Journal: OncoTargets and therapy

Article Title: Identification of 1,2,4-Oxadiazoles-Based Novel EGFR Inhibitors: Molecular Dynamics Simulation-Guided Identification and in vitro ADME Studies

doi: 10.2147/OTT.S357765

Figure Lengend Snippet: IC 50 determination in ( A ) MCF7 and ( B ) MRC5; Three independent experiments were performed, and mean ± standard deviation was reported; GraphPad Prism software was used to calculate IC 50 values.

Article Snippet: MCF7 and MRC5 cell lines were used from ATCC; LDH Cytotoxicity Assay Kit, Item No. 601170 was used from Cayman Chemical; EGFR Kinase assay kit, Catalogues no. 40321 and 40323 were used from BPS Bioscience; Caco-2 (human colon carcinoma) cell line, borrowed from NCCS, Pune; which was initially procured from American Type Culture Collection (ATCC).

Techniques: Standard Deviation, Software

Journal: OncoTargets and therapy

Article Title: Identification of 1,2,4-Oxadiazoles-Based Novel EGFR Inhibitors: Molecular Dynamics Simulation-Guided Identification and in vitro ADME Studies

doi: 10.2147/OTT.S357765

Figure Lengend Snippet: IC 50 determination from EGFR kinase activity assay in ( A ) EFGR WT and ( B ) EGFR T790M ; Data represented as mean ± standard deviation; N = 3, GraphPad Prism software was used to calculate IC 50 values.

Article Snippet: MCF7 and MRC5 cell lines were used from ATCC; LDH Cytotoxicity Assay Kit, Item No. 601170 was used from Cayman Chemical; EGFR Kinase assay kit, Catalogues no. 40321 and 40323 were used from BPS Bioscience; Caco-2 (human colon carcinoma) cell line, borrowed from NCCS, Pune; which was initially procured from American Type Culture Collection (ATCC).

Techniques: Kinase Assay, Standard Deviation, Software

Journal: Cell reports

Article Title: CRACD Loss Induces Neuroendocrine Cell Plasticity of Lung Adenocarcinoma

doi: 10.1016/j.celrep.2024.114286

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: Cat# AA4389603 5-Bromo-2’-deoxyuridine (BrdU) Cayman Cat# 15580 Matrigel GFR, Phenol Red-free, LDEV-free Corning Cat# 356231 Ez-Cytox DoGenGio Cat# EZ-3000 Carboplatin Selleckchem Cat# S1215 Gefitinib SantaCruz Cat# sc-202166 Trametinib Cayman Chemical Cat# 16292 Pitavastatin Selleckchem Cat# S1759 Deposited data Cracd WT and Cracd KO scRNA-seq dataset This paper GEO: GSE229982 Human lung cancer scRNA-seq dataset Salcher et al. 30 https://doi.org/10.5281/zenodo.6411867 Experimental models: Cell lines HEK293T ATCC CRL-3216 A549 ATCC CRM-CCL-185 KP-1 Kim et al. 25 N/A Experimental models: Organisms/strains Mouse: C57BL/6J The Jackson Laboratory JAX: 000664; RRID: IMSR_JAX:000664 Mouse: B6.129S4-Krastm4Tyj/J The Jackson Laboratory JAX: 008179; RRID:IMSR_JAX:007676 Mouse: B6.129P2-Trp53tm1Brn/J The Jackson Laboratory JAX: 008462; RRID: IMSR_JAX:008462Info Mouse: C57BL/6J.

Techniques: Virus, Plasmid Preparation, Recombinant, Modification, cDNA Synthesis, Staining, Cell Recovery, Infection, Transfection, shRNA, Software

Journal: Brain Disorders

Article Title: Investigation for the involvement of microbial FliC and DING proteins in Alzheimer's Disease and Mild Cognitive Impairment and correlation with neurodegeneration and inflammation markers

doi: 10.1016/j.dscb.2023.100091

Figure Lengend Snippet: Fig. 4. Scatter plots of (a) calculated FliC levels against predicted FliC values, and (b) calculated DING proteins levels against predicted DING proteins levels, as analyzed by multivariable regression analysis. The graphs given represent the best-achieved models for the prediction of actual FliC and DING levels in CSF of all the donors enlisted in the current study, as affected by the levels of inflammatory markers COX-1 and COX-2, AD-related biomarkers Аβ42 and tau, and the microbial markers (a) DING or (b) FliC. Multilinear analysis was performed with the process of stepwise elimination, to evaluate the individual effect of the aforementioned markers. The calculated R squared values of the best-achieved models, their respective p values, and equations are provided in the respective plot. Statistical analysis was carried out by employing Graph Pad Prism 8.0 statistical software.

Article Snippet: Аnti-COX-1 (#160,108) and COX-2 (#160,107) rabbit polyclonal antibodies were from Cayman Chemical (Ann Arbor, MI, USA), while mouse monoclonal antibodies Anti-Аβ42 (#sc-28,365) and anti-tau (#AHB0042), were purchased from Santa Cruz (Dallas, TX, USA) and Invitrogen (Waltham, MA, USA), respectively.

Techniques: Software

Journal: Cell

Article Title: TDP-43 Triggers Mitochondrial DNA Release via mPTP to Activate cGAS/STING in ALS

doi: 10.1016/j.cell.2020.09.020

Figure Lengend Snippet: Elevated NF-κB and Type I IFN Signaling Because of TDP-43 In Vitro , Related to Figure 1 (A) Doxycycline (Dox inducible wild-type (WT) or ALS mutant (Q331K) TDP-43 was stably transduced into the mouse neuronal cell line NSC-34. 72 hr after TDP-43 induction, RNA was collected for qPCR of Ifnb1 , Ifna6 , Ifit1 and Tnf or (B) cells were lysed for western blot of p-TBK1, p-IRF3, p-p65, TDP-43 and actin as control. Blots are representative of three independent experiments. (C) IFNβ ELISA was performed on the supernatant from cells in (A). (D) Representative western blot of MAVS, PKR, cGAS, STING, FLAG, TDP-43 and Actin from cells in Figure. 1A. (E) IFNβ ELISA was performed on the supernatant from MEFs after 72hrs induction of WT and Q331K TDP-43. (F) cGAMP ELISA was performed on the lysates of human THP-1 cells overexpressing TDP-43 (WT or Q331K) after 72hrs induction. (G) Images of healthy control and TDP-43-ALS patient iPSC during differentiation into premature MNX1 + motor neurons (day 18) and further into mature MNX1 + /ChAT + motor neurons (day 28). (red - MNX1 or ChAT, green – β3-tubulin and blue - DAPI). (scale: 40 μm). (H) MNX1 and CHAT expression, measured by qPCR in undifferentiated (day 0) and differentiated iPSC-derived MNs (day 28). (I) Representative western blot of p-TBK1, total TBK1, TDP-43, TFAM and Actin for cells in (G) (lysed in 1% NP-40). Data are mean ± SEM from 3-4 independent experiments. P value s were calculated using one-way or two-way ANOVA. ∗ p < 0.05, ∗∗ p < 0.01, ∗∗∗ p < 0.001, ∗∗∗∗ p < 0.0001.

Article Snippet: 2′3′-cGAMP ELISA Kit , Cayman Chemical , Cat# 501700.

Techniques: In Vitro, Mutagenesis, Stable Transfection, Western Blot, Enzyme-linked Immunosorbent Assay, Expressing, Derivative Assay

Journal: Cell

Article Title: TDP-43 Triggers Mitochondrial DNA Release via mPTP to Activate cGAS/STING in ALS

doi: 10.1016/j.cell.2020.09.020

Figure Lengend Snippet: Inflammatory Signaling from TDP-43 Is Dependent on cGAS/STING (A) Vector alone (Ctrl) or plasmids encoding FLAG-tagged wild-type (WT) TDP-43 and the ALS mutation (Q331K) were transiently overexpressed in mouse embryonic fibroblasts (MEFs) genetically deficient for different innate immune sensors. Expression of Ifnb1 and Tnf was measured by qPCR after 72 h and was ablated only when cGAS or STING were genetically deficient. (B) Inducible TDP-43 constructs (WT or Q331K) were transduced into WT or STING CRISPR knockout (KO) THP-1 cells. 72 h after Dox induction, qPCR for IFNB1 and TNF was performed. (C) TDP-43-overexpressing THP-1 cells as in (B) were subjected to western blot analysis of inflammatory signaling pathways related to type I IFN and NF-κB. (D and E) The cGAS inhibitor RU.521 and STING inhibitor H-151 prevent IFNB1 and TNF induction from TDP-43-overexpressing THP-1 cells used in (B) and (E) iPSC-derived motor neurons from ALS patients compared with healthy controls (RU.521, 10 μM; H-151, 1 μM). DMSO was used as a solvent control (0). (F and G) Quantification of cGAMP by ELISA from (F) cell lysates of iPSC-derived motor neurons from healthy controls and ALS patients and from (G) post-mortem spinal cord samples of patients with sporadic ALS (n = 16) or MS (n = 12). Data are mean ± SEM, pooled from 3–5 independent experiments ([A], [B], and [D]–[F]) or representative of 3 independent experiments (C). The p values were calculated using two-way ANOVA to Ctrl in (A), (B), and (D) or unpaired t test between healthy control and ALS patient iPSC-MN lines (G298S, M337V, and A382T) in (E)–(G). ∗ p < 0.05, ∗∗ p < 0.01, ∗∗∗ p < 0.001, ∗∗∗∗ p < 0.0001. See also Figure S1 and .

Article Snippet: 2′3′-cGAMP ELISA Kit , Cayman Chemical , Cat# 501700.

Techniques: Plasmid Preparation, Mutagenesis, Expressing, Construct, CRISPR, Knock-Out, Western Blot, Derivative Assay, Enzyme-linked Immunosorbent Assay

Journal: Cell

Article Title: TDP-43 Triggers Mitochondrial DNA Release via mPTP to Activate cGAS/STING in ALS

doi: 10.1016/j.cell.2020.09.020

Figure Lengend Snippet:

Article Snippet: 2′3′-cGAMP ELISA Kit , Cayman Chemical , Cat# 501700.

Techniques: Recombinant, Transfection, Protease Inhibitor, Modification, Knock-Out, Mutagenesis, Activity Assay, Enzyme-linked Immunosorbent Assay, CRISPR, Software

Journal: Clinical and Translational Science

Article Title: Good Manufacturing Practice‐Grade of Megakaryocytes Produced by a Novel Ex Vivo Culturing Platform

doi: 10.1111/cts.12788

Figure Lengend Snippet: Confirmation of MK differentiation effect from SMC‐expanded hematopoietic stem cells. ( a ) Expansion folds of total cells, CD34 + cells, and CD34 + /CD38 ‐ cells after 5 days of expansion with SMC combination. ( b ) Percentage of CD34 + cells, CD34 + /CD38 ‐ cells, and CD41a + cells after 5 days of expansion with SMC combination. ( c ) Purity of CD41a + /CD42b + MKs differentiated from unexpanded or SMC‐expanded CD34 + cells over time. ( d ) Absolute number of total cells cultured from unexpanded or SMC‐expanded CD34 + cells over time. ( e ) Absolute number of CD41a + /CD42b + MKs cultured from unexpanded or SMC‐expanded CD34 + cells over time. ( f ) Yield of CD41a + /CD42b + MKs per input cord blood hematopoietic stem cells. Data are shown as mean ± SD, n = 3. *** P < 0.001. MKs, megakaryocytes; SMC, small‐molecule/cytokine cocktail.

Article Snippet: SMC was composed of stem cell factor (SCF 100 ng/mL; Biopharmagen, Suzhou, China), Fms‐related tyrosine kinase 3 ligand (100 ng/mL; Biopharmagen), thrombopoietin (TPO 40 ng/mL; Biopharmagen), interleukin (IL) −6 (15 ng/mL; Biopharmagen), stemregenin1 (SR1 1 μM; Selleck Chemicals, Houston, TX), CAY10433 (C433, 0.1 μM; Cayman Chemical, Ann Arbor, MI), and valproic acid (VPA 0.2 mM; Sigma‐Aldrich, St. Louis, MO).

Techniques: Cell Culture

Journal: Clinical and Translational Science

Article Title: Good Manufacturing Practice‐Grade of Megakaryocytes Produced by a Novel Ex Vivo Culturing Platform

doi: 10.1111/cts.12788

Figure Lengend Snippet: Optimization of culture conditions for producing MKs from small‐molecule/cytokine cocktail‐expanded hematopoietic stem cells. ( a ) Absolute number of CD41a + /CD42b + MKs after 9 days of culture with the indicated treatments. ( b ) Percentage of CD41a + and CD42b + cells after 9 days of culture with the indicated treatments. ( c ) Percentage of CD41a + and CD42b + cells over time induced by CC. ( d ) Absolute number of CD41a + /CD42b + MKs from day 7 to day 9 induced by SCF + TPO or CC. Data are shown as mean ± SD, n = 3. * P < 0.05, ** P < 0.01, *** P < 0.001. CC, cytokine cocktail; MKs, megakaryocytes; SCF, stem cell factor; SR1, stemregenin1; TPO, thrombopoietin; VPA, valproic acid.

Article Snippet: SMC was composed of stem cell factor (SCF 100 ng/mL; Biopharmagen, Suzhou, China), Fms‐related tyrosine kinase 3 ligand (100 ng/mL; Biopharmagen), thrombopoietin (TPO 40 ng/mL; Biopharmagen), interleukin (IL) −6 (15 ng/mL; Biopharmagen), stemregenin1 (SR1 1 μM; Selleck Chemicals, Houston, TX), CAY10433 (C433, 0.1 μM; Cayman Chemical, Ann Arbor, MI), and valproic acid (VPA 0.2 mM; Sigma‐Aldrich, St. Louis, MO).

Techniques:

Journal: Clinical and Translational Science

Article Title: Good Manufacturing Practice‐Grade of Megakaryocytes Produced by a Novel Ex Vivo Culturing Platform

doi: 10.1111/cts.12788

Figure Lengend Snippet: Scalable production and characterization analysis of mature MKs. ( a ) Schematic diagram of the stepwise culture protocol from cord blood CD34 + cells to MKs in the roller‐bottle culture system. ( b ) Absolute number of CD41a + /CD42b + MKs at the end of culture. ( c ) Cell size distribution of MKs measured by microscopy. Digital images of cells were captured and cell diameters were measured by Image J software. ( d ) Representative cell morphology of MKs and pro‐platelet‐like structures (red arrows). Scale bar = 20 μm. ( e ) Number of extending shafts from one adherent MK with ≧ 30 cells counted per condition. ( f ) DNA ploidy distribution of MKs. ( g ) The mRNA levels of megakaryopoiesis‐related gene assessed by real‐time quantitative polymerase chain reaction. β‐actin was used as an internal control. ( h ) Yield of CD41a + /CD42b + MKs per input cord blood hematopoietic stem cell. All data are shown as means ± SD, n = 3. * P < 0.05, ** P < 0.01, *** P < 0.001. CB, cord blood; MKs, megakaryocytes; SMC, small‐molecule/cytokine cocktail.

Article Snippet: SMC was composed of stem cell factor (SCF 100 ng/mL; Biopharmagen, Suzhou, China), Fms‐related tyrosine kinase 3 ligand (100 ng/mL; Biopharmagen), thrombopoietin (TPO 40 ng/mL; Biopharmagen), interleukin (IL) −6 (15 ng/mL; Biopharmagen), stemregenin1 (SR1 1 μM; Selleck Chemicals, Houston, TX), CAY10433 (C433, 0.1 μM; Cayman Chemical, Ann Arbor, MI), and valproic acid (VPA 0.2 mM; Sigma‐Aldrich, St. Louis, MO).

Techniques: Microscopy, Software, Real-time Polymerase Chain Reaction, Control

Journal: Cell reports

Article Title: Progesterone Receptor Serves the Ovary as a Trigger of Ovulation and a Terminator of Inflammation

doi: 10.1016/j.celrep.2020.03.060

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: PGE2 enzyme immunoassay (EIA) kit , Cayman , Cat# 514010.

Techniques: Blocking Assay, Plasmid Preparation, Recombinant, Staining, Chromatin Immunoprecipitation, Enzyme-linked Immunosorbent Assay, Software

Journal: eLife

Article Title: Sustained TNF-α stimulation leads to transcriptional memory that greatly enhances signal sensitivity and robustness

doi: 10.7554/eLife.61965

Figure Lengend Snippet:

Article Snippet: The Calcitonin Gene-Related Peptide (human) ELISA Kit (Cayman Chemical, USA 589101) and EnSight Multimode Plate Reader (PerkinElmer, USA) were used to measure CGRP concentration in the cell culture supernatants following the manufacturer’s instructions.

Techniques: Recombinant, Enzyme-linked Immunosorbent Assay, Software

Journal: Cell chemical biology

Article Title: Covalent Ligand Discovery Against Druggable Hotspots Targeted by Anti-Cancer Natural Products

doi: 10.1016/j.chembiol.2017.08.013

Figure Lengend Snippet: Key Resources Table

Article Snippet: Data and Software Availability N/A Additional Resources N/A REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit anti-Vinculin Abcam ab129002 Rabbit anti-p-Akt (S473) CST D9E Mouse anti-total Akt CST 40D4 Bacterial and Virus Strains Biological Samples Chemicals, Peptides, and Recombinant Proteins Withaferin A Sigma W4394 N-Hex-5-ynyl-2-iodo-acetamide (IAyne) Chess Gmbh 3187 Sequencing grade trypsin (porcine) Promega V5111 AcTEV protease Invitrogen 12575015 1,4-benzodioxan- 6-amine Sigma 193232 Chloroacetyl chloride Sigma 104493 Triethylamine Sigma T0886 Sodium Hydride Sigma 452912 Benzyl Bromide Sigma {"type":"entrez-nucleotide","attrs":{"text":"B17905","term_id":"2125654","term_text":"B17905"}} B17905 5,6,7,8-Tetrahydro-2-napthylamine Sigma 678864 Biotin-TEV-azide ( Weerapana et al., 2010 ) Critical Commercial Assays Malachite Green Phosphate Assay Kit Cayman 10009325 Hoechst 33342 dye Invitrogen H3570 Deposited Data Experimental Models: Cell Lines 231MFP ( Jessani et al., 2004 ) HCC38 ATCC CRL-2314 MCF7 ATCC HTB-22 MCF10A ATCC CRL-10317 HEK293T/17 ATCC CRL-11268 Experimental Models: Organisms/Strains C.B17 SCID mice Taconic CB17SC-F Oligonucleotides PPP2R1A SMARTPOOL siRNA Dharmacon L-010259-00-0005 Recombinant DNA PPP2R1A (Myc-DDK-tagged) expression plasmid Origene RC200056 PPP2R2A (Myc-DDK-tagged) expression plasmid Origene MR207137 Software and Algorithms IP2 proteomics pipeline 4.1.1 Integrated Proteomics Applications Other Streptavidin agarose ThermoFisher 20347 Open in a separate window Key Resources Table

Techniques: Virus, Recombinant, Sequencing, Expressing, Plasmid Preparation, Software