Journal: BMC Cancer

Article Title: Bioinformatics identification and validation of m6A/m1A/m5C/m7G/ac4 C-modified genes in oral squamous cell carcinoma

doi: 10.1186/s12885-025-14216-7

Figure Lengend Snippet: Clinical characteristics of risk scores. A OncoPrint of I GF2BP2, HNRNPC, TRMT61B , and NAT10 using the cBioPortal database. Each column represents one patient sample, and each row corresponds to a gene. Different colors or bars indicate various genetic alterations (e.g., mutation, amplification, deep deletion). The bottom legend summarizes the frequency of each alteration type across the cohort. B , C Unpaired ( B ) and paired ( C ) differential analyses for the 4 genes between paraneoplastic and tumor tissues. The expression level of the 4 genes was higher in tumor tissues than in normal tissues. D Immunohistochemistry (IHC) of IGF2BP2, HNRNPC, TRMT61B, and NAT10 in normal versus tumor tissues. Representative tissue microarray images (from the Human Protein Atlas or in-house staining) show the protein localization and intensity. Brown staining indicates positive protein expression, while blue (hematoxylin) represents the nuclear counterstain. The upper panels depict normal oral mucosa, and the lower panels show corresponding OSCC tissues, confirming higher protein expression in tumor samples for most genes. Scale bars (if included) indicate the magnification used

Article Snippet: Representative tissue microarray images (from the Human Protein Atlas or in-house staining) show the protein localization and intensity.

Techniques: Mutagenesis, Amplification, Expressing, Immunohistochemistry, Microarray, Staining

Journal: Frontiers in Microbiology

Article Title: A Multiplex Immunosensor for Detecting Perchlorate-Reducing Bacteria for Environmental Monitoring and Planetary Exploration

doi: 10.3389/fmicb.2020.590736

Figure Lengend Snippet: PRBCHIP, an antibody microarray for detecting perchlorate reducing bacteria. (A) Schematic of the antibody printing pattern layout (by triplicate) in the PRBCHIP as indicated in and in Section “Materials and Methods.” Empty circles correspond to a serial dilution of a fluorescent antibody printed as a control for fluorescence (marked with a yellow dashed line); circles 1–20 represent antibodies raised against different strains; circles 21–24 indicate antibodies produced against proteins (red rectangles); P1–P20 indicate their corresponding pre-immune antibodies (marked with a continuous yellow line); circles labeled as B (BSA) and PP (Protein Printing Buffer) were used as negative control spots. (B,C) Images obtained after fluorescence sandwich microarray immunoassay (FSMI) with PRBCHIP by using cell lysates of Magnetospirillum bellicus VDY (B) and Dechlorobacter hydrogenophilus LT-1 (C) strains as sample. Immunoassays were revealed with anti- M. bellicus VDY (L2C1) and anti- D. hydrogenophilus LT- 1 (L4C1) antibodies, respectively. (D,E) Images obtained for the same samples and revealed with TOP-PRB fluorescent mix, made up of all anti-PRB antibodies shown in plus A-Cld and A-PCR antibodies. Red and white spots are fluorescence signals corresponding to positive immunodetections.

Article Snippet: The microarray images obtained with different immunogen dilutions were quantified and calibration curves were produced ( ) to determine the limit of detection (LOD) for each antibody ( ).

Techniques: Microarray, Bacteria, Serial Dilution, Control, Fluorescence, Produced, Labeling, Negative Control

Journal: Frontiers in Microbiology

Article Title: A Multiplex Immunosensor for Detecting Perchlorate-Reducing Bacteria for Environmental Monitoring and Planetary Exploration

doi: 10.3389/fmicb.2020.590736

Figure Lengend Snippet: Testing the PRBCHIP sensitivity by fluorescent sandwich microarray immunoassay (FSMI). We assayed serial dilutions of cell cultures as samples for FSMI using their corresponding fluorescent antibodies or the TOP-PRB mix. The fluorescent signals in the microarray were quantified and plotted against the sample concentration. (A) Example of the calibration curve for antibody L1C1 raised against Azospira suillum PS and revealed with its tracer antibody and (B) with the TOP-PRB mix, respectively. When Azospira suillum PS was used as tested sample, besides L1C1 (black circles) and L1S2 (white circles), also L8C1 (triangles) showed a comparable signal at high sample concentrations. (C) Calibration curve for the antibody L4C1 raised against D. hydrogenophilus LT-1 revealed with its tracer antibody and (D) revealed with the TOP-PRB mix. In this case, only L4C1 showed positive immunodetections.

Article Snippet: The microarray images obtained with different immunogen dilutions were quantified and calibration curves were produced ( ) to determine the limit of detection (LOD) for each antibody ( ).

Techniques: Microarray, Concentration Assay

Journal: Frontiers in Microbiology

Article Title: A Multiplex Immunosensor for Detecting Perchlorate-Reducing Bacteria for Environmental Monitoring and Planetary Exploration

doi: 10.3389/fmicb.2020.590736

Figure Lengend Snippet: Testing the specificity of the antibodies with the PRBCHIP. Immunogens corresponding to whole-cell extracts of each perchlorate reducing strain, its EPS fractions and proteins were tested by FSMI with its corresponding fluorescent antibody at its appropriate working dilution (see section “Materials and Methods”). (A) Specificities and cross-reactions between different antibodies and immunogens. Microarray images were scanned for fluorescence, quantified and plotted in a heatmap. Each column corresponds to a single PRBCHIP assay with the corresponding strain or protein tested (see section “Materials and Methods”) as the immunogen, while each row represents the antibody code for each printed antibody (as in ) on the microarray. (B) Antibody graph G of 16 nodes (antibodies with low performance were not considered for this analysis) and 28 links associated with our antibody microarray. Each node represents one antibody. The link (arrow) from antibody j to antibody i represents cross-reactivity of weight G ij , where G ij is the extent of cross-reactivity between antibodies i and j referred to the cognate immunogen of antibody j . Self-loops ( G jj = 1) are not shown for clarity.

Article Snippet: The microarray images obtained with different immunogen dilutions were quantified and calibration curves were produced ( ) to determine the limit of detection (LOD) for each antibody ( ).

Techniques: Microarray, Fluorescence

Journal: Frontiers in Microbiology

Article Title: A Multiplex Immunosensor for Detecting Perchlorate-Reducing Bacteria for Environmental Monitoring and Planetary Exploration

doi: 10.3389/fmicb.2020.590736

Figure Lengend Snippet: Deconvolution method applied to two complex natural samples by sandwich microarray immunoassay (FSMI). (A) Deconvolution of the American Pacific sample 140-10_07/07 and (B) deconvolution of the Lost Hammer sediment sample (LH-Sed) after performing both immunoassays with the mixture of all fluorescent-labeled tracer antibodies (TOP-PRB mix). Filled black bars represent the experimental fluorescence intensities F and red bars represent the deconvoluted signals F ′ [see (40–41) for details on obtaining F ′ from F and the matrix G associated to the antibody graph G]. Note that the experimental fluorescence intensities are ≥0 (as they were directly obtained from the FSMI), while the deconvoluted signals might be positive, zero or negative. Analyzing whether the experimental signal of each antibody is positive or close to zero and whether its deconvoluted signal is positive, zero or negative, we obtain a code for each organism (in bold) that yields reliable information about its existence or not in the sample [see supporting information of ].

Article Snippet: The microarray images obtained with different immunogen dilutions were quantified and calibration curves were produced ( ) to determine the limit of detection (LOD) for each antibody ( ).

Techniques: Microarray, Labeling, Fluorescence

Journal: Ecotoxicology (London, England)

Article Title: Application of physiologically based modelling and transcriptomics to probe the systems toxicology of aldicarb for Caenorhabditis elegans (Maupas 1900)

doi: 10.1007/s10646-010-0591-z

Figure Lengend Snippet: Scores plot for PC1 and PC2 from a PCA of normalised whole genome microarray data for C. elegans exposed to control or 16 mg/l aldicarb

Article Snippet: Acquired microarray images were quantified using ImaGene TM (Biodiscovery Inc., CA, USA) using the default flagging and segmentation settings.

Techniques: Microarray, Control

Journal:

Article Title: A protein multiplex microarray substrate with high sensitivity and specificity

doi: 10.1016/j.jim.2010.10.005

Figure Lengend Snippet: The Multiplex Microarray format is as follows: A1= Hepatitis B Core, A2 = Hepatitis C Core, A3 = HTLV-I, A4 = HTLV-II, B1 = T. Palladium, B2 = HIV-1 IIIB, B3 = HIV-2, B4 = Human Serum Albumin, 25 μg/μl packed colloid C1 = Human IgG, 25 μg/μl packed colloid, C2 = Human IgG, 12 μg/μl packed colloid, C3 = Human IgG, 6μg/μl packed colloid and C4 = Human Serum Albumin, 25 μg/μl packed colloid

Article Snippet: Presented in , are developed microarray images that were prepared by conventional direct spotting with the nitrocellulose colloid technology (A1, A2) and onto three commercial substrates: Prolinx (B), S&S FAST (C) and Telechem strepavadin (D).

Techniques: Multiplex Assay, Microarray

Journal:

Article Title: A protein multiplex microarray substrate with high sensitivity and specificity

doi: 10.1016/j.jim.2010.10.005

Figure Lengend Snippet: Light microscope (40X) images of developed colloidal microarrays. The multiplex microarray format is as follows: Each spot in triplicate, Row 1 = anti-norovirus, Row 2 = anti-adenovirus 41 (type specific), Row 3 = anti-adenovirus 40 (type specific), Row 4 = anti-hexon of adenovirus (group specific), Row 5 anti-astrovirus and Row 6 anti-rotavirus.

Article Snippet: Presented in , are developed microarray images that were prepared by conventional direct spotting with the nitrocellulose colloid technology (A1, A2) and onto three commercial substrates: Prolinx (B), S&S FAST (C) and Telechem strepavadin (D).

Techniques: Light Microscopy, Multiplex Assay, Microarray