Journal: The Journal of Biological Chemistry

Article Title: Surfactant protein A down-regulates epidermal growth factor receptor by mechanisms different from those of surfactant protein D

doi: 10.1074/jbc.M117.800771

Figure Lengend Snippet: SP-A binds to EGFR in A549 cells, H441 cells, and CHOK1 cells stably expressing EGFR. A, whole-cell lysate of A549 cells was immunoprecipitated (IP) with anti-EGFR monoclonal antibody Ab-11 or control IgG (0. 8 μg) at 4 °C for 16 h. The samples and BSA (200 ng/lane) were subjected to SDS-PAGE and transferred onto PVDF membranes. The membranes were incubated with or without SP-A (1 μg/ml) for 16 h. The membranes not incubated with SP-A were subjected to Western blotting using an anti-human EGFR monoclonal antibody (WB: EGFR). The membranes incubated with SP-A were then treated with an anti-human SP-A polyclonal antibody (SP-A pAb) or monoclonal antibodies PE10 (SP-A mAb (PE10)) or PC6 (SP-A mAb (PC6)), which was followed by incubation with HRP-labeled anti-rabbit IgG or anti-mouse IgG (upper panel). As a negative control, the membranes in the absence of incubation with SP-A were also incubated with an anti-human SP-A polyclonal antibody (WB: SP-A pAb) or monoclonal antibodies PE10 (WB: SP-A mAb (PE10)) or PC6 (WB: SP-A mAb (PC6)), which was followed by incubation with HRP-labeled anti-rabbit IgG or anti-mouse IgG (lower panel). The data are representative of three independent experiments. B and C, experimental paradigm described in A was performed in H441 cells (B) and CHOK1 cells stably expressing EGFR (C) by using an anti-human SP-A polyclonal antibody, which was followed by incubation with HRP-labeled anti-rabbit IgG. The data are representative of three independent experiments.

Article Snippet: The H441 human lung adenocarcinoma cell line was obtained from ATCC and maintained in RPMI 1640 medium (Sigma) with 10% (v/v) FCS.

Techniques: Stable Transfection, Expressing, Immunoprecipitation, Control, SDS Page, Incubation, Western Blot, Bioprocessing, Labeling, Negative Control

Journal: Scientific Reports

Article Title: Subfamily-selective PCR primers for the human LINE1 L1PA lineage

doi: 10.1038/s41598-025-17649-z

Figure Lengend Snippet: L1PA subfamily-selective PCR primers amplify sequences of interest. ( a ) PCR amplification of human liver genomic DNA using the indicated primers. Agarose gel electrophoresis shows the amplification products. Cropped parts of a single gel are shown, uncropped gel is included in Supplementary Fig. 1. ( b ) Validation of L1PA subfamily-selective primers by amplicon sequencing. Bar chart indicates percentage of all amplified fragments that map to LINE1 and non-LINE1 loci. Predominantly amplified subfamilies are indicated in brackets. Data include multi-mapping reads; a corresponding analysis restricted to unique alignments is presented in Supplementary Fig. 2.

Article Snippet: PCR was performed with FastStartTM Taq-DNA-Polymerase (Roche 12032902001) using genomic DNA from human liver cells (Amsbio CD563105).

Techniques: Amplification, Agarose Gel Electrophoresis, Biomarker Discovery, Sequencing

Journal: medRxiv

Article Title: A broad-based probe-free qPCR assay for detection and discrimination of three human herpes viruses

doi: 10.1101/2020.10.01.20205427

Figure Lengend Snippet: Comparison of Phusion vs Q5 DNA Polymerases for amplification of HSV1. Amplification of serially diluted HSV1 (5.23x 10 5 to 5.23×10 2 copies/reaction) in triplicates with (A) Phusion-LOD of 5.23×10 4 copies and with (B) Q5-LOD of 5.23×10 3 copies.

Article Snippet: Extracted viral DNA was obtained from ATCC with the following product details: HCMV strain AD-169-ATCC VR-538D, HSV1 strain KOS-ATCC VR-1493D and HSV2 strain G-ATCC VR-734.

Techniques: Comparison, Amplification

Journal: medRxiv

Article Title: A broad-based probe-free qPCR assay for detection and discrimination of three human herpes viruses

doi: 10.1101/2020.10.01.20205427

Figure Lengend Snippet: Optimization of annealing temperature in HSV1. Temperature gradient experiments were performed for HSV1 in duplicates from 72°C to 67°C (rounded off) for a 10x dilution series ranging from 5.23×10 4 to 5.23×10 2 genome copies/reaction. As in the case of HCMV, product concentration decreases with decrease in temperature. ∼72°C was thus chosen as the optimum annealing temperature.

Article Snippet: Extracted viral DNA was obtained from ATCC with the following product details: HCMV strain AD-169-ATCC VR-538D, HSV1 strain KOS-ATCC VR-1493D and HSV2 strain G-ATCC VR-734.

Techniques: Concentration Assay

Journal: medRxiv

Article Title: A broad-based probe-free qPCR assay for detection and discrimination of three human herpes viruses

doi: 10.1101/2020.10.01.20205427

Figure Lengend Snippet: Standard curves for HCMV, HSV1 and HSV2. The quantification region (LOQ) is marked with a dashed line while the plateau region at lower concentrations is due to primer dimers. The serial dilution concentrations are as follows: HCMV-8.45×10 7 to 8.45×10° copies/reaction, HSV1-5.23×10 7 to 5.23×10° copies/reaction and HSV2-3.45×10 6 to 3.45×10° copies/reaction.

Article Snippet: Extracted viral DNA was obtained from ATCC with the following product details: HCMV strain AD-169-ATCC VR-538D, HSV1 strain KOS-ATCC VR-1493D and HSV2 strain G-ATCC VR-734.

Techniques: Serial Dilution

Journal: medRxiv

Article Title: Nanopore-based hybridization capture approaches for targeted viral metagenomics and whole-genome sequencing

doi: 10.1101/2025.04.08.25325453

Figure Lengend Snippet: Reference genome coverage of human betaherpesvirus 5 (A) and SARS-CoV-2 (B) from whole genome sequencing with the SureSelect protocol and ONT.

Article Snippet: For human betaherpesvirus 5 (ATCC, VR-538DQ), we used a human DNA content expected for a blood sample (40ng/μl) spiked with4 × 10 4 human betaherpesvirus 5 genome copies per microliter (gc/μl).

Techniques: Sequencing