EMBO/sd-character-level-ner huggingface dataset:
Fig.Figure 6(A) Mitochondrial iron quantified by ICP-MS in quadriceps of C26-tumor bearing mice after iron carboxymaltose supplementation (n=7-8). Data information: For all data, n represents the number of biological replicates. Statistical significance was calculated by unpaired, two-tailed Student's T-test. Data are mean ± SEM. ∗p < 0.05, ∗∗p < 0.01, ∗∗∗p < 0.001 compared to control and #p < 0.05, ##p < 0.01, ###p < 0.001 compared to C26 untreated group. (B) Aconitase activity of quadriceps lysates normalized to protein content (n=3-7). Data information: For all data, n represents the number of biological replicates. Statistical significance was calculated by unpaired, two-tailed Student's T-test. Data are mean ± SEM. ∗p < 0.05, ∗∗p < 0.01, ∗∗∗p < 0.001 compared to control and #p < 0.05, ##p < 0.01, ###p < 0.001 compared to C26 untreated group. (C) Succinate Dehydrogenase activity staining of gastrocnemius transversal sections and resulting intensity quantification (n=3-7). Data information: For all data, n represents the number of biological replicates. Statistical significance was calculated by unpaired, two-tailed Student's T-test. Data are mean ± SEM. ∗p < 0.05, ∗∗p < 0.01, ∗∗∗p < 0.001 compared to control and #p < 0.05, ##p < 0.01, ###p < 0.001 compared to C26 untreated group. (D) Mitochondrial ATP content determined by luminescence assay in the quadriceps (n=3-9). Data information: For all data, n represents the number of biological replicates. Statistical significance was calculated by unpaired, two-tailed Student's T-test. Data are mean ± SEM. ∗p < 0.05, ∗∗p < 0.01, ∗∗∗p < 0.001 compared to control and #p < 0.05, ##p < 0.01, ###p < 0.001 compared to C26 untreated group. (E) Representative Western blot and densitometric quantification of phospho-AMPK and total AMPK (stripped and re-blotted) in the gastrocnemius of C26-tumor bearing mice after iron carboxymaltose supplementation (n=6). Data information: For all data, n represents the number of biological replicates. Statistical significance was calculated by unpaired, two-tailed Student's T-test. Data are mean ± SEM. ∗p < 0.05, ∗∗p < 0.01, ∗∗∗p < 0.001 compared to control and #p < 0.05, ##p < 0.01, ###p < 0.001 compared to C26 untreated group. (F-H) mRNA levels of ACOT 1 (F), MCD (G), and CPT1B (H) normalized to GAPDH in gastrocnemius (n=5-10). Data information: For all data, n represents the number of biological replicates. Statistical significance was calculated by unpaired, two-tailed Student's T-test. Data are mean ± SEM. ∗p < 0.05, ∗∗p < 0.01, ∗∗∗p < 0.001 compared to control and #p < 0.05, ##p < 0.01, ###p < 0.001 compared to C26 untreated group.
Losartan treatment ameliorates histological signs of RDEB fibrosis.Figure 2Cross sections of paraffin-embedded forepaws of C7-hypomorphic mice treated with losartan for 7 weeks, age-matched untreated C7-hypomorphic mice, and wild-type mice were stained with H&amp;amp;E (A, B) and Elastica van Gieson (EvG) (C).A, B H&amp;amp;E staining in low (A) and higher (B) magnification of the same forepaw digits. Note widening of the dermis, rich infiltration of inflammatory cells, and deposition of dense material in untreated C7-hypomorphic forepaw digits compared to wild-type. Losartan effectively reduced dermal width, inflammatory infiltrates, and deposition of dense fibrotic material. However, losartan treatment did not protect against friction-induced dermal-epidermal separation visible as epidermal detachment in untreated and losartan-treated C7-hypomorphic digits. Scale bars = 100 μm. Cross sections of paraffin-embedded forepaws of C7-hypomorphic mice treated with losartan for 7 weeks, age-matched untreated C7-hypomorphic mice, and wild-type mice were stained with H&amp;amp;E (A, B) and Elastica van Gieson (EvG) (C).C EvGstaining of forepaw digits as in (A, B). In wild-type digits, the dermiselastic fibers (black) are densely organized in the papillary dermis. Untreated C7-hypomorphic digits show increased collagen deposition (red) and loosening and disarrangement of elastic fiber organization (black), losartan treatment reduces collagen deposition and improves the appearance of elastic fibers. Scale bar = 50 μm.
Figure 6A. Scheme depicting the setup of optical tweezers for measuring the forces that a sporozoite can generate to pull a bead out of an optical trap. The bead is placed at the apical end of the sporozoite. The graph shows the fraction of sporozoites that pulled the bead out of the optical trap. Black dots: individual experiments. Bars: mean. 73-131 sporozoites were probed for each line. Significance determined by One-way analysis of variance with Tukeys Multiple Comparison test. B. Scheme showing a sporozoite moving through a polymeric network in 3D. The graph shows sporozoite speeds as measured by manual tracking from imaging of sporozoites in a 3D hydrogel. Box‐and‐whisker plots depict the 25% quantile, median, 75% quantile, and nearest observations within 1.5 times the interquartile range (whiskers). Significance determined by Kruskal-Wallis test with Bonferroni's Multiple Comparison test. C. Selected trajectories of 20 moving sporozoites observed over a period of 3 min. Scale bar, 10 μm.
SH-BC-893 reduces food intake and triggers weight loss.Figure 6Food intake during indirect calorimetry studies in mice fed the HFD for 10-12 weeks and then gavaged with vehicle or 120 mg/kg SH-BC-893 at ZT8.5 on days 1 (first exposure) and 3; n=5-8. The means of 4 measurements over 108 minutes (A) or over the dark cycle (ZT12-ZT24) (B) shown ± SEM. In (A), arrows indicate dosing. Grey shading indicates dark period. as in (A,B) but measuring the respiratory exchange ratio (RER); n=6-8. Average RER from ZT12-ZT24 in mice fed the HFD for 22 weeks then treated once at ZT8.5 with vehicle or 120 mg/kg SH-BC-893; n=7-8. Pair-fed mice were fed the amount of food eaten by SH-BC-893-treated animals. Absolute (F) or relative (G) body weight of mice fed the standard diet and gavaged with vehicle (SD, n=10) or a HFD and gavaged with vehicle (n=10), 60 mg/kg (n=9), or 120 mg/kg (n=10) SH-BC-893 on Mondays, Wednesdays, and Fridays beginning on day 47 (arrow in F). Fat (H,I) or lean (J,K) mass in the mice in (F) measured after the 4 weeks of treatment (H,J) or weekly (I,K); n=9-10. Average daily distance run by HFD-fed mice treated with vehicle (n=8) or SH-BC-893 (120 mg/kg, n=6) on Mondays, Wednesdays, and Fridays over 4 weeks when housed with a running wheel. Body weight of mice fed the SD or HFD housed with or without wheels and treated with vehicle or 120 mg/kg SH-BC-893 as indicated over time (M) or after 4 weeks of treatment (N); n=6-10. Mice were fed chow or the HFD for 9-10 weeks then treated with vehicle or 120 mg/kg SH-BC-893 Mondays, Wednesdays, and Fridays for 3 weeks; n=9. Mean absolute (O) or relative (P) caloric intake per mouse in the 24 h after treatment is plotted for each of 8 different treatments; mice were euthanized 4 h after the ninth treatment. Body weight change in the mice in (O,P) over the 24 h after the first treatment (Q) or after the 3 week course of treatment (R); n=9.
miR‐371 cluster, human homolog of miR‐290 cluster, stimulates the metabolic switch and reprogramming of human fibroblasts A–C Cellular glucose uptake (A), lactate production (B), and oxygen consumption rates (C) were measured in IMR90 and H9 cell lines.Figure 6A-C Cellular glucose uptake (A), lactate production (B), and oxygen consumption rates (C) were measured in IMR90 and H9 cell lines. D Western blotting for MBD2, MYC, PKM2, and LDHA in IMR90 and H9 cells. A representative result is shown. E Western blotting for MBD2, MYC, PKM2, and LDHA in IMR90 cells transfected with mimics of miR‐371 cluster. A representative result is shown. F Western blotting showing knockdown of PKM2 and LDHA in IMR90 cells. A representative result is shown. G Tra‐1‐81‐positive colonies were counted on day 35 after infection of IMR90 cells using the indicated factors. H A working model of the miR‐290‐Mbd2‐Myc axis in regulating metabolism and reprogramming. miR‐290/371 cluster posttranscriptionally represses Mbd2, leading to the downregulation of MBD2 protein and reactivation of Mbd2 target gene Myc. Subsequently, Myc activates glycolysis through directly stimulating the transcription of glycolytic enzymes Pkm2 and Ldha. This regulatory circuit orchestrated by miRNAs facilitates metabolic switch in reprogramming and enhances glycolysis in ESCs.
Electron microscopy of the ExE region at LB/NP stage.Figure 3A-H. SEM images of an opened embryo (A), the ExE cavity wall (B) where blood islands are indicated by white arrow, the allantois surface (C-C'), an opened allantois (D) and its zooms (E-E') where filaments are indicated by white arrows, the epiblast-derived side of the amnion (F), the mesoderm-derived side of the amnion (G) and its zoom (G'). H-O. TEM pictures in allantois (H-J), amnion (K-M), chorion (N) and allantois base (O). In H, allantois mesenchyme (Left) and cortex (Right) are separated by a black dashed line. I-J. Junctions in internal (I-I') and external (J-J') allantois cells. In K, the embryonic side of the amnion is on the left, and the ExE side on the right. L-M. Junctions in the epiblast-derived side (L-L') and the mesoderm-derived side (M-M') of the amnion.
Figure 6Kinesin- and Dynein-dependent anterograde and retrograde particles (1 and 2, respectively) are shown harbouring IFT-A, IFT-B and BBS subcomplexes involved in ciliary cargo transport. Under normal conditions, any misassembly or partial disassembly of proteins from the TZ (3) can be recovered by the retrograde IFT machinery (4). Disruption of retrograde transport (and consequently, anterograde transport) leads to an accumulation of TZ proteins in a short, bulbous cilium as well as impaired TZ assembly and function (as observed in our temperature-sensitive IFT-dynein mutant at the restrictive temperature), phenotypes that are reversible when IFT is restored at the permissive temperature Cross-talk between different ciliary modules and distinct classes of ciliopathies. Most ciliary modules are associated with a specific class of ciliopathies; for example, IFT-A and IFT-dynein are linked to skeletal ciliopathies, BBS proteins are associated with Bardet-Biedl syndrome, and transition zone proteins are associated with Joubert Syndrome and Related Disorders (JSRDs), MKS, NPHP and eye-related disorders, but not skeletal ciliopathies. However, a subset of proteins are associated with ciliopathies generally typical of a different module, indicating potential overlap in function. The module-disease connections are shown as solid lines, with the width correlating to the number of causative genes currently identified (1 to 10+, as indicated). MKS, Meckel syndrome; JBTS, Joubert syndrome; COACH, Cerebellar vermis hypoplasia/Oligophrenia/Ataxia/Coloboma/Hepatic fibrosis; OFD, Oral-Facial-Digital syndrome; SLSN, Senior-Løken syndrome; NPHP, nephronophthisis; RP, Retinitis Pigmentosa; CRD, Cone-Rod Dystrophy; LCA, Leber Congenital Amaurosis; BBS, Bardet-Biedl Syndrome; CED, CranioEctodermal Dysplasia; SRTD, Short-Rib Thoracic Dysplasia; JATD, Jeune Asphyxiating Thoracic Dystrophy. SUPPLEMENTARY FIGURE
Figure 4Left graph: IF staining of TDP-43 and HDAC1 during progression of TDP-43 proteinopathies in the frontal cortices from the FTLD-TDP Tg and WT mice. Nuclei were stained with DAPI (in blue). Scale bar: 50 μm. The circled area is emphasized for showing the distribution of immunoreactivity in cell subregions. Scale bar: 15 μm. Right histogram: Quantification of co-localized TDP-43 and HDAC1 immunoreactivity in the cytosol or nucleus in the WT or 1-, 6-, and 12-month-old FTLD-TDP Tg mice. n = 9 sections per mouse, N = 5 mice per group, data are presented as mean ± SEM. *Nucleus: Tg 1m vs. Tg 6m or 12m; #Cytosol: Tg 1m vs. Tg 6m or 12m; @ Tg 6m vs Tg 12m. ****/####/@@@@ p < 0.0001 by multiple comparison. Left graph: IF staining of γH2AX and HDAC1 in the frontal cortices from the 12-month-old FTLD-TDP Tg and WT mice. Nuclei were stained with DAPI (in blue). Arrow head: γH2AX+ nucleus; arrow: mislocalized HDAC1. Scale bar: 50 μm. Right histogram: Quantification of γH2AX+ and HDAC1 mislocalized cells in the WT or 1-, 6-, and 12-month-old FTLD-TDP Tg mice. n = 4 sections per mouse, N = 5 mice per group, data are presented as mean ± SEM. ** p = 0.0079, **** p < 0.0001 by multiple comparison.
Increasing nuclear import by overexpressing importin α rescues nuclear size and lamin aggregation phenotypes in ELYS knockdown cells.Figure 4MCF-10AT1k.cl2 cells were co-transfected with control or ELYS siRNA and plasmids expressing mCherry alone or mCherry-importin α. Cells were stained with an antibody against lamin B2. Representative images are shown. Scale bar, 10 µm. (B) For each experiment, nuclear cross-sectional areas were quantified for 30-172 nuclei per condition (84 nuclei on average) and averaged. Two biological replicates, data from one representative experiment shown. Cells with and without cytoplasmic lamin B2 aggregates were counted and the percentage of cells with aggregates was calculated. For each experiment, 74-218 cells were examined per condition. Two biological replicates, data from one representative experiment shown. For each experiment, nuclear lamin B2 staining intensities were quantified for 34-187 nuclei per condition (85 nuclei on average) and normalized to the mCherry/negative siRNA control. To measure bulk import capacity for importin α/β cargos, cells were co-transfected as in (A) along with a plasmid expressing GFP-3x SV40 NLS. For each experiment, nuclear GFP-NLS intensities were quantified for 22-188 nuclei per condition (73 nuclei on average) and normalized to the mCherry/negative siRNA control. Two biological replicates, data from one representative experiment shown.
Figure 6Wild type C57BL/6 mice were injected with anti-G-CSF antibody alone or in combination with anti-IL-6 antibody one hour prior to CoPP treatment; the injections were repeated daily for 5 days and mice were sacrificed 6 hours after the last CoPP injection. G-CSF and IL-6 concentration in plasma Wild type C57BL/6 mice were injected with anti-G-CSF antibody alone or in combination with anti-IL-6 antibody one hour prior to CoPP treatment; the injections were repeated daily for 5 days and mice were sacrificed 6 hours after the last CoPP injection. CD45+ cells, granulocytes and HSC numbers in PB measured by flow cytometry. HO-1 deficient and control C57BL/6xFVB mice were injected with CoPP three times, every second day and sacrificed 24 hours after last injection. Total leukocyte counts in PB (HO-1+/+: n = 5, HO-1-/- DMSO: n = 6, HO-1-/- CoPP: n = 4 mice per group). Granulocyte percentage among PB leukocytes. HO-1 deficient and control C57BL/6xFVB mice were injected with CoPP three times, every second day and sacrificed 24 hours after last injection. Cytokine and growth factor concentrations in plasma (E - HO-1+/+ n = 5, HO-1-/- DMSO: n = 5, HO-1-/- CoPP: n = 3 mice per group). Results are shown as mean + SEM, two-way Anova with Bonferroni post-test. Nrf2-deficient and control C57BL/6 mice were injected with CoPP daily for 5 days and sacrificed 6 hours after last injection (DMSO: n = 4, CoPP: n = 5 mice per group). CD45+ cell numbers in PB measured by flow cytometry. Granulocyte percentage among PB leukocytes. Nrf2-deficient and control C57BL/6 mice were injected with CoPP daily for 5 days and sacrificed 6 hours after last injection (DMSO: n = 4, CoPP: n = 5 mice per group). Cytokine and growth factor concentrations in plasma
Figure 4A, B. Fluorescence microscopy at 24 hpi showing green fluorescence absorbance at 12 and 24 hpi, and virus replication at 12 and 24 hpi, in vector, HDAC6, or HDAC6-CDM-overexpressing stable RAW264.7 cells in response to VSV-GFP (MOI = 1) infection (A) and PR8-GFP (MOI = 1) infection (B). bar, 100µm. C. ELISA of IFN-b (upper) and IL-6 (lower) levels in the supernatant of (A), (B), and in vector, HDAC6, or HDAC6-CDM-overexpressing stable RAW264.7 cells treated with poly(I:C) (20 μg/ml) or transfected with 5'ppp-dsRNA (1 µg/ml). D, E. Luciferase assay in 293T cells transfected with an IFN-β luciferase promoter and TK-Renilla together with mutant HDAC6 or HDAC6-CDM (100, 200, 400, or 800 ng), followed by PR8-GFP (MOI = 2) infection (D) or by poly(I:C) (E) (1 μg/ml) transfection for another 12 h. F, G. Luciferase assay in 293T cells transfected with RIG-I (F), MDA-5 (G), an IFN-β luciferase promoter, and TK-Renilla together with mutant HDAC6 or HDAC6-CDM (100, 200, 400, or 800 ng). 24 h later, IFN-β activity was measured by luciferase reporter assay.
Variable rescue of the demyelinating polyneuropathy of Prnp0/0 mice by the S3 PrP allele.Figure 4A Sections of sciatic nerve from TgPrP(S3.F88W)-14 female mice (all 610 days old) and TgPrP(S3.F88W)-35 female mice (614, 570 and 614 days old, respectively) were analysed using toluidine blue staining (upper row), with the third panels for each line showing a hypermyelinated phenotype. Scale bar in left panel represents 50 μm. The lower rows show EM analyses of mice of the indicated genotypes. Scale bar is 10 μm for panels 1-4, with the fifth panel showing a high power view to illustrate hypermyelinated fibres in a mouse expressing S3.F88W PrP (scale bar, 5 μm). B Western blot analysis of sciatic nerve protein extracts (10 μg) from female mice after PNGaseF treatment shows a similar hierarchy of PrP expression in Tg lines to that of brain (see Fig3). The asterisk indicates a greater than full-length fragment present in TgPrP(S3.F88W) mice, possibly corresponding to incomplete removal of the N-terminal signal peptide. C Quantification of fibre morphology in aged animals (492-608 days old), representing the percentage of the nerve occupied by fibres versus the total cross-sectional area of the nerve. The S1 and S3.F88W alleles rescue Prnp0/0 nerves to a similar percentage as the WT allele, but the variance and P-value is greater for the two Tg lines expressing the TgPrP(S3.F88W) allele. Unpaired, two-tailed t-test, **P < 0.01, ***P < 0.001, ****P < 0.0001. Sample sizes and exact P-values compared with Prnp0/0 (n = 9) were as follows: TgPrP(WT) n = 6, P = 3.63E-05; Prnp0/0, n = 9; TgPrP(S1)-17 n = 5, P = 3.54E-05; TgPrP(S1)-19 n = 3, P = 6.35E-06; TgPrP(S3.F88W)-14 n = 3, P = 3.70E-03; and TgPrP(S3.F88W)-35 n = 7, P = 7.18E-03.
Figure 7A Irradiated H-2 Kb- positive spleen cells isolated from T cell-deficient mice were pulsed for 2 hours with the N4 agonist OVA peptide and cultured with CD8+ T cells purified from WT OT-I (WT) or Arhgap45−/− OT-I (Arhgap45−/−) mice. Cell proliferation was measured by luminescence after 48 h. Data are representative of 2 independent experiments with 3 mice per genotype (mean and SEM of triplicate are shown). B WT mice that received CTV-labelled WT or Arhgap45−/− OT-I T cells were immunized using laser-assisted, dermal delivery of vaccibodies that deliver OVA to XCR1+ DC. Four days after antigen delivery, the extent of OT-I T cell proliferation was determined by CTV dilution in ear-draining, auricular LNs, in LNs that do not drain the ear, and in the spleen. Data are representative of two experiments with 4 mice per group. C On the basis of the data shown in (B), the index of OT-I proliferation was calculated using FloJo software. Each dot represents an individual mouse. Mean and SD are shown. ns, non-significant.
Proteomic response to heat stressA.Figure 2A. Heat map summarizing quantitative changes in 1554 proteins in heat stressed naïve MCF7 cells and in thermotolerant MCF7aTT cells. The color bar defines the fold changes in protein expression relative to protein levels of MCF7 cells at 37oC. B. Log2 fold change distribution of proteins in the indicated comparisons. The fractions of up- and downregulated proteins are highlighted in red and blue. The conditions compared are shown in the scheme on the top left. C. Heat map showing the enrichment of Gene Ontology functional terms in up- and downregulated proteins shown in (B). p-values were calculated based on the accumulative hypergeometric distribution (Zhou et al. 2019). D. Heatmap showing changes in the expression of chaperones and proteasome subunits in MCF7 cells during heat shock exposure and recovery (MCF7aTT) as determined by SILAC proteomics. E. Naïve MCF7 cells and MCF7aTT cells were exposed to the indicated stress conditions for 3 h, and cell viability was assessed by staining dead cells with trypan blue. The bar graphs represent the percentage of trypan blue excluding cells. (means +/- SD, n = 3, numbers above bars indicate p values calculated with the two-stage linear step-up procedure of Benjamini, Krieger and Yekutieli).
Figure 4Bar graph representing quantification of stiffness measured by atomic force microscopy (Young modulus) of ECM area generated by H1299control or H1299RASSAF1A cells in vitro. Data information: All statistical analyses were performed using Student's t-test (2-tailed) of n=3 for in vitro experiments and error bars represent the mean ± S.E.M. Representative atomic force microscopy (AFM) images showing organization of extracellular matrix generated by H1299control and H1299RASSF1A cells in 3D collagen matrices (2mg/ml). Bar graph representing quantification of stiffness by atomic force microscopy (Young modulus) in of n=5 H1299control and n=3 H1299RASSF1A primary lung tumours on day 30. Data information: All statistical analyses were performed using Student's t-test (2-tailed) of n=3 for in vitro experiments and error bars represent the mean ± S.E.M. Representative topographic images of stiffness map of H1299control and H1299RASSF1A lung primary tumours provided by AFM. AFM images of ECM fibre organization within primary lung tumours generated by H1299control and H1299RASSF1A cells on day 30. Second harmonic generation (SHG) representative Images and Quantification (bars) showing deposition and organization of collagen fibres produced by H1299control and H1299RASSF1A spheroids embedded in collagen I matrix (2mg/ml), treated with siNT, siRNA against P4HA2 or 4μM DPCA to restrict P4HA2 activity. Red arrowheads show highly organized, long collagen fibres. Scale bars 20µm. Data information: All statistical analyses were performed using Student's t-test (2-tailed) of n=3 for in vitro experiments and error bars represent the mean ± S.E.M. SHG images of organization and quantification (bars) of collagen fractions in primary lung tumours and metastases at day 30. Scale bars 10µm. Data information: All statistical analyses were performed using Student's t-test (2-tailed) of n=3 for in vitro experiments and error bars represent the mean ± S.E.M. Representative H&E and quantification (bars) of picrosirius red staining of two independent regions of n=5 H1299control and n=3 H1299RASSF1A primary lung tumours. Scale bars 100µm, zoom 20µm. Data information: All statistical analyses were performed using Student's t-test (2-tailed) of n=3 for in vitro experiments and error bars represent the mean ± S.E.M.