Journal: BMC Microbiology

Article Title: Separation of the bacterial species, Escherichia coli , from mixed-species microbial communities for transcriptome analysis

doi: 10.1186/1471-2180-11-59

Figure Lengend Snippet: Plot of gene expression of sorted/unsorted cells . Plot of one-sample T-test p-values with fold-change in gene expression for all ORFs in microarray study I. Vertical lines show the cutoff of fold-change of 2 (Log 2 ratio of ± 1), while the horizontal line shows the cutoff of p-value 0.05. Genes located in the left-bottom corner (Log 2 ratio <-1 and p-value <0.05) and in the right-bottom corner (Log 2 ratio >1 and p-value <0.05) were considered to have their expressions changed due to dispersion/homogenization and IMS (immuno-magnetic separation) cell sorting. A total of ten genes were selected using these criteria, eight of which also differentially expressed in the independent microarray study II.

Article Snippet: Hybridization was in a Corning Microarray Hybridization Chamber (Corning Inc.) in 42°C water bath.

Techniques: Expressing, Microarray, Homogenization, FACS

Journal: BMC Microbiology

Article Title: Separation of the bacterial species, Escherichia coli , from mixed-species microbial communities for transcriptome analysis

doi: 10.1186/1471-2180-11-59

Figure Lengend Snippet: Genes identified as differentially expressed # between IMS sorted E. coli cells versus unsorted E. coli cells* by the method of cDNA microarray and their differential expression confirmed with another method of qPCR

Article Snippet: Hybridization was in a Corning Microarray Hybridization Chamber (Corning Inc.) in 42°C water bath.

Techniques: Microarray, Expressing

Journal: mBio

Article Title: Exploring the Impact of Ketodeoxynonulosonic Acid in Host-Pathogen Interactions Using Uptake and Surface Display by Nontypeable Haemophilus influenzae

doi: 10.1128/mBio.03226-20

Figure Lengend Snippet: Antigenic specificity of the human anti-Kdn glycan antibodies. Heatmap showing the relative intensity of the fluorophore-conjugated anti-human IgG antibodies binding with the individual glycan on the microarray. Experiment was performed using commercially available pooled human IVIG (last column) as well as individual ( n = 24) sera. Numbers (S-18 through S-81) on the top represent individual healthy human sera. (A) Each block represents the mean intensity of the antibody binding to the specific asialo- and sialoglycan at four independent spots in the microarray. Glycans are grouped by their nonsialylated (asialo-), Neu5Ac-, Neu5Gc-, and Kdn-terminating structures. The complete list of glycan structures represented is provided in panel B. Each column represents the relative binding preference of IgG antibodies in the corresponding serum toward the specific glycan epitopes. The color code of the heatmap is indicated, and the corresponding glycan in each row matched with the list in panel B.

Article Snippet: The slides were left for drying for an additional 8 h. Printed glycan microarray slides were blocked with prewarmed 0.05 M ethanolamine solution (in 0.1 M Tris-HCl [pH 9.0]), washed with warm Milli-Q water, dried, and then fitted in a multiwell microarray chamber (Grace Bio-Labs) to divide into 16 subarrays.

Techniques: Binding Assay, Microarray, Blocking Assay

Journal: mBio

Article Title: Exploring the Impact of Ketodeoxynonulosonic Acid in Host-Pathogen Interactions Using Uptake and Surface Display by Nontypeable Haemophilus influenzae

doi: 10.1128/mBio.03226-20

Figure Lengend Snippet: Appearance of anti-Kdn IgG and IgM antibodies in the first year of human life. Binding of human sera to Kdn- and Neu5Gc-containing glycan epitopes was determined by sialoglycan microarray binding assay. Sera were obtained from cord blood ( n = 15) and the child at 3, 6, and 12 months old and from 9 out of the 15 matched mothers in their third trimester of pregnancy. Control represents sera from blood from healthy human donors (both male and female) ( n = 24). The average relative fluorescence unit (RFU) in arbitrary units (A.U.) against terminal Kdn (A and C) or Neu5Gc (B and D) containing glycan epitopes with underlying structures similar to vertebrate glycoconjugates are shown. Each dot represents the mean RFU values against all the Kdn (A and C)- or Neu5Gc (B and D)-containing glycans, respectively, for individual serum. (A to D) Relative abundance of the human IgG (A and B) and IgM antibodies (C and D) against the corresponding sialoglycoconjugates. Statistical significance was evaluated using one-way ANOVA with Tukey’s multiple comparison test. The mean ± standard error of the mean (SEM) (error bars) values and the adjusted P values are shown in the figure.

Article Snippet: The slides were left for drying for an additional 8 h. Printed glycan microarray slides were blocked with prewarmed 0.05 M ethanolamine solution (in 0.1 M Tris-HCl [pH 9.0]), washed with warm Milli-Q water, dried, and then fitted in a multiwell microarray chamber (Grace Bio-Labs) to divide into 16 subarrays.

Techniques: Binding Assay, Microarray, Fluorescence