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

Journal: BMC Cancer

Article Title: Presence of S100A9-positive inflammatory cells in cancer tissues correlates with an early stage cancer and a better prognosis in patients with gastric cancer

doi: 10.1186/1471-2407-12-316

Figure Lengend Snippet: Expression of S100A9 in gastric cancer and adjacent non-cancerous tissues. ( A ) Different expression value of S100A9 in 72 gastric cancer tissues and paired no-cancerous tissues by analyzing data from illumina Sentrix BeadChip cDNA microarray. (B-E) Immunohistochemical staining of S100A9 in gastric cancer tissues ( B ) metastatic lymph nodes ( C ), chronic gastritis ( D ), and adjacent non-cancerous gastric mucosa ( E ). S100A9 localization was revealed as brown or red granulated loci in the cytoplasm of infiltrating inflammatory cells, especially in mononuclear phagocytes and neutrophil granulocytes. (magnification 200×).

Article Snippet: Expression of S100A9, S100A8 and S100A8/A9 were also detected in Cybrdi tissue microarray slides (IC00-01-001, Cybrdi, Xi'an, China) containing chronic gastritis with metaplasia (57 cases) and gastric carcinoma tissues (23 cases).

Techniques: Expressing, Microarray, Immunohistochemical staining, Staining

Journal: BMC Cancer

Article Title: Presence of S100A9-positive inflammatory cells in cancer tissues correlates with an early stage cancer and a better prognosis in patients with gastric cancer

doi: 10.1186/1471-2407-12-316

Figure Lengend Snippet: Immunofluorescence images of S100A9, S100A8 and S100A8/A9 proteins in tissue microarray slides containing gastric cancer tissues (A-J) and chronic gastritis tissues (K-T), and chronic appendicitis tissues with exacerbation (U-Y). S100A9 and S100A8 were detected by monoclonal antibody, prelabeled with the Zenon Alexa Fluor Mouse IgG Labeling Kit (with green and red fluorescence respectively). The nucleus was stained by DAPI. S100A8/A9 heterodimers were detectable using the dimer-specific antibody 27E10 from BMA Biomedicals prelabeled with green fluorescence. The co-localization of S100A9 and S100A8 or S100A8/A9 was showed in merged pictures ( D , I , N , S , X ) and larger merged pictures ( E , J , O , T , Y ). White arrow in 3 T shows co-localization of S100A9 and S100A8/A9 in chronic gastritis. Bar length, 50 μm.

Article Snippet: Expression of S100A9, S100A8 and S100A8/A9 were also detected in Cybrdi tissue microarray slides (IC00-01-001, Cybrdi, Xi'an, China) containing chronic gastritis with metaplasia (57 cases) and gastric carcinoma tissues (23 cases).

Techniques: Immunofluorescence, Microarray, Labeling, Fluorescence, Staining