Journal: Molecular & cellular proteomics : MCP

Article Title: Identification of novel proteins associated with both alpha-synuclein and DJ-1.

doi: 10.1074/mcp.M600182-MCP200

Figure Lengend Snippet: FIG. 4. Affinity purification and WB validation of mortalin, grp94, calnexin, clathrin, and nucleolin in -synuclein and DJ-1 protein complexes. MES cells were treated with 20 nM rotenone (R) or DMSO (D) for 3 days and then lysed in Nonidet P-40 lysis buffer, respectively. The total cell lysate was purified with -synuclein or DJ-1 affinity column. Afterward equal amounts of protein (20 g) from the total cell lysate (input) and elutes were analyzed by WB with antibodies against -synuclein, DJ-1, mortalin, grp94, calnexin, clathrin, or nucleolin, respectively.

Article Snippet: Antibodies used include: -synuclein for Western blot (WB) (BD Pharmingen), -synuclein for IP (Cell Signaling Technology, Beverly, MA), -synuclein for immunofluorescent staining (Chemicon, Temecula, CA), DJ-1 (Novus Biologicals, Littleton, CO), mortalin/grp75 (Stressgen, San Diego, CA), nucleolin (Novus Biologicals), calnexin (BD Pharmingen), grp94 (Stressgen), and clathrin (Chemicon).

Techniques: Affinity Purification, Biomarker Discovery, Lysis, Purification, Affinity Column

Journal: Molecular & cellular proteomics : MCP

Article Title: Identification of novel proteins associated with both alpha-synuclein and DJ-1.

doi: 10.1074/mcp.M600182-MCP200

Figure Lengend Snippet: FIG. 5. Co-localization of mortalin, nucleolin, calnexin, grp94, and clathrin with -synuclein and DJ-1 in MES cells. MES cells were fixed and triple stained with antibodies against -synuclein (Column A, red); DJ-1 (Column B, green); and mortalin, nucleolin, calnexin, grp94, or clathrin (Column C, blue) simultaneously. The images were visualized with a confocal microscope. Merged im- ages are shown in white when three antibodies are co-localized (Column D).

Article Snippet: Antibodies used include: -synuclein for Western blot (WB) (BD Pharmingen), -synuclein for IP (Cell Signaling Technology, Beverly, MA), -synuclein for immunofluorescent staining (Chemicon, Temecula, CA), DJ-1 (Novus Biologicals, Littleton, CO), mortalin/grp75 (Stressgen, San Diego, CA), nucleolin (Novus Biologicals), calnexin (BD Pharmingen), grp94 (Stressgen), and clathrin (Chemicon).

Techniques: Staining, Microscopy

Journal: bioRxiv

Article Title: Different localization of fluorescently labeled N- and C-termini of nucleolin variants in human glioblastoma cell culture

doi: 10.1101/596916

Figure Lengend Snippet: 2D Western blot hybridization of the Sus\fP2 (A,B) and MSC (C,D) cell culture lysate. A – antibodies against the N-terminus of nucleolin (#N2662, Sigma, USA). B – antibodies against the C- terminus of nucleolin (#A300-711A, Bethyl, USA). The presence of multiple protein products recognized by antibodies against the N-terminus but not antibodies against the C-terminus is noticeable.

Article Snippet: Primary antibodies were used: anti-GFP in a titer of 1:8000 (AB011, Evrogen, Russia), anti-NCL in a titer of 1:7000 (#a300-711A, Bethyl, USA), anti-FLAG M2 in a titer of 1:8000 (#F3165-.2MG, Sigma, USA).

Techniques: Western Blot, Hybridization, Cell Culture

Journal: eLife

Article Title: Long non-coding RNA Neat1 and paraspeckle components are translational regulators in hypoxia

doi: 10.7554/elife.69162

Figure Lengend Snippet: Figure 6. p54nrb-interacting proteins, nucleolin and RPS2, control the FGF1 IRES activity. (A–C) Quantification of RPS2 (A), hnRNPM (B) and nucleolin (C) RNA expression in HL-1 cells transfected with siRNAs against Rps2, hnRNPM or nucleolin mRNA, respectively. RNA expression was measured by RT- qPCR and normalized to control siRNA. One representative experiment is shown with n=3 biological replicates. Student two-tailed t-test was performed with n=3 or Mann-Whitney test with n=9; *p<0.05, **p<0.01, ***<0.001, ****p<0.0001. (D) Capillary Simple Western of nucleolin following nucleolin knock-down. The full raw unedited gel is provided in Figure 6—figure supplement 1A (Figure 6—figure supplement 1—source data 1). (E) FGF1 IRES activity with knock-down by siRNA interference of candidate ITAF nucleolin in HL-1 in normoxia or hypoxia 1% O2 was performed as in Figure 2. The IRES activity values have been normalized to the control siRNA. Histograms correspond to means ± standard deviation of the mean, with a non- parametric Mann-Whitney test *p<0.05, **p<0.01. The mean has been calculated with nine cell culture biological replicates, each of them being already the mean of three technical replicates (27 technical replicates in total but the M-W test was performed with n=9). Detailed values of biological replicates are presented in Supplementary file 6. (F) Capillary Simple Western of endogenous FGF1 following nucleolin knock-down. Histograms correspond to means ± standard deviation. The source data or capillary Simple Western are provided in Figure 1—figure supplement 1B (Figure 6—figure supplement 1—source data 1).

Article Snippet: Capillary Western Diluted protein lysate was mixed with fluorescent master mix and heated at 95 °C for 5 min. Three μL of protein mix (1 mg/mL maximal concentration) containing Protein Normalization Reagent, blocking reagent, wash buffer, target primary antibody (rabbit anti- eIF2α [Cell Signaling Technology 9721]) diluted 1:50, mouse anti- phospho- eIF2α [Cell Signaling Technology 2103] diluted 1:50, mouse antip21 antibody [Santacruz, sc- 6246] diluted 1:50, rabbit anti- P54nrb diluted 1:200 [Santacruz, sc- 67016], rabbit anti- PSPC1 diluted 1:100 [bethyl laboratory, A303- 205A], mouse anti- SFPQ diluted 1:100 [Abcam, Ab11825]; rabbit anti- FGF1 diluted 1:25 [Abcam Ab207321], rabbit anti- Nucleolin diluted 1:50 [Novus biological, NB600- 241], secondary- HRP (ready to use rabbit or mouse ‘detection module’, DM- 001 or αDM- 002), and chemiluminescent substrate were dispensed into designated wells in a manufacturer- provided microplate.

Techniques: Control, Activity Assay, RNA Expression, Transfection, Quantitative RT-PCR, Two Tailed Test, MANN-WHITNEY, Simple Western, Knockdown, Standard Deviation, Cell Culture

Journal: bioRxiv

Article Title: Dependency Map correlation analysis reveals WDR89 as a genome maintenance factor

doi: 10.64898/2026.01.28.698016

Figure Lengend Snippet: WDR89 is a nucleolar protein that responds to double-strand DNA break-inducing stresses. ATM-dependent nucleolar accumulation of WDR89 upon genotoxic stress. (A) WDR89 localizes predominantly in the nucleus and overlaps largely with nucleolin. (B) Quantification of WDR89 nuclear staining intensity following ionizing radiation. (C) Quantification of WDR89 nuclear staining intensity following genotoxic chemical treatments. (D) Confirmation of DNA damage by γH2AX foci staining of the conditions in C. (E) Effect of ATM inhibitor treatment on WDR89 nuclear intensity changes after IR. (F) Western blot of chromatin fractionation for WDR89 and the indicated markers. For panels in B, C, D and E, ****p<0.0001, by ANOVA with Tukey’s post-hoc test or by T-test where appropriate.

Article Snippet: Immunofluorescence staining was performed using anti-γ-H2AX antibodies (Abcam, ab81299, Santa Cruz, sc-517348), an anti-Nucleolin antibody (Novus, NBP2-44610), anti WDR89 antibody (Bethyl, A301-872A) or p53 antibody (Cell Signaling, #9282) at 1:250 dilution and Alexafluor 568 goat anti-rabbit secondary and Alexafluor 488 goat anti-mouse antibodies (Invitrogen) at 1:400 dilution.

Techniques: Staining, Western Blot, Fractionation

Journal: Experimental & Molecular Medicine

Article Title: (Non)canonical Wnt signaling, cytoarchitecture and stemness: new insights from primary nonmetastatic, primary metastatic, regional and distant metastatic models of adrenocortical carcinoma

doi: 10.1038/s12276-025-01507-z

Figure Lengend Snippet: a Cellular localization of vimentin in all three models. b – d The localization of E-cadherin and N-cadherin in TVBF-7 ( b ) NCI-H295R ( c ) and MUC-1 ( d ) spheroids. e – g The cellular localization of MMP9 ( e ) Nucleolin ( f ) and Lamin B1–β-catenin–DAPI ( g ) in tumor spheroids of all three models. Scale bar, 50 μm.

Article Snippet: Nucleolin , STJ140144, St John’s Laboratory (London, UK) , 1/200.

Techniques: