Journal: bioRxiv

Article Title: HPeV-3 predominated among Parechovirus A positive infants in the summer of 2013-2014 in Queensland, Australia

doi: 10.1101/182436

Figure Lengend Snippet: Phylogenetic analysis of the HPeV VP3/VP1 sequences (approximately 256nt in length) inferred using the Neighbor-Joining method The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (500 replicates) are shown next to the branches The evolutionary distances are presented as the number of base substitutions per site. All ambiguous positions were removed for each sequence pair. Open boxes indicate divergent genotypes with sequences intersected by those of other genotypes. Trees and evolutionary analyses were conducted using MEGA7 from alignments constructed using Geneious v8.1.8 and [ , ].

Article Snippet: The RT-PCR included 600 nM external sense and antisense oligonucleotide primers (HPeV_VP3/1_OS, HPeV_VP3/1_OAS, Geneworks, Australia) in a 20 µl one-step RT-PCR reaction mix (SensiFAST OneStep Mix, Bioline, Australia) with RNase inhibitor and 3 mM MgCl 2 .

Techniques: Sequencing, Construct

Journal: Journal of Translational Medicine

Article Title: SITC/iSBTc Cancer Immunotherapy Biomarkers Resource Document: Online resources and useful tools - a compass in the land of biomarker discovery

doi: 10.1186/1479-5876-9-155

Figure Lengend Snippet: Structure of the Biomarker References and Online Resources Provided

Article Snippet: A. Primer Design Software B. Transcription Factors Binding Sites Prediction Software C. Design of Antisense Oligonucleotides, Nucleic Acid Probes, siRNA Software D. miRNA Prediction E. Alternative Splicing Analysis F. Linkage Disequilibrium Analysis G. Analysis Support, Laboratory Optimization and Other Useful Websites H. Nanotechnology I. Clinical Trials Registries.

Techniques: Biomarker Discovery, Clinical Proteomics, Gene Expression, High Throughput Screening Assay, Hybridization, Methylation, Chromatin Immunoprecipitation, Expressing, Next-Generation Sequencing, Sequencing, Software, Binding Assay, Alternative Splicing

Journal: Cancer Science

Article Title: High levels of DJ-1 protein and isoelectric point 6.3 isoform in sera of breast cancer patients

doi: 10.1111/cas.12673

Figure Lengend Snippet: Mean level of DJ-1 in serum, and the expression profile of its isoforms, in breast cancer and non-cancerous groups. (a) Mean levels of DJ-1 protein in sera from breast cancer and non-cancerous groups. In sera from the breast cancer group ( n = 180), the mean level of DJ-1 protein was 42.7 ng/mL, whereas that in the non-cancerous group ( n = 300) was 28.3 ng/mL. There was a significant difference in the mean levels between the two groups ( P = 0.019). Data are means of three independent experiments with SE. (b) DJ-1 isoform patterns of three representative cancer cases. (c) Two-dimensional Western blot detection of DJ-1 isoforms shown as an LAS3000 image with molecular weight. Intensity of each isoelectric spot was semiquantified as a peak of signal intensity that was drawn by ImageQuant TL 8.1 software. The vertical axis shows signal intensity, and the horizontal axis shows the pI. The highest peak was detected at pI 6.3 in all cancer cases. (c) DJ-1 isoform patterns of three representative non-cancerous cases. DJ-1 isoform image and its semiquantified graph are shown in the same manner as (b). The vertical axis shows signal intensity, and the horizontal axis shows the pI. The highest peak was detected at the acidic side (pI 5.7, 5.9, 5.9) in each non-cancerous case. The y -axis is the signal intensity drawn by ImageQuant TL 8.1 software. (d) Mean levels of DJ-1 at pI 6.3 in the sera of abnormally high DJ-1 in breast cancer and non-cancerous groups. The mean level, calculated by the ratio of isoform peaks, of DJ-1 at pI 6.3 from sera of 11 cancerous cases (40.6 ng/mL) was significantly higher than that from 6 non-cancer cases (3.5 ng/mL) ( P = 0.0017). Data are the mean of three independent experiments with SE.

Article Snippet: In situ hybridization was also carried out using 20 pmol of 3′-end biotin-labeled DJ-1 oligonucleotide probes per slide (sense primer, 5′-ATGACTTCCAAGCTGGCCGT-3′; antisense primer, 5′-CTTGTAAGAATCAGGCCGTCT-3′) (Nihon Gene Research Laboratories, Miyagi, Japan).

Techniques: Expressing, Western Blot, Molecular Weight, Software

Journal: Cancer Science

Article Title: High levels of DJ-1 protein and isoelectric point 6.3 isoform in sera of breast cancer patients

doi: 10.1111/cas.12673

Figure Lengend Snippet: Expression of DJ-1 protein and mRNA in a breast cancer biopsy specimen. (a) The breast cancer nest is located in the center of the H&E stained specimen. Non-cancerous ducts are seen in the right lower corner. Bar = 50 μm (originally 400 high power fields). (b) Immunohistochemistry of DJ-1, in the same area as in (a). The immunoreactivity in the cancerous area is marked by arrowheads, and was analyzed by the image analyzer WinROOF. The average intensity of DJ-1 staining in the non-cancerous ducts located in the right corner was determined as the threshold value by applying the hue–lightness–saturation color space. The expression of DJ-1 in the cancerous area was judged as low because the intensity of DJ-1 staining was lower than the threshold value in the cancerous area. (c) In situ hybridization of DJ-1, in the same area as in (a, b). Upregulation of DJ-1 mRNA was detected in the cancerous lesion (arrowheads).

Article Snippet: In situ hybridization was also carried out using 20 pmol of 3′-end biotin-labeled DJ-1 oligonucleotide probes per slide (sense primer, 5′-ATGACTTCCAAGCTGGCCGT-3′; antisense primer, 5′-CTTGTAAGAATCAGGCCGTCT-3′) (Nihon Gene Research Laboratories, Miyagi, Japan).

Techniques: Expressing, Staining, Immunohistochemistry, In Situ Hybridization