Journal: eLife

Article Title: Maternal obesity blunts antimicrobial responses in fetal monocytes

doi: 10.7554/eLife.81320

Figure Lengend 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.

Article Snippet: Approximately 5x10 5 MACS purified UCB monocytes were cultured with RSV (Human respiratory syncytial virus ATCC VR-1540, Manassas, VA) or E. coli ( Escherichia coli (Migula) Castellani and Chalmers ATCC 11775, Manassas, VA) or left untreated in RP10 medium for 16 hr at 37 °C.

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

Journal: eLife

Article Title: Maternal obesity blunts antimicrobial responses in fetal monocytes

doi: 10.7554/eLife.81320

Figure Lengend 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.

Article Snippet: Approximately 5x10 5 MACS purified UCB monocytes were cultured with RSV (Human respiratory syncytial virus ATCC VR-1540, Manassas, VA) or E. coli ( Escherichia coli (Migula) Castellani and Chalmers ATCC 11775, Manassas, VA) or left untreated in RP10 medium for 16 hr at 37 °C.

Techniques: Functional Assay

Journal: eLife

Article Title: Maternal obesity blunts antimicrobial responses in fetal monocytes

doi: 10.7554/eLife.81320

Figure Lengend 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.

Article Snippet: Approximately 5x10 5 MACS purified UCB monocytes were cultured with RSV (Human respiratory syncytial virus ATCC VR-1540, Manassas, VA) or E. coli ( Escherichia coli (Migula) Castellani and Chalmers ATCC 11775, Manassas, VA) or left untreated in RP10 medium for 16 hr at 37 °C.

Techniques: Functional Assay, Expressing, In Vitro, Infection

Journal: eLife

Article Title: Maternal obesity blunts antimicrobial responses in fetal monocytes

doi: 10.7554/eLife.81320

Figure Lengend 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.

Article Snippet: Approximately 5x10 5 MACS purified UCB monocytes were cultured with RSV (Human respiratory syncytial virus ATCC VR-1540, Manassas, VA) or E. coli ( Escherichia coli (Migula) Castellani and Chalmers ATCC 11775, Manassas, VA) or left untreated in RP10 medium for 16 hr at 37 °C.

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

Journal: eLife

Article Title: Maternal obesity blunts antimicrobial responses in fetal monocytes

doi: 10.7554/eLife.81320

Figure Lengend 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.

Article Snippet: Approximately 5x10 5 MACS purified UCB monocytes were cultured with RSV (Human respiratory syncytial virus ATCC VR-1540, Manassas, VA) or E. coli ( Escherichia coli (Migula) Castellani and Chalmers ATCC 11775, Manassas, VA) or left untreated in RP10 medium for 16 hr at 37 °C.

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

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

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

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

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

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 , S. salivarius ATCC 25975, S. aureus ATCC 19701, S. marcescens ATCC 99006, E. coli ATCC 29998, K. pneumoniae ATCC 13883, P. vulgaris ATCC 8427 and P. aeruginosa ATCC 10145.

Techniques: Activity Assay

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 , S. salivarius ATCC 25975, S. aureus ATCC 19701, S. marcescens ATCC 99006, E. coli ATCC 29998, K. pneumoniae ATCC 13883, P. vulgaris ATCC 8427 and P. aeruginosa ATCC 10145.

Techniques: Inhibition, Concentration Assay

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 , S. salivarius ATCC 25975, S. aureus ATCC 19701, S. marcescens ATCC 99006, E. coli ATCC 29998, K. pneumoniae ATCC 13883, P. vulgaris ATCC 8427 and P. aeruginosa ATCC 10145.

Techniques: Concentration Assay, Isolation

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

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

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

Journal: International Journal of Molecular Sciences

Article Title: Evaluation of Chitosans as Coagulants—Flocculants to Improve Sand Filtration for Drinking Water Treatment

doi: 10.3390/ijms24021295

Figure Lengend Snippet: Average log 10 reduction values (LRVs) with standard deviation error bars for E. coli KO11 in water treated by chitosan coagulation followed by Accusand and silica sand column filtration, based on 17 successive samples collected throughout the 57-day experiment period.

Article Snippet: Test waters were spiked with E. coli KO11 (ATCC# 55124) and male-specific (F+) coliphage (bacteriophage) MS2 (ATCC# 15597-B1).

Techniques: Standard Deviation, Coagulation, Filtration

Journal: International Journal of Molecular Sciences

Article Title: Evaluation of Chitosans as Coagulants—Flocculants to Improve Sand Filtration for Drinking Water Treatment

doi: 10.3390/ijms24021295

Figure Lengend Snippet: Average, minimum and maximum differences in log 10 reduction values between duplicate filters for each sand type and chitosan dose over the 57-day filter operating time.

Article Snippet: Test waters were spiked with E. coli KO11 (ATCC# 55124) and male-specific (F+) coliphage (bacteriophage) MS2 (ATCC# 15597-B1).

Techniques:

Journal: International Journal of Molecular Sciences

Article Title: Evaluation of Chitosans as Coagulants—Flocculants to Improve Sand Filtration for Drinking Water Treatment

doi: 10.3390/ijms24021295

Figure Lengend Snippet: Results of the Wilcoxon rank-sum test comparing cumulative median log 10 reduction values of E. coli KO11, MS2, and turbidity by sand type, stratified by dose. Reported p -values were adjusted using the Bonferroni correction, m = 4.

Article Snippet: Test waters were spiked with E. coli KO11 (ATCC# 55124) and male-specific (F+) coliphage (bacteriophage) MS2 (ATCC# 15597-B1).

Techniques: