Journal: Viruses

Article Title: Humoral Immune Response Profile of COVID-19 Reveals Severity and Variant-Specific Epitopes: Lessons from SARS-CoV-2 Peptide Microarray

doi: 10.3390/v15010248

Figure Lengend Snippet: Schematic representation of the study design, microarray protocol, and data analysis. ( a ) Sample acquisition and heat inactivation of virus, ( b ) SARS-CoV-2 whole proteome microarray design, ( c ) microarray staining and image acquisition, ( d ) data analysis pipeline.

Article Snippet: PEPperCHIP ® Peptide Microarray slides were brought to room temperature, assembled onto the PEPperCHIP ® incubation tray (PEPperPRINT GmbH, Germany), and equilibrated using the staining buffer for 15 min.

Techniques: Microarray, Virus, Staining

Journal: Viruses

Article Title: Humoral Immune Response Profile of COVID-19 Reveals Severity and Variant-Specific Epitopes: Lessons from SARS-CoV-2 Peptide Microarray

doi: 10.3390/v15010248

Figure Lengend Snippet: Heatmaps for IgA and IgG response showing major immunogenic regions identified in the SARS-CoV-2 whole proteome microarray. The printed proteome constitutes ORF1a/b polyprotein encoding 16 non-structural proteins (1–10 and 12–16), structural proteins (S, N, E, and M), and the accessory proteins (ORF3a, 6, 7a, 8, and 10).

Article Snippet: PEPperCHIP ® Peptide Microarray slides were brought to room temperature, assembled onto the PEPperCHIP ® incubation tray (PEPperPRINT GmbH, Germany), and equilibrated using the staining buffer for 15 min.

Techniques: Microarray

Journal: Experimental Biology and Medicine

Article Title: Annona atemoya leaf extract ameliorates cognitive impairment in amyloid-β injected Alzheimer’s disease-like mouse model

doi: 10.1177/1535370219886269

Figure Lengend Snippet: Molecular mechanisms responsible for anti-AD effects of AAL extract. (a) HT22 cells were exposed to H2O2 in the absence or presence of AAL extract (50 μg/mL) for 6 h. Antibody microarray assay was performed using the phospho-specific antibody microarray slide (Full Moon BioSystems). For data acquisition, GenePix 4100A scanner (Axon Instrument, USA) was used. The normalization data were analyzed using Genowiz 4.0™ (Ocimum Biosolutions). The phosphorylation ratio was calculated and represented as fold changes of indicated phosphoproteins after H2O2 treatment normalized to total protein expression (upper panel). Total protein quantification is shown (lower panel). (b) HT22 cells were exposed to H2O2 with or without various concentrations of AAL extract (0, 12.5, 25, or 50 μg/mL) for 6 h. Cell lysates were prepared from HT22 cells and equal amounts of protein were subjected to Western blotting using anti-phospho-CaMK2 β/ν/δ, GRK2, EGFR, Myc, FER, caveolin-1, NFκB p65, and MLRN 2 antibodies to validate the Ab microarray. (c) Protein extracts were prepared from hippocampal tissues in an Aβ-induced AD mouse model. Vehicle or various concentrations of AAL extract (50, 100, or 200 mg/kg) were administered to Aβ mice for 23 days. Western blotting was performed for anti-phospho-EGFR and phospho-GRK2. The validity of the two phospho-antibodies was determined using pre-stained protein marker (Bio-Rad). GAPDH was used as an internal control. Shown blots are representative results from three independent experiments.

Article Snippet: Molecular mechanisms responsible for anti-AD effects of AAL extract. (a) HT22 cells were exposed to H 2 O 2 in the absence or presence of AAL extract (50 μg/mL) for 6 h. Antibody microarray assay was performed using the phospho-specific antibody microarray slide (Full Moon BioSystems).

Techniques: Microarray, Phospho-proteomics, Expressing, Western Blot, Staining, Marker, Control

Journal: Molecular Plant Pathology

Article Title: Distinguishing bacterial pathogens of potato using a genome‐wide microarray approach

doi: 10.1111/j.1364-3703.2008.00482.x

Figure Lengend Snippet: Percentage of probes that recognized four bacterial species tested by microarray analysis.

Article Snippet: Image and data analysis Microarray slides were scanned with a GenePix 4200 AL scanner (Axon Instruments, Foster City, CA) using a pixel resolution of 5 μm.

Techniques: Microarray

Journal: Molecular Plant Pathology

Article Title: Distinguishing bacterial pathogens of potato using a genome‐wide microarray approach

doi: 10.1111/j.1364-3703.2008.00482.x

Figure Lengend Snippet: Scanned images of the signals detected on the microarray. A view of the whole microarray with eight subarrays is shown in (A), whereas areas covered by c. 800 probes (of the total of 9676 probes of one subarray) are shown at higher magnification in B and C. Total DNA extracted from pure cultures of bacteria and pooled from several strains of each species was used for hybridization. (A) Two samples were hybridized on each of the eight subarrays. The sample labelled with Cy5 (red) in all eight subarrays was Pectobacterium atrosepticum. The other samples labelled with Cy3 (illustrated as green) were (1) Streptomyces scabies, (2) Dickeya sp., (3) P. carotovorum, (4) Clavibacter michiganensis, (5) P. atrosepticum and (6–8) S. turgidiscabies. The amount of DNA per sample was 500 ng in subarrays 1–6. Signals were clear also with 50 ng of sample DNA (dilution 1 : 10, subarray 7). The image shown here was scanned using constant laser power and detector gain, and signals in subarray 8 (5 ng of DNA; dilution 1 : 100) cannot be seen. However, using increased detector gain, the most species‐specific signals (highest signal intensity) could be detected on subarray 8. (B) Magnification of a part of subarray 5: two samples of P. atrosepticum labelled each with a different dye. Intensive yellow spots (equal hybridization) correspond to probes specific to P. atrosepticum, whereas the spots with faint signal indicate non‐specific hybridization. (C) Magnification of part of the subarray 1: P. atrosepticum labelled with Cy5 and S. scabies labelled with Cy3. A ‘black spot’ (no signal) indicates no hybridization with the probe. The probes were designed to be gene‐specific, taking the whole‐genome sequence information of the species into consideration. Results indicate that most probes detect only the respective species based on which the probes were designed.

Article Snippet: Image and data analysis Microarray slides were scanned with a GenePix 4200 AL scanner (Axon Instruments, Foster City, CA) using a pixel resolution of 5 μm.

Techniques: Microarray, Bacteria, Hybridization, Sequencing

Journal: Molecular Plant Pathology

Article Title: Distinguishing bacterial pathogens of potato using a genome‐wide microarray approach

doi: 10.1111/j.1364-3703.2008.00482.x

Figure Lengend Snippet: Pooled DNA of the strains of Clavibacter michiganensis ssp. sepedonicus (Cms) (labelled with Cy3) and Pectobacterium atrosepticum (Pat) (labelled with Cy5) analysed on the microarray. (A) Scatterplot shows signal intensities from each probe on the array. Signals for Cms are given on the x‐axis and those for Pat on the y‐axis. Data reveal that the samples are not detected with common probes giving high signal intensities. (B) The scatterplot presented in a logarithmic domain places the probes within four groups: (1) high signal intensities for both samples (very few probes); (2) non‐specific probes detecting both samples (relatively low signal intensities); (3) probes giving high signal intensities only for Pat; and (4) probes giving high signal intensities only for Cms. In (C) (Cms) and (D) (Pat), the histograms of the logarithmic signal intensities show three peaks (histograms smoothened by the kernel density method). A threshold value of ~10 separates the two right‐most peaks (II and III) corresponding to the non‐specific and specific probes, respectively, as shown in B. The threshold value corresponds to the raw (non‐logarithmic) intensity value of c. 1000. In (E) (Cms) and (F) (Pat) the hybridization signal intensities are indicated per groups of probes. In the boxplot, the horizontal line in the middle of the box indicates the median value of the data. The box itself shows the first and third quartile of data. Whiskers outside the box indicate the range of data up to 1.5× the box height from both ends. Data beyond these limits are shown as circles. The intensity values of all probes are shown; however, in the final classification, the probes with intensities below the threshold obtained from the intensity histogram would be eliminated. Abbreviations used in the probe group names: Pat, P. atrosepticum; Sca, S. scabies; Cms, C. michiganensis spp. sepedonicus; IGS, 16S–23S intergenic spacer; Pca, P. carotovorum; IGS Dic, probes to the IGS of Dickeya spp.; Stu, S. turgidiscabies; Rso, R. solanacearum; nip, gene for necrosis‐inducing protein; Dic Nip30‐Nip50, probes of different lengths (30–50 nt) designed for the nip gene of D. dadantii; PAI, pathogenicity island.

Article Snippet: Image and data analysis Microarray slides were scanned with a GenePix 4200 AL scanner (Axon Instruments, Foster City, CA) using a pixel resolution of 5 μm.

Techniques: Microarray, Hybridization

Journal: Molecular Plant Pathology

Article Title: Distinguishing bacterial pathogens of potato using a genome‐wide microarray approach

doi: 10.1111/j.1364-3703.2008.00482.x

Figure Lengend Snippet: Pooled DNA of the strains of Streptomyces scabies (Sca) and S. turgidiscabies (Stu) analysed on the microarray. (A) Scatterplot showing signal intensities from each probe on the array. Signals for Sca are given on the x‐axis and those for Stu on the y‐axis. (B) The scatterplot presented on a logarithmic scale places the probes within four groups: (1) high signal intensities for both samples [of the total of 3894 probes designed to target genes of Sca, 1462 probes (c. 40%) show high signal intensities also for Stu]; (2) non‐specific probes giving relatively weak signals for both samples; (3) probes giving high signals only for Stu; and (4) probes giving high signals only for Sc. In (C) (Sca) and (D) (Stu), the histograms of the logarithmic signal intensities show three peaks corresponding to the groups of probes in B, as explained in Fig. 2. In (E) (Sca) and (F) (Stu) the hybridization signal intensities are indicated per three groups of probes. Interpretation of the boxplots is as in Fig. 1. The data indicate that the probes targeting the 16S–23S intergenic spacer (IGS) can be used to distinguish the two species.

Article Snippet: Image and data analysis Microarray slides were scanned with a GenePix 4200 AL scanner (Axon Instruments, Foster City, CA) using a pixel resolution of 5 μm.

Techniques: Microarray, Hybridization