Journal: Cell host & microbe

Article Title: Longitudinal human antibody repertoire against complete viral proteome from Ebola virus survivor reveals protective sites for vaccine design

doi: 10.1016/j.chom.2020.01.001

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: Zaire EBOV VP40 Matrix protein , Sino Biologicals , 40446-V07E.

Techniques: Recombinant

Journal: Cell Death & Disease

Article Title: Effects of short-chain fatty acids in inhibiting HDAC and activating p38 MAPK are critical for promoting B10 cell generation and function

doi: 10.1038/s41419-021-03880-9

Figure Lengend Snippet: A Purified splenic B cells were polarized to Bregs after a 2-day coculture with indicated SCFAs or Trichostatin A (TSA, an HDAC inhibitor with high efficiency) in the presence of LPS; the nuclear protein was prepared and tested for HDAC inhibition by ELISA. B – D B10 cell frequency in purified splenic B cells cultured with or without sodium acetate ( B ), HDAC inhibitors TSA or vorinostat ( C ), or HAT inhibitor (HATi) anacardic acid ( D ) under the existence of CD40 mAb or LPS for 2 days. Results were shown as representative FACS plots or bar graphs. The data are presented as mean ± SD from three independent experiments. * P < 0.05, ** p < 0.01, and *** p < 0.001 compared to Ctrl or as indicated.

Article Snippet: In some experiments, cells were treated with inhibitors or metabolites, including HDACis TSA (1–10 nM; Beyotime) and vorinostat (100–500 nM; MCE), GPR41 agonist AR420626 (1–10 μM; APExBIO), GPR43 agonist (1–10 μM; Sigma-Aldrich) or antagonist GLPG0974 (500 nM; Sigma-Aldrich), GPR109A agonist niacin (1 mM; Sigma-Aldrich), HAT inhibitor anacardic acid (1–10 μM; MCE), ERK1/2 inhibitor U0126 (5 μM; MCE), p38 inhibitor SB 203580 (5 μM; MCE), or JNK inhibitor SP600125 (1 μM; MCE).

Techniques: Purification, Inhibition, Enzyme-linked Immunosorbent Assay, Cell Culture

Journal: Cell death discovery

Article Title: Plac8-ERK pathway modulation of monocyte function in sepsis.

doi: 10.1038/s41420-024-02012-4

Figure Lengend Snippet: Fig. 1 Expression of plac8 and ERK activation in peripheral blood mononuclear cells of septic patients and normal individuals. A Flow cytometry analysis of peripheral blood CD14+ and CD16+ cell subsets. B Flow cytometry analysis of CD14+ and CD16+ cell subsets. C qRT- PCR analysis of gene expression. D ELISA analysis of cytokine expression. E Western blot analysis of protein expression. F Western blot analysis of protein expression. G Flow cytometry analysis of cell cycle. H Cell proliferation index PI = (S + G2M)/(G0/1 + S + G2M). * indicates P < 0.05 compared to the normal group. Data is presented as mean ± standard deviation. Data analysis was performed using an independent samples t-test, and the experiment was repeated three times.

Article Snippet: After blocking with 0.5% BSA, the membranes were incubated overnight with primary antibodies: rabbit anti-CD14 (ab182032, 1:1000, Abcam, UK), CD16 (Cat No. 16559-1-AP, 1:1000, Proteintech), plac8 (Cat No. 12284-1-AP, 1:200, Proteintech), ERK1/2 (ab17942, 1:1000, Abcam, UK), p-ERK1/2 (ab223500, 1:1000, Abcam, UK), and GAPDH (ab8245, 1:1000, Abcam, UK).

Techniques: Expressing, Activation Assay, Flow Cytometry, Quantitative RT-PCR, Gene Expression, Enzyme-linked Immunosorbent Assay, Western Blot, Standard Deviation

Journal: Cell death discovery

Article Title: Plac8-ERK pathway modulation of monocyte function in sepsis.

doi: 10.1038/s41420-024-02012-4

Figure Lengend Snippet: Fig. 2 Effects of plac8 on peripheral blood mononuclear cell proliferation in septic patients. A qRT-PCR analysis of gene expression. B Western blot analysis of protein band. C Western blot analysis of protein expression. D ELISA analysis of cytokine expression. E Cell proliferation measured by CCK-8 assay, cell proliferation (%) = [OD (treatment group) −OD (blank group)] / [OD (control group) −OD (blank group)] × 100%. * indicates P < 0.05 compared to si-Plac8-NC or Plac8-NC group. Data is presented as mean ± standard deviation. An independent samples t-test was used to compare two groups, and two-way ANOVA was used to compare at different time points. The experiment was repeated three times.

Article Snippet: After blocking with 0.5% BSA, the membranes were incubated overnight with primary antibodies: rabbit anti-CD14 (ab182032, 1:1000, Abcam, UK), CD16 (Cat No. 16559-1-AP, 1:1000, Proteintech), plac8 (Cat No. 12284-1-AP, 1:200, Proteintech), ERK1/2 (ab17942, 1:1000, Abcam, UK), p-ERK1/2 (ab223500, 1:1000, Abcam, UK), and GAPDH (ab8245, 1:1000, Abcam, UK).

Techniques: Quantitative RT-PCR, Gene Expression, Western Blot, Expressing, Enzyme-linked Immunosorbent Assay, CCK-8 Assay, Control, Standard Deviation

Journal: Cell death discovery

Article Title: Plac8-ERK pathway modulation of monocyte function in sepsis.

doi: 10.1038/s41420-024-02012-4

Figure Lengend Snippet: Fig. 5 Effects of plac8 on monocyte cell survival and proliferation in the mouse model. A Flow cytometry analysis of CD14+ and CD16+ cell subsets. B Flow cytometry analysis of peripheral blood CD14+ and CD16+ cell subsets. C Western blot analysis of protein band. D Western blot analysis of protein expression. E ELISA analysis of cytokine expression. F Detection of cell proliferation. G Flow cytometry analysis of cell cycle. H Cell proliferation index PI. * indicates P < 0.05 compared to si-Plac8-NC or Plac8-NC group. Data is presented as mean ± standard deviation. Independent samples t-test was used to compare two groups, and two-way ANOVA was used for comparison at different time points. The experiment was repeated three times.

Article Snippet: After blocking with 0.5% BSA, the membranes were incubated overnight with primary antibodies: rabbit anti-CD14 (ab182032, 1:1000, Abcam, UK), CD16 (Cat No. 16559-1-AP, 1:1000, Proteintech), plac8 (Cat No. 12284-1-AP, 1:200, Proteintech), ERK1/2 (ab17942, 1:1000, Abcam, UK), p-ERK1/2 (ab223500, 1:1000, Abcam, UK), and GAPDH (ab8245, 1:1000, Abcam, UK).

Techniques: Flow Cytometry, Western Blot, Expressing, Enzyme-linked Immunosorbent Assay, Standard Deviation, Comparison

Journal: Cell death discovery

Article Title: Plac8-ERK pathway modulation of monocyte function in sepsis.

doi: 10.1038/s41420-024-02012-4

Figure Lengend Snippet: Fig. 6 The role and mechanism of Plac8-mediated ERK signaling pathway activation in the proliferation and activation of peripheral blood monocytes in septic patients.

Article Snippet: After blocking with 0.5% BSA, the membranes were incubated overnight with primary antibodies: rabbit anti-CD14 (ab182032, 1:1000, Abcam, UK), CD16 (Cat No. 16559-1-AP, 1:1000, Proteintech), plac8 (Cat No. 12284-1-AP, 1:200, Proteintech), ERK1/2 (ab17942, 1:1000, Abcam, UK), p-ERK1/2 (ab223500, 1:1000, Abcam, UK), and GAPDH (ab8245, 1:1000, Abcam, UK).

Techniques: Activation Assay

Journal: Scientific reports

Article Title: Parallel Reaction Monitoring reveals structure-specific ceramide alterations in the zebrafish.

doi: 10.1038/s41598-019-56466-z

Figure Lengend Snippet: Figure 1. A Parallel Reaction Monitoring-based approach for ceramide quantification. (a) MS2 of d18:1/16:0 ceramide standard in positive ionisation mode. Fragment structures are based on published assignments43,44. (b) Schematic of Parallel Reaction Monitoring. (c) Example PRM chromatograms for C41:1 ceramide from 48 hpf zebrafish embryos, demonstrating presence of multiple LCB-acyl chain isomers with the same m/z. RT: retention time. (d) MS2 spectrum of C41:1 ceramide from 48 hpf zebrafish embryos, the four major LCB fragments are labelled. (d,e) m/z 200-m/z 350, the four major LCB fragments and additional LCB-derived minor fragments are labelled. Unlabelled minor fragments: m/z 224.2371 (d16:1 LCB), m/z 238.2525 (d17:1 LCB).

Article Snippet: Materials. d18:1/16:0 (860516), d18:1/17:0 (860517), d18:1-d7/15:0 (860681), d18:1-d7/18:0 (860677) and d18:1-d7/24:1 (860679) ceramides were purchased from Avanti Polar Lipids.

Techniques: Targeted Proteomics, Derivative Assay

Journal: Cell Discovery

Article Title: Structural basis of a two-antibody cocktail exhibiting highly potent and broadly neutralizing activities against SARS-CoV-2 variants including diverse Omicron sublineages

doi: 10.1038/s41421-022-00449-4

Figure Lengend Snippet: a Binding profiles of F61 and D2 to different spike proteins (WIV04-S1, WIV04-RBD, WIV04-NTD, Delta-S1, Delta-RBD and Omicron-RBD) were determined by ELISA. F61 and D2 bound to diverse RBD and S1 fragments but not WIV04-NTD with EC 50 values less than 4.5 ng/mL, indicating that they were both RBD-specific antibodies. Experiments were performed in duplicate, n = 2. Data are represented as means ± SD (upper panel) and means (down panel). b Binding kinetics ( K D ) of the monoclonal antibodies (mAbs) with Delta-RBD, Omicron-RBD (BA.1 and BA.2) were measured by SPR. c mAbs blocked SARS-CoV-2 WT-RBD binding to ACE2 measured by FACS. The X-axis represented the fluorescence intensity of human antibodies labeled by FITC, and the Y-axis represented the fluorescence intensity of RBD-mFc labeled by Taxes Red. Percentages of cells that scored negative, single positive, or double positive are shown in each quadrant.

Article Snippet: ELISA plates were coated with SARS-CoV-2 protein including WT-S1, WT-NTD, WT-RBD, Delta-S1, Delta-RBD and Omicron-RBD (Sino Biological, China) at 4 °C overnight.

Techniques: Binding Assay, Enzyme-linked Immunosorbent Assay, Fluorescence, Labeling

Journal: Cell Discovery

Article Title: Structural basis of a two-antibody cocktail exhibiting highly potent and broadly neutralizing activities against SARS-CoV-2 variants including diverse Omicron sublineages

doi: 10.1038/s41421-022-00449-4

Figure Lengend Snippet: a Overall structure of SARS-CoV-2 S in complex with F61 Fab. The tilt angle of RBD is defined by the angle between the long axis of RBD (red line) and its projection on the horizontal plane (black ellipse). Angle between them is indicated. SARS-CoV-2 RBD is colored in cyan, other domains in gray, heavy chain of F61 in magenta and light chain of F61 in violet. Related to Supplementary Fig. . b Overall structure of SARS-CoV-2 S in complex with D2 Fab. The tilt angle of RBD is defined by the angle between the long axis of RBD (red line) and its projection on the horizontal plane (black ellipse). Angle between them is indicated. SARS-CoV-2 RBD is colored in cyan, other domains in gray, heavy chain of D2 in orange and light chain of D2 in light orange. Related to Supplementary Fig. . c Overall structures of SARS-CoV-2 Omicron S in complex with F61 Fab and D2 Fab. Color schemes are the same as a and b . Related to Supplementary Fig. . d Structural superposition of RBD-fab and RBD-ACE2 (PDB ID: 6M0J) structures and the footprints of F61, D2 and ACE2 on the RBD, and structure of Omicron-RBD-F61-D2 with footprints of F61 and D2 on the RBD. ACE2 is colored in blue. The footprints of F61, D2 and ACE2 are represented as magenta, orange and blue, respectively. Other color schemes are the same as a and b .

Article Snippet: ELISA plates were coated with SARS-CoV-2 protein including WT-S1, WT-NTD, WT-RBD, Delta-S1, Delta-RBD and Omicron-RBD (Sino Biological, China) at 4 °C overnight.

Techniques: