EMBO/sd-character-level-ner huggingface dataset:
Figure 4A Telomere restriction fragment analysis of genomic DNA from wt cells and cells carrying two tiTELs (CAF110) grown for 24 h in EMM medium containing THI and TSA as indicated. DNA was digested with HindIII and hybridized first with a nmt1 probe and successively with a telomeric probe. Marker molecular weights are on the left in kilobases. Numbers at the bottom indicate gel lanes. B Genomic DNA from cells carrying two tiTELs and deleted for trt1+ (CAF113) was analyzed as in (A). Marker molecular weights are on the left in kilobases. Numbers at the bottom indicate gel lanes. C ter1+ cells carrying two tiTELs (CAF110, left panel) or trt1Δ cells carrying one tiTEL (MKSP2104, central panel) were cultured in EMM medium in presence of THI for 24 h (THI+) or in absence of THI for 24, 48 or 72 h. In the right panel, cells carrying two tiTELs (CAF110) were treated with TSA for 24 h in the presence or absence of THI. TiTEL telomeric sequences were amplified from genomic DNA and sequenced using a PacBio platform. The statistical analysis for each set of conditions is displayed above each panel. P values for each comparison were derived from the Student's t test between each condition and the THI+ sample using Welch's correction when appropriate. The new population of longer tiTELs appearing in trt1Δ cells upon prolonged transcription induction is indicated in red (center panel).
Figure 3(A) Immunofluorescence staining against CD16/CD32 or Arg-1 in Cb of ASMko mice (red). Microglia were identified by F4/80 or Iba-1 staining (green). DAPI staining shows cell nuclei. Scale bar, 50 μm. (B) Mean ± SEM number of Arg-1 and CD16/CD32 positive microglia per area in Cb from ASMko and wt mice (n = 6 mice per group). (C) Mean ± SEM levels of TNFa protein in the Cb from ASMko and wt mice measured by ELISA (n = 7 mice per group, Student´s t-test). (D) Mean ± SEM levels of TNFa mRNA in Cb of ASMko and wt mice determined by qRT-PCR (n = 7 mice per group, Student´s t-test). (E) Survival after LPS challenge in ASMko and wt mice treated or not with dexamethasone (n = 8 mice per group). (F) Immunofluorescence staining against MBP in Cb of ASMko and wt mice treated or not with PLX for 2 months. Scale bar, 50 μm. (G) Mean ± SEM MBP intensity in the different mouse groups (n = 7 mice per group, Two-way Anova, Bonferroni post hoc). (H) High magnification of immunofluorescence staining against MBP in ASMko mice treated or not with PLX for 2 months. White arrows show MBP aggregates indicative of myelin debris. Scale bar, 50 μm. (I) Mean ± SEM number of MBP aggregates per cell area in the different mouse groups (n = 7 mice per group, Student´s t-test). (J) High magnification images and their 3D rendered replicates from cerebellar wt and ASMko microglia identified by Iba-1 and of the myelin marker MBP. Scale bars, 10 μm. (K) Amplified image and its 3D rendered replicate of amoeboid microglia containing myelin debris (arrowheads) in the ASMko cerebellum. The orthogonal projection of this cell in the lower panels confirms the presence of the myelin debris inside the cell and underneath the plasma membrane (arrowhead). DAPI staining shows cell nuclei. Scale bars, 10 μm. (L) Mean ± SEM percentage of microglia showing internalised myelin debris in wt and ASMko mice (n = 7 mice per group).
Figure 7A In AtWT, PIFs promote hypocotyl elongation as a response to warm temperature (28ºC). High ChHFR1 activity is expected to inhibit this response by repressing PIFs more effectively in ChWT and attenuate hypocotyl elongation at 28ºC. B Seedlings were grown for 7 days in W at either 22ºC, 2 days at 22ºC then transferred to 28ºC for additional 5 days (22ºC > 28ºC) or for 7 days at 28ºC, as represented in the panel. C Hypocotyl length of seedlings of (left) AtWT, pifq, pif7-2, ChWT, (middle) 35S:GFP-ΔNt-HFR1 (ΔNtHFR1), hfr1-5 and (right) chfr1-1 and chfr1-2 lines grown at warm temperatures. Hypocotyl lengths are the means ± SE of three biological replicates. Asterisks mark significant differences (Student t-test: * p-value <0.05, ** p-value <0.01) relative to the same genotype grown at 22ºC (left and right graphs, black asterisks), and between the indicated pairs (middle graph, red asterisks). D In AtWT, PIF-mediated DIS involves a reduction of chlorophyll levels. HFR1 activity might inhibit DIS through repression of PIFs. If PIF activity is attenuated in ChWT, DIS would be delayed in this species compared to AtWT. E Seedlings were grown for 7 days in W and then transferred to total darkness for several days to induce senescence, as illustrated at the right panel. F Relative chlorophylls levels of (left) AtWT, pifq, ChWT, (middle) ΔNtHFR1, hfr1-5 and (right) chfr1-1 and chfr1-2 lines after DIS was promoted for the indicated time. For each genotype, values are relative to pigment levels at time 0 (7 days in W). Data are the means ± SE of four independent biological replicates. G Aspect of 4-day old dark-grown seedlings of AtWT, pifq, pif7-2, hfr1-5 and ΔNt-HFR1 (left panel), and AtWT, ChWT and chfr1-1 (right panel).
Figure 4(A-A''') Immunostaining of Smo protein (red) and full-length Ci (light blue) in discs expressing en-Venus. Smo is expressed at higher levels in the P compartment and in a stripe 5-10 cells wide just anterior to the A-P compartment boundary. White arrowhead indicates cells just anterior to the A-P compartment boundary. (B-C) Effect of expressing an RNAi against the ENaC channel rpk in the dorsal compartment of the disc using ap-Gal4. Knockdown of Rpk in the dorsal compartment results in decreased accumulation of the Hh signal transducer Smo (B, B'), and the activator form of Ci (B, B''). The expression of ptc, visualized using an anti-Ptc antibody (C), a downstream target gene of Hh signaling, is also diminished. The Rpk RNAi line BL:39053 is used in all panels shown, but the phenotype was validated with a second RNAi line (BL:25847).
Figure 1A) Shear-dilation relations of Tek-Cre::Lama5-/- and Lama4-/- mesenteric resistance arteries and corresponding wild type controls show a reduced response of Tek-Cre::Lama5-/- arteries and an enhanced response of Lama4-/- arteries. Data shown are mean changes in vessel diameter (Δ µm) ± s.e.m. from 8 experiments with 16 wild type and 16 KO arteries; KO and wild type were analysed as pairs in each experiment. **P<0.01, paired t-test. The dose-response curves of arteries from wild type, Tek-Cre::Lama5-/- (B) and Lama4-/- mice (C) and wild type littermates stimulated with methacholine do not show significant differences (n.s.). Data are expressed as percent relaxation of the maximum force developed in presence of 0.3 µM U46619, and are mean values ± s.e.m from 7 experiments with 1 wild type and 1 KO artery in each experiment.
Figure 6(A) Western blot analyses for the protein level of key regulators of actin polymerization in the cytoplasm and nucleus of HCC cells with treatment as indicated. Tublin and Lamin B1 were used as loading controls for the cytoplasm and nucleus, respectively (n = 3 independent experiments). (B) Western blot analyses for the protein level in tissues of mouse liver tumor induced by Akt/β-catenin (n = 3 independent experiments). (C) Representative immunofluorescence images of HCC cells co-transfected with mDia2-GFP and other constructs as indicated (n = 3 independent experiments). Scale bars, 20μm. (D) Representative images of immunofluorescence assay for mDia2 and phalloidin staining for HCC cells with treatment as indicated (n = 3 independent experiments). WT-mDia2: expression vector encoding wild type mDia2. mDia2-NLS del.: expression vector encoding truncated mDia2 lacking NLS peptide. Scale bars, 20μm. Representative IHC images of mDia2 nuclear translocation in human (E) HCC tissues. NT, non-tumor liver tissues, n=100; MT, metastatic tumor tissues, n=58; NMT, non-metastatic tumor tissues n=42. Scale bars, 25μm. (F) Positive rates of mDia2 in nucleus and cytoplasm was calculated based on the IHC assay in (E). Graphs show mean ± s.e.m. One-way ANOVA. **P < 0.01. Representative IHC images of mDia2 nuclear translocation in mouse (G) HCC tissues. NT, non-tumor liver tissues, n=100; MT, metastatic tumor tissues, n=58; NMT, non-metastatic tumor tissues n=42. Scale bars, 25μm. (H and I) Spearman correlation analysis between the positive rates of nuclear mDia2 and the TFAM expression level (or positive rates of nuclear F-actin) based on the IHC assay in (E).
Figure 7A. Cardiac mitochondrial iron in ABCB8 KO and WT mice with indicated treatment harvested 4 weeks after the tamoxifen treatment. ANOVA followed by post-hoc Tukey test was performed. * P=0.02 WT-vehicle vs. WT-BPD. * P= 0.001 WT-vehicle vs. ABCB8 KO-vehicle. * P=0.004 ABCB8 KO-vehicle vs. ABCB8 KO-BPD. N=8 for WT-vehicle and N=7 for all other groups. B. Ejection fraction in ABCB8 KO and WT mice with indicated treatment 4 weeks after gene knockout. ANOVA followed by post-hoc Tukey test was performed. * P<1E-8 WT-vehicle vs. ABCB8 KO-vehicle. * P<1E-8 ABCB8-vehicle vs. ABCB8 KO-BPD. N=8 for WT-vehicle and N=7 for all other groups. C. Fractional shortening in ABCB8 KO and WT mice with indicated treatment 4 weeks after gene knockout. ANOVA followed by post-hoc Tukey test was performed. * P<1E-8 WT-vehicle vs. ABCB8 KO-vehicle. * P<1E-8 ABCB8-vehicle vs. ABCB8 KO-BPD. N=8 for WT-vehicle and N=7 for all other groups. D. Nppa expression in mice subjected to sham or I/R procedure. ANOVA followed by post-hoc Tukey test was performed. * P=0.017 WT-vehicle vs. ABCB8 KO-vehicle. * P=0.01 ABCB8-vehicle vs. ABCB8 KO-BPD. N=8 for WT-vehicle and N=7 for all other groups.E. Nppb expression in mice subjected to sham or I/R procedure. ANOVA followed by post-hoc Tukey test was performed. * P=0.001 WT-vehicle vs. ABCB8 KO-vehicle. * P=0.0003 ABCB8-vehicle vs. ABCB8 KO-BPD. N=8 for WT-vehicle and N=7 for all other groups.F. Myh7 expression in mice subjected to sham or I/R procedure. ANOVA followed by post-hoc Tukey test was performed. * P=0.011 WT-vehicle vs. ABCB8 KO-vehicle. * P=0.045 ABCB8-vehicle vs. ABCB8 KO-BPD. N=8 for WT-vehicle and N=7 for all other groups. All data are expressed as mean ± SEM. N.S. = not signigicant.
Figure 7Efficacy of BO-110 as an adjuvant (preventing relapse after surgical removal of the primary lesion). Shown are representative examples of Vegfr3Luc mice implanted with mCherry-SK-Mel-147 and imaged for luciferase emission (prior to and after tumor removal. Animals were left to recover from surgery (4 days) and then treated for 2 weeks (4 dosis) with 0.8 mg/Kg BO-110 or vehicle control (n= 8 for control and n=10 for treatment arm). Scale, p/s/cm2/sr x106.   mCherry emission from tumor cells of the animals in (A). Scale, p/s/cm2/sr x109.   Kaplan-Meier survival curves of animals treated as in (A). 8/8 animals treated with vehicle (V) control had to be sacrificed for humane reasons 110 days after surgery. 9/10 animals in the BO-110 arm (BO) remained tumor-free 8 months after stopping treatment. The grey box marks the period of treatment with BO-110. Statistical significance was determined by logrank test.
cGAMP loading of VLPs increases the magnitude of the CD4 and CD8 T cell responses elicited after immunisation.Figure 2Immunisation with cGAMP-VLPs enhances VLP-specific CD4 T cell responses. BMMCs from C57BL/6 mice were pulsed overnight with cGAMP-VLPs and used to stimulate cells from spleens of immunised mice. Cells were co-cultured for six hours prior to evaluation of CD4 T cell responses by ICS. CD4 T cells were gated as live, MHC-II-, CD4+, CD8-. CD4 T cells expressing IL2, IFNγ or TNFα were analysed as shown in (A). Immunisation with cGAMP-VLPs enhances VLP-specific CD4 T cell responses. BMMCs from C57BL/6 mice were pulsed overnight with cGAMP-VLPs and used to stimulate cells from spleens of immunised mice. Cells were co-cultured for six hours prior to evaluation of CD4 T cell responses by ICS. The percentage of total CD4 T cells producing each cytokine is shown in (B) Immunisation with cGAMP-VLPs enhances VLP-specific CD4 T cell responses. BMMCs from C57BL/6 mice were pulsed overnight with cGAMP-VLPs and used to stimulate cells from spleens of immunised mice. Cells were co-cultured for six hours prior to evaluation of CD4 T cell responses by ICS. the percentage of CD4 T cells co-producing 1, 2 or 3 cytokines is shown in (C). Immunisation with cGAMP-VLPs facilitates induction of HIV-1 Gag-specific polyfunctional CD8 T cell responses. Cells from spleens of immunised mice were stimulated with the HIV-SQV peptide. IFNγ-producing cells were enumerated by ELISPOT 24 hours after stimulation with peptide (D). Immunisation with cGAMP-VLPs facilitates induction of HIV-1 Gag-specific polyfunctional CD8 T cell responses. Alternatively, cells were analysed by ICS six hours after stimulation with peptide. CD8 T cells were gated as live, CD90.2+, CD8+. CD8 T cells expressing CD107a, IFNγ, TNFα or IL2 were analysed as shown in (E). Immunisation with cGAMP-VLPs facilitates induction of HIV-1 Gag-specific polyfunctional CD8 T cell responses. Panel F shows the percentage of total CD8 T cells upregulating CD107a and/or producing each cytokine, and panel G shows the percentage of CD8 T cells co-producing 1, 2 or 3 cytokines.
Figure 1(A) Immunoblot showing p-C/EBP β, C/EBP β, AEP, APP, and Tau expression and proteolytic processing in mouse colon. (B) Immunofluorescent staining of C/EBP β (red) and AEP (green), cleaved APP C586 (red) and AEP (green), cleaved Tau N368 (red) and AT8 (green), cleaved Tau N368 (red) and Aβ (green), cleaved APP C856 (red) and cleaved Tau N368 (green), cleaved APP C586 (red) and MAP2 (green), T22 (red) and AT8 (green), Aβ (red) and Thioflavin S (green) in colons of 3xTg mice. Scale bar: 20μm. (C) AEP activity assay with colon lysates from age-dependent 3xTg mice. Data represent the mean± SEM; representative data of three samples; ***P=0.0001(***P< 0.001), ****P < 0.0001 compared with control, one-way ANOVA. (D) C/EBP β and AEP immunofluorescent staining of colons from age-matched healthy control and AD patients. White arrows indicate that C/EBP β and AEP were co-localized in AD patient's colon. (E) AEP and cleaved APP C586 fragments immunofluorescent staining of colons from age-matched healthy control and AD patient. White arrows indicate that AEP and cleaved APP C586 were co-localized in AD patient's colon. (F) AEP and cleaved Tau N368 fragments immunofluorescent staining of colons from age-matched healthy control and AD patient. Scale bar: 20 μm. White arrows indicate that APP C586 and AEP were co-localized in AD patient's colon.
ΔPrPs are non-complex glycosylated and retained intracellularly.Figure 2A. N-linked glycans of ΔPrPs are not complex-type. Immunoblot comparing EndoH- and non-digested lysates of ΔPrP159 and Δ159-175 transfected cells. Left panel was probed with mAb 3F4 mAb, detecting transiently expressed ΔPrPs. On the right panel, the membrane was re-probed with mAb 4H11, detecting total PrP. Arrowheads depict deglycosylated ΔPrPs. B. The additional band of Δ159-167 represents a third N-glycan sensitive to EndoH. Upon EndoH digestion, all bands converge into a non-glycoform band (lane 3 and 4). In Δ159-167(169) the third glycosylation site is not present anymore. C. ΔPrPs are mainly distributed in intracellular compartments rather than on the cell surface. Confocal microscopy images of N2a cells transiently transfected with (3F4) MoPrP, Δ159 or Δ159-175, either permeabilized (right) or non-permeabilized (left) with 0.2% TX100 after fixation. Cells were immuno-labeled with mAb 3F4. (3F4) MoPrP-expressing cells show bright immunopositivity on the cell surface, whereas ΔPrPs are not observed on the cell surface. Also intracellular staining differs strongly between (3F4) MoPrP and ΔPrP expressing cells Scale bars, 25 µm.
LRRC8 subunit‐ and osmolarity‐dependent caspase induction in HCT116 cells.Figure 4LRRC8 subunit‐ and osmolarity‐dependent caspase induction in HCT116 cellsA, BCisplatin‐induced caspase activity in the continuous presence of 200 μM cisplatin under isotonic conditions (A), or after 1 h exposure to 200 μM cisplatin under iso‐ and hypotonic conditions (B), was followed over time in WT, HAP1−/−, LRRC8D−/−, and LRRC8 −/−HCT116 cells. Results from HAP1−/− and LRRC8D−/− were obtained with two different clonal cell lines each and averaged.CCaspase activation after 1‐h exposure to 4 μM staurosporine under iso‐ or hypotonic conditions of WT, HAP1−/−, LRRC8D−/−, and LRRC8 −/−HCT116 cells.Data information: Data are presented as mean ± SEM, n = 3-6. *P < 0.05; **P < 0.01; and ***P < 0.001. Similar results were obtained in three independent experiments. Fold change in (A) refers to t = 0. Control experiments indicated that hypotonicity per se had no effect (Appendix Fig S4).
A neuropathy-related mutation identified in the KIF1A gene.Figure 1(A) Family pedigree of CMT2 patients. The probands I and II were genetically confirmed to carry the p.E239K variant in KIF1A. Their father also had foot drop symptoms and was clinically diagnosed with neuropathy in his 70s, while their mother was asymptomatic. (B) Domain architecture of human KIF1A showing the position of the E239K mutation. KIF1A is composed of a motor domain, neck-linker and neck-coil in the N-terminal force producing region, a regulatory domain in the middle, and a cargo recognition and binding domain in the C-terminal region. (C) Multiple sequence alignment showing amino acids 214-253 of human KIF1A. E239 is located at β7 and is highly conserved in kinesin-3 members throughout evolution. hs, Homo sapiens; mm, Mus musculus; dm, Drosophila melanogaster; ce, Caenorhabditis elegans.
Shp2 ablation or inhibition inhibits self‐renewal and induces senescence in cultured PyMT tumor cells Scheme of Shp2 ablation in cultures of PyMT;Shp2fl/fl tumor cells using retroviruses, which expressed CreERT2‐GFP or control GFP.Figure 1Scheme of Shp2 ablation in cultures of PyMT;Shp2fl/fltumorcells using retroviruses, which expressed CreERT2‐GFP or control GFP. Western blot analysis of Shp2 in control and Shp2 ko cells. Immunofluorescence analysis of Ki67 on control and Shp2 ko cells at day 7. Scale bar, 50 μm.Quantification of the numbers of Ki67+cells shown in (C). Error bars represent SEM (n = 3). **P 0.01. phere formation by control and Shp2 ko cells at day 7. Scale bar, 200 μm.Quantification of the numbers of spheres formed by control and Shp2 ko cells shown in (E). Error bars represent SEM (n = 3). **P 0.01. Growth kinetics of spheres formed by control and Shp2 ko cells by counting sphere cells at day 4, 7, and 12. Error bars represent SEM (n = 3). SA‐β‐gal staining on spheres formed by control and Shp2 ko cells at day 7. Scale bar, 100 μm.Quantification of the numbers of senescent cells in the spheres shown in (H). Error bars represent SEM (n = 3). **P 0.01. Western blot analysis of H3K9me3, p27, p53 pS18 (Ser18‐phosphorylated p53), total p53, Shp2, and α‐tubulin in control and Shp2 ko cells. SA‐β‐gal staining on spheres formed by control cells and those treated by the Shp2 inhibitor GS493 at 15 μM at day 7. Scale bar, 100 μm.Quantification of the numbers of senescent cells shown in (K). Error bars represent SEM (n = 3). **P 0.01.Quantification of the numbers of spheres formed by control cells and those treated by the Shp2 inhibitor GS493 at 15 μM. Error bars represent SEM (n = 3). **P 0.01. Statistical significance was assessed by Student's unpaired t‐test.
Figure 4A. The gene-specific RNA to protein correlation factors are shown for all the 55 genes with a box-plot showing the average correlation factor for each gene and the variation observed in the nine cell lines and eleven tissues. All the values for each of the cell lines and tissues are found in Table EV7. B. The gene-specific correlation between protein copy number (x-axis) and predicted protein copy number based on the RNA levels (RNA-based prediction) is shown for four tissues and four cell lines. The other seven tissues and five cell lines are also shown in Figure EV5 and predicted copy numbers can be found in Table EV9.
Figure 2A-C Expression pattern of pWOX5::GFP in WT (A), scr-3 (B) and plt1-4 plt2-2 (C) at 5 DAG. D Quantification of GFP fluorescence in the QC of pWOX5::GFP transgenic seedlings, as shown in (A-C). GFP signal intensity in each genotype was normalized relative to that in the WT. Data information: In (D) n denotes the total number of scored samples. Individual values (black dots) are shown. Data represent mean ± SD of three independent replicates. In (D) different lowercase letters indicate significant differences by one-way ANOVA followed by Tukey's multiple comparison test (P < 0.01). E RT-qPCR analysis of the relative expression levels of WOX5 in WT, scr-3, and plt1-4 plt2-2 roots. Total RNA was extracted from 5 mm root tip sections of seedlings at 5 DAG. Data information: In (E) , **P < 0.01 (Student's t-test). Scale bars: 20 µm. F Primary root length of the indicated genotypes at 5 DAG. Data information: In (F) n denotes the total number of scored samples. Individual values (black dots) are shown. Data represent mean ± SD of three independent replicates. In (F), different lowercase letters indicate significant differences by one-way ANOVA followed by Tukey's multiple comparison test (P < 0.01). G-J Representative confocal images of the indicated genotypes at 5 DAG. White arrows indicate the QC. K Quantification of GFP fluorescence in the QC of pSCR::GFP and pSCR::GFP-SCR transgenic seedlings, as shown GFP signal intensity of each genotype was normalized relative to that of the WT. Data information (K), n denotes the total number of scored samples. Individual values (black dots) are shown. Data represent mean ± SD of three independent replicates. (K), **P < 0.01 (Student's t-test). Scale bars: 20 µm. L-Q Root stem cell niche phenotypes of the indicated genotypes at 5 DAG. White dashed lines indicate the QC region. The numbers denote total number of scored samples, with similar phenotypes showing in (L-Q).
Figure 1(A) Oxidation of ketone bodies requires the enzymes SCOT and BDH1 and yields acetyl-CoA which enters the tricarboxylic acid (TCA) cycle. (B) Immunoblot of SCOT, BDH1 and the loading control VCP across various organs obtained from adult C57Bl/6J mice. (C, D) Quantification of SCOT and BDH1 expression levels relative to VCP in various murine organs. Data are presented as mean ± SD. n=3; *, p<0.05; ***, p<0.001 unpaired Student's t-test. (E) Immunoblot of SCOT, BDH1, CD31 and the loading control VCP in murine endothelial cells isolated from heart, muscle, lung and adipose tissue. (F) Immunoblot of SCOT, BDH1, CD31 and the loading control VCP in human cardiac ECs, HUVECs and adipose tissue ECs. (G) Immunoblot of SCOT, BDH1, CD31 and VCP in cardiac endothelial cells (EC) and non-endothelial cell fraction (non-EC) isolated from adult C57Bl/6J mice. (H) Immunoblot of SCOT, BDH1 and β-actin in immortalized murine cardiac endothelial cells (MCEC). (I, J) Ketone body concentration in cell culture medium of MCEC treated with 2 mM D-β-hydroxybutyrate (β-OHB) or 2 mM acetoacetate (AcAc) after 24 hours. Data are presented as mean ± SD. n=3; *, p<0.05; ***, p<0.001 unpaired Student's t-test.