Journal: The Journal of Biological Chemistry

Article Title: The unique prodomain of T-cadherin plays a key role in adiponectin binding with the essential extracellular cadherin repeats 1 and 2

doi: 10.1074/jbc.M117.780734

Figure Lengend Snippet: Adiponectin binding analysis in T-cadFc capture and surface plasmon assays. A, representative immunoblot for adiponectin (APN) in bound fractions of T-cadFc capture assay using the strategy depicted in Fig. 2A. Increasing concentrations of purified adiponectin were applied as the input fraction. Trimer equivalents of adiponectin concentrations of all fractions were determined experimentally by ELISA. B and C, saturable binding curve (B) and its Scatchard plot of ELISA-based binding assay (C). The binding constant (KD) was calculated as the slope of the approximation straight line. D, SPR analysis of purified adiponectin (APN) and full-length T-cadFc. ∼100 response units of T-cad fused with human IgG-Fc were trapped by anti-human IgG Fc antibody immobilized on the sensor surface, and each concentration (333–1.1 nm trimer equivalent) of purified adiponectin was injected at time = 0. Each sensorgram was adjusted to that of purified adiponectin = 0 nm (not shown). Kinetics constants (ka and kd) were analyzed using BIACORE T200 evaluation software v1.0, assuming a 1:1 binding model.

Article Snippet: Anti-human IgG-Fc antibody was immobilized over all four flow cells using the Human Antibody Capture Kit TM (GE Healthcare) according to the instructions supplied by the manufacturer.

Techniques: Binding Assay, Western Blot, Purification, Enzyme-linked Immunosorbent Assay, Concentration Assay, Injection, Software

Journal: Cell Death & Disease

Article Title: Obesity impairs cardiolipin-dependent mitophagy and therapeutic intercellular mitochondrial transfer ability of mesenchymal stem cells

doi: 10.1038/s41419-023-05810-3

Figure Lengend Snippet: Key resources table.

Article Snippet: 39 , RNeasy Mini Kit (250) , Qiagen , 74106.

Techniques: Recombinant, Control, Staining, Isolation, Enzyme-linked Immunosorbent Assay, Live Dead Assay, TUNEL Assay, ATP Assay, Protease Inhibitor, cDNA Synthesis, Saline, Purification

Journal: Cell reports

Article Title: Chromatin Landscape Underpinning Human Dendritic Cell Heterogeneity

doi: 10.1016/j.celrep.2020.108180

Figure Lengend Snippet:

Article Snippet: Anti-human CD117/c-kit purified (clone 104D2) , Biolegend , Cat# 313202; RRID:AB_314981.

Techniques: Purification, Recombinant, Produced, SYBR Green Assay, Saline, Lysis, Electron Microscopy, Labeling, Staining, Cell Isolation, Enzyme-linked Immunosorbent Assay, Control, Antibody Labeling, Reverse Transcription, DNA Library Preparation, Generated, Microarray, Software

Journal: Cells

Article Title: The Cysteine Protease Legumain Is Upregulated by Vitamin D and Is a Regulator of Vitamin D Metabolism in Mice.

doi: 10.3390/cells13010036

Figure Lengend Snippet: Figure 1. Vitamin D3 increases legumain expression, activity, and secretion in pre-osteoblastic cells. (A) The nucleotide sequence of the LGMN gene promoter region with annotations of potential vitamin D-responsive elements (VDRE; red) relative to the transcription start site (TSS). (B–F) Human BMSC- TERT cells (20,000 cells/cm2) were incubated with 1,25(OH)2D3 (B–F; 10, 50 or 100 nM), 25(OH)D3 (C–F; 100, 250, 500 or 1000 nM) or an equal volume of ethanol (control, 0 nM) in osteoblast induction medium for seven days before harvesting. (B) Legumain mRNA expression relative to housekeeping control (GAPDH) (2−∆∆CT; n = 3). (C) One representative immunoblot of legumain (proform 56 kDa, mature form 36 kDa) and GAPDH (housekeeping) in cell lysates (n = 3). (D) Quantification of the 36 kDa mature legumain immunoband (IB) intensity as arbitrary units (ARBU) relative to GAPDH in immunoblots represented in C (n = 3). (E) Legumain activity (dF/s) in cell lysates adjusted for the total protein concentration (µg/mL) (n = 6–9). (F) Secreted legumain (pg/mL) in conditioned media measured by ELISA and adjusted for the total protein concentration in the corresponding cell lysates (n = 3–5). (B,D–F) Data represent mean ± SEM. (B,D) Kruskal–Wallis test. (E,F) One-way ANOVA. * p < 0.05 vs. 0 nM 1,25(OH)2D3 or 25(OH)D3. Numbers (n) represent individual biological replicates.

Article Snippet: Plasma VDBP concentrations Cells 2024, 13, 36 5 of 16 were measured using a mouse VDBP ELISA kit (R&D Systems, Catalog # DY4188-05, RRID: AB_2943630).

Techniques: Expressing, Activity Assay, Sequencing, Incubation, Control, Western Blot, Protein Concentration, Enzyme-linked Immunosorbent Assay

Journal: Cells

Article Title: The Cysteine Protease Legumain Is Upregulated by Vitamin D and Is a Regulator of Vitamin D Metabolism in Mice.

doi: 10.3390/cells13010036

Figure Lengend Snippet: Figure 2. Treatment with 25(OH)D3 increases legumain levels and activity in wild-type mice. Wild-type mice (Lgmn+/+) were treated with 50 µg/kg 25(OH)D3 (n = 7) or an equal volume vehicle (n = 7, control) subcutaneously every two to three days (four times in total). Tissues were harvested 24 h after the final injection (day 8). (A) Legumain mRNA expression relative to the geometric mean of CT values of four housekeeping controls in kidney, liver, and spleen (2−∆∆CT; n = 5). (B) One representative immunoblot of legumain and GAPDH in kidney, liver, and spleen (n = 3). (C) Quantifi- cation of the 36 kDa mature legumain immunoband (IB) intensity as arbitrary units (ARBU) relative to GAPDH (housekeeping) in kidney, liver, and spleen from immunoblots represented in (C) (n = 3). (D) Legumain activity (dF/s) in kidney, liver, and spleen adjusted for total protein concentration (µg/mL, n = 5). (E) Legumain plasma concentration (ng/mL) measured by ELISA (n = 5). (F) Cor- relation between legumain (ng/mL and 1,25(OH)2D3 (pmol/L) concentrations in plasma (n = 5). (A,C,E) Two-tailed unpaired Student’s t-test. (D) Mann–Whitney test. Data represent mean ± SEM. * p < 0.05. (F) Simple linear regression. Numbers (n) represent individual biological replicates.

Article Snippet: Plasma VDBP concentrations Cells 2024, 13, 36 5 of 16 were measured using a mouse VDBP ELISA kit (R&D Systems, Catalog # DY4188-05, RRID: AB_2943630).

Techniques: Activity Assay, Control, Injection, Expressing, Western Blot, Protein Concentration, Clinical Proteomics, Concentration Assay, Enzyme-linked Immunosorbent Assay, Two Tailed Test, MANN-WHITNEY

Journal: Cells

Article Title: The Cysteine Protease Legumain Is Upregulated by Vitamin D and Is a Regulator of Vitamin D Metabolism in Mice.

doi: 10.3390/cells13010036

Figure Lengend Snippet: Figure 3. Legumain is required for VDBP processing and regulation. (A) Purified VDBP from human plasma (1.9 µM) was incubated in legumain assay buffer (pH 5.8) at 37 ◦C with or without purified active bovine legumain (2 µM) for 5 h before gel electrophoresis and immunoblotting of VDBP (n = 1). (B–H) Wild-type (Lgmn+/+) and legumain-deficient (Lgmn−/−) mice were treated with 50 µg/kg 25(OH)D3 (n = 6–7) or an equal volume vehicle (n = 7, control) subcutaneously every two to three days (four times in total). Tissues were harvested 24 h after the final injection (day 8). (B) One representative immunoblot of VDBP and GAPDH (housekeeping) in kidney and liver (n = 4). (C–F) Quantification of VDBP immunoband (IB) intensity as arbitrary units (ARBU) relative to GAPDH in immunoblots represented in (B) (n = 4). (C) Hepatic VDBP 45 kDa immunoband. (D) Renal VDBP 45 kDa immunoband. (E) Hepatic VDBP 55 kDa immunoband. (F) Renal VDBP 55 kDa immunoband. (G) Plasma VDBP concentration (µg/mL) was measured by ELISA (n = 6–7). (H) Hepatic VDBP mRNA expression relative to the geometric mean of CT values of four house- keeping controls (2−∆∆CT, n = 5). (C–H) Data represent mean ± SEM. Two-way ANOVA. # p < 0.05, ## p < 0.01, ### p < 0.001 vs. different genotype, same treatment. Numbers (n) represent individual biological replicates.

Article Snippet: Plasma VDBP concentrations Cells 2024, 13, 36 5 of 16 were measured using a mouse VDBP ELISA kit (R&D Systems, Catalog # DY4188-05, RRID: AB_2943630).

Techniques: Purification, Clinical Proteomics, Incubation, Nucleic Acid Electrophoresis, Western Blot, Control, Injection, Concentration Assay, Enzyme-linked Immunosorbent Assay, Expressing

Journal: Cells

Article Title: The Cysteine Protease Legumain Is Upregulated by Vitamin D and Is a Regulator of Vitamin D Metabolism in Mice.

doi: 10.3390/cells13010036

Figure Lengend Snippet: Figure 5. Graphical representation of the suggested interplay between vitamin D and legumain. Left panel: Vitamin D (VD3) promotes legumain expression and activity through transcriptional upregulation of the legumain gene (LGMN). The free fraction of circulating VD3 metabolites diffuse through plasma membranes. 25-hydroxyvitamin D (25(OH)D3) is hydroxylated by 1α-hydroxylase (CYP27B1), forming the active metabolite 1α,25-dihydroxyvitamin D (1,25(OH)2D3). 1,25(OH)2D3 binds to the nuclear vitamin D receptor (VDR) and promotes transcription of legumain (LGMN). Synthesized prolegumain is either sorted and activated in the endolysosomal system or released to the extracellular environment. Right panel: In the proximal tubular epithelium, 25(OH)D3 bound to vitamin D binding protein (VDBP) is internalized from the tubular lumen through a megalin/cubilin- mediated process. The vitamin D metabolite is released, enabling subsequent hydroxylation by 1α-hydroxylase (CYP27B1) or 24-hydroxylase (CYP24A1), and VDBP is cleaved by legumain in the endolysosomal system. VDBP cleavage by legumain might be important in controlling the systemic level of vitamin D metabolites. Created with BioRender.com (accessed on 11 December 2023).

Article Snippet: Plasma VDBP concentrations Cells 2024, 13, 36 5 of 16 were measured using a mouse VDBP ELISA kit (R&D Systems, Catalog # DY4188-05, RRID: AB_2943630).

Techniques: Expressing, Activity Assay, Clinical Proteomics, Synthesized, Binding Assay

Journal: PLoS ONE

Article Title: Antigenic and immunosuppressive properties of a trimeric recombinant transmembrane envelope protein gp41 of HIV-1

doi: 10.1371/journal.pone.0173454

Figure Lengend Snippet: a) Glycosylation analysis of purified gp41. The protein was denatured and left untreated or incubated with Endoglycosidase H (EndoH) or with PNGase F (PNGase) as indicated. The exclusive sensitivity to PNGase F digestion suggests that the protein is properly post-translationally modified with N-linked sugar residues. b) Analysis of the purified protein using native PAGE, The migration of gp41 at ~160 kDa suggests a trimeric state of the protein. c) Binding of different monoclonal antibodies to recombinant gp41. Binding was measured in a capture ELISA at 4 or 37°C incubation temperature with indicated antibodies coated to the plate. 2nd, secondary anti HIS-HRP probe only, human, anti-gp120 control antibody, mouse, anti gp120 control antibody. For details on the monoclonal antibodies, please see . Different levels of binding and a temperature sensitive recognition pattern was observed for selected antibodies. d) Results of surface plasmon resonance studies using recombinant gp41 and various monoclonal antibodies. Single cycle kinetics were determined by capturing the indicated anti-gp41 antibodies to the chip via covalently linked anti-mouse or anti human IgG, followed by five injections of gp41 at increasing concentrations. Data shown (ΔRU) represent double referenced sensograms with relative signal intensities obtained by subtraction of flow cell 2 (gp41 antibody) and flow cell 1 (no antibody). Measurement curves (black) and fitted curves (red) are indicated.

Article Snippet: Affinity measurements were performed on a Biacore X100 device (GE Healthcare, Germany) at 37°C using the human or mouse antibody capture kit and CM5 sensor chips according to manufacturer’s recommendations (GE Healthcare, Germany).

Techniques: Purification, Incubation, Modification, Clear Native PAGE, Migration, Binding Assay, Recombinant, Enzyme-linked Immunosorbent Assay, SPR Assay