EMBO/sd-character-level-ner huggingface dataset:
(A) Scheme of DDLprotein domains and gene structures with molecular lesions of five mutants. N-terminal NLS (nuclear localization signal) and C-terminal FHA domains are labeled. The dark grey bars indicate exons and lines in between indicate introns. The light grey bars indicate 5' and 3' UTR. The ddl-1, ddl-2 and ddl-3 mutants are in the Ws background, whereas ddl-6 (SALK_045025) and ddl-7 (SAIL_1281_F08) are in the Col-0 background. ddl-1, ddl-2, ddl-6 and ddl-7 are T-DNA insertional lines whereas ddl-3 is a TILLING line with a point mutation.
A, B. Comparisons of RNAseq and ChIPseq data. Wt strain (A) and ∆rnjA (B). The x-axis shows the relative RNAP occupancy at a given gene (normalized ChIPseq coverage). The y-axis shows the relative abundance of the transcript (normalized RNAseq coverage; each dot is one gene). The genes are color-coded, ranging from yellow (low RNA abundance) to red (high RNA abundance) in wt. The ∆rnjA strain has higher RNAP occupancy mainly among the genes with less abundant transcripts. The color coding in (B) reveals no dramatic overall changes in the vertical direction (RNA abundance). If anything, some of the low abundance transcripts decreased further in level in the mutant strain. The main difference (mostly among the low abundance transcripts) is their shift in the horizontal direction to the right (towards higher occupancy with RNAP). Data represent mean values of three independent experiments.
(E) In vitro colony replating ability of HSCs from Ctrl, 4-months old Npm1 cKO and 2-years old WT mice determined by limiting-dilution assay. Overall test for differences in stem cell frequencies between any of the groups calculated by Chisq test, * p<0.05, ***p<0.001, **** p <0.0001. The slope of the line is the log-active cell fraction. The dashed lines give the 95% confidence interval.
Hierarchical clustering of 694 genes correlated with the first two PCs identified three major distinct cell lineages (p < 1 × 10-6). Each column represents a single-cell and each row represents one gene. Cells were re-ordered according to the value of PC1 or PC2. Genes in clusters 'a, b' and 'c, d' were re-ordered by correlations with PC2 and PC1, respectively. The color of the cell type and cell source are indicated in (C). Lineage-specific TFs are listed on the right.
A Schematic representation of the UbG76V-GFP chimeric repoter and its associated internal control (mRFP or mCherry, in red). The amino acid sequences for ubiquitin are in yellow, whereas the sequences for GFP are in green. The UbG76V-GFP chimera, which contains a mutation in the terminal residue of ubiquitin, cannot be cleaved. The resulting protein is a substrate for poly-ubiquitination (indicated by the circles labeled with "u") and degradation by the proteasome. High levels of reporter poly-ubiquitination and/or proteasome activity result in little or no GFP fluorescence.
DU145 cells were transfected with the indicated siRNA (control, siCTRL; UBTD1, siUBTD1pool). (B) Quantification of CTGF1, CYR61 and BIRC5 mRNA levels.
(B) Representative images of HeLa cells with or without the perinuclear clusters of GFP-LC3-positive vesicles (right) and quantification of the number of cells with this phenotype 48 h after transient transfection with siRNAs against FYCO1 (left). Error bars represent SDs based on three independent experiments.
A) HeLa cells were cultured in complete growth or starvation (STV) media for 30'. Cell lysates were immunoprecipitated (IP) with anti‐TFG antibody or IgG as a negative control. Immunoprecipitated complexes were analysed by WB to detect TFG, ULK1, ATG13, and FIP200 as indicated.
Influence of Ctcflos KD on Prdm16 alternative splicing. (M) Levels of Prdm16 long and short isoforms in Ctcflos tr1 (ASO1) KD and control cells. Signal intensities quantified from PCR gel picture subtracted by background and normalized to overall mean signal intensity of the respective biological replicate. Mean and individual values. Two-way ANOVA (Šídák-test), *p<0.05, ****p<0.0001.
(M) Co-transfection of ARE Wild type (WT) or Mutant (Mut) ADAR2 promoter pGL3-Luciferase constructs into UMUC3 cells with/without shAR (left panel), and J82 cells with/without oeAR (right panel). The luciferase assay was used to detect promoter activity.
A Quantitative RT-PCR evaluation of KDM6A mRNA expression in kidney glomeruli isolated from wild-type and KDM6A-knockout (KO) mice. *P < 0.05, significant difference versus wild-type controls (Wilcoxon two-sample test; n = 8).
Schematic model of this study. Mammalian Atg8 proteins directly bind Stx16 through its LIR motif, which controls the proper localization of the Stx16 SNARE complex at the endolysosomal compartments. The Stx16 SNARE complex functions in the maintenance of lysosomal homeostasis upon autophagy induction, thus controlling mTOR activity.
Composite images of representative chimaeric embryos made with control (Mta1Flox/∆Mta2+/+Mta3Flox/Flox) or Mta123∆ ES cells. ES-derived cells express the Kusabira Orange fluorescent marker. Sox2 indicates epiblast cells and Cdx2 is expressed in trophectoderm cells. Arrows indicate examples of K-Orange expressing cells in the mutant embryos. Scale bars = 20µm.
A. Transmembrane topology of PC1 and PC2 proteins, showing the cleavage at the N-terminal GPS site (in circles), the "HLT" tripeptide where the cleavage happens, and the two mutations, L3040H and T3041V, that abolish GPS cleavage.
(H) Expressing phosphor-mimic TauS199E (TauS199E) further increased the transcription activity of Wnt/TCF/LEF1 by Tau in HEK293 cells (n=7 biological replicates each group). Data information: Data are expressed as mean ± SEM, *, P<0.05; **, P<0.01, ***, P<0.001 vs Vec ; ##, P<0.01, ###, P<0.001 vs Tau (H). Data were analyzed by , one-way ANOVA
L, Fluorescent image of c-Fos expression in Parvalbumin (Pv)-positive interneurons in CA3. Scale bar: 50 µm. M, A higher percentage of Pv-positive interneurons in CA3 expressed c-Fos in KO mice (n = 4 mice, WT; n = 4 mice, KO).
(B) CD45.2 frequency within GCs on Day 8 in CLK adoptively transferred mice with different precursor frequency. Adoptively transferred mice with different precursor frequency were immunized with eOD-GT8 60 mer, on Day 8, the splenocytes were isolated and the CD45.2 populations were detected by FACS with the marker SSL+B220+CD95+CD38-CD45.2+. Gated plots represent the CD45.2 frequency within GCs. (C) Quantification of the frequency of CD45.2 and CD45.2 binders. Upper graph shows the quantification of CD45.2 frequency among GC in three adoptively transferred mouse models after the immunization of eOD-GT8 60mer. The graphs below show the frequency of GC CD45.2 binders. X-axis represents the different precursor frequency group. Y-axis represents the percentage of GC (upper) and GC CD45.2 B cells (lower) respectively. Each circle represents one mouse. Mice from two independently repeated experiments were analyzed, n=5-10 mice/group. Bars indicate geometric mean and geometric SD from mice in each group. Significant differences were calculated with Student's t-test and shown as: p > 0.05, no statistical significance (ns), *p < 0.05, **p <0.01, ***p < 0.001, ****p < 0.0001. All p value analyses were calculated by GraphPad Prism V8.0.
AGS and TIFA-KO cells were infected with H. pylori for the times shown. Co‑IP with an anti‑TRAF6 antibody or isotype‑matched antibody (IgG) was performed. Eluates and total cell lysates were analyzed by immunoblotting using the indicated antibodies.
Du145TXR-derived xenograft male nude mice received the indicated treatments. (C) weights measured at the indicated time points are shown. One-way ANOVA was used to analyze statistical differences in (C). Mean with ± SD. Data information: data were obtained from 4-5 tumors per group.
(A, B) Clonogenic assays were performed with HeLa and TRIM16KO cells, untreated or treated with As2O3 or MG132.
D. TUNEL assay shows the presence of some apoptotic cells in Ad-TFEB-infected cultures, but not in control cultures infected with adenovirus alone (n = 3). Bar: 10 µm for all panels.
(D) Schematic summary of structural alignment of bacterial S6 and yeast Mrp17 shown in panel (A) highlighting internal targeting signal (grey outline), additional features of Mrp17 structure (two TBMs), and six glutamate residues (E's) at the C-terminus of bacterial S6 (top); schematic of chimeric constructs of EcS6: S6/Mrp17ITS with Mrp17 amino acids 30-60 incorporated instead of the homologous region of S6 and fused to DHFRmut (middle), S6/Mrp17ITS+ that is similar to S6/Mrp17ITS but has 7 amino acids mutated to lysines (bottom).
(C) HT29 cells were infected with Shigella WT, S325, or ∆ospD3 and incubated for 8 h. Infected cells were subjected to Giemsa staining. Arrows indicate cells in which the cytoplasm disappeared. Scale bar: 20 μm.
F) Specific tetanic force was measured in 15-week-old mice using an in vivo muscle-function analyzer. WT, n = 11; Dup18-30 n = 15 mice.
C Generic EMT score of the adherent and non-adherently growing CTC-ITB-01 fractions in relation to tumor samples from different cancer entities. Scaling ranges from 1 (completely epithelial) to -1 (entirely mesenchymal). The adherent fraction is shown with a black dot, the non-adherent fraction with a black triangle, and the mean score per cancer entity by a black line. D Generic EMT score of the adherent and non-adherently growing CTC-ITB-01 fractions in relation to established cancer cell lines. Scaling ranges from 1 (completely epithelial) to -1 (entirely mesenchymal). The adherent fraction is shown with a black dot, the non-adherent fraction with a black triangle, and the mean score per cancer entity by a black line.
b, Simulation of the "strength of coupling" as a function of the number of unique phase-coupling molecule types under the many-for-all model. Each simulation generated 200 cells for which an R2 value was calculated. R2 values were averaged across 200 simulations. The shaded area represents the standard deviation of R2 across the simulations.
(A) The occurrence of mC-ATG5 puncta in WT L. major promastigotes expressing mC-ATG5 incubated in nutrient-rich medium at log phase at 26°C.
B The dose-response curves for six drugs with potential antiviral effects. The drug-induced inhibition of virus infection (count of N protein positive cells) was quantified using the area under the curve (AUC) values.
(C) BMDMs were incubated with rRv2626c-CA, rRv2626c-DN, or rVehicle for the indicated times and then cell viability measured with MTT assay.
D. Viability of primary human PMNs following incubation with WT and mutant toxin pairings using the viability dye CellTiter. Insert: 2 μg per lane of purified recombinant toxins visualized by Coomassie Blue staining on a 12% SDS-PAGE gel. E = LukE, D = LukD, Emut1 = LukEmut1, Dmut = LukDmut. Bars indicate Mean ± SEM, with n = 4 donors.
C The ADP/ATP ratios in the ubiquitination reaction mixtures. The reaction mixtures containing 2 μM PknG K181M and 5 μM ATP were incubated at 37°C for 30 min in the absence (reaction 1) or presence (reaction 2) of 5 μM Ub and 5 μM UbcH7. LC-MS MultiQuant software was used to calculate the normalized abundance of each compound (including AMP, ADP, and ATP) by measuring the peak area intensity.
F Representative spectral karyotype (SKY) images of metaphase spreads obtained from C57#1 DLP mouse prostate organoids cultured in normal conditions (ENRAD) or upon adaptation without A83-01. Widespread genomic instability is observed following adaptation. Scale bars = 5 µm. G-H Representative telomere FISH images - and quantification (n = 2 biological replicates, 20 metaphases per condition) - in C57#1 DLP mouse prostate organoids cultured in normal conditions (ENRAD) or upon adaptation without A83-01. Widespread telomeric instability is observed following adaptation (arrows indicate telomere doublets, One-way ANOVA, scale bars = 10 µm).
(D) RNF114-dependent TAB1 degradation during early embryo development. (a-c) Representive time lapse embryo images were shown for each treatment. Scale bar = 20um. (a'-c') Quantification of the GFP fluorescent signals for respective treatments in (a-c). n=14, 9 or 12 for the NC, Rnf114 siRNA1# or Rnf114 siRNA2# treatment group respectively. Gray traces: Tab1-GFP fluorescent signals were normalized to the first time point; Black trace: average signal of all embryos for each treatment.
H Synapsin1+ puncta quantitation (one-way ANOVA, F3,34 = 10.07, P < 0.0001; Dunnett's multiple comparisons test vs untreated: Nefiracetam, **P < 0.01 and Z = 2.998; PHA 543613, P > 0.05 and Z = 1.266; WT83/Q83X cell lines were used; N = 8-10 each). Left: representative image of Synapsin1+ immunofluorescent staining; Right: Synapsin1+ puncta quantification. Scale bar = 20 µm.
B) H2AQ105me levels upon arrest (2.5 hours) at different cell cycle stages. Treatment is given above the lanes.
F. Number of oocysts per infected mosquito. Numbers of analyzed mosquitoes are shown above the graph. Data pooled from at least three independent cage feeds originating from independently infected mice. Box‐and‐whisker plots depict the 25% quantile, median, 75% quantile, and nearest observations within 1.5 times the interquartile range (whiskers). Statistical analysis: (F) Kruskal-Wallis test with (F) Bonferroni's Multiple Comparison test.
H,I, Immunostaining for Tbr2 (red) and Ngn1 (green) in Gpr124KO cortices after exposure of the pregnant dams to 21% O2 (H) or 80% O2 (I). J-L Quantification of neurogenic (Ngn1+) RGs and BPs (J), newborn BPs (K) or expanding (Tbr2- Ngn1-) RGs (L) in Gpr124KO cortices after exposure of the pregnant dams to 21% O2 or 80% O2 (mean±SEM; N=4 for 21% O2 and N=5 for 80% O2; * p<0.05, ** p<0.01). M,N, Immunostaining for Tbr2 (red) and Ngn1 (green) in control cortices after exposure of the pregnant dams to 21% O2 (M) or 80% O2 (N). O-Q Quantification of neurogenic (Ngn1+) RGs and BPs (O), newborn BPs (P) or expanding (Tbr2-Ngn1-) RGs (Q) in control cortices after exposure of the pregnant dams to 21% O2 or 80% O2 (mean±SEM; N=5; ** p<0.01). Full, dotted and dashed lines indicate basal and apical boundaries of the cortex or boundaries of the cortical zones, respectively. CP, cortical plate; IZ, intermediate zone; SVZ, subventricular zone; VZ, ventricular zone. Scale bar: 100 µm
F, ChIP analysis of H1299 cells transfected with a Flag-tagged p53 or an empty plasmid together with a USP7-specific siRNA or a control siRNA (siCont.) as indicated. Data information: Bars and error bars are mean±s.d., n=3 independent repeats.
(B) and (C) Iron uptake mutants restore ∆vxrAB growth on 10% sucrose. The indicated strains were grown to exponential phase (OD600~0.5) in LB medium and spot-plated on 10% Sucrose plates with or without additional iron sulfate. An example is shown in (B), quantification of cfu is shown in (C). Data information: Data are average of 3 independent biological replicates, error bars represent standard deviation. ∗∗∗ P<0.0003; ∗∗∗∗ P<0.0001 (paired t-test).
Abro1+/+, Abro1−/−, BMDMs transduced with lentiviruses expressing GFP, ABRO1-GFP or BRCC3-GFP CBA analysis of IL-1β in culture supernatants
(A) TSC2−/−, p53−/− MEFs stably reconstituted with wild-type raptor or S722A/S792A mutant raptor were transfected with GFP-LC3, treated with 2 mM AICAR or control vehicle for 4 h, and then analyzed by fluorescent microscopy. The number of GFP-LC3 dots per GFP-positive cell was counted (mean ± s.d.; n = 60). The scale bars represent 10 µm.
by immunoblotting using the indicated antibodies. Dimerisation assay in 293T cells transiently transfected with ATG16L1-GFP and the indicated S-tagged ATG16L1 constructs and analysed
C Cells expressing GFP-p97-EQ were treated as in (A) and stained with antibodies as indicated.D Quantification of the total number of K63- or K48-ubiquitinated vesicles per cell, and number of p97-EQ positive K63- or K48-ubiquitinated vesicles (mean ± SD).E Percentage of GFP-p97-EQ vesicles positive for K63 or K48 chains was determined (mean ± SD).
Western blot analysis of CHX chase kinetics in U2OS cells, comparing the degradation rate of Flag-RNF8-WT and Flag-RNF8-RING*. Endogenous RNF8 was depleted by shRNF8 targeting only endogenous RNF8.   Graph represents the quantifications of (E) (ns P>0.05, ****P<0.0001; two-way ANOVA, n=3, mean +SEM).
(A) Enlarged (EM) and swollen (WM) mitochondria seen by transmission electron microscopy (TEM) in Δatg5 promastigotes under standard growth conditions. WT is shown at bottom right. Scale bar, 500 nm.
HME control (vec) and KO1 cells were pre-treated with IFNβ for 2 days, followed by a 10-min treatment with H2O2. Cytoplasmic, membrane-bound and soluble nuclear fractions of cell lysates were analyzed by the Western method; staining with anti-AIF and anti-HDAC2 staining was used to characterize membrane and nuclear fractions, respectively. Anti-PAR detects all PAR-modified proteins, which appear as smears.
A. Immunofluorescence images of 10 μm-thick sections of CP from third ventricle villi of Mpdz+/+ and Mpdz-/- mice were immunolabeled as shown. The areas in the square frames are magnified in the bottom panels.
d, Thioester formation between Apg8 and Apg3. Δapg3, Δapg7 and Δapg10 cells were transformed with both Myc-APG8 and Apg3, or only Apg3, on 2µ plasmids. Cell extracts were immunoprecipitated with anti-Myc antibody, and subjected to immunoblot (IB) using anti-Myc and anti-Apg3 antibody. DTT-, no DTT; DTT+, 100 mM DTT; asterisk, Apg8-Apg3 conjugate; diamond, possible Myc-Apg8 dimer.
A) UMAP projection representing the 16 clusters of cells identified in the WI sample. Note the presence of two additional clusters, LMLM-1 and LM-2, compared to the NI sample. The two clusters correspond to the lamellocytes.
(G) T47D-MTVL cells transfected with control or HP1y siRNAs, were incubated with 10 nM R5020 for 6h and RNA-seq experiments were performed as described in methods section. The differentially expressed genes where considered when presented a fold change greater than 1.5 and P-value <0.05.
Phosphopeptide peak intensity normalized to total TRF1 signal in samples containing only TRF1 plus mTOR
(b) After the generation of parkin-labelled mitochondrial tubules following treatments in a, discrete DFCP1 foci (green, middle panel, ER-associated omegasomes) formed along the parkin-labelled mitochondria (white arrows indicate DFCP1 spots that colocalized with parkin). Bottom panel: merged image of parkin and DFCP1. Scale bar, 10 μm.
(D) Western blot of test translations using the (CGA-CCG) dicodon stalling mRNA reporter shown in (A). The mRNA reporter was added to a yeast in vitro translation extract obtained from a ski2∆uS10-3HA strain. Expression of the translation products (free His- and V5 tagged truncated uL4 protein and the same protein attached to tRNA) was visualized with an anti-V5 antibody.
(A) Distribution of antimycin A resistance scores for wild isolates, compared to standard laboratory strain (red vertical line). Resistance scores are the ratio of fitness on rich glucose media with vs without 500 µg/L antimycin A. Fitness was estimated based on colony size on solid media, corrected for spatial and plate effects After quality control, we obtained quantitative fitness scores for 154 strains, with a signal-to-noise ratio of 29.8 and an unexplained variance of 0.12.
Representative traces tracking bead displacements Histogram shows relative bead displacement for the first and last pulse, n=27 control and n=37 tamoxifen
(A) SEC-profiles of the IFT-B1 and IFT-B2 complexes as well as the 15-subunit reconstituted IFT-B complex. IFT-B1 and IFT-B2 elute at similar volumes, but after mixing the resulting high-molecular weight complex is clearly shifted towards a smaller elution volume. The Coomassie-stained SDS-PAGE gel on the right shows the peak fractions of the individual runs.
Five weeks-old Arabidopsis wild-type Col-0 plants were placed in the 22°C and 45°C growth chambers and total RNA was isolated from leaf samples collected at indicated times. Transcript levels were determined using real-time qRT-PCR. Error bars indicate SE (n = 3).
A. A human brain random cDNA library was screened in a Y2H assay using C9orf72S as bait. A clone coding for aa46-205 of Rab1a, comprising most of the GTP-binding G-box domain and the C-terminal CC-motif was found to interact with C9orf72S.
E-F Confocal images of early Stage 12 embryos from the controls, from lines expressing nlacZ and RNAis against atos or pths in macrophages (mac>) as a second control, and lines expressing RNAis targeting atos or pths along with individual components of the dTORC1 pathway in macrophages, including Nrpl2, Iml1, and TSC1. Germband edge: dotted white line. Data information: Scale bar: 30µm
B, Quantification of pAkt substrate staining in T3 patients (total number of patients = 6, n = 2 in each group). Mean +/- SEM.
During transcription, an R-loop is formed at the GAA tract, which can promote triplex or H-loop formatio We propose this structure is dissociated by replicative helicase into the purine-rich leading strand and DNA:RNA hybrid on the lagging strand. In the wake of the replicative helicase, the triplex / H-loop may reform between DNA:RNA hybrid and purine-rich sequence, blocking the leading strand polymerase. In wild type cells, PrimPol is recruited to the single stranded gap, where repriming allows DNA synthesis to remain coupled to fork progression. In the absence of Primpol, however, the activity of replicative helicase exposes long stretches of ssDNA. RNA polymerase II gains access to such template, leading to unscheduled DNA:RNA hybrid formation
Percentage of phage particles in the extended, intermediate, and contracted states after 5, 20 and 80 minutes of incubation with L. monocytogenes cell walls. The numbers above the bars show the number of particles contained in the tomograms. The average length of the tail and the standard deviation for each of the three states is given next to the color legend.
Scheme of SIRF assay. Nascent DNA was pulse-labelled with EdU. Upon fork stalling, proteins located at stalled forks are in close proximity to EdU. EdU was then biotinylated using click reaction, followed by incubating with biotin and target protein antibodies. PLA amplification was used to visualize the localization of target proteins at EdU-labeled stalled forks.
a, heatmaps showing the differentially-expressed genes according to the selected KEGG pathways calculated in comparison to mock-infected hamsters. * indicates Benjamini-Hochberg adjusted p-value<0.05 in the comparison between saline and ivermectin within the same sex. Color gradient represents the transcription log2 fold change comparing infected and mock-infected.
B: Cells were treated as in (A) and after 2 hours from the release α-factor was re-added to prevent cells from undergoing a second cell cycle. Cell samples were collected at the indicated time points for western blot analysis of the indicated proteins. Pgk1 was used as loading control. Cyc: cycling cells.
D. Electrostatic surface of the SARS-CoV-2 N-NTD. Blue denotes positive charge potential, while red indicates negative charge potential. The potential distribution was calculated by Pymol. The values range from −5 kT (red) to 0 (white) and to +5 kT, where k is the Boltzmann constant and T is the temperature.
c, Increased mortality in LAMP-2 deficient outbred (C57B6/Jx129SV) mice. Forty-two control (closed circles) and LAMP-2-deficient mice (open circles) were monitored over 300 days.
Scatter plot representing the levels of CSF PGRN in healthy controls (depicted in blue) and the different stages of the Alzheimer's continuum (depicted in red). The analysis and graphs were performed excluding CSF PGRN outliers (1 'healthy control', 1 'Preclinical AD A+/TN-', 4 'AD CDR = 0.5' and 1 'AD CDR = 1'). Including them yielded a similar result and CSF PGRN was still significantly higher in the 'AD CDR = 1' group compared to the 'healthy controls' (P = 0.001) and 'Preclinical AD A+/TN-' (P = 0.0001) groups. Abbreviations: A: amyloid-β biomarker status; AD: Alzheimer's disease; CDR: clinical dementia rating; CSF, cerebrospinal fluid; N: neurodegeneration biomarker status; T: tau pathology biomarker status.