Journal: Journal of Clinical Medicine

Article Title: Effects of Caloric Restriction with Protein Supplementation on Plasma Protein Profiles in Middle-Aged Women with Metabolic Syndrome—A Preliminary Open Study

doi: 10.3390/jcm8020195

Figure Lengend Snippet: Absolute changes in the plasma levels of several proteins in female patients with metabolic syndrome after the 12-week dietary interventions analysed using an ELISA kit: caloric restriction (CR) or caloric restriction with protein supplementation (CRPS). Box plots represent values between the 25th and 75th percentile. The solid line within the box is the median value, and the symbol within the box is the mean value. The circles are values that are 1.5 times the interquartile range above the upper quartile and below the lower quartile. Units of raw data are ng/mL. * p < 0.05 in comparison with postintervention measurements between the groups and according to the Quade’s test with baseline measurements as covariates.

Article Snippet: Commercial available plasma C4b-binding protein (C4BP), complement component C6 (C6), complement component C8 gamma chain (C8G), and vitamin K–dependent protein S (PROS) were respectively measured using the following commercial ELISA kits: (1) C4BP ELISA kit (#EC2202-1, Assaypro, St. Charles, MO, USA); (2) C6 ELISA kit (#EC6101-1, Assaypro, St. Charles, MO, USA); (3) C8G ELISA kit (#EC8120-1, Assaypro, St. Charles, MO, USA); and (4) PROS ELISA kit (#AB190808, Abcam, Cambridge, UK).

Techniques: Clinical Proteomics, Enzyme-linked Immunosorbent Assay, Comparison

Journal: Journal of Clinical Medicine

Article Title: Effects of Caloric Restriction with Protein Supplementation on Plasma Protein Profiles in Middle-Aged Women with Metabolic Syndrome—A Preliminary Open Study

doi: 10.3390/jcm8020195

Figure Lengend Snippet: Heat maps showing different baseline and postintervention protein plasma levels. A significant correlation was observed with the selected increment clinical variables between baseline and postintervention in the CR ( A ) and CRPS ( B ) groups. The left red–blue scale heatmaps show the estimates of Spearman’s correlation coefficients, whereas the right yellow-scale heat maps show the p -values for the same protein–clinical variable pairs. AG: android/gynoid fat ratio, ALB: albumin, TBF: total body fat, BMI: body mass index, CRP: C-reactive protein, FBG: fasting blood glucose, HOMA: homeostatic model assessment for insulin resistance, IL6: interleukin 6, LDL-C: low-density lipoprotein cholesterol, MONO: mononuclear, NEU: neutrophil, PLA: platelet, QUICKI: quantitative insulin sensitivity check index, TC: total cholesterol, WBC: white blood cell, A2M: alpha-2-macroglobulin, C1RL: Complement C1r subcomponent–like protein, C4BPA: C4b-binding protein alpha chain, C6: complement component C6, C8G: complement component C8 gamma chain, Protein S: vitamin K-dependent protein S, CR: caloric restriction, CRPS: caloric restriction with protein supplementation.

Article Snippet: Commercial available plasma C4b-binding protein (C4BP), complement component C6 (C6), complement component C8 gamma chain (C8G), and vitamin K–dependent protein S (PROS) were respectively measured using the following commercial ELISA kits: (1) C4BP ELISA kit (#EC2202-1, Assaypro, St. Charles, MO, USA); (2) C6 ELISA kit (#EC6101-1, Assaypro, St. Charles, MO, USA); (3) C8G ELISA kit (#EC8120-1, Assaypro, St. Charles, MO, USA); and (4) PROS ELISA kit (#AB190808, Abcam, Cambridge, UK).

Techniques: Clinical Proteomics, Binding Assay

Journal: Frontiers in Oncology

Article Title: Establishment, characterization, and drug screening of low-passage patient individual non-small cell lung cancer in vitro models including the rare pleomorphic subentity

doi: 10.3389/fonc.2023.1089681

Figure Lengend Snippet: Antibodies used for flow cytometry.

Article Snippet: LYPD3 , APC , Sino Biological Europe GmbH, Düsseldorf, Germany , 11836-H08H.

Techniques: Cytometry

Journal: Frontiers in Oncology

Article Title: Establishment, characterization, and drug screening of low-passage patient individual non-small cell lung cancer in vitro models including the rare pleomorphic subentity

doi: 10.3389/fonc.2023.1089681

Figure Lengend Snippet: Flow cytometry. Histogram overlays of unstained controls (dotted lines for all three cell lines) and measurements for HROLu55 (green), HROLu22 (blue), and HROBML01 (red) for the epitopes CD326, PD-L1, EGFR, CD26, LYPD3, DSG3, CCD59, CD27, and CD90 are shown.

Article Snippet: LYPD3 , APC , Sino Biological Europe GmbH, Düsseldorf, Germany , 11836-H08H.

Techniques: Flow Cytometry

Journal: Molecular Neurobiology

Article Title: Novel Exosome Biomarker Candidates for Alzheimer’s Disease Unravelled Through Mass Spectrometry Analysis

doi: 10.1007/s12035-022-02762-1

Figure Lengend Snippet: AACT exosomal levels in dementia and AD cases monitored by distinct antibody-based approaches. AACT levels were assessed through immunoblot analysis or commercial ELISA assays in serum-derived exosomes from Controls (CDR = 0 and MMSE −) and individuals with dementia (CDR ≥ 1 and MMSE +) from UA-cohort ( a , d ), and AD clinically diagnosed cases from UA-cohort ( b , e ) or UMG-cohort ( c , f ). For WB, each point represents the relative densitometry ratio. For ELISA, each point represents the mean concentration value obtained for each individual. The solid horizontal line shows mean, and error bars indicates standard deviations. Abbreviations: AD, Alzheimer’s disease; C, Controls; CDR, Clinical Dementia Rate; MMSE, Mini-Mental State Examination. * p ≤ 0.05

Article Snippet: Further, AACT and C4BPα levels were also evaluated by enzyme-linked immunosorbent assay (ELISA), in serum-derived exosomes of the same individuals, using the commercial Human AACT ELISA Kit (ab217779; Abcam) or the Human C4 binding protein A ELISA Kit (NBP2-60,550; Novus Biologicals), according to manufacturer’s instructions.

Techniques: Western Blot, Enzyme-linked Immunosorbent Assay, Derivative Assay, Concentration Assay

Journal: PeerJ

Article Title: A new 12-gene diagnostic biomarker signature of melanoma revealed by integrated microarray analysis

doi: 10.7717/peerj.49

Figure Lengend Snippet: The 200 genes with largest s r values that were selected as the proposed gene signature of melanoma.

Article Snippet: These included: COL11A1 (Abcam, ab64883), CXCL13 (R & D Systems, AF801), PTPRF (NeuroMab, 75-193), SHC4 (Proteintech, 12641-1-AP), which were incubated overnight at 4 °C followed by secondary antibody (1:300) for 1 h (donkey anti-goat (Invitrogen, A11055), donkey anti-mouse (Invitrogen, A21202), donkey anti-rabbit (Invitrogen, A21206), Alexa green).

Techniques:

Journal: PeerJ

Article Title: A new 12-gene diagnostic biomarker signature of melanoma revealed by integrated microarray analysis

doi: 10.7717/peerj.49

Figure Lengend Snippet: Pathways where the 12 genes closely interact with melanoma driver genes (BRAF, NRAS, cKIT and MITF).

Article Snippet: These included: COL11A1 (Abcam, ab64883), CXCL13 (R & D Systems, AF801), PTPRF (NeuroMab, 75-193), SHC4 (Proteintech, 12641-1-AP), which were incubated overnight at 4 °C followed by secondary antibody (1:300) for 1 h (donkey anti-goat (Invitrogen, A11055), donkey anti-mouse (Invitrogen, A21202), donkey anti-rabbit (Invitrogen, A21206), Alexa green).

Techniques: Infection

Journal: PeerJ

Article Title: A new 12-gene diagnostic biomarker signature of melanoma revealed by integrated microarray analysis

doi: 10.7717/peerj.49

Figure Lengend Snippet: A new signaling network for melanoma. The signaling network is based on the complex interactions of the 12 signature genes (labeled in red) and the 4 melanoma driver genes ( BRAF, cKit, NRAS, MITF ) in 3 signaling pathways (MAPK, Ca 2+ and WNT). Nine of these 12 genes (i.e., EGFR, FGFR2, FGFR3, IL8, PTPRF, CXCL13, TNC, COL11A1, and SHC4 ) closely interact with three driver genes ( NRAS, BRAF, and MITF ) in the MAPK signaling pathway: the remaining 3 genes include WNT4, PPP2R2C and CHP2 , which also play important roles in WNT and Ca 2+ signaling pathways.

Article Snippet: These included: COL11A1 (Abcam, ab64883), CXCL13 (R & D Systems, AF801), PTPRF (NeuroMab, 75-193), SHC4 (Proteintech, 12641-1-AP), which were incubated overnight at 4 °C followed by secondary antibody (1:300) for 1 h (donkey anti-goat (Invitrogen, A11055), donkey anti-mouse (Invitrogen, A21202), donkey anti-rabbit (Invitrogen, A21206), Alexa green).

Techniques: Labeling, Protein-Protein interactions

Journal: PeerJ

Article Title: A new 12-gene diagnostic biomarker signature of melanoma revealed by integrated microarray analysis

doi: 10.7717/peerj.49

Figure Lengend Snippet: Immunocytochemical analysis of human melanocytes and melanoma cells in vitro . COL11A1, CXCL13, PTPRF and SHC4 proteins were upregulated (green fluorescence) in melanoma cells. Inserts show higher power views of expression, including when associated with the perinuclear region of the cell.

Article Snippet: These included: COL11A1 (Abcam, ab64883), CXCL13 (R & D Systems, AF801), PTPRF (NeuroMab, 75-193), SHC4 (Proteintech, 12641-1-AP), which were incubated overnight at 4 °C followed by secondary antibody (1:300) for 1 h (donkey anti-goat (Invitrogen, A11055), donkey anti-mouse (Invitrogen, A21202), donkey anti-rabbit (Invitrogen, A21206), Alexa green).

Techniques: In Vitro, Fluorescence, Expressing

Journal: PeerJ

Article Title: A new 12-gene diagnostic biomarker signature of melanoma revealed by integrated microarray analysis

doi: 10.7717/peerj.49

Figure Lengend Snippet: Immunohistochemical analaysis of COL11A1, CXCL13, PTPRF and SHC4 in normal human skin epidermis. Melanocytes were detected with an antibody (NKi/beteb) raised against the melanocyte-specific marker gp100 (red, arrows). COL11A1, CXCL13, PTPRF (shown in green) were not detected in normal epidermal melanocytes. SHC4 was expressed strongly in proliferating keratinocytes in the basal layer on the epidermis, and to some extent also in melanocytes (i.e. double positive cells in orange-yellow).

Article Snippet: These included: COL11A1 (Abcam, ab64883), CXCL13 (R & D Systems, AF801), PTPRF (NeuroMab, 75-193), SHC4 (Proteintech, 12641-1-AP), which were incubated overnight at 4 °C followed by secondary antibody (1:300) for 1 h (donkey anti-goat (Invitrogen, A11055), donkey anti-mouse (Invitrogen, A21202), donkey anti-rabbit (Invitrogen, A21206), Alexa green).

Techniques: Immunohistochemical staining, Marker

Journal: PeerJ

Article Title: A new 12-gene diagnostic biomarker signature of melanoma revealed by integrated microarray analysis

doi: 10.7717/peerj.49

Figure Lengend Snippet: Immunohistochemical analaysis of COL11A1, CXCL13, PTPRF and SHC4 in primary and metastatic melanoma. Double staining of test protein (shown in green) and pigment cell lineage-specific marker gp100 (in red, arrows). Both immunoreactivites were merged with yellow/orange fluorescence indicating co-localization of these proteins in melanoma cells.

Article Snippet: These included: COL11A1 (Abcam, ab64883), CXCL13 (R & D Systems, AF801), PTPRF (NeuroMab, 75-193), SHC4 (Proteintech, 12641-1-AP), which were incubated overnight at 4 °C followed by secondary antibody (1:300) for 1 h (donkey anti-goat (Invitrogen, A11055), donkey anti-mouse (Invitrogen, A21202), donkey anti-rabbit (Invitrogen, A21206), Alexa green).

Techniques: Immunohistochemical staining, Double Staining, Marker, Fluorescence

Journal: The FEBS journal

Article Title: Stimulation of Pol III-dependent 5S rRNA and U6 snRNA gene expression by AP-1 transcription factors.

doi: 10.1111/febs.14104

Figure Lengend Snippet: Fig. 1: In silico prediction and validation of putative AP-1 binding sites in Pol III-target gene

Article Snippet: All rights reserved. subunit of RNA polymerase III (POLR3D) were obtained from Proteintech (Rosemont, IL, USA).

Techniques: In Silico, Biomarker Discovery, Binding Assay

Journal: The FEBS journal

Article Title: Stimulation of Pol III-dependent 5S rRNA and U6 snRNA gene expression by AP-1 transcription factors.

doi: 10.1111/febs.14104

Figure Lengend Snippet: Fig. 5: Recruitment of AP-1 transcription factors to Pol III-transcribed gene promoters. (A)

Article Snippet: All rights reserved. subunit of RNA polymerase III (POLR3D) were obtained from Proteintech (Rosemont, IL, USA).

Techniques:

Journal: The FEBS journal

Article Title: Stimulation of Pol III-dependent 5S rRNA and U6 snRNA gene expression by AP-1 transcription factors.

doi: 10.1111/febs.14104

Figure Lengend Snippet: Fig. 6: Epigenetic changes at Pol III-transcribed gene promoters mediated by AP-1 factors.

Article Snippet: All rights reserved. subunit of RNA polymerase III (POLR3D) were obtained from Proteintech (Rosemont, IL, USA).

Techniques:

Journal: Frontiers in Immunology

Article Title: Toxoplasma gondii Recruits Factor H and C4b-Binding Protein to Mediate Resistance to Serum Killing and Promote Parasite Persistence in vivo

doi: 10.3389/fimmu.2019.03105

Figure Lengend Snippet: Toxoplasma gondii recruits AP regulator Factor H and CP/LP regulator C4b-binding protein to the parasite surface. 1 × 10 6 Type II ME49 parasites were incubated in 10% NHS for 0–60 min at 37°C. Western blots (left panels) of C4BP (A) (rabbit α-human C4BP, AssayPro 1:500) and FH (B) (goat α-human Factor H, CompTech 1:20,000) binding. Serum or purified protein was used as a positive control and heat inactivated serum (hiNHS) was used as a negative control. Blots were stripped and re-probed with anti-SRS29B (SAG1) for loading control. Images are from one representative of three independent experiments with similar results. Right panels (A,B) represent flow cytometric assays of C4BP (A) and FH (B) binding to the parasite surface for 0–60 min. Heat inactivated NHS (hiNHS) serum was used as a negative control. Flow cytometry data are shown as mean ± SEM from three independently performed experiments.

Article Snippet: The following antibody dilutions were used: rabbit anit-SRS29B (formerly SAG1, 30 kDa) 1:5,000, rabbit anti-C4BP (alpha chain, 70 kDa) (AssayPro) 1:1,000, goat anti-C3 (C3, C3b, iC3b) and goat anti-Factor H (full length protein, 155 kDa) antibodies (CompTech) were both used at 1:20,0000, anti-rabbit HRP 1:10,000 (Sigma), and anti-goat HRP 1:5,000 (Santa Cruz Biotechnology, Inc.).

Techniques: Binding Assay, Incubation, Western Blot, Purification, Positive Control, Negative Control, Flow Cytometry

Journal: Frontiers in Immunology

Article Title: Toxoplasma gondii Recruits Factor H and C4b-Binding Protein to Mediate Resistance to Serum Killing and Promote Parasite Persistence in vivo

doi: 10.3389/fimmu.2019.03105

Figure Lengend Snippet: Factor H and C4b-binding protein contribute to serum resistance. Factor H (FH) and C4b-binding protein (C4BP) were blocked by pre-incubating 10% NHS with 1:100 or 1:400 dilution of goat α-human FH (CompTech) or rabbit α-human C4BP (AssayPro) for 1 h on ice before adding to 1 × 10 6 parasites and incubating for 60 min at 37°C. Flow cytometric analysis of C5b-9 formation (A) and parasite viability (B) after 60' in 10% NHS blocked with 1:100 or 1:400 of α-C4BP (gray bars) α-FH (open bars) antibodies. 10% heat inactivated serum (hiNHS) was used a negative control. Flow cytometry data are shown as mean ± SEM from three independently performed experiments. Significant differences between the compared groups was determined using multiple Student's t test with Holm-Sidak correction for multiple comparisons, * p < 0.05, *** p < 0.001, **** p < 0.0001.

Article Snippet: The following antibody dilutions were used: rabbit anit-SRS29B (formerly SAG1, 30 kDa) 1:5,000, rabbit anti-C4BP (alpha chain, 70 kDa) (AssayPro) 1:1,000, goat anti-C3 (C3, C3b, iC3b) and goat anti-Factor H (full length protein, 155 kDa) antibodies (CompTech) were both used at 1:20,0000, anti-rabbit HRP 1:10,000 (Sigma), and anti-goat HRP 1:5,000 (Santa Cruz Biotechnology, Inc.).

Techniques: Binding Assay, Negative Control, Flow Cytometry