Journal: Cell reports

Article Title: IPMK Mediates Activation of ULK Signaling and Transcriptional Regulation of Autophagy Linked to Liver Inflammation and Regeneration

doi: 10.1016/j.celrep.2019.02.013

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: Beclin , Cell Signaling , 3738; RRID: AB_490837.

Techniques: Generated, Plasmid Preparation, Recombinant, Purification, SYBR Green Assay, DNA Purification, Staining, In Situ, shRNA, Software

Journal: Molecular Cancer Research

Article Title: The Opposing Effect of Hypoxia-Inducible Factor-2α on Expression of Telomerase Reverse Transcriptase

doi: 10.1158/1541-7786.mcr-07-0065

Figure Lengend Snippet: FIGURE 4. HIF-2a occupancy on the hTERT promoter, recruitment of p300, and changes in histone H3 acetylation in A498 and U251 cells under hypoxic conditions. A. Schematic presentation of the hTERT promoter and locations of the ChIP PCR amplicons relative to the translational start codon (ATG). The putative HREs in region a are indicated (16). Region b was also found to interact with HIF-1a according to Anderson et al. (10). B. The ChIP assay for the presence of HIF-2a, p300, and histone H3 acetylation at the hTERT promoter in hypoxia-treated A498 and U251 cells. The precipitated DNA was subject to PCR analysis using the primer pairs specific to the hTERT promoter regions a and b. Input is sonicated chromatin without immunoprecipitation, but reverse cross-linked and purified together with ChIP samples. HRE, hypoxia-responsive element; H and N, the cells were cultured under hypoxic and normal oxygen conditions, respectively. Ab, no antibody controls. H3-Ac, the antibody against acetylated histone H3.

Article Snippet: The membranes were probed with the specific mouse monoclonal antibody against HIF-1a or HIF-2a rabbit polyclonal antibody (Novus Biologicals), followed by a secondary anti-mouse or rabbit horseradish peroxidase–conjugated immunoglobulin G, and developed with the enhanced chemiluminescence method (Amersham).

Techniques: Sonication, Immunoprecipitation, Purification, Cell Culture

Journal: The Journal of biological chemistry

Article Title: Alzheimer disease-specific conformation of hyperphosphorylated paired helical filament-Tau is polyubiquitinated through Lys-48, Lys-11, and Lys-6 ubiquitin conjugation.

doi: 10.1074/jbc.M512786200

Figure Lengend Snippet: FIGURE 5. Anti-polyubiquitin staining of affinity-purified PHF-Tau. Following SDS- PAGE separation of MC1 affinity-purified PHF-Tau on a 10% polyacrylamide gel, Western blot was performed with an anti-polyubiquitin antibody. Immunoreactivity was visual- ized by enhanced chemiluminescence (left panel). Secondary antibody (goat anti-mouse IgG-horseradish peroxidase) control for nonspecific immunoreactivity is also depicted (right panel).

Article Snippet: Blots were incubated with a monoclonal mouse anti-polyubiquitin antibody (Novus Biologicals) 1:500 overnight at 4 °C.

Techniques: Staining, Affinity Purification, SDS Page, Western Blot, Control

Journal: The Journal of biological chemistry

Article Title: Alzheimer disease-specific conformation of hyperphosphorylated paired helical filament-Tau is polyubiquitinated through Lys-48, Lys-11, and Lys-6 ubiquitin conjugation.

doi: 10.1074/jbc.M512786200

Figure Lengend Snippet: FIGURE 6. Relative quantification of Lys-6, Lys-11, and Lys-48 polyubiquitin linkages by SRM. Polyubiquitin linkages at Lys-6 (A), Lys-11 (B), and Lys-48 (C) of ubiquitin (ubiquitinated and unmodified peptides) were quantified by specific precursor-to-product ion transition monitoring (Table 4). D shows chromatograms for all three ubiquitinated peptides on the same scale for visual comparison of the relative peak areas.

Article Snippet: Blots were incubated with a monoclonal mouse anti-polyubiquitin antibody (Novus Biologicals) 1:500 overnight at 4 °C.

Techniques: Quantitative Proteomics, Ubiquitin Proteomics, Comparison