EMBO/sd-character-level-ner huggingface dataset:
(F) Distribution of distance to nucleus, normalized on cell size, quantified by image (as in d) segmentation (see Material and Method, Confocal microscopy and early/late quantification) of EEA-1+ endosomes. Results are from three independent experiments for a total of 1193 early endosomes in 12 siCTL cells (99 ± 7 endosomes per cell) and 1282 early endosomes in 22 siHOOK3 cells (58 ± 5 endosomes per cell) and analyzed by a two-tailed heteroscedastic Student's t-test, p≤ 0,001 ***.
B mRNA expression of SQLE in the mouse liver of p53+/+ and p53-/- mice with normal or HFD diet.
(D) Effects of lysosomes on the degradation of Htt-552. PC12 cells were trasfected with Htt-552 as described above and cell lysates were incubated with isolated lysosomes. The degradation of Htt-552-18Q and Htt-552-100Q after incubating with intact lysosomes was assessed with Western blot analysis. Values are the mean±SE of three independent experiments. **P<0.01 (compared with Htt-552-18Q without treatment); ##P<0.01 (compared with Htt-552-100Q without treatment).
(B) Depolarized mitochondria are selectively targeted for autophagy after a multi‐hour time lag. APs are labeled with LC3:GFP, which translocates from the cytosol to the AP's isolation membrane. MTR, a membrane potential dye that stains mitochondria irreversibly and is retained during depolarization, is used to pulse label mitochondria in INS1 cells (14 min, 50 nM) at different time points before detection of APs content. At the time set for detection, cells were treated with pepstatin A (10 μM) and E64d (10 μM) for 30 min to arrest digestion inside the APs, and then subjected to confocal microscopy (see schematic illustration of the Materials and methods). MTR pulse is used here to report on Δψm during the staining period. While mitochondria outside APs show bright MTR fluorescence, those localized in APs varied in fluorescence based on the time at which they were pulsed with MTR. Note that mitochondria inside APs have dim MTR FI if they were pulsed with MTR 1 h before autophagy was detected (circle, top panel), but bright MTR FI if pulsed 24 h before detection of autophagy (circle, bottom panel). Scale bar, 10 μm.
(B) Representative confocal images of stage 17 embryonic heads highlighting the expression of Dfd (purple), Myosin in muscles (blue) and FasII in axonal projections (green) in control (elav>RFP) animals and animals mis-expressing the Hox TFs Lab, Dfd and Scr by means of the elav-GAL4 driver. A zoom on the projections (FasII staining) of MN2a and MN3 to the MHE and MHD muscles of an early stage 17 Drosophila embryo are shown. Asterisks highlight the location of MN2a and MN3, respectively. MN2a is identified by the FasII expressing axonal projection emerging from a Dfd expressing MN, which normally innervates the Dfd expressing MHE muscle (as shown in the elav>RFP control), while MN3 is identified as the MN underneath MN2a, which normally innervates the MHD muscle (as shown in the elav>RFP control). The panel on the right side represents a schematic drawing of the confocal image shown on the left side, summarizing the innervation of the anterior muscles (LR, MHE, MHD) by projections emerging from MN2a (magenta) or MN3 (cyan) in control and mis-expression conditions.
Gene expression profile of MDA231-LM2 cells treated with paclitaxel (PAX) for 48 hours. Highlighted are examples of JNK signature genes that are induced by PAX treatment.
C. TF solubilizes proOmpA*. proOmpA*1 (5 μM) was incubated (50 μl; Buffer C; < 0.2 M urea; 37°C; 60 min) alone or in the presence of TF. Proteins in the soluble fraction were analyzed on 15% SDS-PAGE and Coomassie-blue stained. Lane 2: 2.84 μg proOmpA*. Representative experiment shown; n= 5 biological replicates
C) Wt and Sfrp1-/- mice immunized with MOG and sacrificed 16 days post immunization. Cryostat sections of the thoracic spinal cords were stained with antibodies against CD4, Iba1, GFAP and MBP. Images show the region dorsal fasciculus. White arrowheads point to the disruption of the pia surface in wt. Scale bar 100μm. D) Quantification of CD4+ infiltrated lymphocytes, Iba1 normalised immunoreactivity, MBP normalised immunoreactivity and MBP immune-reactive area in the dorsal fasciculus of spinal cord sections from wt and Sfrp1-/- mice 16 days after immunization (n=16 acquisitions, white dots; from N=4 animals, black dots, per genotype). Error bars represent Standard Error. Statistic refers to number of acquisitions.
H. Heatmap showing the expression level of selected maternal genes, mitochondrial translation genes and mitochondrial respiratory chain genes regulated by MOS mutation or ERK1/2 inactivation.
(F) gba+/+and gba−/− cells treated with 3 nM decylTPP and MitoQ10 for 48 hr were subjected to immunoblotting using the indicted antibodies. All data in this figure represent the mean ± SEM, *p < 0.05.
d, Quantification of fission activity. For each movie, the whole frame was divided into squares of 10 per 10 µm and the number of small vesicles per 100 µm2 counted. The mean of three independent experiments is shown with SEM.
N. Quantification of esg-GFP+ cells, Dl+ cells, and pH3+ cells in experiments (K-M). n is indicated. The numbers of quantified guts from left to right are 16, 18, 19, 16, 18, 19, 16, 18, and 19. Data information: Error bars represent SDs. The statistical tests used in other panels were student's t-tests. *p < 0.05, **p < 0.01, ***p < 0.001, ****p < 0.0001, and non-significant (NS) represents p > 0.05.
b, Atg18 was covalently labeled with the green fluorescent dye Alexa488 TFP (ThermoFisher) and used in experiments as in a, with rhodamine-phosphatidylethanolamine-labeled (Rh-PE) GUVs containing the indicated phosphoinositides. Scale bar 5 µm
F. Cell numbers of injected (CD45.2+) Treg cells and FOXP3+ cells were determined by flow cytometry.
p53+/+ HepG2 cells were stably overexpressed SQLE or vector control. Cell proliferation (D) are shown respectively.
(A) Scatter plot comparing polysome association score (defined as fold-change between abundance in polysome libraries vs. total RNA) and RDR6-dependent siRNA levels of TEs found de-repressed in ddm1 (brief description of RDR6 dependency). Quartiles of siRNA levels are confined by gray vertical lines. For comparison and reference, polysome association and RDR6-dependent siRNA levels of protein coding and non-coding transcripts are displayed as boxplots. Copia93 elements: EVD (AT5G17125) + ATR (AT1G34967), are circled. Inlet: Polysome association score of TEs in quartile 4, EVD mRNA isoforms are displayed separately.
(C) ARPE-19 cells incubated with Tunicamycin as indicated in (A) were immunostained with antibody against CHOP. Scale bar, 10 µm. Data are representative of three independent experiments.
(J) Immunoblotting analysis for GLUT1 protein expression upon MIG-6 overexpression in GFP and HAUSP knockdown BT549 cells.
(g) Model for MBd fate in cells. The newly formed MBd is preferentially inherited by the daughter cell with the older centrosome (top panel). The inherited MBd (black ring) is recognized by binding of the NBR1 autophagic receptor (grey circle) with the midbody protein CEP55 (magenta). The MBd is then encapsulated by the autophagosome (yellow circle), and degraded after fusion of autophagosome and lysosome (red circle) in differentiated cells. This pathway prevents MBd accumulation. In contrast, stem cells efficiently accumulate MBds through successive divisions and evasion of NBR1-mediated autophagy. Furthermore, differentiated and stem cells possess overall high and low autophagic activity, respectively. Uncropped images of blots are shown in Supplementary Fig. S6.
(D) Translation efficiency of UUG-enriched, leucine-enriched, proline-enriched and random genes in each sample. A gene was considered enriched in a certain codon when the proportion of this codon in the gene was at least 3-fold higher than the proportion of the same codon across the transcriptome. Data information: In n = 3 biological replicates. In (D), boxplots show the median (central band) and IQR (boxes) ± 1.5 x IQR (whiskers), Welch's t-test, p-value < 0.05.
D-F. Example pictures of the GABAergic nervous system cell bodies, commissures, axonal gaps and axonal breaks larger than 50 µm per worm in chd-7(gk290) mutants expressing unc-47p::mCherry.
Growth curve (B) of Hepa1-6 cells derived xenografts in the subcutaneous implantation mice model in six treatment groups for 12 days (n=5).
(A) Bright-field images (10x (left) and 4x (right) magnification) from shScr, sh1 and sh2 at day 8 of differentiation. Scale bars, 200 µM.
E: Rates of GVBD, PB1 emission, and normal spindle assembly in WT, Cnot6l-/- and Btg4-/- oocytes cultured in vitro. Error bars, s.e.m. ***P < 0.001 by two-tailed Student"s t test. n.s.: non-significant. The numbers of analyzed oocytes were indicate
(a) SAR405 induces late endosome-lysosome swelling. RKO cells were treated with DMSO (upper panels) or with 10 μM SAR405 for 16 h (lower panels). The late endosomes-lysosomes compartment was assessed using Lysotracker green (left) or Alexa 488-conjugated anti-Lamp1 antibodies (right), as indicated. Nuclei were stained using Hoechst 33342 (blue). One representative image chosen from three independent experiments, showing fluorescence imaged using a Zeiss microscope (X40), is shown for each condition. Arrows indicate accumulation of swollen late endosome-lysosomes. Scale bars, 20 μm.
A-E The JurkatTat LTR-luciferase cell line was treated with the EC50/4, EC50, EC50*4 of PH01 - PH05, alone or in combination with 300 nM SAHA, 100 nM Chaetocin, 1 µM Ionomycin, or 10 nM PEP005 as indicated. Luciferase activity was measured after 24 h, and the results are presented as percent activation relative to results from PMA treatment (percent activation for the EC50 of each compound are shown here).
(E) Immunoblots of protein lysates from Null- or TFEB/3 knockout-MEF cells treated as described in (A). Data are representative of three independent experiments.(F-H) Quantification of CHOP (F), PUMA (G) and NOXA (H) protein levels in Null- or TFEB/3 knockout-MEF cells treated as indicated in (E) (mean ± SD of the indicated protein to actin ratio from three independent experiments, student's t-test analysis versus the corresponding time point in Null-MEF cells, ns= not significant, *p < 0.05, **p < 0.01).
PARP-1 inhibitor Olaparib protects WT cells from H2O2 treatment to the same extent as NEDP1 KO. U2OS cells were plated in 96 well plates and 24 hours later pre-treated with Olaparib (10 μM) for 1 hour before treatment with the indicated concentration of H2O2. 24 hours later, cell viability was measured using the CellTiterGlo assay. NEDP1 deletion protects cells from H2O2 treatment to the same extent as PARP-1 inhibition in WT cells. Olaparib does not provide additional protection to NEDP1 cells from H2O2 treatment.
(D) Immunostaining assay of PAX6 (green) in control and V1-PAKI cells on day 10 of neural differentiation. Scale bar, 100 μm.
b, Immunohistochemistry using an anti-calbindin antibody on cerebellum sections from control (Atg5flox/+; nestin-Cre) and Atg5flox/flox; nestin-Cre mice at six weeks of age. Scale bar, 25 µm.
GC-MS analyses of the major metabolites of Urea cycle in SW-1116-Vector, SW-1116-LOC113230 or SW-1116-shASS1 cells, respectively.
f) Heat map of gene expression for key regulators of DNA replication in PDK3 OE vs control RNCMs.
clonogenic assay of H358 cells treated for 48 h with vehicle, AZD4547 (5 µM) and BI2536 (5 nM), in the presence or absence of Q-VD-OPh (20 µM). Data shown as mean ± SD (n=3). ***P<0.001 and ****P<0.0001 by two-way ANOVA with Tukey's multiple comparisons test.
C Representative light micrographs of adult Drosophila eyes expressing the indicated transgenes under the control of the GMR-Gal4 driver. The Drosophila were fed with or without CQ. Drosophila (GMR-Gal4/+) was used as the control.
A-C Plots and Pearson correlation analysis of reciprocals of EC50 vs. the force-dependent in-situ koff at 5 pN (A), 10 pN (B) 15pN (C).
(B) Workflow depicting the in vivo CRISPR-SAM screen to identify tumor-promoting genes. Parental cells and CRISPR-SAM cell library were xenografted on nude mice (3x106 cells/mouse, n=6 and n=10, respectively) and tumor growth was monitored during 5 months. Seven tumors were collected and analyzed by DNA-Seq to identify the sgRNAs
(D) Boxplot represents the quantification of PMEPA1 protein level normalized to β-actin levels across groups. The p-values were determined by unpaired t-test for D *p < 0.05, **p < 0.01, ***p < 0.001.
G) PARGi (5 μM, 24 hours) treated WT and Ews-/- cells were subjected to cellular viability assay. Error bars represent as mean ±SEMs, and technical repeats (n=3). Significance determined by Two-way ANOVA.
(c-e) Tertiary siRNA screening. Pooled siRNAs against candidate RAB GTPases identified from the secondary screen or TKS5, used as control, were transfected into MCF10.DCIS.com cells. Cells plated onto fluorescently conjugated gelatin (red) were stimulated with 100 ng/ml HGF overnight in the presence or absence of GM6001, followed by staining with FITC-phalloidin (green) and DAPI (blue) (c). Data are the mean ± SEM (d, error bars; n > 100 cells/experiment in at least 4 independent ones).
The Kaplan-Meier curve demonstrates increased survival of starved cct3A(RNAi) animals when treated with palmitic acid/palmitoylcarnitine (PA/PC). Percentages indicate the number of survivals at the indicated time points. Three asterisks indicate P < 0.001 with log-rank (Mantel-Cox) test.
D Comparison of heart weight / body weight (HW/BW) in WT and Cuedc2-/- mice. ** p = 0.036, n = 15 in young WT and Cuedc2-/- mice, n = 10 in old WT mice and n = 12 in old Cuedc2-/- mice.
atg18 cells expressing plasmids carrying Atg18-GFP or Atg18FGGG-GFP, a mutant in the lipid binding sites, were stained with FM4-64. a, Confocal z-stacks were taken before and 2, 6 and 10 min after addition of 0.4 M NaCl. Stacks were processed into maximum projections using ImageJ. Scale bar: 5 µm.
D. Mouse embryonic fibroblasts (MEF) were infected with ZIKV (MOI=5) for 48 hrs after which IFN-α (200 U/mL) was added for 2 hrs. Samples were processed for immunofluorescence assay as described in panel C. Representative panels are shown. The experiment was repeated two times.
D: Scatter plot comparing transcripts between WT and Cnot6l-/- oocytes (at GV, MI and MII stages) and zygotes derived from these oocytes. Transcripts decreased or increased more than five folds in Cnot6l-/- oocyte samples were high-lighted with blue or red, respectively
a) Schematic drawing of the lentiviral vectors used. LV indicates conventional integrating lentiviral vector and NILV indicates non-integrating lentiviral vector, generated by using packaging plasmid with deficient integrase. S/MAR indicates that the vector contains a scaffold matrix attachment region element and S/MARrev means that the element is positioned in the reverse orientation. LTR: Long terminal repeat; CMV prom: cytomegalovirus immediate early gene promoter; GFP: green fluorescent protein; 2A: viral self-cleaving T2A sequence; puro: puromycin.
D. Quantification of Golgi objects in cells pre-treated with ISRIB (1 µM) for 3 h and then exposed to SA (30 min) in the presence of ISRIB. ***p<0.002, Student's unpaired two-tailed t-test.
Percentage of Zscan4+ cells in cultures treated with varying combinations of sodium acetate, sodium L-lactate or D-ribose. Shown are the mean ± s.d. of 2 independent cell cultures, performed across biological replicates. Boxes indicate the range between the first and third quantile, the band depicts the median and the whiskers extend no further than 1.5-times the interquartile range.
B: Growth charts of 2 probands each showing typical growth patterns of self-limited DP, without compromised linear growth before puberty. Solid horizontal black lines connect green dots representing bone age to red dots at the equivalent chronological age.
The protein level of ASS1 was examined by immunoblotting in SW-1116-Vector and SW-1116-LOC113230 cells overexpressing ASS1WT or ASS1K234R .
In the EPM task, the time spent in the open arms was significantly decreased in cKO mice compared to that in the control (CTL) group (nCTL=20, ncKO=12, unpaired Student t-test). B. In the LDB task, the time spent in the light zone by cKO mice was significantly decreased compared to that spent by the CTL mice (nCTL=20, ncKO=12, unpaired Student t-test). C. In the PA task, the entry latency of cKO mice was significantly decreased compared to that of the CTL mice (nCTL=20, ncKO=12, unpaired Student t-test)..D. Nestlet shredding behaviors of the cKO group were also decreased compared to those of the CTL group. The weight of the shredded nestlets of the cKO group was significantly lower than that of the CTL group (nCTL=20, ncKO=12, unpaired Student t-test).
(E) A functional CDGSH iron‐binding domain is necessary, but not sufficient for the interaction between the cytosolic domains of NAF‐1 and BCL‐2. HA‐BCL‐2 ΔTM was in vitro translated in rabbit reticulocyte lysate and equivalent aliquots were added to each GST pull‐down reaction. GST‐fusion proteins used were GST alone, GST‐NAF1‐C, GST‐NAF1‐C‐mut (C99S C101S C110S H114Q), and GST‐MitoNEET‐C. The proteins were detected using anti‐HA and anti‐GST
(D) IFNγ-primed WT, Irgm2-/-, Casp11-/- and Irgm2-/- Casp11-/- BMMs were transfected with LPS using lipofectamine LTX and LDH release was measured at 2 hpt.
B. Western blot analysis of Tace using lysates from Pmp22+/- and WT sciatic nerves at different stages of development. The arrowhead indicates the pro-protein and the arrow shows the cleaved active form of Tace. Representative of two independent experiments.
C: FIP3 expression was analyzed by Western blot. Quantification of bands was performed with ImageJ and normalized to a non-specific band of 35 kDa used as loading control.
(C) Kaplan-Meier plot for progression-free survival stratifying RCC patients with high and low APELIN serum levels 3-5 months after the start date of sunitinib treatment. *P=0.0367; Log rank test.
(c-f) lung wet weight (f) in Sham-operated WT mice and miR-212/132 null and WT mice 3 weeks after TAC surgery (n=4-7). Scale bar, 50 μm.
B-E. Study of gene and protein hypothalamic expression of the MCH peptide (D, E) in icv LPS injected mice. Real-time PCR analysis for MCH (D) at different times after injection (from 1h to 24h), normalized to values in control icv saline injected mice (n=6 per group).
(C) and (D) Effects of knockdown and overexpression of LAMP-2A on Htt-552 levels. PC12 cells were transiently transfected with LAMP-2A plasmid, vector control or LAMP-2A siRNA for 72 h and Htt-552 for 48 h. Lysates were subjected to Western blot analysis with anti-Htt 2166, anti-human LAMP-2A antibodies. Values are the mean±SE of three independent experiments. *P<0.05 (compared with Htt-552-18Q without treatment); #P<0.05 (compared with Htt-552-100Q without treatment).
(E) K48-linked ubiquitin chains accumulate in a cdc48 mutant (cdc48-3). Ub-K48 ChIP followed by qPCR for same loci as in (D) are depicted. See also Fig. EV1C-D. Data represent means ± SD (n = 2).
(C) Quantification of different phenotypes manifesting in MN2a and MN3 after Hox mis-expression in comparison to control animals: MN2a axons projecting to the MHE muscle, representing the wild-type (wt) innervation pattern of MN2a (magenta); MN3 axons projecting to the MHD muscle, representing the wild-type (wt) innervation pattern of MN3 (cyan); MN2a or MN3 axons projecting to muscles other than the MHE or MHD termed wiring defects (dark grey); abnormal synaptic morphologies at MN2a or MN3 derived axon terminals termed terminal defects (light grey). Note, each genetic experiment was performed in parallel to an adequate control experiment using the same driver line crossed to a line that controls expression of either UAS-RFP or UAS-GFPRNAi. Each experiment was performed in triplicates, innervation rates were calculated from n=16 for elav>lab, n=18 for elav>Dfd and n=25 for elav>Scr. p-values between two genetic conditions were calculated by a two-sided Fisher test. # p <0 .1, * p < 0.05, **<0.01.
F: Conservation of signal duration decoding to response amplitude in two prominent model systems for ERK signal duration: NGF and HRG cause more sustained ERK signalling compared to EGF treatment in PC12 and MCF7 cells respectively. Decoding of signal duration to response amplitude is clearly governed by ILGs.
(E) Subcellular localization of ERGIC-53 in fibroblasts by indirect immunofluorescent confocal microscopy. Representative immunofluorescence images of ERGIC-53 (green) and GM130 (red) in fibroblasts from P1, P2 and a control cell line. Scale bar: 20 µm. PCC (right panel) for GM130 versus ERGIC-53 (C1: n=74, C2: n=95, C3: n=59, P1: n=72 and P2: n=76). (*** = p≤ 0.001, one-way ANOVA was followed by Tukey's post-hoc test). Shown are means ± SEM. Immunofluorescence images shown are one example of a total of two biological replicates.
(B) Sashimi plots comparing muscle RNA sequencing reads in P1 (red) and two control muscle samples (blue and green) at the exons 3-5 of BET1.
(B) COS7 cells coexpressing DRP1‐DN and mtDsRed (red) were fixed, permeabilized and stained with a monoclonal antibody against nitrotyrosine (green). Control cells were infected with mtPA‐GFP lentivirus. DRP1‐DN cells show increased nitrotyrosine immunoreactivity in mitochondria, particularly in the distal and enlarged ends. Scale bar, 15 μm (see also Supplementary Figure S9).
(A - C) Fluorescence images (upper) and quantifications (lower) of GFP-tagged CST-1 (A  B) or GFP-labeled F-actin (C) and mCherry tagged plasma membrane and histone in WT and mig-2 null mutant animals. The membrane protrusions in the white boxes are enlarged 3 times at the bottom. Yellow dashed lines indicate the cell periphery. White lines indicate the line to measure the fluorescence intensity. Green lines denote the CST-1 fluorescence intensity; red lines denote the plasma membrane fluorescence intensity; double-headed arrows denote the distance between the GFP signal and cell periphery. Scale bars, 5 μm. (D) Distance between GFP::CST-1 or GFP::Moesin ABD and the plasma membrane at the leading edge in WT and mig-2 null mutants. Error bars indicate SD. N = 9 - 14. ***, P  0.001 by Student's t test.
(B) Conjugation of ubiquitin to BAK K113C impairs BAK apoptotic function. Mitochondrially-enriched membranes from MEFs expressing BAK or BAK K113C were cross-linked (CuPhe) with UbG76C and treated with cBID for 30 min at 30°C. Supernatant (S) and pellet (P) fractions were then immunoblotted for BAK under non-reducing conditions, or cytochrome c or ubiquitin under reducing conditions. Representative of three independent experiments. Note that the incorporation of recombinant UbG76C on higher molecular weight proteins is likely due to incomplete reduction on reducing SDS-PAGE.
B. Same as in A) using the YAP/TAZ activity signature of Zhang et al. (2009) (p<0.0001, n=701).
HCT-116 or HT-29 cells were treated with 10 μg/mL cycloheximide or 0.1μM mithramycin for 30 min and then with 2mM sodium butyrate (NaB) for 24 h. Representative Western blots of the expression of LC3-II are shown. The level of LC3-II expression was quantified by densitometry and normalized to GAPDH (ratio of LC3-II:GAPDH). The fold change from control cells is shown. Means and standard deviation (SD) of three independent experiments are shown. One-way ANOVA was used for statistical analysis. * P<0.05, ** p<0.01, compared to the control group. (C-D) HCT-116 cells treated with mithramycin;  (G-H) HT-29 cells treated with mithramycin. cancel
B Example histograms of smFRET efficiency of Syx1 in complex with Munc18-1 WT in the absence and presence of the MUN domain, and within the SNARE complex. C−E Example histograms of smFRET efficiency of Syx1 bound to Munc18-1 QKAA (C), KKEE (D), and L348R (E) in the absence or presence of the MUN domain. The QKAA mutation strongly impaired the shift of smFRET efficiency in the presence of the MUN domain.