EMBO/sd-character-level-ner huggingface dataset:
Figure 5(A) Experimental design in a unilateral 6-OHDA rat model of PD. Rats were lesioned unilaterally with 6-OHDA into three sites of the right striatum (3 x 2 µg). After two weeks, rats received intrastriatal injections of recombinant human netrin-1, recombinant human GDNF or PBS (VEH). Amphetamine-induced behaviour was assessed every two weeks for 12 weeks then brains were taken to perform IHC analyses. (B) Cumulative amphetamine-induced ipsilateral rotations. Progression of amphetamine-induced ipsilateral rotations over time (right panel). Mean + SD are shown, n=11-12 animals in each group. Tukey post hoc analysis after two-way RM ANOVA, **** P <0.0001 compared to the initial rotation score at week 2. Comparison of the treatment's effect between groups (left panel). Mean + SD are shown, n=11-12 animals in each group. Tukey post hoc analysis after two-way RM ANOVA, *P < 0.05, **P < 0.01 compared to vehicle group. (C) Dopamine fibres in the striatum of 6-OHDA-lesionned rats, ten weeks after treatment. Representative images of coronal sections of the striatum showing TH IHC staining (left panel), intact side on the left and 6-OHDA lesioned side on the right. (Scale bar, 2000 µm). Optical density measurement of TH-positive fibres in the lesioned side of the striatum (bar graph, right panel). Individual values and mean ± SD are shown, N > 10 animals in each group. Tukey post hoc analysis after one-way ANOVA, *P < 0.05, **P < 0.01 compared to vehicle group. Images are oriented with the dorsal part of the tissue at the top, and ventral part at the bottom (D) Dopamine cell bodies in the SN of 6-OHDA-lesionned rats, ten weeks after treatment. Representative images of coronal sections of the SN (lesioned side) showing TH-positive cell bodies stained by IHC (left panel) (Scale bar, 2000 µm). TH-positive cell count in the SN (right panel). Individual values and mean + SD are shown, N > 10 animals in each group. Tukey post hoc analysis after one-way ANOVA, **P < 0.01 compared to vehicle group. Images are oriented with the dorsal part of the tissue at the top, and ventral part at the bottom.
Figure 5(A) RLS analysis for YSC5106 wild-type, nat4∆, H4R3K and double mutant strains. Values in parenthesis indicate mean lifespan. Statistical significance was determined by one-way ANOVA test: **** p ≤ 0.0001. (B) Gene expression analysis of the indicated stress-induced genes in YSC5106 WT, nat4∆, H4R3K and double mutant strains. Expression levels were normalized to RPP0, whose expression remains unchanged.
LAT is not required for CAR microcluster formation or SLP76 activation following CD19 stimulation in human primary T cells.Figure 7A. Western blot showed that LAT is efficiently depleted in human primary T cells using CRISPR. Shown are the means ± SD. n = 4 independent experiments. B. CAR T cells were stimulated on SLBs coated with biotin-OKT3 (left) or biotin-CD19 (right) supplemented with ICAM-1. TIRF microscopy revealed clustering of Alexa647-labeled streptavidin-Biotin-OKT3 or CD19. Scale bar, 5 µm. C. Quantification of clustering of OKT3 or CD19 as normalized variance. n > 200 cells from two independent donors were scored for each condition. Central band: mean; Box: quartiles; Whisker: rest of the distribution. ****, p < 0.0001; n.s. p = 0.48. D. Immunofluorescence analysis revealed membrane-localized phosphorylated SLP76. Cells were plated on supported lipid bilayer coated with ICAM-1 only (control) or ICAM-1 supplemented with CD19 or OKT3 as indicated. The white dashed circle indicated cell boundary. Scale bar, 5 µm. E. Quantification of pSLP76 level on the membrane. n > 200 cells were scored, and the cells were isolated from two independent donors. Central band: mean; Box: quartiles; Whisker: rest of the distribution. ****, p < 0.0001; n.s. p = 0.11. F. T cells were incubated with Raji B cells at a 4:1 ratio and IL-2 production was measured by ELISA at 24 hr. Data were pooled from three donors. *, 0.005 < p < 0.05; **, 0.0005 < p < 0.005. Unpaired two-tailed t-test was applied.
Striatal infusion of the high dose of cholesterol partially rescues synaptic activity and ultrastructure of excitatory synapses in HD MSNs.Figure 2(A) Schematic representation of the electrophysiological parameters analyzed in the infused striatum of 12-week-old mice following 4 weeks of striatal infusion of cholesterol. (B) Spontaneous EPSCs were recorded from striatal MSNs (wt=6; R6/2 ACSF=5; R6/2 chol-high=5) at a holding potential of -70 mV. (C-D) Average amplitude (C) and average frequency (D) of EPSCs from wt, R6/2 ACSF, and R6/2 chol-high MSNs. Data information: The data are shown as scatterplot graphs with means±standard error. Each dot corresponds to the value of each cell recorded Statistics: one-way ANOVA with Newman-Keuls post-hoc test (*p<0.05; **p<0.01; ***p<0.001; ****p<0.0001). (E-G) Number of excitatory synapses per volume of striatum by using FIB/SEM followed by 3D reconstruction. (E) Representative tissue block of striatum (10 µm x 15 µm x 10 µm) used for the 3D analysis. (F) Representative FIB-SEM segmentation and reconstruction of excitatory synapses (yellow) in 200 serial sections of striatum for a total volume of 500 µm3, of wt, R6/2, R6/2 ACSF, and R6/2 chol-high mice. (G) Density of excitatory synapses in at least 1500 μm3 of striatal tissue from wt, R6/2, R6/2 ACSF, and R6/2 chol-high mice (N=3 animals/group). Data information: The data are shown as scatterplot graphs with means±standard error. Each dot corresponds to the value of , the number of synapses counted/µm3 in different blocks of striatal tissue (G) Statistics: one-way ANOVA with Newman-Keuls post-hoc test (*p<0.05; **p<0.01; ***p<0.001; ****p<0.0001). (H-I) TEM images (H) and 2D profile (I) of pre-synaptic terminal sections contain SVs and mitochondria (m). Docked vesicles are indicated by a white arrowhead (H) and black circle (I) and are defined as a vesicle with its center located within 20 nm from the presynaptic membrane. Scale bar: 100 nm. (J, K) Quantification showing the total SVs/µm2 (J) and the docked SVs/µm (K) in R6/2, R6/2 ACSF, and wt striatal synapses (N=3 animals/group). N=60 excitatory synapses/group were counted. Data information: The data are shown as scatterplot graphs with means±standard error. Each dot corresponds to the number of total SVs/µm2 (J) and docked SVs/µm of active zone (K) counted in each synapse. Statistics: one-way ANOVA with Newman-Keuls post-hoc test (*p<0.05; **p<0.01; ***p<0.001; ****p<0.0001).
SseL reduces the accumulation of ubiquitinated aggregates and ALIS in macrophages.Figure 5(A) Single confocal sections of RAW264.7 macrophages infected with GFP-expressing strains of S. Typhimurium (green) for 10 h and immunolabelled for ubiquitin (Ub, red) (scale bars, 5 µm). (B) Quantification of infected macrophages containing ubiquitinated aggregates 10 h after bacterial uptake. Cells were processed as in (A) and analysed by fluorescence microscopy. A minimum of 50 cells were counted for each bacterial infection per experiment and values are the mean ± SEM of at least 3 independent experiments. * p<0.05; *** p<0.001. Uninfected cells (uninf) were from the same wells as infected and therefore were exposed to extracellular bacteria. (C) Immunoelectron microscopy of RAW264.7macrophages infected with the ΔsseL mutant bacteria for 12 h. Arrows and arrowheads indicate ubiquitin (15 nm gold particles) and p62 (10 nm gold particles), respectively (scale bar, 0.5 µm). (D and E) Single confocal sections of RAW264.7 macrophages infected with GFP-expressing strains of S. Typhimurium (blue) and immunolabelled for ubiquitin (Ub, red) and (D) p62 (green) or (E) LC3 (green). The far right panels show merged images of p62 or LC3, ubiquitin and Salmonella. Arrows indicate Arrows indicate SCV-associated ubiquitin labelling with p62 or LC3 (scale bars, 5 µm). Cell outlines and nuclei are delineated by white lines.
Effect of RK-33 on Wnt signaling via DDX3.Figure 8A β-catenin (red) and DDX3 (green) expression in H1299 cells. After overexpressing β-catenin, both DDX3 and β-catenin accumulate in the nucleus. Scale bar is 10 μm. B Immunoprecipitation with DDX3 or H3K4Me3 (control) and immunoblotted with β-catenin in A549 and H1299 cells. Outlined boxes indicate spliced lanes. C Immunoprecipitation with β-catenin or H3K4Me3 (control) and immunoblotted with DDX3 in A549 and H1299 cells. Outlined boxes indicate spliced lanes. D, E β-catenin/TCF4 activity was determined by the TOP/FOP reporter assay. Co-transfection with β-catenin is indicated below. F-I H1299 and A549 cells were treated with RK-33 (0, 1, 2, and 3 μM) and co-transfected with β-catenin in (F, H). Treatment with RK-33 decreased TCF4 activity in both cell lines. J, K Normalized mRNA expression of TCF4-regulated proteins (Axin-2, c-Myc, Cyclin D1) and DDX3 were measured by qRT-PCR in H1299 cells after knockdown of DDX3 (J) and treatment with RK-33 (K). All experiments were repeated three times.
regulates the migration of PGCs in vivo.Figure 3A. The results of IHC examining using anti-DDX4 antibody shows that the overexpression of LncBMP4 increases the number of PGCs in the genital ridge, and interference with LncBMP4 reduces the number of PGCs in the genital ridge. The number of PGCs was counted through the Segmentation module of Image J software. Scale bars:200 μm (top row),40 μm (bottom row) (Data are shown as mean ± SEM, n = 3 independent experiments, * p < 0.05, ** p < 0.01, **** p < 0.0001, one-way ANOVA). B. The number of PGCs in the genital ridge, following the overexpression or interference of LncBMP4, as determined by flow cytometry (Data are shown as mean ± SEM, n = 3 independent experiments, **** p < 0.0001, one-way ANOVA). C. The number of PGCs labeled with PkH26 (red) that migrated to the genital ridge in a frozen section, the number of PGCs labeled with PkH26 (red) was counted using Image J software. Scale bar: 70 µm (Data are shown as mean ± SEM, n = 6 independent experiments, ** p < 0.01, **** p < 0.0001, one-way ANOVA.). D. The effect of overexpression and interference of LncBMP4 on the proliferation of PGCs was detected by EDU proliferation assay. Scale bar: 100 µm (n = 3 independent experiments).
Figure 8Schematic model showing the mechanism of EML4-ALK V1 and V3 cytoplasmic foci formation. EML4-ALK V1 foci are formed by dynamic cross-linking interactions between the EML4 trimerization domain (TD), dimerization of ALK domains and additional interactions via the 12N Blade/Blades 1-5 domains. The shorter EML4-ALK V3 variant forms foci via interactions of EML4 TD and ALK kinase dimerization. In both variants, EML4-ALK trimers arises from the stoichiometric mismatch between the trimeric EML4 N-terminus and the dimers formed by ALK in its active conformation which leads to the formation of foci in the cytoplasm that exclude large complexes such as microtubules. The EML4-ALK foci act as signalling platforms by recruiting several proteins and allowing signal transduction. When the ALK kinase domain is monomeric cross-linking does not occur and the inactive EML4-ALK V3 trimers instead localise to microtubules through the EML4 TD and basic region, whereas inactive EML4-ALK V1 trimers are diffusely localised in the cytoplasm.
Fig.Figure 1A. Parental HEK293T, HET, HOM1 and KO1 cells were treated with the indicated ligands for 1 h. Data information: In all cases, whole cell extracts were Western blotted using the indicated antibodies. Representative experiments are shown. The levels of pSMAD1/5 relative to Actin were determined and are expressed as a fold change relative to the parental HEK293T untreated sample Act, Activin A; Par, parental HEK293T cells, KO1, ACVR1 KO clone 1. B. Cells were stimulated with increasing (doubling) doses of Activin A (0.625-20 ng/mL) for 1 h. Data information: In all cases, whole cell extracts were Western blotted using the indicated antibodies. Representative experiments are shown. The levels of pSMAD1/5 relative to Actin were determined and normalized to the 20 ng/mL ligand dose in parental HEK293T cells Act, Activin A; Par, parental HEK293T cells, KO1, ACVR1 KO clone 1. C. Cells were treated with BMP2 for 1 h. D. Cells were stimulated with increasing (doubling) doses of BMP4/7 (0.625-20 ng/mL) for 1 h. Data information: In all cases, whole cell extracts were Western blotted using the indicated antibodies. Representative experiments are shown. The levels of pSMAD1/5 relative to Actin were determined and are expressed as a fold change relative to the parental HEK293T untreated sample or normalized to the 20 ng/mL ligand dose in parental HEK293T cells Act, Activin A; Par, parental HEK293T cells, KO1, ACVR1 KO clone 1.
Deletion of ACH1 or MPC1 Shortens Chronological Lifespan and Leads to Excess Release of Cellular Acetate (A-C) Chronological lifespan (CLS) analyses in SC 2% glucose medium of wild-type (WT) cells compared to Δacs1 (A), Δmpc1 (B), or Δach1 (C) cells (see also ).Figure 3(A-C) Chronological lifespan (CLS) analyses in SC 2% glucose medium of wild-type (WT) cells compared to Δacs1 (A), Δmpc1 (B), or Δach1 (C) cells (see also Figure S3). Survival was determined by colony-forming capacity (clonogenicity). Data represent means ± SEM (n = 4) of a representative aging experiment.(D-F) Propidium iodide (PI)-positive cells analyzed by flow cytometry to quantify age-induced cell death of experiments shown in (A)-(C). Data represent means ± SEM (n = 4) (see also Figure S4).(G-I) Extracellular acetate assessed from crude culture supernatants obtained at indicated time points of experiments shown in (A)-(C). Data represent means ± SEM (n = 4).∗p < 0.05 and ∗∗∗p < 0.001. (A-C) Chronological lifespan (CLS) analyses in SC 2% glucose medium of wild-type (WT) cells compared to Δmpc1 (B) cells (see also Figure S3). Survival was determined by colony-forming capacity (clonogenicity). Data represent means ± SEM (n = 4) of a representative aging experiment.(D-F) Propidium iodide (PI)-positive cells analyzed by flow cytometry to quantify age-induced cell death of experiments shown in (A)-(C). Data represent means ± SEM (n = 4) (see also Figure S4).(G-I) Extracellular acetate assessed from crude culture supernatants obtained at indicated time points of experiments shown in (A)-(C). Data represent means ± SEM (n = 4).∗p < 0.05 and ∗∗∗p < 0.001. (A-C) Chronological lifespan (CLS) analyses in SC 2% glucose medium of wild-type (WT) cells compared to Δach1 (C) cells (see also Figure S3). Survival was determined by colony-forming capacity (clonogenicity). Data represent means ± SEM (n = 4) of a representative aging experiment.(D-F) Propidium iodide (PI)-positive cells analyzed by flow cytometry to quantify age-induced cell death of experiments shown in (A)-(C). Data represent means ± SEM (n = 4) (see also Figure S4).(G-I) Extracellular acetate assessed from crude culture supernatants obtained at indicated time points of experiments shown in (A)-(C). Data represent means ± SEM (n = 4).∗p < 0.05 and ∗∗∗p < 0.001.
Figure 1A In silico analysis of humanGATA6and NKX2-1 shows similar gene structures (top) with two promoters (grey boxes) driving the expression of two distinct transcripts (middle and bottom); exons as black (non-coding) and white (coding) boxes. GATA6, GATA Binding Factor 6; NKX2-1, NK2 homeobox 1; Em, Embryonic; Ad, Adult. B Box plots of the Em/Ad expression ratios of GATA6 (left) and NKX2-1 (right) in FFPE lung tissue sections from controls (Ctrl, n=61) or lung cancer (LC, n=51) patients. Isoform-specific expression of the indicated genes was analyzed by qRT-PCR after total RNA isolation from tissue samples. Each point represents one sample. C Box plots of Em/Ad of GATA6 (top) or NKX2-1 (bottom) show that high Em/Ad ratios in LC samples are maintained among ethnic groups (left) and gender (right). GER, samples collected in Germany; MEX, samples collected in Mexico. D Box plots of Em/Ad of GATA6 (left) or NKX2-1 (right) in FFPE lung tissue sections from controls or LC patients. Samples were staged according to the TNM Classification (UICC, 7th edition).
Figure 2(A) Comparable maximum projections of confocal sections of the dorsal wing pouch portion of third instar larval imaginal discs. A cartoon of full length Snap29 is shown above the control panel. (B) Quantification of the Snap29 signal as in panel A, considering > 30 KTs per sample. Relative mRNA expression of the downregulated genes versus control, measured by Q-PCR, is shown above the graph. Note that efficient depletion of Zw10 does not affect Snap29 localization to KTs. (C) Comparable maximum projections of confocal sections of dorsal wing pouches in which Snap29 has been downregulated and the indicated Snap29 form over-expressed. Cartoons of the expressed Snap29 mutant forms are shown above the panels. Anti-pH3 labels mitotic cells and CenpC marks KTs. (D) Quantification of Snap29 as in panel C, considering > 28 KTs per sample. Note that expression of a form of Snap29 lacking the SNARE1 domain does not rescue Snap29 localization to KTs in Snap29 RNAi cells.
Figure 9A-C Immunolabeling of SYCP3 (red) and telomere FISH (PNA-Tel, green) in Pds5AB cKO spread spermatocytes at the indicated stages. Data information: Sex bivalents (XY) are indicated. Scale bar, 10 μm. D 300% magnification of selected zygotene-like and pachytene-like bivalents presenting regular (left) or altered (i-iv) telomere FISH signals.Double immunolabeling of SYCP3 (red) and RAP1 (blue) and telomere FISH (PNA-Tel, green) in Pds5AB cKO spread spermatocytesDouble immunolabeling of SYCP3 (red) and RAP1 (blue) and telomere FISH (PNA-Tel, green) in Pds5AB cKO spread spermatocytes at the indicated stages. Asterisks indicate the position of the enlarged chromosomes/bivalents shown in a 300% magnification displaying telomere stretches, multiple telomere, distant telomeres and telomere-less. White arrowheads indicate telomeres with an altered organization of telomeric DNA into multiple telomere signals with RAP1 signals and telomere stretches Data information: Sex bivalents (XY) are indicated. Scale bar, 10 μm. Double immunolabeling of SYCP3 (red) and RAP1 (blue) and telomere FISH (PNA-Tel, green) in Pds5AB cKO spread spermatocytes at the indicated stages. Asterisks indicate the position of the enlarged chromosomes/bivalents shown in a 300% magnification displaying telomere stretches, multiple telomere, distant telomeres and telomere-less. White arrowheads indicate telomeres with an altered organization of telomeric DNA into multiple telomere signals without RAP1 signals telomere stretches Pink arrowheads in (T) indicate a telomere presenting a regular telomere FISH signal without a RAP1 signal. Data information: Sex bivalents (XY) are indicated. Scale bar, 10 μm. Double immunolabeling of SYCP3 (red) and RAP1 (blue) and telomere FISH (PNA-Tel, green) in Pds5AB cKO spread spermatocytes at the indicated stages. Asterisks indicate the position of the enlarged chromosomes/bivalents shown in a 300% magnification displaying telomere stretches, multiple telomere, distant telomeres and telomere-less.
Figure 5(A) Schematic of domain distribution of wildtype human ArfGAP1 (amino acids 1-406) and the COPI defective mutant of ArfGAP1 (amino acids 1-394). Critical residues of various domains are highlighted. (B) RagA/B knockout (KO) human embryonic kidney 293A (HEK293A) cells were transfected with HA-tagged wildtype ArfGAP1, the HA-tagged ArfGAP1 R50K mutant, or empty vector (EV, control) for 72 hours. Cell lysates were immunoprecipitated with anti-HA beads. IP or WCL samples were probed for HA and mTORC1 components (mTOR, Raptor and mLST8). Vinculin was probed for as a control. (C) RagA/B KO HEK293A cells were transfected with HA-tagged wildtype ArfGAP1, HA-tagged ArfGAP1 L207D/V279D, or RFP1 (control) for 24 hours. Cell lysates were analyzed as in (B). (D) Top - Input of GST, GST-tagged ArfGAP1, and GST-tagged ArfGAP1 L207D/V279D that was us in the in vitro binding assays. Bottom - Flag-tagged mTOR, Flag-tagged Raptor, and Flag-tagged mLST8 were overexpressed in HEK293A cells. Cell lysates were immunoprecipitated (IP) with anti-Flag beads and incubated with either GST (control), GST-tagged ArfGAP1, or GST-ArfGAP1 L207D/V279D. IP or WCL samples were probed for Flag or GST. (E) RagA/B KO HEK293A cells were transfected with HA-tagged wildtype ArfGAP1, 1-394 truncation of ArfGAP1, or RFP1 as a control for 24 hours. Cell lysates were immunoprecipitated with anti-HA beads. Immunoprecipitates (IP) or whole cell lysate (WCL) samples were probed for HA, AP-2, or β-COP. Actin served as a loading control. (F) RagA/B KO HEK293A cells were transfected with HA-tagged ArfGAP1, HA-tagged ArfGAP1 1-394, or RFP1 (control) for 24 hours. Cell lysates were immunoprecipitated with anti-HA beads. Cell lysates were analyzed as in (B). (G) RagA/B KO HEK293A cells were co-transfected with HA-tagged ArfGAP1, HA-tagged ArfGAP1 L207D/V279D, or RFP1 (control) together with Myc-S6K1. Cells were starved of amino acids (-AA) for 2 hours and then 4 mM of Gln or Asn were added for 2 hours. Cell lysate were immunoprecipitated (IP) with anti-Myc beads. IP or WCL samples were probed for HA, Myc, and phosphorylated S6K1 at threonine 389 (pS6K1). Actin served as a loading control.
Figure 9(A) Images showing UHMK1, p-NCOA3 (S1062/T1067), and ATIC protein expression in two human GC specimens. Scale bars=100μm. (B) Pearson correlation analysis about of the levels of UHMK1, p-NCOA3 (S1062/T1067) and ATIC proteins in patients with GC (n=120) by IHC. (C) (Ci)OS data from GC patients stratified by the level of UHMK1. (Cii) Combination of UHMK1 and p-NCOA3 (S1062/T1067) expression predicts more exact OS of GC patients. Survival curves were plotted according to Kaplan-Meier method, with the log-rank test applied for comparison. (D) Schematic depicting the function of UHMK1 in GC. H. pylori-induced upregulation of UHMK1 or human GC-associated UHMK1 mutation enhances the level of NCOA3 phosphorylation at S1062/T1067; this event greatly increases the association of NCOA3 with ATF4, which activates the de novo purine biosynthesis pathway and promotes the development of GC. Interestingly, activated ATF4 transcriptionally upregulated UHMK1 expression.
Model Summarizing the Nuclear Structure Changes Observed Upon Different Treatments RNase treatment of cells before crosslinking results in reduction of long-range interactions specifically at B-type compartments, and in the preservation TAD boundaries.Figure 6RNase treatment of cells before crosslinking results in reduction of long-range interactions specifically at B-type compartments, and in the preservation TAD boundaries. On the other hand, transcriptional inhibition leads to significant weakening of TAD boundaries without drastic alterations in genomic compartmentalization.
Figure 2(A) Comparison of the dynamic behavior of the GFP-tagged Chs5 and Bch1 with the GFP-tagged Sec28, Cop1, Clc1 and Apm1. The mean of 20-30 FRAP measurements from different cells is shown. Calculated parameters are shown in Table 2. (B) Binding kinetics of the GFP-tagged Chs5 and ChAPs at the TGN is different. Data processing was carried out as in (A). (C) Quantification of the relative expression levels of the exomer components in GFP-tagged strains. A representative immunoblot of yeast lysates is shown; Pgk1 serves as loading control. The asterisks depict the analyzed bands. The plot shows average and SD of three independent biological experiments. The relative expression levels are normalized to Chs6 (depicted by the red line).