EMBO/sd-character-level-ner huggingface dataset:
Figure 1A) H&E and immunohistochemistry reveal that β-catenin accumulates in tumors emerging in one-year-old female miR-424(322)/503-/- mice. The panel is a representative image of n=5 independent tumors. The scale bar indicates 100 micrometers (µM). B) Bar graphic showing that human breast cancers with deletion of the miR-424/503 locus have higher protein levels of β-catenin (RPPA). P-value is calculated based on one-sided Wilcoxon rank-sum test. In the box-plots in B and C the relative expression of β-catenin in the RPPA data from TCGA is shown. The yellow line indicates the median and the bars indicate the 75th percentile (Q3)+1.5 interquartile range (IQR). C) The bar graph shows that human breast cancers with low expression levels of miR-424 and miR-503 have higher protein levels of β-catenin. P-value is calculated based on one-sided Wilcoxon rank-sum test. D) GSEA indicating that tumors with deletion of the miR-424/503 locus present higher canonical Wnt-signaling activity. Independent analysis for TCGA and METABRIC data sets are shown. . P-values were obtained from the GSEA pipeline based on permutation tests. E) The graphic shows the enrichment of miR-424/503 deletions in the BL2 and M subtypes of TNBC. The red line shows the overall fraction of miR-424/503 deletions in TCGA samples. The enrichment in subtypes is estimated by the binomial test. The asterisks indicate the columns that the p-values above are linked to.
S proteasome from S.Figure 3A. Unique residue pairs obtained by Wang et al. for the human 26S proteasome (PDB|5GJR). B. Unique residue pairs obtained by sequential digestion for the S. cerevisiae 26S proteasome (PDB|4CR2). Sequential digestion returned the highest number of residue pairs so far identified by CLMS for the 26S proteasome. Tryptic residue pairs are represented in green and non-tryptic in orange. C. Long distance (blue) and within distance (pink) between residue pairs were mapped into one of the states of the proteasome (4cr2) showing the accumulation of those into the base of the complex. Residue pairs satisfying other states are represented in yellow. The bar plot shows the distribution of all residue pairs in the complex showing that long distance links locate mainly in the base. D. Unique residue pairs were mapped into the 3 states described by Unverdorben et al. showing the rearrangement of Rpn5 relative to Rpt4. E. Our data supports Rpn1 being translated and rotated to be positioned closer to the AAA-ATPase. F. Structural rearrangements of the AAA-ATPase dependent heterohexameric ring throughout four states for the RPT6 and RPT1 mapped to the 4 states described by Wehmer et al. G. Structural rearrangements of the AAA-ATPase dependent heterohexameric ring throughout four states for the RPT4 and RPT6.
Figure 2BLI sensorgrams of intermediate VHHs A SARS-CoV-2 RBD-loaded sensors were incubated with nanobodies at the indicated concentrations for 300 s, followed by dipping in assay buffer for 600 s. The response curves (black) were fitted using either a 1:1 (for VHH-72) or 2:1 (for Re6B06 and Re9F06) binding models to obtain KDs. Fitted curves are shown in red. For Re6B06 and Re9F06, some secondary binding with weaker affinity at high VHH concentrations was observed (denoted as KD2). BLI sensorgrams of high-affinity VHHs B Nanobody-loaded sensors were dipped into wells containing RBD at the indicated concentrations for 600 s, and then incubated with assay buffer for 1 h. The response curves (black) were fitted using a mass transport model. Fitted curves are shown in red.
Figure 4Immunoblot analysis of IκBα phosphorylation and degradation as well as p65/RelA phosphorylation in healthy control or OTULING281R fibroblasts primary fibroblasts in response to stimulation with TNF (10 ng/mL). Data are representative of three independent experiments. Immunoblot analysis of phosphorylation of the MAP kinases p38 and JNK in healthy control or OTULING281R primary fibroblasts in response to stimulation with TNF (10 ng/mL). Data are representative of three independent experiments. Densitometry analysis of p65/RelA phosphorylation as presented in (A) from three independent experiments. ELISA analysis of IL-8 secretion in response to TNF stimulation (10 ng/mL) in healthy control or OTULING281R primary fibroblasts. Bars represent mean ± SEM (n=4). Immunoblot analysis of the native TNF-RSC purified by immunoprecipitation from healthy control or OTULING281R primary fibroblasts. Data are representative of three independent experiments.
Sodium butyrate increased expression of LC3-II.Fig 3HCT-116 (A) or HT-29 (B) cells were treated with the indicated concentrations of sodium butyrate (NaB) for 24 h. Representative blots showed expression of Beclin1, ATG3, and LC3 as well as GAPDH, the loading control. C. Electron microscopy images of control and NaB (2mM) treated HCT-116 cells. ER, endoplasmic reticulum; Mt, mitochondrion; AL.
Figure 6Figure 6. Model for Mmi1/exosome YTH-mediated control of cell differentiation and heterochromatin gene silencing mediated by its targeting of nascent lncRNA and the induction of their transcription termination. The YTH domain of Mmi1 co-transcriptionally binds to specific lncRNAs expressed from either euchromatin or heterochromatin regions. We propose that Mmi1 binding to a euchromatic nascent lncRNA (in green) induces the recruitment of the exosome and together they degrade the lncRNA and promote robust termination of the lncRNA transcription, which otherwise will inhibit the expression of the downstream protein-coding gene (in blue). In the case of nam1-byr2 locus, the efficient transcription termination prevents the occurrence of read-through transcription from nam1 gene, which represses byr2 MAPKKK gene, a critical regulator of the entry into sexual differentiation. In parallel, Mmi1 co-transcriptional binding to the heterochromatic pericentromeric lncRNAs also recruits the exosome and contributes to heterochromatin gene silencing by degrading the nascent lncRNAs as well as by inducing precocious termination of their transcription. STOP sign, site of Mmi1-dependent lncRNA transcription termination.
Figure 2Representative FACS plots of retinas and sclera-choroid-RPE cell complexes from naïve and burned mice 3 days (D3) after laser-burn. Quantification of mononuclear phagocytes (Ly6G-, F4/80+, CD11b+) in retinas and sclera-choroid-RPE cell complexes at D3 relative to Naïve; n = 5 (Naïve), 4 (CNV). Quantification of NRP1+ mononuclear phagocytes (Ly6G-, F4/80+, CD11b+, NRP1+) in retinas and sclera-choroid-RPE cell complexes at D3 relative to Naïve; n = 5 (Naïve), 4 (CNV). mRNA expression of Nrp1 in BMDM relative to LysM-Cre/Nrp1+/+; n = 3 (LysM-Cre/Nrp1+/+), n = 4 (LysM-Cre/Nrp1fl/fl). Quantification of NRP1 protein expression in LysM-Cre/Nrp1+/+ and LysM-Cre/Nrp1fl/fl BMDM; n= 6. Representative Western Blot showing NRP1 expression in LysM-Cre/Nrp1+/+ (Ctrl) and LysM-Cre/Nrp1fl/fl (Nrp1fl/fl). Representative confocal images of NRP1 and IBA1-stained mononuclear phagocytes on choroidal flat mounts from LysM-Cre/Nrp1+/+ and LysM-Cre/Nrp1fl/fl mice at D3. Arrow heads indicate NRP1-positive mononuclear phagocytes. Scale bar: 20μm. H. Representative confocal images of IBA-1-stained mononuclear phagocytes on choroidal flat mounts from LysM-Cre/Nrp1+/+ and LysM-Cre/Nrp1fl/fl mice at D7 and D14. Examples of macrophage quantification (yellow stars) are presented in side panels. Scale bar: 20μm. I, J. Total number of IBA-1-positive mononuclear phagocytes counted around laser impact area on confocal images of choroidal flat mounts at D7 (I) and D14 (J); n = 19 burns (D7 LysM-Cre/Nrp1+/+), n = 25 burns (D7 LysM-Cre/Nrp1fl/fl) n = 37 burns (D7 LysM-Cre/Nrp1+/+), n = 23 burns (D7 LysM-Cre/Nrp1fl/fl), 3-5 mice with ~4 burns per eye. K. Compilation of representative compressed Z-stack confocal images of FITC-dextran-labeled CNV and IB4-stained laser impact area from LysM-Cre/Nrp1+/+ and LysM-Cre/Nrp1fl/fl mice at D14. Scale bar: 20μm. L-N. Quantification of area of FITC-dextran-labeled CNV (L), isolectin B4 (IB4 )-stained laser impact area (M) and the ratio of FITC/IB4 per laser-burn (N) relative to LysM-Cre/Nrp1+/+ at D14; n = 23 burns (LysM-Cre/Nrp1+/+), n = 27 burns ( LysM-Cre/Nrp1fl/fl).
Facilitated OGS and early EMT form a positive feedback loop (A-B) Expression of Hif1α was modulated via a retrovirus system or small-molecule compounds, oligomycin (1 µM) and 2-DG (5 mM), during reprogramming.Figure 4Expression of Hif1α was modulated via a retrovirus system or small-molecule compounds, oligomycin (1 µM) and 2-DG (5 mM), during reprogramming. The expression of mesenchymal markers (A) Expression of Hif1α was modulated via a retrovirus system or small-molecule compounds, oligomycin (1 µM) and 2-DG (5 mM), during reprogramming. The expression of mesenchymal markers cell migration (B) was determined with qPCR and live-cell imaging, respectively, on day 6. (C) HIF1α induces EMT by transcriptionally activating key mesenchymal transcriptional factors, including Snai1/2, Twist1/2, and Zeb1/2. Although to a less extent, inducing OGS directly with Pdk1/2 or small molecules also activate these factors. Repsox (1 μM) was used on day 2-7 to inhibit early EMT during reprogramming with 5C medium. TGFβ (TGFβ1/2/3, 1ng/ml each) on day 2-7, LSD1i (SP2509, 10 nM), and sequential introduction of Yamanaka factors (OK+M+S) were used to induce early EMT during reprogramming with mES medium (D). Repsox (1 μM) was used on day 2-7 to inhibit early EMT during reprogramming with 5C medium. Except for OK+M+S group, the four Yamanaka factors were delivered simultaneously. Energy metabolism was determined on day 6 with Seahorse instrument (E-F). Repsox (1 μM) was used on day 2-7 to inhibit early EMT during reprogramming with 5C medium. The expression of glycolysis markers was determined on day 6 with qPCR (G). (H) Key mesenchymal transcriptional factors, including Snai1/2, Twist1/2, and Zeb1/2 induce OGS by transcriptionally activating Hif1α and glycolysis genes. (I) Early EMT and facilitated OGS form a positive feedback loop to induce pluripotency.
a,b) Differential interaction of UVRAG with the RINT-1–ZW10–NAG tethering complex and the beclin-1–Bif-1–PI(3)KC3 autophagy complex after treatment with rapamycin (a) and HBSS (b).figf7(a,b) Differential interaction of UVRAG with the RINT-1-ZW10-NAG tethering complex and the beclin-1-Bif-1-PI(3) KC3 autophagy complex after treatment with rapamycin (a) and HBSS (b). Cells (HEK293T) treated with rapamycin (50 nM) in a or with HBSS in b were subjected to immunoprecipitation with anti-UVRAG (first panel), anti-RINT-1 (second panel) or anti-PI(3) KC3 (third panel), followed by immunoblotting with the indicated antibodies. Input (10%) shows endogenous protein expression. See Supplementary Fig. S9 for uncropped data. (c) Gel filtration analysis of UVRAG complex formation under normal conditions (untreated, UT) and after rapamycin-induced autophagy (50 nM). Affinity-purified UVRAG complexes from HCT116 cells stably expressing Flag-UVRAG were fractionated by Superose-6 gel filtration column and the eluates were analysed by western blotting for UVRAG, RINT-1, ZW10, beclin 1, PI(3) KC3 and Bif-1 proteins. Whole-cell lysates (2.5%) were used as the input (lane-1). The elution profile of each protein was quantified by densitometry analysis and normalized. Relative densitometry units were plotted against fraction number. Black arrows indicate the positions of the molecular weight size markers. Red arrows indicate the peak shift of the UVRAG eluates.
Figure 8Cells expressing a nearly functional FtsZ-mVenus fluorescent fusion as their sole copy of ftsZ were monitored after transition into carbon starvation. Two low motile MG1655 strains, one (wild-type) containing clpX and one without (ΔclpX), were grown in M9 glucose to steady-state. At time zero, M9 media without glucose was flushed through device. Cells rapidly ceased elongation as measured by phase contrast imaging at 2 minute intervals. Fluorescent images were taken every hour throughout to measure both total Ftsz-mVenus per cell and localization patterns Thin individual lines show the total fluorescent per cell in a single lineage (wild-type in solid blue, n = 154. ΔclpX in dotted red, n = 144). Thick solid lines are the time average across individual lineages for each subset (wild-type in blue, ΔclpX in red). After starvation, cells containing clpX degrade FtsZ faster than cells which do not. Fluorescent signals are normalized to the average value for their respective subset at time 0 Distributions of cellular fluorescence for each subset at times corresponding to the top panel. Cellular fluorescence varies widely as total FtsZ per cell is a function of cell size; a typical size distribution is shown at left. FtsZ concentration is roughly constant at steady-stat Student"s t-test P value shown for when distributions differ with significance level α = 0.01. Representative images from cells in a single lineage with and without clpX. Wild-type strains may contain the characteristic FtsZ ring at midcell after shift down but it dissipates after several hours. ΔclpX strains display an abnormal FtsZ localization pattern even in steady-state. After shift down, the FtsZ may disassemble and reform along the cell body in distinct puncta. Image timing corresponds to the abscissa in the top
Figure.Figure 7(A-B) Ctrl or YY1iKO ASCs were treated with CHX (Cycloheximide) for 90 mins and Hif1α protein was measured by flow cytometry. The numbers indicate the degradation rate after CHX treatment. N=3 mice. (C) The relative degradation rate was calculated by the ratio of degradation rate in YY1iKO (11.14% ± 1.71%) vs Ctrl (5.08% ± 0.796%). N=3 mice. (D) Lysates from C2C12 myoblasts (GM) were subjected to co-immunoprecipitation (Co-IP) assays with anti-YY1 or anti-IgG antibodies and blotted with anti-Hif1α or anti-YY1 antibodies. (E) The above lysates were also IPed with anti-Hif1α or anti-IgG antibodies and blotted with anti-YY1 or anti-Hif1α antibodies. (F) ASCs from YY1iKO mice were infected with pRlenti-Hif1α (P402A/P564A) (Hif1α-DM) viruses to overexpress a non-degradable Hif1α protein or GFP-expressing viruses. ASCs from Ctrl mice were also infected with the GFP viruses. 36 hrs after infection, the expression of target glycolytic genes was detected by RT-qPCR. Hsp90ab1 was used as the normalization control. (G) SCs were isolated from Ctrl or YY1iKO mice and infected with the above viruses. EdU labeling was then performed for 5.5 hrs. The percentage of MyoD+EdU+ cells over the total number of MyoD+ cells was quantified. Scale bar = 100 µm. N=3 mice. Heat maps indicating gene expression levels (Log2[FPKM]) of pentose cycle enzymes (H) in YY1iKO vs Ctrl. Heat maps indicating gene expression levels (Log2[FPKM]) of amino acid transporter (I) in YY1iKO vs Ctrl. (J) YY1(WT) or YY1(S365D) mutant was expressed in YY1iKO ASCs and EdU labeled for 6 hrs. (K) Similarly, YY1 (WT) or YY1 (1-394) mutant was expressed and EdU labeled for 6hrs. A GFP expressing plasmid was used the negative control. The percentage of Pax7+/EdU+ cells over the total number of Pax7+ cells was quantified. Error bars represent s.d.'s of the mean. Student's t-test (two-sided): N.S = non-significant, *P<0.05, **P<0.01, ***P<0.001.
Figure 7A. WB analysis of PARP, cleaved-PARP, caspase-3 and cleaved-caspase-3 under L-OHP B. TUNEL of nuclear DNA fragmentation exposed to L-OHP. Scale bar, 20µm. C. Flow cytometry of the cell apoptosis ratio under L-OHP with down- or up-regulation of lnc-AP/pep-AP in two groups of CRC cells, which was quantified in bar charts on the right (n = 3, biological replicates, mean±SEM, Dunnett-t test). Data information: * for P < 0.05; ** for P < 0.01; NS for no significance. Control referred to the corresponding plasmid vector and si-NC was the abbreviation of commercial normal control of siRNA. D. lipid-ROS measurement with down- or up-regulation of lnc-AP/pep-AP in HCT116 and HCT116/L-OHP cells. E. CCK-8 assay of the inhibition ratio by L-OHP with inhibitors of apoptosis Z-VAD-FMK or ferroptosis Fer-1 in HCT116/L-OHP and SW480/L-OHP cells (n = 3, biological replicates, mean±SEM). Data information: * Control referred to the corresponding plasmid vector
Figure 6A-L Only buffer (A), ferric iron (B), ferrous iron (C), ferrous iron-loaded DJA6 (D), DJA6J deletion (H), DJA6C224S (I), DJA6C241S (J), DJA6C267S (K), or DJA6C280S (L) was added to the reaction mixture (SUFBC2D complex, NFS2, SUFE1, MgCl2, NADPH and ATP). DMSO was added to the reaction mixture as a control to the iron chelator deferiprone (DFP) treatment (E). The reaction mixture containing ferrous iron-loaded DJA6 was treated with the iron chelator DFP (F). The reaction mixture containing ferrous iron was treated with the iron chelator DFP (G). UV-visible absorption spectra of the re-purified SUFBC2D complex from the reaction mixture were taken every 10 min for 50 min under anaerobic condition after addition of L-cysteine to initiate the reaction. A peak at 420 nm represents the iron-sulfur cluster in SUFBC2D complex. All data were based on three biological replicates, and similar results were observed.
is required for spinal cord regeneration but does not regulate the length of the cell cycle (A) NF40 tadpoles with the following genotypes foxm1-/- (mut), foxm1+/- (het) and foxm1+/+ (wt) were amputated and left to regenerate for 7 days.Figure 2(A) NF40 tadpoles with the following genotypes foxm1-/- (mut), foxm1+/- (het) and foxm1+/+ (wt) were amputated and left to regenerate for 7 days. The images show representative tails at 3 and 7 dpa. The white arrowheads indicate the amputation site. (B) Quantification of the rate of regeneration. The ratio of the length of the regenerate to the length that has originally be amputated was compared for the whole tail at 3 and 7 dpa. The graph represents the mean+/-SD of 5 independent experiments from 3 different clutches with at least 5 tadpoles in each experiment. (C) Experimental set up for EdU labelling, foxm1 knockout and wt tadpoles were amputated and left to regenerate for 3 days. Tadpoles were then injected with EdU and 2 days later the tails were fixed, sectioned and stained for EdU and DAPI. (D) Representative images of EdU (red) and DAPI (blue) staining at 5 dpa. (E) The graph represents the mean +/- SD of EdU+ cells over the total number of cells in the spinal cord of 5 to 12 tadpoles. Each data point represents a tadpole, with an average of 9 sections analysed per animal. (F) Experimental set up for Dual-Pulse S-phase Labelling: NF50 tadpoles at 3 dpa were injected with EdU and three hours later, the same tadpoles were injected with BrdU. Six hours after the first injection, the tails were fixed, sectioned and labelled for Sox3, Edu, BrdU and DAPI. (G) Representative images of EdU (green), BrdU (magenta), Sox3 (white) and DAPI (blue) staining at 3 dpa. (H) Quantification of images in (G). The graph represents the mean +/- SD of 6 tadpoles with an average of 13 sections per tadpole analysed.
Sleep and activity of flies with silenced expression of TOR signaling pathway and autophagy genes.Fig 4(A)-The total activity of flies recorded on the second day of experiment (mean +/- SD). Silencing the Tsc1 gene in per-positive cells increased the total activity of the flies [U Mann-Whitney Test, * for p≤0,05]. (B)-Total sleep of flies in the dark phase (mean +/- SD). The flies with silenced expressions of Tor or Atg7 gene had lengthened sleep durations in the dark [U Mann-Whitney Test, ** for p≤0,01, * for p≤0,5]. (C)-The sleep metrics of flies with silenced expression of the Tor gene in per-positive cells (x axis shows the time in hours). These flies were less active than control flies during the morning peak of activity but were more active during the evening peaks. (D)-The sleep metrics of flies with silenced expression of the Tsc1 gene in per-positive cells. The experimental flies were more active than control flies during the entire recorded period, regardless of the time of day. (E)-The sleep metrics of flies with silenced expression of the Rheb gene in per-positive cells. Experimental flies were less active during morning peaks of activity in comparison to control flies. (F)-The sleep metrics of flies with silenced expression of the Atg7 gene in per-positive cells. (G)-The sleep metrics of flies with silenced expression of the Atg5 gene in per-positive cells.
Figure 8(a) Detrended spatial profile of NGN2::mScarlet-I intensity from transverse slice of E10.5 spinal cord from heterozygous knock-in mouse in ventral-dorsal direction;red indicates motorneuron (MN) domain, blue interneuron domain (IN). (b) Auto-correlation analysis of detrended NGN2::mScarlet-I intensity spatial profiles from motorneuron and interneuron domains; multiple peaks indicating spatial periodicity; significant peaks (red triangle) lie outside black dotted lines indicating 95% significance based on bootstrap approach (see Materials and Methods) and non-significant peaks (black triangle). (c) Ratio of NGN2:HES5 spatial period in the same tissue; grey dots show ratio for single image from 4 experiments; line shows overall median and error bars 95% confidence limits. (d) Peak to peak distance in auto-correlation plots of de-trended NGN2::mScarlet-I spatial profile in motorneuron (MN) and interneuron (IN) domains as a measure of spatial period in NGN2 expression along dorsal-ventral axis of spinal cord; Grey data points represent mean peak to peak distance in a single slice, n=33, left and right ventricle analysed separately in 4 experiments; black line shows overall mean, error bars show SD; 2-tailed Mann-Whitney test with exact p-value *** p=0.0003. (e) Detrended spatial profile of Venus::HES5 (black) and NGN2::mScarlet-I (red) intensity from the same transverse slice of E10.5 spinal cord in ventral-dorsal direction. (f) Example cross-correlation function of Venus::HES5 with NGN2::mScarlet-I (blue), Venus::HES5 with brightfield signal (black), and NGN2::mScarlet-I with brightfield signal (red) from the same transverse slice of E10.5 spinal cord; markers indicate the presence of two types of co-ordination namely in-phase (red arrowhead) and out-of-phase (black arrowhead). (g) Phase shift showing absolute lag distance corresponding to in-phase peak in Venus::HES5 vs NGN2::mScarlet-I cross-correlation function of spatial intensity profiles from the same slice. 34 individual data points from 6 slices, 2 experiments; red line indicates average inter-nuclear distance in D-V; bars show mean±SD; 2-tailed Mann-Whitney test not significant, p=0.32. (h) Pseudo-color look-up tables applied to mean nuclear Venus::HES5 and NGN2 staining intensity in motorneuron (MN) and interneuron (IN) domains. Venus::HES5 microcluster and single NGN2 high cell (red arrow) in IN domain; Alternating high-low expression of Venus::HES5 in MN, red arrows show high cells. (i) Graphical summary: Through a combination of experimental and computational work we characterised the HES5 dynamic expression in the mouse E10.5 ventral spinal cord. We found evidence that progenitors located in two domains (motorneuron, MN and interneuron, IN) give rise to distinct spatiotemporal characteristics that are indicative of differences in coupling strength and can explain increased differentiation rates observed in MN.