Escherichia fergusonii and Escherichia coli Isolated from Patients with Inflammatory Bowel Disease/Ischemic Colitis and Their Antimicrobial Susceptibility Patterns

    doi: 10.3390/antibiotics12010154

    Figure Lengend Snippet: Differentiating adk gene nucleotides of E. coli against E. fergusonii strains.

    Article Snippet: We extracted 645 bp adk gene sequences of type species and representatives of E. coli and E. fergusonii species, including E. coli ATCC 11775 T (CP033092), E. coli O157:H7 (BA000007), E. coli K12 (U00096), E. fergusonii ATCC 35469 T (CU928158), and E. fergusonii RHB19-C05 (CP057657), from respective whole genome sequences and aligned all the adk gene sequences of 83 isolates with adk gene sequences from E. coli KCTC 2441 T , E. coli 25922, and E. fergusonii KCTC 22525 T using a multalign interface server [ ].

    Techniques: Sequencing

    Overview of selected records reporting antibacterial activity of polyphenols sourced from date kernel extracts.

    Journal: Frontiers in Pharmacology

    Article Title: A systematic review of antibacterial activity of polyphenolic extract from date palm ( Phoenix dactylifera L.) kernel

    doi: 10.3389/fphar.2022.1043548

    Figure Lengend Snippet: Overview of selected records reporting antibacterial activity of polyphenols sourced from date kernel extracts.

    Article Snippet: , Met, E th, Ace , E. coli O157-H7 ATCC 51659 and P. aeruginosa NRRL B-272; S. aureus ATCC 13565 and B. subtilis BTN7A.

    Techniques: Activity Assay

    (A) Boxplot of pooled median ± range of zone of inhibition (ZOI) results reported in included studies against four pathogens gram positive: S. aureus , B. subtilis and gram negative: E. Coli , P. aeruginosa (values in parentheses indicate number of studies). (B) Boxplot of pooled median ± range of minimum inhibitory concentration (MIC) results reported against S. aureus and E. Coli in included studies (values in parentheses indicate number of studies).

    Journal: Frontiers in Pharmacology

    Article Title: A systematic review of antibacterial activity of polyphenolic extract from date palm ( Phoenix dactylifera L.) kernel

    doi: 10.3389/fphar.2022.1043548

    Figure Lengend Snippet: (A) Boxplot of pooled median ± range of zone of inhibition (ZOI) results reported in included studies against four pathogens gram positive: S. aureus , B. subtilis and gram negative: E. Coli , P. aeruginosa (values in parentheses indicate number of studies). (B) Boxplot of pooled median ± range of minimum inhibitory concentration (MIC) results reported against S. aureus and E. Coli in included studies (values in parentheses indicate number of studies).

    Article Snippet: , Met, E th, Ace , E. coli O157-H7 ATCC 51659 and P. aeruginosa NRRL B-272; S. aureus ATCC 13565 and B. subtilis BTN7A.

    Techniques: Inhibition, Concentration Assay

    (A) Boxplot of pooled median ± range of minimum inhibitory concentration (MIC) results reported against S. aureus in included studies (values in parentheses indicate number of studies). *Gallic acid was isolated from the date seed extract and used for the test. (B) Boxplot of pooled median ± range of minimum inhibitory concentration (MIC) results reported E. coli in included studies (values in parentheses indicate number of studies). *Gallic acid was isolated from the date seed extract and used for the test. (C) Boxplot of pooled median ± range of minimum bactericidal concentration (MBC) results reported against S. aureus and E. coli in included studies (values in parentheses indicate number of studies).

    Journal: Frontiers in Pharmacology

    Article Title: A systematic review of antibacterial activity of polyphenolic extract from date palm ( Phoenix dactylifera L.) kernel

    doi: 10.3389/fphar.2022.1043548

    Figure Lengend Snippet: (A) Boxplot of pooled median ± range of minimum inhibitory concentration (MIC) results reported against S. aureus in included studies (values in parentheses indicate number of studies). *Gallic acid was isolated from the date seed extract and used for the test. (B) Boxplot of pooled median ± range of minimum inhibitory concentration (MIC) results reported E. coli in included studies (values in parentheses indicate number of studies). *Gallic acid was isolated from the date seed extract and used for the test. (C) Boxplot of pooled median ± range of minimum bactericidal concentration (MBC) results reported against S. aureus and E. coli in included studies (values in parentheses indicate number of studies).

    Article Snippet: , Met, E th, Ace , E. coli O157-H7 ATCC 51659 and P. aeruginosa NRRL B-272; S. aureus ATCC 13565 and B. subtilis BTN7A.

    Techniques: Concentration Assay, Isolation