Journal: bioRxiv

Article Title: Vascular endothelial growth factor-D improves lung vascular integrity during acute lung injury

doi: 10.1101/2024.12.16.628787

Figure Lengend Snippet: A) NICHES analysis of AFs, mesothelial cells, pericytes, gCap, and aCap in human microvascular niche yields a quantitative cell-cell signaling atlas of AF-aCap, AF-gCap, Mesothelial-aCap, Mesothelial-gCap, Pericyte-aCap, and Pericyte-gCap visualized by low-dimensional UMAP embedding. B) FeaturePlot of top differentially expressed L/R pairs ANGPT1 - TEK , SLIT2 - ROBO4 , VEGFD - KDR , BMP5-BMPR2 , ADM - RAMP2 , WNT5A - FZD6 , PTN - RACK1 , OXT - EDNRB , and ADCYAP1 - VIPR1 from NICHES analysis C) Top 10 differentially expressed L/R pairs between different cell-cell interaction signals processed through NICHES and plotted in DoHeatmap. D) Immunostaining of representative L/R pairs from AF to microvascular endothelial cells, including SLIT2 - ROBO4 , ADM - RAMP2 , BMP5 - BMPR2 , and VEGFD - VEGFR2 in human lung section. ITGA8 is a marker for AF; PRX is a marker for microvascular endothelial cells. Scale bar 20 μm.

Article Snippet: The protein levels of SLIT2, ADM, BMP5, and VEGFD in samples harvested from different timepoints were determined using corresponding ELISA kits: SLIT2 (# NB030384), ADM (# NBP2-78738), BMP5 (# NBP2-69996), VEGFD (# NBP2-78890), all from Novus Biologicals.

Techniques: Immunostaining, Marker

Journal: bioRxiv

Article Title: Vascular endothelial growth factor-D improves lung vascular integrity during acute lung injury

doi: 10.1101/2024.12.16.628787

Figure Lengend Snippet: A) C57Bl/6 mice were injected with LPS for 18 hours, followed by a collection of bronchioalveolar lavage (BAL) fluid. The expression level of VEGF-D was measured in the BAL fluid in mice with or without LPS challenge. B) Mice were injected with LPS, followed by treatment with VEGF-D (225 μg/kg). The BAL fluid and histological samples were collected after 18 hours of treatment. C) The FITC-albumin probe was injected retro-orbitally 16 hours after the LPS challenge. The amount of probe in BAL fluid was quantified after another 2 hours. The FITC-albumin levels in BAL fluid in the control and experimental groups were determined. D) The BAL fluid was spun down at 5,000 g for 10 minutes and resuspended in 300 μL of 1XPBS. The number of cells in the BAL from different conditions was determined using a hemacytometer. n = 12 – 14 per group. E) LPS and LPS+VEGFD lungs were excised, fixed in 4% paraformaldehyde, embedded in paraffin, and used for histochemical analysis after haematoxylin and eosin staining. Images are representative of 6–9 lung specimens for each condition. Scale bar 150 μm. F) Lung pathological index was performed by a blinded reviewer from 1 to 4, where 4 was the worst pathology. The score was used for both peribronchial and alveolar inflammation. The average of two scores was taken to obtain a range between 1 (no inflammation or pathology) and 4 (maximum inflammation and pathology). The lung pathological index was calculated in LPS and LPS+VEGFD conditions. G-I) The expression level of TNF-α and IL-6 were measured in BAL fluid from LPS and LPS+VEGFD conditions using corresponding ELISA kits. Mice without LPS challenge were used as control. N = 12 - 14 per treatment group. Data presented as mean ± SEM. * and ** indicate p<0.05 and p<0.01, respectively.

Article Snippet: The protein levels of SLIT2, ADM, BMP5, and VEGFD in samples harvested from different timepoints were determined using corresponding ELISA kits: SLIT2 (# NB030384), ADM (# NBP2-78738), BMP5 (# NBP2-69996), VEGFD (# NBP2-78890), all from Novus Biologicals.

Techniques: Injection, Expressing, Control, Staining, Enzyme-linked Immunosorbent Assay

Journal: Cell reports

Article Title: Impaired islet function and normal exocrine enzyme secretion occur with low inter-regional variation in type 1 diabetes

doi: 10.1016/j.celrep.2024.114346

Figure Lengend Snippet:

Article Snippet: Human Pancreatic Lipase ELISA Kit , Novus Biologicals , Cat# NB016815.

Techniques: Recombinant, Enzyme-linked Immunosorbent Assay, Software, Microscopy

Journal: iScience

Article Title: Amitriptyline revitalizes ICB response via dually inhibiting Kyn/Indole and 5-HT pathways of tryptophan metabolism in ovarian cancer

doi: 10.1016/j.isci.2024.111488

Figure Lengend Snippet: Expression of MYD88, IDO1, and IL4-I1 in EOC cells after LPS-induced combination with AMI (A−C) RT-qPCR and Western blot verification of MYD88 and IDO1 expression in A2780, OVCAR3, and ID8 EOC cells after LPS-induction (1 μg/ml). (D−F) mRNA expression of MYD88 and IDO1 by the combination of LPS with AMI in A2780, OVCAR3 (AMI: 50, 100μm) and ID8 (AMI: 30, 60μm) EOC cells. (G−H) MYD88 and IDO1 expression was not detected in A2780 EOC cells according to the pre-WB results. Therefore, only the expression of MYD88 and ID8 protein levels in OVCAR3 and ID8 were performed in the combined treatment. (Protein expression of MyD88 and IDO1 relative to Tubulin in EOC cells treated with different concentrations of drugs). (I) mRNA expression of IL4I1 on A2780, OVCAR3, and ID8 EOC cells after LPS combined with AMI treatment was analyzed by RT-qPCR, in which IL4I1, as a secreted protein, was detected in the levels in the EOC cells culture supernatant with Elisa. Each assay was performed in triplicate, and data are presented as mean ± SD ( n = 3).

Article Snippet: ELISA kit- TNF-α (Mouse) , Novus Biologicals , VAL609.

Techniques: Expressing, Quantitative RT-PCR, Western Blot, Enzyme-linked Immunosorbent Assay

Journal: iScience

Article Title: Amitriptyline revitalizes ICB response via dually inhibiting Kyn/Indole and 5-HT pathways of tryptophan metabolism in ovarian cancer

doi: 10.1016/j.isci.2024.111488

Figure Lengend Snippet: The killing activity of T lymphocytes against EOC cells and expression of CD39 after AMI stimulation (A) Expression of CD8 + CD39 + in T lymphocytes after exposure to different concentrations of AMI-treated (AMI concentrations refer to the preceding) EOC cells culture supernatants for 12 or 24 h as analyzed by FCM. (B) The killing activity of corresponding T lymphocytes (effector cells) to parental EOC cells (target cells) or AMI-treated EOC cells (target cells) shown are from the effector/target ratio at 1:1, 5:1, and 10:1. Supernatant 0h, 24h, and 48h represent the stimulation of T lymphocytes by supernatants collected at different times from EOC cells treated with AMI, respectively. (C) Measure the levels of TNF-α and IFN-γ in lymphocyte culture supernatants stimulated with AMI-treated EOC cell culture supernatants by Elisa assays. Each assay was performed in triplicate, and data are presented as mean ± SD ( n = 3). In Elisa results, ∗ indicates compared to the lymphocytes without any treatment (LN), # indicates compared to the lymphocytes stimulated with DMSO-treated EOC cell culture supernatant. #, ##, ### and #### indicates p < 0.05, p < 0.01, p < 0.001, and p < 0.0001 respectively.

Article Snippet: ELISA kit- TNF-α (Mouse) , Novus Biologicals , VAL609.

Techniques: Activity Assay, Expressing, Cell Culture, Enzyme-linked Immunosorbent Assay

Journal: iScience

Article Title: Amitriptyline revitalizes ICB response via dually inhibiting Kyn/Indole and 5-HT pathways of tryptophan metabolism in ovarian cancer

doi: 10.1016/j.isci.2024.111488

Figure Lengend Snippet: AMI reshapes TIME, the serum level of IL-4I1 and TRP metabolites peripheral blood of EOC-bearing mice (A and B) Tryptophan metabolites in the serum of unimplanted tumor-bearing mice (normal mice) and compared with implanted tumor-bearing mice (controls). (C and D) Tryptophan metabolites in the serum of normal mice (without implanted tumors) before and after the use of AMI. (E−H) EOC-bearing mice receiving PD-1 inhibitor - combined AMI therapy, LC-MS/MS was used to detect the amount of KYN, KYNA, TRP, and the ratio of KYN/TRP in the serum of EOC-bearing mice. (I) IL4I1 in EOC-bearing mice serum by Elisa. (J) LC-MS/MS was used to detect the amount of AHR ligands (I3P, IAA, I3A, and ILA) in the serum of EOC-bearing mice. Data are presented as mean ± SD ( n = 3).

Article Snippet: ELISA kit- TNF-α (Mouse) , Novus Biologicals , VAL609.

Techniques: Liquid Chromatography with Mass Spectroscopy, Enzyme-linked Immunosorbent Assay

Journal: iScience

Article Title: Amitriptyline revitalizes ICB response via dually inhibiting Kyn/Indole and 5-HT pathways of tryptophan metabolism in ovarian cancer

doi: 10.1016/j.isci.2024.111488

Figure Lengend Snippet:

Article Snippet: ELISA kit- TNF-α (Mouse) , Novus Biologicals , VAL609.

Techniques: Recombinant, Bicinchoninic Acid Protein Assay, Membrane, Isolation, Enzyme-linked Immunosorbent Assay, Lactate Dehydrogenase Assay, Software

Journal: American Journal of Respiratory and Critical Care Medicine

Article Title: Protection of Human Lung Cells against Hyperoxia Using the DNA Base Excision Repair Genes hOgg1 and Fpg

doi: 10.1164/rccm.200112-130oc

Figure Lengend Snippet: Figure 1. Construction and ex- pression of retroviral vector con- taining the hOgg1 or E. coli Fpg coding regions. (a) Mam- malian expression construct. From 5-end: LTR, spleen focus-form- ing virus (SFFV), multiple clone sites with the mIFN- insert (EcoRI and SalI sites), internal ri- bosome entry site, EGFP, and 3-end LTR. The transcript con- tains EGFP, the vector’s splice donor and splice acceptor sites, and BER gene. (b) Expression of EGFP in A549 cells. Phase contrast (A, C) and fluorescence (B, D) microscopy of retroviral- transduced A549 cells express- ing EGFP/hOgg1 (A, B—popu- lation; C, D—Clone 10) (400).

Article Snippet: Each blot was incubated with rabbit polyclonal antibodies to hOgg1 (Novus Biologicals, Littleton, CO) at a dilution of 1:500 at room temperature for 1–1.5 hours.

Techniques: Retroviral, Plasmid Preparation, Expressing, Construct, Virus, Fluorescence, Microscopy

Journal: American Journal of Respiratory and Critical Care Medicine

Article Title: Protection of Human Lung Cells against Hyperoxia Using the DNA Base Excision Repair Genes hOgg1 and Fpg

doi: 10.1164/rccm.200112-130oc

Figure Lengend Snippet: Figure 2. Expression and activity analysis of hOgg1-transduced A549 cells. (A) Northern blot analysis of hOgg1 mRNA. Clones 2, 5, 10, 15, and 16 expressing different amounts of hOgg1 mRNA. (B) Western blotting analysis of hOgg1 protein. Clones 2, 5, 10, 15, and 16 express- ing different amounts of hOgg1 protein. (C) hOgg1 enzyme activity detected by oligonucleotide cleavage assay. Control, oligonucleotide without cleavages; Clones 2, 5, 10, 15, and 16 expressing different amounts of enzyme activity. Ten micrograms of cell-free extract reacted with 2.5 pM -[32P]-dATP–labeled 8-oxoguanine–containing 23-bp oli- gonucleotide for 60 minutes at 37 C. The cleavage product of reaction was a 9-bp oligonucleotide. (D) Nouthern blot analysis of Fpg DNA ex- pression.

Article Snippet: Each blot was incubated with rabbit polyclonal antibodies to hOgg1 (Novus Biologicals, Littleton, CO) at a dilution of 1:500 at room temperature for 1–1.5 hours.

Techniques: Expressing, Activity Assay, Northern Blot, Clone Assay, Western Blot, Cleavage Assay, Control, Labeling

Journal: American Journal of Respiratory and Critical Care Medicine

Article Title: Protection of Human Lung Cells against Hyperoxia Using the DNA Base Excision Repair Genes hOgg1 and Fpg

doi: 10.1164/rccm.200112-130oc

Figure Lengend Snippet: Figure 4. Effect of variable hOgg1 expression on DNA damage in hy- peroxia. (A) Various A549 cell clones expressing different amounts of hOgg1 activity were incubated in 95% O2 for 72 hours, and DNA dam- age was detected by Comet assay (*p 0.05, compared with the vector control). (B) Relationship between hOgg1 enzymatic activity and resis- tance to hyperoxia. hOgg1 activity (oligonucleotide cleavage assay)

Article Snippet: Each blot was incubated with rabbit polyclonal antibodies to hOgg1 (Novus Biologicals, Littleton, CO) at a dilution of 1:500 at room temperature for 1–1.5 hours.

Techniques: Expressing, Clone Assay, Activity Assay, Incubation, Single Cell Gel Electrophoresis, Plasmid Preparation, Control, Cleavage Assay

Journal: American Journal of Respiratory and Critical Care Medicine

Article Title: Protection of Human Lung Cells against Hyperoxia Using the DNA Base Excision Repair Genes hOgg1 and Fpg

doi: 10.1164/rccm.200112-130oc

Figure Lengend Snippet: Figure 3. Effect of DNA BER protein expression in A549 cell population on O2-induced DNA damage. A549 cells expressing either hOgg1 or Fpg were in- cubated in 95% O2 or room air for 72 hours. DNA damage was measured by Comet assay, and tail length was defined as the distance between the leading edge of the nucleus and the end of the tail. (A) A549 cell population expressing hOgg1. (B) Comet assay showing de- creased DNA damage in hOgg1- transduced A549 pop- ulation. (C) A549 cell population ex- pressing Fpg. *p 0.05, com- pared with the vector control.

Article Snippet: Each blot was incubated with rabbit polyclonal antibodies to hOgg1 (Novus Biologicals, Littleton, CO) at a dilution of 1:500 at room temperature for 1–1.5 hours.

Techniques: Expressing, Single Cell Gel Electrophoresis, Plasmid Preparation, Control

Journal: American Journal of Respiratory and Critical Care Medicine

Article Title: Protection of Human Lung Cells against Hyperoxia Using the DNA Base Excision Repair Genes hOgg1 and Fpg

doi: 10.1164/rccm.200112-130oc

Figure Lengend Snippet: Figure 6. Effect of variable hOgg1 expression on cell survival in hyper- oxia. (A) A549 cell clones expressing different amounts of hOgg1 were incubated in hyperoxia, and cell survival was measured by colony form- ing assay (*p 0.05, compared with the vector control). (B) Relation- ship between hOgg1 enzymatic activity and resistance to hyperoxia- induced toxicity (r 0.55, p 0.05).

Article Snippet: Each blot was incubated with rabbit polyclonal antibodies to hOgg1 (Novus Biologicals, Littleton, CO) at a dilution of 1:500 at room temperature for 1–1.5 hours.

Techniques: Expressing, Clone Assay, Incubation, Plasmid Preparation, Control, Activity Assay

Journal: American Journal of Respiratory and Critical Care Medicine

Article Title: Protection of Human Lung Cells against Hyperoxia Using the DNA Base Excision Repair Genes hOgg1 and Fpg

doi: 10.1164/rccm.200112-130oc

Figure Lengend Snippet: Figure 5. Effect of DNA BER protein expression on cell survival. A549 cells expressing hOgg1 or Fpg were incubated in 95% O2, and cell sur- vival was measured by colony forming assay. Cell survival was expressed as percentage of surviving colonies in hyperoxia to surviving colonies in room air. (A) A549 cell population expressing hOgg1. (B) A549 cell pop- ulation expressing Fpg. *p 0.05, compared with the vector control.

Article Snippet: Each blot was incubated with rabbit polyclonal antibodies to hOgg1 (Novus Biologicals, Littleton, CO) at a dilution of 1:500 at room temperature for 1–1.5 hours.

Techniques: Expressing, Incubation, Plasmid Preparation, Control

Journal: American Journal of Respiratory and Critical Care Medicine

Article Title: Protection of Human Lung Cells against Hyperoxia Using the DNA Base Excision Repair Genes hOgg1 and Fpg

doi: 10.1164/rccm.200112-130oc

Figure Lengend Snippet: Figure 7. Protection from hydrogen peroxide–induced toxicity. Detection of DNA damage by the Comet assay: (A) A549 cell population expressing hOgg1. (B) A549 cell population express- ing Fpg. Detection of cell survival by the colony forming assay: (C) A549 cell population expressing hOgg1. (D) A549 cell pop- ulation expressing Fpg. *p 0.05, compared with the vector control.

Article Snippet: Each blot was incubated with rabbit polyclonal antibodies to hOgg1 (Novus Biologicals, Littleton, CO) at a dilution of 1:500 at room temperature for 1–1.5 hours.

Techniques: Single Cell Gel Electrophoresis, Expressing, Plasmid Preparation, Control