EMBO/sd-character-level-ner huggingface dataset:
Parental and VAR cells were treated as indicated for 24 hours and allowed to grow in drug-free medium for 15-20 days to form colonies, which were counted using ImageJ.
HUVECs were treated with Sema3C-conditioned medium for 10 min and lysed, and Nrp-1 was immunoprecipitated. Bound Sema3C was detected by Western blotting.
(C, D) Ubiquitination of CREBH and CREBH K294R were measured after co-transfected C-terminal of HRD1.
(B) Representative confocal micrographs of F-actin (grey signal) polarization at B-T cell contacts after 1-2h of co-culture. Cell conjugates were stained with Phalloidin to visualize F-actin. Scale bar, 5µm.
A For macrophage depletion models, mice (six weeks) were injected with GdCl3 (15 mg/kg). After the induction of macrophage depletion in the mice, pancreatitis was induced by cerulein, LPS, and ANGPTL4 for 24 h (n = 10, each group). H&E staining of pancreatic tissue, and levels of amylase and lipase in the serum. Scale bar represents 100 µm
The promoter design is based on the CYC1 core promoter. The relevant structural elements of the CYC1 core promoter elements, which are required for transcription, were conserved in the synthetic promoter design. These elements comprised two TATA boxes at position -221 and -117 (relative to the start of the CYC1 ORF), and the 5'UTR of the CYC1 core promoter (including transcriptional start site, TSS). In the promoter design, three CggR operator sites were inserted adjacent to the two TATA boxes. All functional elements were conserved (blue colored region) during the optimization of the promoter sequence. Nucleotide sequences between the functional elements (grey colored region) were allowed to be optimized by the algorithm. Nucleotides that got optimized are indicated with a black line. A total of 75 sequence versions were generated, where each sequence differed in one mutation from the progenitor sequence. The sequences were optimized for low nucleosome affinity. After optimization, all sequences were checked for synthesis feasibility. The synthesis of the sequences was feasible (green) until the 46th round. After this round, the sequences (not feasible in red) reached a GC content insufficient for proper synthesis. The promoter sequence, which was generated in round 38 (black), showed the best compromise between minimal nucleosome affinity and the possibility to synthesize the sequence.
(b) Suppression of Htt103Q toxicity in yeast by Gpx1, Hyr1 (Gpx3) and mGpx1. The viability of the parental strain, Y258, and of cells overexpressing yeast GPxs was determined using spotting assays. Equal numbers of cells were serially diluted fivefold and plated on medium containing glucose to assess cell numbers and containing galactose (GAL) to induce the expression of Htt103Q and the indicated ORF.
A, B BMDCs were treated with OxPAPC or DPPC (40 μg/ml) for 60 min followed by R837 stimulation (5 μg/ml). (B) mRNA was harvested after 2 h, and expression of IL-6 and IL-12 was measured by real-time PCR and normalized to G6pdx. Unpaired two-tailed t-test. Data (mean ± SD) are representative of three independent experiments.
(d) CEM cells that either lacked Bcl-2 or expressed high levels of Bcl-2 received truncated Atg5 or GFP by lentiviral gene transfer. In the absence of Bcl-2, induction of apoptosis as assessed by DNA fragmentation was observed due to enforced expression of truncated Atg5 within two days. Apoptosis was largely blocked in cells expressing high levels of Bcl-2. GFP transfection did not affect viability of the cells in this system.
Single IHC exhibits different modes of Ca2+-control of release. The overlaid ΔF image of Rhod-FF (red) and iGluSnFR (green) shows synaptic Ca2+-influx and glutamate release at three neighboring modiolar synapses (individual synapses are color coded based on their clusters).
(F) Schematic diagram of human PARP1 functional domains and strategy for engineering a series of PARP1 deletion mutants.
(A) Venn diagrams showing overlaps of differentially expressed genes in the mutants relative to the WT. Up- and down-regulated genes were independently analyzed. The data were generated from two biological replicates. Differentially regulated genes were called when log2(fold change)>1 or <-1; P<0.01.
Apoptosis levels in cultured control (Cnt) and Atg12cKO HSCs and GMPs (n = 3). Results are expressed as percent caspase activation compared to +cytokines Cnt HSCs (100%).
(E) Body height and tibia length of the WT and L-HRD1 KO mice 5 weeks after AAV-shCrebh injection (n=5 for each group).
(A) H&E, PAS and AB staining of lung sections in KLN mice with vehicle or a combinational therapy of phenformin (Phen) and LY-411575. Representative images were shown. Scale bar, 150 μm (left panel), 50 μm (right panel).
(F) Western Blot analysis of the CREBH WT or K48 only ubiquitination level after HRD1 C-terminal co-expression.
(B) Brains of w1118 larvae were stained with anti-ALIX (white), anti-Cnn (white) or anti-Asl (white) and Hoechst (blue) and their centrosomal intensities were calculated in 41, 44 and 40 metaphase NBs, respectively. The average ratios of centrosomal intensities (strongest/weakest) (±S.E) of ALIX, Cnn and Asl calculated from 77, 76 and 56 NBs, respectively, are indicated below the micrographs (from at least three experiments). Scale bars, 5 μm
(d) Wild-type and pep4Δ cells expressing RPL25-GFP were analysed as in b; 0.1 mM of PMSF was added to pep4Δ cells at the time of starvation to block all vacuolar proteases completely. The LI-COR imaging system was used to quantify the ratio between cleaved GFP and full-length protein as described in Methods. The last time point of wild-type cells containing RPL25-GFP was set to 1 arbitrary unit (a.u.). One of two independent experiments is shown.
C Immunofluorescence images showing BrdU incorporation in parental and resistant WM3248 cells after PLX4032 (2 &amp;amp;#x3BC;M) or DMSO treatment for 24 hr.
(B) U2OS cells (WT) and U2OS H2AX knockout cells reconstituted with empty vector (H2AX KO+EV), wild type H2AX (H2AX KO+WT), or the E141A mutant (E141A) H2AX were treated with H2O2 (2 mM in PBS, 5 minutes) or MMS (1 mM in medium, 30 minutes), subsequently; the cells were cultured in fresh DMEM medium for 2 weeks. The numbers of colony formation were counted. Values are mean ± SD of three assays.
A. Schematics illustrate the soluble Bax monomer and the MOM-bound Bax monomers, dimers and tetramers. The helices α2-α9 are depicted as cylinders with the indicated colors, and the helix α1 is omitted for simplicity. The MOM-bound tBid, depicted as a star, enhances cytosolic Bax interaction with the membrane (step I) and binds to the groove of Bax, thereby releasing α9 from the groove to the membrane (step II). The tBid binding also unfolds the Bax separating the latch (α6-α8) from the core (α2-α5) (step III). After tBid dissociates, the activated Bax monomer either embeds more hydrophobic regions such as α5 and α6 into the membrane (step IV) or binds other activated Bax monomer forming a BH3-in-groove dimer on the membrane surface (step V). After α5 is released into the membrane, the remnant BH3-in-groove dimer is rearranged to a α2-α3-α4 dimer (step VI). A Bax tetramer is then formed by two BH3-in-groove dimers via an additional dimer interface formed by two membrane-embedded α9 helices either intersected (step VII) or in parallel (step VIII). These Bax complexes may be in equilibrium with one another, but the BH3-in-groove dimerization is a prerequisite for the other dimerizations. In principle, combinations of these dimer interfaces would be sufficient to generate higher order oligomers, although other dimer interfaces have been discovered.B. A lipidic pore in the MOM is illustrated with BH3-in-groove dimers located on the cytosolic surface of the membrane and α9 monomer and dimer at the rim. Note that the BH3-in-groove dimers are partially embedded in the cytosolic monolayer, generating membrane tension that induces the pore, while the α9 monomer and dimer are integrated into the highly curved monolayer to reduce the line tension, thereby stabilizing and expanding the pore.
F-K Representative fundus fluorescein angiography images of C57BL6/J (F-H) and Ifnar1-/- (I-K) mice 3, 7 and 14 days after laser-induced damage.L Quantification of vascular leakage by analyzing pixel intensities at 3, 7 and 14 days after laser-induced retinal damage in C57BL6/J controls versus Ifnar1-/- mice. Values show mean ± SD. (n = 14-22 eyes; One-way ANOVA followed by Tukey's post-test: ***p < 0.0001).
F) Degree of colocalization of indicated fluorescent proteins in STED images was determined as described in Materials and Methods. For each group, 12 granules from 3 animals (4 granules per animal) were quantified. Black line indicates mean of the degree of colocalization in each group.
Co-localization (yellow merged) of the T22-GFP-H6-FdU (green) and the CXCR4 receptor (red) and release of T22-GFP-H6-FdU into the cytosol in CXCR4+ tumor cells 5h after a 100ug dose of nanoconjugate, as measured by dual anti-GFP/anti-CXCR4 immunofluorescence (IF). DAPI (blue nuclear staining). Fluorescence emission was measured in the green and red channels using the Image J software and expressed as mean Area (A)±s.e.m (µm2) (N=10, 2 tumor fields x 5 mice; 200X). Note the significant (P=0.003) increase in the area occupied by the green dots (nanoconjugate realeased to the cell cytosol) in T22-GFP-H6-FdU-treated tumors, compared to free oligo-FdU-treated control tissues. Scale bar, 50 µm.
E Similar experiments, performed by click reactions in 143B COX1 mutant cells (m.6930G>A), derived from a patient, or in COA6KO HEK293T cells, in comparison to the respective controls.
D HeLa cells expressing inducible E2F7-EGFP (left destruction graph) or E2F8-EGFP (right destruction graph) were blocked with thymidine for 16h, then released in fresh medium with doxycycline. Imaging was performed at 3-min intervals, as in Figure 2E. The x-axis is set to 0 at the frame of anaphase onset. Graphs show mean ± s.e.m. wild-type (wt) shown from Figure 2E in gray. E2F7-EGFP-KENmut n=13 from 2 independent experiments, E2F8-EGFP K/Kmut n=26 from 3 independent experiments.
FP competition binding of C5 (also used in C) and Tat-P4-(C5)2 to PICK1 with 5FAM-Tat-C5 (20 nM) as tracer.
(B) Wild‐type, rho0, Δnpr2, and Δatg7 cells expressing prNPR1‐NPR1‐HA were exposed to amino‐acid starvation medium supplemented with galactose in the absence (upper panels) or presence (lower panels) of rapamycin. The hyperphosphorylated (Npr1‐P) and dephosphorylated (Npr1) forms of Npr1 are indicated. Cells were analysed at indicated time points by whole cell extraction and western blot analysis using α‐HA and α‐Cdc11 antibodies.
I PPI network for the 153 DEGs based on STRING database. Node colors indicate fold changes; node sizes indicate link numbers.
B Ape1‐mRuby atg19Δ cells containing GFP‐Atg19 wild‐type or GFP‐Atg19‐3A were analyzed in log phase. Scale bar, 5 μm.
HUVECs were suspended in conditioned medium with VEGF (25 ng/ml) and plated on Matrigel. Branch points of the capillary-like network were counted after 18 h. n = 4 independent experiments; scale bar, 200 μm. Control vs. Sema3C, *P = 0.0375 and control vs. Sema3CΔ13, *P = 0.0162.
B. Gene synteny analysis of the genomic loci encoding vcdRP (formerly known as vcr082) in various Vibrio strains. Homologous genes are depicted using the same colors.
B Representative confocal images of a dendrite (top) and an axon (bottom) in which mitochondrial translation products were labeled with HPG (magenta). HOMER1 and VGLUT1 were used as post- and presynapse markers, respectively (green) and DiO stained randomly neurites (gray). In each neurite, an exemplary region was selected and the DiO was outlined to mark the outer edge of the region. As a control, cells were treated with Chloramphenicol (Chl) to inhibit mitochondrial translation. Scale bars, 5 µm.
Biotin-RNA pulldowns were performed with nuclear extracts of oncosphere cells using full-length HAND2-AS1 transcript (sense), antisense, and one HAND2-AS1 intron control, followed by mass spectrometry. Band 1: INO80, band 2: RUVBL2.
143B, 143B ρ0 cells were harvested for mitochondrial isolation. Purified mitochondria were treated with DMSO or EDC (20 mM) for 30 min at 37 ℃, and then were analyzed by Western blotting with the indicated antibodies.
bat cells were infected with VSV-particles pseudotyped with the lineage B chimeric spike panel. Pseudotypes were either left untreated or incubated with trypsin before addition to the cells. Luciferase was measured and normalized to particles produced without pseudotype. Shown are the data for 3 replicates.
Ray-traced picture of the wildtype CggR and R250A mutant structure. Carbon atoms of the FBP ligand are in turquoise while the part of the side chain that is eliminated by the R250A mutation is in green. Hydrogen bonds are indicated with dashed lines.
H-J. AT-MSCs were transfected with 50 nM miR-21 inhibitor or control inhibitor, and were exposed to r.h. TGF-β1 2 days after transfection at indicated concentrations for another 24 h, and subsequently subjected to the analysis of expression of miR-21 (H), Smad7 protein (I) and human TGF-β1 mRNA (J). Data is given as mean ± SEM of three independent experiments.
Western blotting assays for p53, LRP130, FOXO4 and p21 expression in A459 and H1299 cells treated with 100nM of rapamycin or vehicle (DMSO) for 48h.
(A) Schematic experimental flow of the analysis of IS formation and function between NEF-expressing CD4OT-II cells and antigen-specific BHEL cells. BHEL cells were stimulated with LPS in the presence (+Ag) or absence (-Ag) of HEL-OVA antigen. B cells and T cells were labelled with different CellTrackerTM dyes before seeding on PLL-coated cover glasses and analyzed by microscopy.
d. Microscopic images showing PIN2-Dendra fluorescent signal five hours after photoconversion of PIN2-Dendra into its red form. Depletion of the red signal and recovery of the green signal over a 6 hours period was followed in parallel in 5 DAG old roots12 HAT to ammonium or nitrate supplemented media. Note the increase in the intensity of the green signal in roots transferred to nitrate. Graph represents the mean signal + SD (n=6 roots per condition, 20 cells per root analyzed). The experiment was repeated 3 times. Scale bar=20 µm.
(A-D) Primary cultures from D. melanogaster embryos expressing GFP-Atg8a under the control of Dmef2-Gal4, stained with Phalloidin (actin) in red. Inset are magnifications of areas denoted by dotted line. (A) In untreated control cultures, GFP-Atg8a localizes throughout the muscle cytoplasm and nuclei. (B) Addition of rapamycin (Rap) for 12 hrs results in the formation of small GFP-Atg8a labeled punctae. (C) Addition of chloroquine (CQ) for 12 hrs results in the accumulation of large GFP-Atg8a labeled vesicles that localize around the nucleus and between the myofibers. (D) Addition of both CQ and Rap for 12hrs, triggers the formation of greater numbers of enlarged vesicles in the muscles than either drug alone. (E) Knockdown of the core autophagy gene, Atg1, prevents the formation of GFP-Atg8a vesicles in CQ+Rap treated cultures. (F) Quantification of the mean ratio of GFP-Atg8a punctae area to total muscle area per well (n = 4). Error bars indicate SEM with **p<.01; ***p<.001.
F BMMΦ were stimulated with LP and 10µM nutlin3a and quantified for inos transcript levels by qRT-PCR at indicated times as fold change to unstimulated. Depicted are means ± SEM from 4 independent experiments. *p < 0.05, **p < 0.01 (two-tailed unpaired t-test).
(B) Key endogenous genes controlling Golgi (sedV, geaA, hypB) or post-Golgi trafficking (rabE, ap1σ, claH) were genetically replaced by versions transcribed under the highly repressible thiAp promoter via targeted homologous recombination. In the absence of thiamine from the growth medium (derepressed conditions) the relative proteins are expressed, while upon addition of thiamine at the onset of conidiospore germination (ab initio repression) the expression of these proteins is tightly repressed. Proteins are detected by a standard western blot analysis using either anti-FLAG or anti-GFP antibodies for Golgi and Post-Golgi proteins. Equal loading and protein steady state levels are normalized against the amount of actin, detected with a specific antibody.
G Representative micrographs of PR-IHC on glands from 5-month-old MM134 xenografts from hosts treated for 2 months with vehicle (left) or E2 (right) pellets. Scale bars, 200 μm. Right, bar plot showing percentage of PR+ cells in MM134 and SUM44 xenografts with n>1000 cells per condition on glands from 3 different mice. Data represent mean ± SEM unpaired, Student's t-test, two-tailed; *** p < 0.001, **** p < 0.0001.
Relative expression of fibronectin (I), collagen I (J) and collagen III (K) mRNA normalized to GAPDH.
Heatmaps of AIB1-YAP co-activated, YAP activated, AIB1-YAP corepressed, and YAP repressed genes shown in panel (A). Red and blue indicate high and low levels, respectively. RNA-sequencing was performed in triplicate and statistics in Panel (A-B) were calculated by EdgeR with Benjamini-Hochberg multiple test correction in R.
(c) Fluorescence microscopy of DHE→Eth conversion in wild-type and Δspe1 cells indicating ROS production. Scale bars, 10 μm.
C Control or LAPTM4B knockdown MDA‐MB‐231 cells were starved overnight, cell surface EGFR was labeled with immuno‐gold on ice. Cells were then stimulated with EGF for 1 h at 37°C and fixed for the EM study. Scale bar, 200 nm. See Materials and Methods for details.D Relative amounts of immuno‐gold‐labeled EGFR in the MVE lumen versus MVE limiting membrane were quantified. Over 80 endosomes for each siRNA treatment from three independent experiments were used for quantification (mean + SD; ***P 0.001, one‐tailed t‐test).
(c) TSC2 and RagA/B independently affect S6K phosphorylation. HA-S6K (20 ng) was transfected into HeLa cells with or without RNAi against human TSC2, RagA and RagB as indicated.
Figure 6: Cognitive decline in 8-month old Fmn2 -/- mice is rescued by the HDAC inhibitor Vorinostat.. E. Left panel: The escape latency in the water maze test was significantly improved in the Fmn2-/- Vorinostat group when compared to the placebo group (P < 0.0001, F = 4,86; n=10/group). Right panel: Swim speed was not altered amongst groups
(A-C) Tracks generated through automated tracking were plotted to a common origin to visualize parasite dispersal P. berghei (A), P. yoelii (B) and P. falciparum (C) at 5, 10, 30 and 60 min after intradermal inoculation. For each timepoint, the tracks are representative of the average displacement of the entire sporozoite population. Track numbers used for each timepoint were: 5 min, 40 tracks; 10 min, 32 tracks; 30 min, 25 tracks; 60 min, 21 tracks. (D-F) Displacement of P. berghei (D), P. yoelii (E) and P. falciparum (F) sporozoites 5-120 min after inoculation in box and whisker plots with whiskers displaying the 10-90 percentiles and values below and above the whiskers shown individually. Horizontal lines show median displacement at each time point. Percentage values in boxes indicate the fraction of tracks displacing over 75 micrometers at each time point. Within a given species, the difference in sporozoite displacement between 5 min and 120 min is statistically significant (Kruskal-Wallis test: P. berghei p<0.0001, P. yoelii p<0.0001, P. falciparum p<0.01). Comparisons between species showed no statistically significant difference in displacements for any given time point, with the exception of the 10 min time point in which there was a significant difference between P. berghei and P. falciparum (Kruskal-Wallis test, *p<0.05). For panels (D-F), a varying number of videos were processed for each time point after inoculation: (D) Same dataset as used for Figure 2D: 5 min (3 videos/203 tracks), 10 min (6 videos/292 tracks), 20 min (4 videos/184 tracks), 30 min (6 videos/235 tracks), 60 min (7 videos/162 tracks) and 120 min (6 videos/151 tracks). (E) 5 min (7 videos/714 tracks), 10 min (16 videos/1514 tracks), 20 min (4 videos/415 tracks), 30 min (4 videos/319 tracks), 60 min (4 videos/255 tracks), and 120 min (4 videos/180 tracks). (F) 5 min (6 videos/389 tracks), 10 min (6 videos/464 tracks), 20 min (3 videos/184 tracks), 30 min (2 videos/195 tracks), 60 min (2 videos/239 tracks), and 120 min (2 videos/103 tracks).
(E) Decrease of steady-state levels of respiratory chain subunits in Clpp-knockout hearts relative to wild type (set to 1). VDAC or TOMM20 were used as loading controls. Bars present mean levels ± SD. Student's t-test was used to determine the level of statistical difference (n=4).
A. Schematic view of the mutants generated to evaluate the functional role of the C575 intra-subunit bonds. HEK293T cells expressing λ chains were transfected with µHaloC575A-C414A (HC575A, depicted in red in the figure), µC414A (µ, in blue) or both mutants together.
(B) M (above) and Z (below) α1-antitrypsin, at a concentration of 0.2mg/ml in PBS+5% v/v glycerol, were heated at a range of temperatures between 48°C-65°C for 4 hours in the presence and absence of GSK716, as indicated. The oligomerisation state was determined by non-denaturing PAGE electrophoresis; the lane denoted 'M' contains the unheated monomeric control.
(A) The promoter region was divided into 7 building blocks: block 1 with 239 bp of a potential -1 nucleosomal sequence; block 2 with 73 bp sequence representing the ecdysone receptor binding region; block 3-6 with 131 bp sequence representing the native and perturbative core promoter regions from different architectures; block 7 with 240 bp of a potential +1 nucleosomal sequence. (B) Synthetic promoter design - building blocks. The promoter region (sketch in lower panel) was divided into 7 building blocks: block 1 with 239 bp sequence representing a potential -1 nucleosome; block 2 with 73 bp sequence representing the ecdysone receptor binding region; block 3-6 with 131 bp sequence representing the native and perturbative core promoter regions from different architectures; block 7 with 240 bp sequence representing a potential +1 nucleosome. (
a) Volcano plot highlighting differentially expressed genes (DEGs, false-discovery rate [FDR] <0.01; red upregulated and blue downregulated) at each study time point versus pre-vaccination (4 months of age) 4 hours post-vaccination (719 DEGs, n=28). P-values were obtained from the moderated t-statistic, after adjustment for multiple testing (Benjamini and Hochberg's method). The top 10 genes, ranked by FDR, are labelled.
B. A53T α-syn-EGFP and A53T α-syn-mCherry OE SH-SY5Y cells were cocultured in the presence of 5 μM saracatinib (sara) or 10 μM SKI-1, respectively, with 50 μM RA for 5 days.
NEMO degradation assay. (A) HEK293T cells were transfected with different doses of Strep-tagged MARCH2 in the presence HA-tagged NEMO plasmid.
(D) Numbers of rosette leaves of the WT and mutant plants shortly after bolting. Rosette leaves from at least 20 plants were counted for each genotype. Values are mean ± SD. ** P<0.01, student's t test.