Journal: Materials Today Bio

Article Title: Age-mimicking hydrogel stiffness recapitulates the mechanical niche of the hippocampus to regulate neural stem cell senescence

doi: 10.1016/j.mtbio.2026.102985

Figure Lengend Snippet: Age-associated hippocampal stiffening and its replication via laminin-modified hydrogels . (a) The strategy of in vivo EdU labeling and marker immunostaining for analyzing NSC proliferation and neurogenesis across various mouse age groups. ( b ) Co-staining of GFAP, EdU, and DCX in the hippocampus across different ages. Representative images showing a reduction in active radial glia-like stem cells and neuroblasts/newborn neurons with increasing age. GFAP (green), DCX (red), EdU (gray), and DAPI (blue). Scale bar, 100 μm. ( c-e ) Quantification of active radial glia-like stem cells (GFAP + EdU + ) ( c ), neuroblasts (DCX + EdU + ) ( d ), and newborn neurons (DCX + ) (e) in the SGZ area as in ( b ). n = 3 or 4 mice per group. ( f ) Schematic showing the measurement of hippocampal tissue stiffness using the Pavone nanoindenter and the design of hyaluronic acid (HA)–laminin hydrogels with tunable stiffness to mimic hippocampal mechanical properties at different postnatal ages. Soft, medium, and stiff hydrogels correspond to the mechanical characteristics of hippocampal tissues from 1-, 4-, and 12-week-old mice, respectively. ( g ) Representative images of the dentate gyrus in mouse brain slices across age groups, captured under Pavone nanoindentation microscopy. The SGZ regions measured by the nanoindentation probe are demarcated by paired colorful dashed lines. ( h ) Quantification of Young’s modulus in the hippocampal SGZ region of mice at different ages using Pavone nanoindentation. Brain slices were obtained from four mice per age group. Measurements were taken from n = 227 spots (1 week), n = 149 spots (4 weeks), n = 241 spots (8 weeks), n = 157 spots (12 weeks). (i ) Schematic illustration of the synthesis of HA@HA and HA@HA–Laminin hydrogels. Hyaluronic acid (HA) was first crosslinked with adipic dihydrazide (ADH) using EDC/HCl activation under acidic conditions (pH 3–4) to form HA@HA. Subsequently, laminin was conjugated to the HA network via CDI-mediated coupling to generate HA@HA–Laminin hydrogels. ( j ) Quantification of Young’s modulus of Soft, Medium, and Stiff HA-laminin hydrogels using the same Pavone nanoindentation used for tissue (Soft hydrogel, n = 44 spots; Medium hydrogel, n = 37 spots; Stiff hydrogel, n = 29 spots). ( k ) Immunostaining of YAP1 protein shows the subcellular localization of YAP1 in NSCs cultured on HA-laminin hydrogels of varying stiffness. Dashed lines indicate representative cells with YAP1 predominantly in the cytoplasm (indicated by arrowheads), while solid lines represent cells with YAP1 primarily in the nucleus (indicated by arrows). Scale bar, 20 μm. ( l ) Quantification of YAP1 distribution in NSCs as in ( k ) (n = 4 wells). For all quantification data, statistical significance was determined using one-way ANOVA with Tukey’s multiple comparison tests. Data are presented as mean ± SD (∗∗p < 0.01, ∗∗∗p < 0.001, ∗∗∗∗p < 0.0001).

Article Snippet: The sections were incubated overnight at 4 °C with primary antibodies: GFAP (Sigma, AB5541, 1:1000), GFAP (Invitrogen, 13-0300, 1:1000) Doublecortin (Abcam, AB18723, 1:500) and Yap1 (Proteintech, 13584-1-AP, 1:800).

Techniques: Modification, In Vivo, Labeling, Marker, Immunostaining, Staining, Microscopy, Activation Assay, Cell Culture, Comparison

Journal: Developmental cell

Article Title: Flow-Dependent Endothelial YAP Regulation Contributes to Vessel Maintenance.

doi: 10.1016/j.devcel.2017.02.019

Figure Lengend Snippet: Figure 2. Yap1/TEAD-Dependent Transcription Becomes Active in Perfused Vessels (A) The constructs used to monitor Yap1 responses in EC by using fli1 promoter (EC-specific TEAD reporter). (B) Projection view of confocal stack fluorescence images of the trunk region in Tg(fli1:Gal4db-TEAD2DN-2A-mC);(UAS:GFP);(fli1:Myr-mC) WT (left) and ho- mozygous yap1ncv101 mutant embryos (right) at 50 hpf. Lateral views, anterior to the left. Upper panels, GFP images (green); lower panels, merged images (GFP, green; Myr-mC, red). White arrows indicate GFP signal-positive ECs of lumenized blood vessels. Representative images of four independent experiments are shown. (C) Projection view of confocal images of the trunk region in Tg(fli1:Gal4db-TEAD2DN-2A-mC);(UAS:GFP);(fli1:Myr-mC) embryos (at 32 and 50 hpf as indicated at the left) injected with Qdot 655 (white) into the heart to visualize perfused vessels. Left, GFP images (green); right, merged images (Qdot 655, white; GFP, green; Myr-mC, red). While a significant population of ECs of perfused vessels expresses GFP (white arrows), ECs of non-perfused vessels do not (magenta arrows). (D) Projection view of confocal images of the trunk region of fixed Tg(fli1:EGFP-YAP) embryos (at 27–50 hpf as indicated at the top) immunostained with anti-GFP antibody (green) together with DAPI (blue). White and orange arrowheads indicate EGFP-YAP in the cytoplasm and nucleus, respectively. (E) Graph shows percentage of the number of the ECs in which EGFP-YAP is excluded from the nucleus (N < C, white bars) and those in which EGFP-YAP is localized in the nucleus (N > C or N = C, black bars) at the indicated stages of the dorsal aorta (DA) and the arterial intersomitic vessels (aISVs) among the total number of observed ECs (indicated at the top) from 7 to 10 embryos. (F) Time-sequential two-photon images of ISVs in Tg(fli1:EGFP-YAP) embryos that were about to form lumen (from 37 hpf). Elapsed time (min) is indicated at the left. Yellow asterisks indicate newly formed lumens connecting to the circulation. White and orange arrowheads indicate EGFP-YAP in the cytoplasm and nucleus, respectively. Representative images of seven independent experiments are shown. Scale bars, 10 mm. See also Figure S2.

Article Snippet: After removing chorionic membrane and yolk sac, wild-type or homozygous yap1ncv101 mutant embryos were directly lysed in 1 x SDS sample buffer and subjected toWestern blot analysis with a rabbit anti-YAP antibody (Novus Biologicals) recognizing zebrafish Yap1 and with an anti-b-actin antibody.

Techniques: Construct, Mutagenesis, Injection

Journal: Developmental cell

Article Title: YAP Partially Reprograms Chromatin Accessibility to Directly Induce Adult Cardiogenesis in Vivo

doi: 10.1016/j.devcel.2019.01.017

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: Rabbit YAP1 antibody , Novus biologicals , Cat#NB110-583538.

Techniques: Virus, Plasmid Preparation, Recombinant, Imaging, SYBR Green Assay, Gene Expression, Control, Software, Next-Generation Sequencing

Journal: Theranostics

Article Title: Remodeling cancer stemness by collagen/fibronectin via the AKT and CDC42 signaling pathway crosstalk in glioma

doi: 10.7150/thno.50613

Figure Lengend Snippet: The integrin αvβ3/CDC42/F-actin/YAP/NUPR1/Nestin signaling pathway is activated in collagen/FN-cultured glioma cell (A) Expression of CDC42, F-actin, and β-actin in LN229 cells and T98G cells cultured in a flask or 3D Collagen/FN gel. (B) Expression of CDC42, F-actin, and β-actin in LN229 cells and T98G cells cultured in 3D Collagen/FN gel treated with PBS or SB273005 (5 nM, 24). (C) Cell fraction of cytosol (C) and nucleus (N) was analyzed by Western blotting. Expression of YAP1 in LN229 cells or LN229 CDC42 OE cells cultured in a flask or 3D Collagen/FN gel and treated with PBS or SB273005 (5 nM, 24 h). (D) Western blotting analysis of proteins immunoprecipitated (IP) with anti-YAP1 from LN229 cells cultured in a flask or 3D Collagen/FN gel for 48 h. (E) ChIP analysis of YAP1 or TEAD4 binding to the NUPR1 promoter in LN229 cells. YAP1 and TEAD4 increased the luciferase activity of the NUPR1 promoter in LN229 cells. (F) Expression of NUPR1 and Nestin in LN229 cells and T98G cells cultured in a flask or 3D Collagen/FN gel. (G) Expression of NUPR1in LN229 and T98G cells cultured in 3D Collagen/FN gel, treated with PBS or SB273005 (5 nM, 24 h) and transfected with CDC42 OE lentivirus. (H) Representative photographs of LN229-NC cells and LN229-CDC42 OE cells cultured in 3D Collagen/FN gel. Scale bar represents 20 µm (I) Representative photographs of LN229-NC cells and LN229-Nestin shRNA cultured in 3D Collagen/FN gel. Scale bar represents 20 µm (J) Quantification of colony sizes in (H) and (I) (K) Proliferation of 3D collagen/FN pre-cultured LN229-vec cells, LN229-CDC42 OE cells, LN229-NC cells, and LN229-Nestin shRNA cells (L) Colony formation of 3D collagen/FN pre-cultured LN229-vec cells, LN229-CDC42 OE cells, LN229-NC cells, and LN229-Nestin shRNA cells. Mean ± SEM, n.s, no significant difference, *p < 0.05, **p < 0.01.

Article Snippet: The proteins were immuno-precipitated with anti-YAP1 (MAB8094, RD, USA) or IgG conjugated to protein G agarose (11243233001, Roche, USA) at 4 ºC overnight.

Techniques: Cell Culture, Expressing, Western Blot, Immunoprecipitation, Binding Assay, Luciferase, Activity Assay, Transfection, shRNA

Journal: Nature Communications

Article Title: Tubular cell polyploidy protects from lethal acute kidney injury but promotes consequent chronic kidney disease

doi: 10.1038/s41467-022-33110-5

Figure Lengend Snippet: a Matrix plot of hPTC clusters showing hypertrophy genes. b Monocle2 pseudotime trajectory of hPTC clusters and “facet” trajectory (right) showing cluster distribution in order of appearance. c Monocle2 trajectory of hPTC coloured by pseudotime, mean ribosome gene expression difference, cell cycle phases, YAP1 mRNA accumulation, E2F-markers (E2F1, E2F7, E2F8) and YAP1-targets (ANKDR1, BIRC5, CTGF, CDK1, CCNB1, AKT1). d Cell cycle distribution of mCherry-hPTC. e Gene expression of sorted polyploid mCherry-hPTC over diploid mCherry-hPTC ( n = 4). f Matrix plot of cluster 9 characteristic genes. g Cell cycle distribution of mCherry-hPTC treated with DMSO or with verteporfin (VP). A representative experiment out of 6 is shown. h Percentage of polyploid mCherry-hPTC in DMSO-treated or VP-treated culture ( n = 6). Statistical significance was calculated by two-sided Mann-Whitney test; numbers on graphs represent exact p values. Box-and-whisker plots: line = median, box = 25–75%, whiskers = outlier (coef. 1.5).

Article Snippet: 100 μg of chromatin was diluted into ChIP dilution buffer containing protease and phosphatase inhibitor (Merck) and incubated with specific antibodies against YAP1 (10 μg/IP, Novus Biologicals, NB110-58358) or normal rabbit IgG (7 μg/IP Thermo Fisher Scientific, 02-6102) overnight at 4 °C.

Techniques: Gene Expression, MANN-WHITNEY, Whisker Assay

Journal: Nature Communications

Article Title: Tubular cell polyploidy protects from lethal acute kidney injury but promotes consequent chronic kidney disease

doi: 10.1038/s41467-022-33110-5

Figure Lengend Snippet: a UMAP of experimental time distribution and b cluster distribution of mouse PTC at day 2 (t2) and 30 (t30) after IRI. c UMAP showing ribosome gene expression difference and d hypertrophy genes (Top2a, Mcm7, Ccna2, Ccnb2, Tmsb10, S100a11). e UMAP showing E2F-markers (E2f1, E2f7, E2f8) and f YAP1-targets (Ankdr1, Birc5, Ctgf, Cdk1, Ccnb1, Akt1) in PTC. g Matrix plot of PTC at 2 and 30 days after IRI, showing hypertrophy genes. h Monocle2 trajectory of PTC clusters and trajectory of PTC coloured by pseudotime, mean ribosome gene expression difference, cell cycle phases, E2F-markers (E2f1, E2f7, E2f8) and YAP1-targets (Ankdr1, Birc5, Ctgf, Cdk1, Ccnb1, Akt1). i Monocle2 “facet” trajectory showing cluster distribution in order of appearance. j Violin plots showing ribosome distribution in clusters grouped by ribosome gene expression. Median distribution is represented by the white dot; the black bar in the centre of the violin represents the interquartile range between the first and third quartile; the black lines stretched from the bar represent the lower/upper adjacent values defined as first interquartile −1.5 and third interquartile +1.5, respectively. k Bar plot showing the binned normalized counts distribution in each cluster group. IRI ischemia reperfusion injury.

Article Snippet: 100 μg of chromatin was diluted into ChIP dilution buffer containing protease and phosphatase inhibitor (Merck) and incubated with specific antibodies against YAP1 (10 μg/IP, Novus Biologicals, NB110-58358) or normal rabbit IgG (7 μg/IP Thermo Fisher Scientific, 02-6102) overnight at 4 °C.

Techniques: Gene Expression

Journal: Nature Communications

Article Title: Tubular cell polyploidy protects from lethal acute kidney injury but promotes consequent chronic kidney disease

doi: 10.1038/s41467-022-33110-5

Figure Lengend Snippet: a qRT-PCR analysis of YAP1 targets in DMSO and verteporfin (VP) treated mCherry-hPTC ( n = 4). CTGF was used as a positive control. YAP1 was used as a negative control. # Significance between DMSO and VP treated mCherry-hPTC for each gene analysed, p = 0.028. b qRT-PCR quantification of E2F7, E2F8 and AKT1 in scramble, YAP1, and TAZ knock-down (KD) mCherry-hPTC ( n = 4). # Significance between scramble and YAP1-KD mCherry-hPTC for each gene analysed, p = 0.028. Scramble and TAZ-KD conditions are not significantly different. Chromatin immunoprecipitation assay showing YAP1 binding on c CTGF, d E2F7, e E2F8 and f AKT1 promoters in DMSO and VP treated mCherry-hPTC ( n = 4). #Significance between DMSO and VP treated mCherry-hPTC, p = 0.028. g KD efficiency of E2F7, E2F8 and AKT1 GapmeRs ( n = 4). #Significance between scramble and KD mCherry-hPTC, p = 0.028. h Cell cycle distribution of mCherry-hPTC transfected with scramble, E2F7, E2F8 and AKT1 GapmeRs. A representative experiment out of 4 is shown. i Percentage of polyploid mCherry-hPTC in scramble-treated, E2F7-KD, E2F8-KD and AKT1-KD cultures ( n = 4). # Significance between scramble and KD mCherry-hPTC, p = 0.028. hPTC: human proximal tubular cells. Statistical significance was calculated by two-sided Mann-Whitney test. Box-and-whisker plots: line = median, box = 25–75%, whiskers = outlier (coef. 1.5). Bar plots: line = mean, whisker = outlier (coef. 1.5).

Article Snippet: 100 μg of chromatin was diluted into ChIP dilution buffer containing protease and phosphatase inhibitor (Merck) and incubated with specific antibodies against YAP1 (10 μg/IP, Novus Biologicals, NB110-58358) or normal rabbit IgG (7 μg/IP Thermo Fisher Scientific, 02-6102) overnight at 4 °C.

Techniques: Quantitative RT-PCR, Positive Control, Negative Control, Knockdown, Chromatin Immunoprecipitation, Binding Assay, Transfection, MANN-WHITNEY, Whisker Assay

Journal: Nature Communications

Article Title: Tubular cell polyploidy protects from lethal acute kidney injury but promotes consequent chronic kidney disease

doi: 10.1038/s41467-022-33110-5

Figure Lengend Snippet: a FACS plots of Pax8/FUCCI2aR (Pax8/WT) ( n = 6) and Pax8/FUCCI2aR/YAP1ko (Pax8/YAP1 ko ) ( n = 6) showing diploid (2C), tetraploid (4C) and octaploid or greater (≥8C) TC. Colours match the FUCCI2aR reporter. b Percentage of cycling TC in healthy (t0) mice and after IRI ( n = 6). c Percentage of polyploid TC in healthy (t0) mice and after IRI ( n = 6). (§) Significance within Pax8/WT mice: t0 vs t2 p = 0.015, t0 vs t3 p = 0.002, t0 vs t5 p = 0.002, t2 vs t3 p = 0.002, t2 vs t5 p = 0.026, t3 vs t5 p = 0.002. (†) Significance within Pax8/YAP1 ko mice t0 vs t2 p = 0.002, t0 vs t3 p = 0.002, t2 vs t3 p = 0.04. d Glomerular filtration rate (GFR) measurement ( n = 8). (t0 = healthy, t2 = day 2 after IRI, t3 = day 3 after IRI, t5 = day 5 after IRI). e FACS plots of Pax8/WT ( n = 6) and Pax8/YAP1 ko ( n = 6) TC after nephrotoxic injury, showing diploid (2C), tetraploid (4C) and octaploid or greater (≥8C) TC. f Percentage of cycling TC in healthy (t0) mice and after nephrotoxic injury ( n = 6). g Percentage of polyploid TC in healthy mice (t0) and after nephrotoxic injury ( n = 6). h Percentage of dead TC after nephrotoxic injury ( n = 6). i Total FUCCI2aR TC number after nephrotoxic injury ( n = 4). j Survival analysis of mice after nephrotoxic injury. Kaplan-Meier analysis showed a significant difference at Log rank comparison X2 = 17.663, p = 0.0004 ( n = 24 Pax8/WT, n = 14 Pax8/YAP1 ko , none censored). k Blood urea nitrogen measurement ( n = 10). l Potassium level in the serum ( n = 10). m Kidney weight ( n = 18), p = 0.0000016. n Picture of Pax8/WT and Pax8/YAP1 ko kidneys 2 days after nephrotoxic injury. o Cell surface area of mCherry + TC at day 1 and 2 after nephrotoxic injury. 30 TC for each mouse (t1 n = 2; t2 n = 2) were counted. (t0 = healthy, t1 = day 1 after nephrotoxic AKI, t2 = day 2 after nephrotoxic AKI, p = 5.4 × 10 −10 ). Statistical significance was calculated by two-sided Mann-Whitney test; numbers on graphs represent exact p values or are provided in the legend. Box-and-whisker plots: line = median, box = 25–75%, whiskers = outlier (coef. 1.5).

Article Snippet: 100 μg of chromatin was diluted into ChIP dilution buffer containing protease and phosphatase inhibitor (Merck) and incubated with specific antibodies against YAP1 (10 μg/IP, Novus Biologicals, NB110-58358) or normal rabbit IgG (7 μg/IP Thermo Fisher Scientific, 02-6102) overnight at 4 °C.

Techniques: Filtration, Comparison, MANN-WHITNEY, Whisker Assay

Journal: Nature Communications

Article Title: Tubular cell polyploidy protects from lethal acute kidney injury but promotes consequent chronic kidney disease

doi: 10.1038/s41467-022-33110-5

Figure Lengend Snippet: a Representative pictures for immunohistochemistry of active-YAP1 staining. Bars 100 µm. A representative experiment out of 4 is shown. b Picture of Pax8/FUCCI2aR/SAV1 ko (Pax8/SAV1 ko ) and Pax8/WT kidneys. c Kidney weight in Pax8/WT ( n = 30) and Pax8/SAV1 ko mice ( n = 16), p = 7.2 × 10 −6 . FACS plots of TC in d Pax8/WT and in e Pax8/SAV1 ko mice, showing diploid (2C), tetraploid (4C) and octaploid or greater (≥8C) TC. Colours match the FUCCI2aR reporter ( n = 8). f Percentage of polyploid TC ( n = 8). g Representative pictures of Masson’s trichrome staining ( n = 8). Bars 100 µm. h Tubular score evaluated on Masson’s trichrome staining ( n = 8). i Sequential scanning of kidney section stained for fibronectin. DAPI counterstains nuclei. Bars 500 µm. j Quantification of fibronectin deposition by digital morphometry ( n = 8). k Senescence-associated β-galactosidase assay ( n = 8). Bars 100 µm. l Percentage of β-galactosidase + TC ( n = 8). m GFR measurement for 30 days ( n = 5). Statistical significance was calculated by two-sided Mann-Whitney test; numbers on graphs represent exact p values or are provided in the legend. Two-way ANOVA test of significance followed by Bonferroni post-test was employed for graph m. Data are expressed as mean ± SEM in graph m. Box-and-whisker plots: line = median, box = 25–75%, whiskers = outlier (coef. 1.5).

Article Snippet: 100 μg of chromatin was diluted into ChIP dilution buffer containing protease and phosphatase inhibitor (Merck) and incubated with specific antibodies against YAP1 (10 μg/IP, Novus Biologicals, NB110-58358) or normal rabbit IgG (7 μg/IP Thermo Fisher Scientific, 02-6102) overnight at 4 °C.

Techniques: Immunohistochemistry, Staining, MANN-WHITNEY, Whisker Assay

Journal: Nature Communications

Article Title: Tubular cell polyploidy protects from lethal acute kidney injury but promotes consequent chronic kidney disease

doi: 10.1038/s41467-022-33110-5

Figure Lengend Snippet: a Representative sequential scanning of kidney biopsy from a CKD after AKI patient showing CDK4, p-H3 and Phalloidin staining ( n = 45). DAPI counterstains nuclei. Bar 250 µm. b , b ’ Higher magnification of kidney section with split images. Bar 50 µm. c Percentage of polyploid TC in CKD after AKI ( n = 45) vs healthy patients ( n = 18). d Percentage of polyploid TC in “early” ( n = 14) and “late” groups ( n = 31). e Representative sequential scanning of kidney biopsy from a CKD after AKI patient showing YAP1 and Phalloidin staining ( n = 8). PicoGreen counterstains nuclei. Bar 250 µm. e ’ Higher magnification of kidney section with split images. Bar 25 µm. f DNA content quantification of YAP1 + nuclei vs YAP1 − nuclei of TC over diploid TC ( n = 8, for each biopsy 25 YAP1 + /Phalloidin + and 25 YAP1 − /Phalloidin + nuclei respectively were quantified), p = 2.19 × 1011. g Scoring of glomerular sclerosis (GS) and interstitial fibrosis and tubular atrophy (IFTA) in kidney biopsies of “late” group ( n = 16). h Representative sequential scanning of biopsies stained for fibronectin ( n = 16). DAPI counterstains nuclei. Bars 250 µm. i Linear correlation between polyploid TC and fibronectin deposition quantified by digital morphometry in the “late” group ( n = 16) was assessed by Pearson correlation coefficient. Statistical significance was calculated by two-sided Mann-Whitney test; numbers on graphs represent exact p values or are provided in the legend. Box-and-whisker plots: line = median, box = 25–75%, whiskers = outlier (coef. 1.5).

Article Snippet: 100 μg of chromatin was diluted into ChIP dilution buffer containing protease and phosphatase inhibitor (Merck) and incubated with specific antibodies against YAP1 (10 μg/IP, Novus Biologicals, NB110-58358) or normal rabbit IgG (7 μg/IP Thermo Fisher Scientific, 02-6102) overnight at 4 °C.

Techniques: Staining, MANN-WHITNEY, Whisker Assay

Journal: Nature Communications

Article Title: Tubular cell polyploidy protects from lethal acute kidney injury but promotes consequent chronic kidney disease

doi: 10.1038/s41467-022-33110-5

Figure Lengend Snippet: a Blood urea nitrogen measurement in healthy WT mice ( n = 5) and after nephrotoxic injury ( n = 7). b qRT-PCR for YAP1-downstream target CTGF in nephrotoxic injury after CA3 treatment ( n = 7). c FACS plots of TC in Pax8/FUCCI2aR mice after nephrotoxic injury, showing diploid (2C), tetraploid (4C) and octaploid or greater (≥8C) TC ( n = 8). Colours match the FUCCI2aR reporter. d Percentage of total and ≥8C cycling polyploid TC in Pax8/FUCCI2aR mice after nephrotoxic injury ( n = 8). e Total number of FUCCI2aR TC after nephrotoxic injury ( n = 8). f PAS staining in WT mice at day 30 after nephrotoxic injury ( n = 7). Bars 50 µm. g Senescence-associated β-galactosidase assay in WT mice at day 30 after nephrotoxic injury ( n = 7). Bars 100 µm. h Percentage of β-galactosidase + TC ( n = 7). i Sequential scanning of kidney sections stained for fibronectin in WT mice at day 30 after nephrotoxic injury ( n = 7). Bars 500 µm. DAPI counterstains nuclei. j Quantification of fibronectin deposition by digital morphometry ( n = 7). k Blood urea nitrogen measurement in Pax8/WT and Pax8/YAP1 ko mice after nephrotoxic injury ( n = 8). l FACS plots of TC after nephrotoxic injury showing diploid (2C), tetraploid (4C) and octaploid or greater (≥8C) TC ( n = 8). Colours match the FUCCI2aR reporter. m Percentage of total and ≥8C cycling polyploid TC (n = 8). n Percentage of β-galactosidase + TC ( n = 8). o Quantification of fibronectin deposition by digital morphometry ( n = 8). p Blood urea nitrogen measurement in Pax8/WT mice after nephrotoxic injury ( n = 7). q FACS plots of TC in Pax8/FUCCI2aR mice after nephrotoxic injury, showing diploid (2C), tetraploid (4C) and octaploid or greater (≥8C) TC ( n = 7). Colours match the FUCCI2aR reporter. r Percentage of total and ≥8C cycling polyploid TC ( n = 7). s Percentage of β-galactosidase + TC ( n = 7). t Quantification of fibronectin deposition by digital morphometry ( n = 7). t30: day 30 after nephrotoxic AKI. t4 recombination: doxycycline administered 4 days after nephrotoxic AKI. Senolytic treatment: quercetin+dasatinib. PAS: Periodic-acid schiff. Statistical significance was calculated by two-sided Mann-Whitney test; numbers on graphs represent exact p values. Data are expressed as mean ± SEM in graph a, k, and p. Box-and-whisker plots: line = median, box = 25–75%, whiskers = outlier (coef. 1.5).

Article Snippet: 100 μg of chromatin was diluted into ChIP dilution buffer containing protease and phosphatase inhibitor (Merck) and incubated with specific antibodies against YAP1 (10 μg/IP, Novus Biologicals, NB110-58358) or normal rabbit IgG (7 μg/IP Thermo Fisher Scientific, 02-6102) overnight at 4 °C.

Techniques: Quantitative RT-PCR, Staining, MANN-WHITNEY, Whisker Assay

Journal: Cancer research

Article Title: Recycling endosomes in mature epithelia restrain tumorigenic signaling

doi: 10.1158/0008-5472.CAN-18-4075

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: Mouse anti – YAP1 (clone 2F12) , Novus Biologicals , H00010413-M01, RRID: AB_10694607.

Techniques: Plasmid Preparation