Journal: Molecular cell

Article Title: Dietary supplement chondroitin-4-sulfate exhibits oncogene-specific pro-tumor effects on BRAF V600E melanoma cells

doi: 10.1016/j.molcel.2018.02.010

Figure Lengend Snippet: Key Resources Table

Article Snippet: Two-Step RT-PCR kit , TaKaRa/Clontech , Cat# RR019A.

Techniques: Virus, Recombinant, RNA Extraction, Transfection, SYBR Green Assay, Protease Inhibitor, Enzyme-linked Immunosorbent Assay, Malachite Green Assay, Activity Assay, shRNA, Sequencing, Mutagenesis, CRISPR, Plasmid Preparation, Software, Expressing

Journal: Journal of biomedical materials research. Part A

Article Title: Effects of hyaluronic acid conjugation on anti-TNF-α inhibition of inflammation in burns

doi: 10.1002/jbm.a.34829

Figure Lengend Snippet: Binding affinity experiments. Association and dissociation curves for (a.) (anti-TNF-α)-HA and (b.) anti-TNF-α. Vertical line separates association, on the left from dissociation. c. Comparison of initial loading of biotinylated antibody and conjugate onto streptavidin tips. Greater thickness is observed for the conjugate possibly due to interactions with HA chains.

Article Snippet: The experimental parameters consisted of the following dipping sequence: PBS 1 min (baseline), anti-TNF-α or (anti-TNF-α)-HA (10 μg/mL antibody) 20 min (loading), biocytin (10 μg/mL) 3 min (quench), PBS 5 min (wash), PBS 5 min (baseline), recombinant rat TNF-α (R&D systems Inc, Minneapolis, MN) 20 min (association), PBS 60 min (dissociation).

Techniques: Binding Assay

Journal: Journal of biomedical materials research. Part A

Article Title: Effects of hyaluronic acid conjugation on anti-TNF-α inhibition of inflammation in burns

doi: 10.1002/jbm.a.34829

Figure Lengend Snippet: Masson’s trichrome images of burn edges. Granulation tissue started to appear four days after eschar removal in the deep dermal region, with the most robust granulation tissue in the (anti-TNF-α)-HA treated sites. HA, anti-TNF-α and anti-TNF-α + HA treatments shows slower granulation tissue formation, while saline treated wound sites display the slowest granulation tissue formation. On day 4, newly forming eschar (#) is observed in most of the wound sites, and on day 7, necrosis has grown significantly particularly in saline and anti-TNF-α treated burn sites. Adjacent tissue (*) appears healthiest day 7 in the (anti-TNF-α)-HA treated sites. Scale bar = 1mm.

Article Snippet: The experimental parameters consisted of the following dipping sequence: PBS 1 min (baseline), anti-TNF-α or (anti-TNF-α)-HA (10 μg/mL antibody) 20 min (loading), biocytin (10 μg/mL) 3 min (quench), PBS 5 min (wash), PBS 5 min (baseline), recombinant rat TNF-α (R&D systems Inc, Minneapolis, MN) 20 min (association), PBS 60 min (dissociation).

Techniques:

Journal: Journal of biomedical materials research. Part A

Article Title: Effects of hyaluronic acid conjugation on anti-TNF-α inhibition of inflammation in burns

doi: 10.1002/jbm.a.34829

Figure Lengend Snippet: H & E staining. Day 7 images of the burn at the interface of wound edge and newly formed eschar shows densely populated multinucleated inflammatory immune cells apparent in saline and anti-TNF-α treatments. These immune cells, indicated with an arrow, are less densely populated in HA and anti-TNF-α + HA, with the fewest and most sparse found with (anti-TNF-α)-HA treatments. Scale bar = 200 μm.

Article Snippet: The experimental parameters consisted of the following dipping sequence: PBS 1 min (baseline), anti-TNF-α or (anti-TNF-α)-HA (10 μg/mL antibody) 20 min (loading), biocytin (10 μg/mL) 3 min (quench), PBS 5 min (wash), PBS 5 min (baseline), recombinant rat TNF-α (R&D systems Inc, Minneapolis, MN) 20 min (association), PBS 60 min (dissociation).

Techniques: Staining

Journal: Journal of biomedical materials research. Part A

Article Title: Effects of hyaluronic acid conjugation on anti-TNF-α inhibition of inflammation in burns

doi: 10.1002/jbm.a.34829

Figure Lengend Snippet: Vimentin immunostaining was used to assess viable tissue, by measuring thickness of nonviable tissue. Trichrome images were referenced if it was not immediately clear where the viable tissue ended. By day 7, (anti-TNF-α)-HA has decreased the thickness of necrosis significantly. (Anti-TNF-α)-HA treated burn sites have significantly thinner nonviable zones than saline and anti-TNF-α treated sites and denser vimentin staining in the viable region. Thickness of nonviable tissue in anti-TNF-α treated sites is not significantly different from saline treatments, but trends towards a slight reduction in nonviable tissue. *: p<0.05; error bars = mean +/− SD

Article Snippet: The experimental parameters consisted of the following dipping sequence: PBS 1 min (baseline), anti-TNF-α or (anti-TNF-α)-HA (10 μg/mL antibody) 20 min (loading), biocytin (10 μg/mL) 3 min (quench), PBS 5 min (wash), PBS 5 min (baseline), recombinant rat TNF-α (R&D systems Inc, Minneapolis, MN) 20 min (association), PBS 60 min (dissociation).

Techniques: Immunostaining, Staining

Journal: Journal of biomedical materials research. Part A

Article Title: Effects of hyaluronic acid conjugation on anti-TNF-α inhibition of inflammation in burns

doi: 10.1002/jbm.a.34829

Figure Lengend Snippet: Macrophage infiltration counts. On day 1, macrophage count appears to be most affected by (anti-TNF-α)-HA, and slightly by anti-TNF-α treatment. Anti-TNF-α treatments appeared to decrease macrophage counts the most by days 4 and 7. (Anti-TNF-α)-HA treatment attenuated slightly by day 7, but was still significantly decreased compared to saline control (* p<.001, bars p<.05; error bars are mean +/− SD).

Article Snippet: The experimental parameters consisted of the following dipping sequence: PBS 1 min (baseline), anti-TNF-α or (anti-TNF-α)-HA (10 μg/mL antibody) 20 min (loading), biocytin (10 μg/mL) 3 min (quench), PBS 5 min (wash), PBS 5 min (baseline), recombinant rat TNF-α (R&D systems Inc, Minneapolis, MN) 20 min (association), PBS 60 min (dissociation).

Techniques:

Journal: Journal of biomedical materials research. Part A

Article Title: Effects of hyaluronic acid conjugation on anti-TNF-α inhibition of inflammation in burns

doi: 10.1002/jbm.a.34829

Figure Lengend Snippet: IL-1β concentration in extracted burn tissue. IL-1β concentration peaks at day 1, and attenuates on day 4 in saline and (anti-TNF-α)-HA treated wound sites, however IL-1β levels are significantly lower than those in saline treated sites throughout the experimental period (* p<0.01 day 4, and p<0.05 day 7). Anti-TNF-α treatment exhibited the opposite response to saline and (anti-TNF-α)-HA, inhibiting IL-1β day 1 compared to saline, but then steadily loses effect by days 4 and 7. Error bars = mean +/− SD.

Article Snippet: The experimental parameters consisted of the following dipping sequence: PBS 1 min (baseline), anti-TNF-α or (anti-TNF-α)-HA (10 μg/mL antibody) 20 min (loading), biocytin (10 μg/mL) 3 min (quench), PBS 5 min (wash), PBS 5 min (baseline), recombinant rat TNF-α (R&D systems Inc, Minneapolis, MN) 20 min (association), PBS 60 min (dissociation).

Techniques: Concentration Assay

Journal: Bangladesh Journal of Botany

Article Title: Broad bean wilt virus 2 in commelina communis L. in China

doi: 10.3329/bjb.v52i20.68222

Figure Lengend Snippet: Fig. 1. Yellow mosaic symptoms on Commelina communis Another diseased sample was used for RNA extraction using the RNASimple Total RNA Kit (DP419), and then cDNA was synthesized using the TIANScript II RT Kit (KR107-01) from Tiangen Biotech (Beijing) Co., Ltd. Seven pairs of primers were used to amplify the whole genome of the virus, and the PCR products were detected on 1% agarose gel. Seven expected fragments were obtained and purified using a TIANgel Purification Kit (DP219-02) from Tiangen Biotech (Beijing) Co., Ltd. The recovered products were connected to the pMD-18T clone vector with a DNA ligation Kit Ver.2.1 (6022) from Takara Biomedical Technology (Beijing) Co., Ltd and then transferred into competent cells of the DH5α strain (CB101-02) from Tiangen Biotech (Beijing) Co., Ltd. The positive fragments were sent to Sangon Bioengineering (Shanghai) Co., Ltd for sequencing. Viral genomic organization was analyzed using the ORF Finder program. A homology comparison was performed on the amino acid sequence analysis of the viral cp gene. A Neighbor-joining phylogenetic tree based on the RNA 2 polyprotein was constructed using Mega

Article Snippet: Another diseased sample was used for RNA extraction using the RNASimple Total RNA Kit (DP419), and then cDNA was synthesized using the TIANScript II RT Kit (KR107-01) from Tiangen Biotech (Beijing) Co., Ltd.

Techniques: RNA Extraction, Synthesized, Virus, Agarose Gel Electrophoresis, Purification, Plasmid Preparation, DNA Ligation, Sequencing, Comparison, Construct

Journal: Scientific Reports

Article Title: Establishment and genomic characterization of the new chordoma cell line Chor-IN-1

doi: 10.1038/s41598-017-10044-3

Figure Lengend Snippet: Identification of kinases differentially expressed in Chor-IN-1 cell line vs . a panel of chordoma cell lines. ( a ) Heatmap representing the expression levels of the most differentially expressed kinases in Chor-IN-1 cell line, as obtained by NGS analysis using TREx, Illumina, San Diego, CA, USA. Colormap shades reflect relative low to high expression levels, ranging from green (log2 = 0) to red (log2 = 14). ( b ) RT-qPCR validation of selected genes (indicated with a star in the heatmap). Histogram bars represent RT-qPCR relative quantification results, carried out as described in M&M and normalized using U-CH1 as a reference sample.

Article Snippet: A custom panel interrogating 487 human kinases was selected from the available pre-designed assays for TruSeq Targeted RNA expression kit (TREx Illumina, San Diego, CA, USA) using the Design Studio software (Illumina, San Diego, CA, USA).

Techniques: Expressing, Quantitative RT-PCR, Biomarker Discovery, Quantitative Proteomics