Journal: Arthritis Research & Therapy

Article Title: Anti-PM/Scl antibodies are found in Japanese patients with various systemic autoimmune conditions besides myositis and scleroderma

doi: 10.1186/s13075-015-0573-x

Figure Lengend Snippet: Detection of anti-PM/Scl antibodies in immuoprecipitation analysis. TnT-IPP: immunoprecipitation of biotinylated recombinant PM/Scl-100 and PM/Scl-75. Recombinant proteins were subjected to 4% to 20% SDS-PAGE and analyzed by immunoblotting with streptavidin-alkaline phosphatase and substrate. In., the input was half the dose for immunoprecipitation. Lanes A to K correspond to the anti-PM-Scl-100 and/or −75-positive patients shown in Figure . Lane N: healthy control serum. HeLa-IPP: immunoprecipitation analysis using radiolabeled HeLa cell extracts. Lanes A to L correspond to the patients shown in Figure and Table . Lanes A to K correspond to anti-PM-Scl-100 and/or −75-positive patients shown in Figure . Lane M: [Methyl- 14 C] methylated protein MW markers (PerkinElmer Japan, Yokohama, Japan). Lane L: anti-U1-RNP-positive serum with equivocal titers for both antibodies in ELISA. Lanes 1 to 4 show the reference sera; lane 1, anti-PM/Scl-positive serum; lane 2, anti-MDA5-positive serum; lane 3, anti-TIF1-γ-positive serum; lane 4, anti-Mi-2-positive serum. Arrow and arrowhead corrspond to the PM/Scl-100 and PM/Scl-75 antigens, respectively. IPP, immunoprecipitation; TnT, in vitro translation and transcription product.

Article Snippet: Lane M: [Methyl- 14 C] methylated protein MW markers (PerkinElmer Japan, Yokohama, Japan).

Techniques: Immunoprecipitation, Recombinant, SDS Page, Western Blot, Control, Methylation, Enzyme-linked Immunosorbent Assay, In Vitro

Journal: Clinical cancer research : an official journal of the American Association for Cancer Research

Article Title: Identification and validation of a 3-gene methylation classifier for HPV-based cervical screening on self-samples

doi: 10.1158/1078-0432.CCR-17-3615

Figure Lengend Snippet: Hierarchical clustering of the 28 Infinium 450K BeadChip probes, each probe corresponds to a DNA methylation marker. Low (blue) to high (purple) DNA methylation levels (arcsine square-root transformed beta values) are displayed for each DNA methylation marker (cg-numbers of the probes). (A) DNA methylation data of self-samples from hrHPV-positive controls (green; n=28) and from women with CIN3 (orange; n=36). The samples are ordered by predicted probability. The 12 DNA methylation markers above the black line showed the most discriminative DNA methylation profile between women with and without CIN3. (B) DNA methylation data of self-samples from women with SCC (red; n=4).

Article Snippet: The 12 DNA methylation markers above the black line showed the most discriminative DNA methylation profile between women with and without CIN3. ( B ) DNA methylation data of self-samples from women with SCC (red; n=4). table ft1 table-wrap mode="anchored" t5 caption a7 Infinium BeadChip probe Chr.

Techniques: DNA Methylation Assay, Marker, Transformation Assay

Journal: Clinical cancer research : an official journal of the American Association for Cancer Research

Article Title: Identification and validation of a 3-gene methylation classifier for HPV-based cervical screening on self-samples

doi: 10.1158/1078-0432.CCR-17-3615

Figure Lengend Snippet: The 12 candidate DNA methylation markers from the discovery screen.

Article Snippet: The 12 DNA methylation markers above the black line showed the most discriminative DNA methylation profile between women with and without CIN3. ( B ) DNA methylation data of self-samples from women with SCC (red; n=4). table ft1 table-wrap mode="anchored" t5 caption a7 Infinium BeadChip probe Chr.

Techniques: DNA Methylation Assay

Journal: Clinical cancer research : an official journal of the American Association for Cancer Research

Article Title: Identification and validation of a 3-gene methylation classifier for HPV-based cervical screening on self-samples

doi: 10.1158/1078-0432.CCR-17-3615

Figure Lengend Snippet: DNA methylation levels represented by the square-root transformed ΔΔCt ratios (y-axis) in (A) lavage self-samples from hrHPV-positive controls (n=214) and women with CIN3 (n=31; x-axis), and (B) brush self-samples from hrHPV-positive controls (n=174) and women with CIN3 (n=72; x-axis). The 3 genes left of the black line are included in the 3-gene methylation classifier. * p < .05; *** p < .001; NS: not significant.

Article Snippet: The 12 DNA methylation markers above the black line showed the most discriminative DNA methylation profile between women with and without CIN3. ( B ) DNA methylation data of self-samples from women with SCC (red; n=4). table ft1 table-wrap mode="anchored" t5 caption a7 Infinium BeadChip probe Chr.

Techniques: DNA Methylation Assay, Transformation Assay, Methylation

Journal: Annals of Translational Medicine

Article Title: Circulating tumour DNA analysis for early detection of lung cancer: a systematic review

doi: 10.21037/atm-23-1572

Figure Lengend Snippet: Studies on the use of ctDNA analysis for early detection of lung cancer

Article Snippet: 36175411 , Stackpole et al. , 2022 ( ) , Pan-cancer , cfDNA methylation markers , 23,748 cancer-specific hypermethylation markers, 28,197 cancer-specific hypomethylation markers, 7,547 tissue-specific hypermethylation markers, 7,212 tissue-specific hypomethylation markers , Lung cancer (N=126), other cancers (N=150); stage I/II/III/IV =33/23/30/40, histological subtype (LUAD/LUSC) =77/49 , Non-cancer (healthy individuals and patients of various noncancer diseases (e.g., cirrhosis, pancreatitis, hepatitis, diabetes, etc.), N=203) , Integrating four marker types (all cancer types (n=217) vs. noncancer (n=191): sen./spec.=80.7%/97.9%, AUC =0.974.

Techniques: Biomarker Discovery, Concentration Assay, Amplification, Mutagenesis, Control, Clinical Proteomics, Methylation, DNA Methylation Assay, Computed Tomography, In Situ, Marker, Comparison, Diagnostic Assay, Genome Wide, RNA Expression

Journal:

Article Title: The Lantibiotic Mersacidin Inhibits Peptidoglycan Synthesis by Targeting Lipid II

doi:

Figure Lengend Snippet: (A and B) Interaction of mersacidin with isolated lipid II. Various amounts of [14C]lipid II and either [14C]mersacidin or unlabeled mersacidin were incubated and subjected to PAGE under nondenaturing conditions (A) or in the presence of 1% SDS in the sample buffer and 0.1% SDS in the running buffer (B). Lane 1, 0.4 nmol of [14C]mersacidin and 0.4 nmol of [14C]lipid II; lane 2, 0.8 nmol of [14C]mersacidin and 0.4 nmol of [14C]lipid II; lane 3, 0.4 nmol of [14C]mersacidin and 0.8 nmol of [14C]lipid II; lane 4, 4 nmol of unlabeled mersacidin and 0.4 nmol of [14C]lipid II; lane 5, 0.4 nmol of [14C]mersacidin; lane 6, 0.4 nmol of [14C]lipid II. The lipid II bands mark the upper boundary of the separating gel. Most of the stacking gel was removed prior to autoradiography. (C and D) SDS-PAGE of M. luteus ATCC 4698 after adsorption of [14C]mersacidin to the cells. (C) Autoradiogram; (D) Coomassie stain of gels run in parallel. Lanes 7 and 12, 5 mg of cells (wet weight); lanes 8 and 13, 2.5 mg of cells; lanes 9 and 14, 1 mg of cells; lane 10, 0.25 nmol of [14C]mersacidin; lane 11, 14C-methylated Rainbow molecular mass marker (Amersham-Buchler).

Article Snippet: Lanes 7 and 12, 5 mg of cells (wet weight); lanes 8 and 13, 2.5 mg of cells; lanes 9 and 14, 1 mg of cells; lane 10, 0.25 nmol of [ 14 C]mersacidin; lane 11, 14 C-methylated Rainbow molecular mass marker (Amersham-Buchler).

Techniques: Isolation, Incubation, Autoradiography, SDS Page, Adsorption, Staining, Methylation, Marker

Journal: Intestinal Research

Article Title: Is methylation analysis of SFRP2 , TFPI2 , NDRG4 , and BMP3 promoters suitable for colorectal cancer screening in the Korean population?

doi: 10.5217/ir.2017.15.4.495

Figure Lengend Snippet: Primer Sequences, PCR Product Sizes, and Annealing Temperatures Used in MSP Assays

Article Snippet: In our study, we selected 4 methylation markers, SFRP2 , TFPI2 , NDRG4 , and BMP3 , which are known to be involved in CRC and were included in a recent multitarget stool DNA test.

Techniques:

Journal: Intestinal Research

Article Title: Is methylation analysis of SFRP2 , TFPI2 , NDRG4 , and BMP3 promoters suitable for colorectal cancer screening in the Korean population?

doi: 10.5217/ir.2017.15.4.495

Figure Lengend Snippet: Results of the stool DNA methylation-specific PCR assay performed with samples obtained from patients with colorectal cancer (C) and advanced adenoma (A) and healthy controls (N). SFRP2 , secreted frizzled-related protein 2; TFPI2 , tissue factor pathway inhibitor 2; NDRG4 , N-myc downstream-regulated gene 4; BMP3 , bone morphogenetic protein 3.

Article Snippet: In our study, we selected 4 methylation markers, SFRP2 , TFPI2 , NDRG4 , and BMP3 , which are known to be involved in CRC and were included in a recent multitarget stool DNA test.

Techniques: DNA Methylation Assay