EMBO/sd-character-level-ner huggingface dataset:
Effect of cl-HK2pep on glucose phosphorylation in 4T1 cell extracts (J), where both total hexokinase activity and HK1/HK2 specific activities are measured.
C9 DPR reporter constructs show cell-type variability in the number of cells that are DPR positive and the overall DPR levels. Transient cotransfections of HEK293T cells robustly undergo G4C2 -Dendra2 non-AUG-dependent translation compared to NSC34 or rat primary cortical neurons. DPR positive cells and DPR fluorescent intensity were analyzed and calculated 24 h post-transfection only in cells expressing the co-transfected NES-mIFP construct. DPR fluorescent intensity was normalized to NES-mIFP fluorescent intensity to adjust for cell specific AUG-dependent translation levels; represented as fold-change relative to HEK293T. HEK293T: n = 5 with m > 500 cells analyzed per n. NSC34: n = 5 with m > 500 cells per n. Rat primary cortical neuron: n = 5 with m > 40 cells per n. (***P < 0.001, **P < 0.01, *P <0.05) See also Figure EV1-2.
Expression of priA, priJ or priH enhancers in the posterior midgut as seen by lacZ reporters (X-Gal staining, blue), and pri-Gal4 gene trap expressing GFP (green).
(A) At the Golgi, the recruitment of PI4KB can be controlled through the action of ACBD3. PI4KB can recruit c10orf76 to the Golgi, with this playing a role in the dynamics and localization of GBF1 and active Arf1-GTP and their downstream effectors (1). Active, membrane localized Arf1-GTP can activate PI4KB (2). (B) In a c10orf76-knockout cell, there is decreased recruitment of GBF1 and active Arf1, with this potentially describing the decreased levels of PI4P. (C) In enterovirus infected cells there are multiple mechanisms that can alter PI4P levels and Arf1 activation. The 3A proteins from different viruses can activate PI4KB, primarily through hijacking ACBD3 (i), as well as directly binding to GBF1 (ii). Viruses that require c10orf76 to replicate rely on the PI4KB-c10orf76 interface, emphasising the importance of manipulating PI4KB-c10orf76 and GBF1/Arf1-GTP dynamics to facilitate viral replication.
A, B SAXS profiles of the H1-nuclesomal arrays in 0 (TE), 1, 2.5 mM MgCl2 (A) and 5, 10 mM MgCl2 (B) are shown as plots of log(I × S2) vs. 1/S (I, intensity; S, scattering vector (1/nm)).
(f,g) Immunoblot for the indicated proteins of immunoprecipitates (IP) of endogenous Cx43 and Atg16 from WT MEFs maintained in the presence (f,g) or absence of serum (4 h; g). I: input; FT: flow through.
I Agarose gel showing levels of spliced and unspliced XBP-1 in primary mouse skin fibroblasts treated as indicated with TGFβ and 4μ8C.
(A) IRF7 protein expression in pDC isolated from Irf7-/- (pink, bottom), C57BL/6 (WT, black, top) and Ifnar1-/- (red, middle) uninfected (empty histograms, Ø, left) vs MCMV-infected mice (filled histograms, MCMV, right). For each condition histograms are representative of one out of 4-6 mice from 2 independent experiments
C. The domain organization of Arabidopsis UVR8. It consists of a UV-B-sensing β-propeller core (residues 12-381) and a long C-terminus containing the VP motif. Constructs and peptides used and their residue endings are indicated.
Western blot analysis of total cell lysates of macrophages from a SARS-CoV-2 naïve individual (SC-naïve) (top) and COVID-19 infected individual (bottom). Macrophages were stimulated with LPS or S-protein (4h) followed by 2h of nigericin treatment. Control cells were left unstimulated. Antibodies against NLRP3 (110kDa) and β-actin (loading control) were used for detection. Representative example of three individual experiments.
(D) COCO injections (P1, P7 and P14) do not result in ONL thinning in P28 retinas. Scale bar, 40 μm. (E) Quantification of apoptotic cells (cleaved caspase-3; CC3) in control and COCO-injected mice (p-values are versus PBS treatment). (n=4).
H BZR1-mediated hypocotyl elongation phenotype is dependent on the function of BIC1 and BIC2. The Col-0, 35S:BZR1-MYC, bic1bic2, 35S:BZR1-MYC/bic1bic2 seedlings were grown on medium supplemented with 1 μM BRZ plus different concentrations of eBL for 6 days and then the hypocotyl lengths were measured. Data are means ± SD (n>20).
Lipid peroxidation was measured by C11-BODIPY 581/591 after cold stress for 5 h. Representative plots are shown in (D). Quantification data (E), whose raw value were normalized by the C11-BODIPY 581/591 of the WT A549 cells after cold stress application, are presented as mean ± SEM; n = 4, biological replicates. ****p < 0.0001, ***p < 0.001, **p < 0.01, n.s.: not significant, by one-way ANOVA followed by Tukey's multiple comparison test.
E. A majority of hyper-methylated genomic regions were within the genes (31.9% in exons and 48.8% in introns in count-base analysis and 50.0% in exons and 31.2% in introns in length-base analysis). In contrast, almost half (47.9%) of the hypo-methylated regions were in intergenic regions (51.3% in count-base analysis and 47.9% in length-base analysis); only 4.3% of the regions in count-base analysis and 5.2% in length-base analysis were in exons, and 3.1% in count-base analysis and 11.5% in length-base analysis were in promoter regions (0.5 kb or 2.0 kb upstream of the transcription starting site).
D Sequence conservation of stimulation-dependent modified serine (red) and lysine (green) residues amongst mammals. The degree of conservation is indicated by color saturation.
D) Parasites per vacuole were determined 24 h p.i. with similar conditions and staining as described in (C) except MOIs used were 0.5 and 1 for RH (n=3) and Pru (n=3), respectively.
Schematic representation of Rab8a protein. To prevent C-terminal geranylgeranylation, the Cys204 residue was substituted with a serine residue. Alternatively, two truncated proteins (N100 and ∆N100 fragments of Rab8a) were prepared for this experiment.
A. Schematic showing %GA content and positions along the human RAB13 3'UTR targeted by the indicated PMOs. Red rectangles indicate the location of GA-rich motifs. Graphs present PDI measurements of RAB13 RNA (upper panel) or NET1 RNA (another APC-dependent RNA; bottom panel) detected in MDA-MB-231 cells treated with the indicated PMOs. PDI=1 indicates a diffuse distribution. p-values: **<0.01, ***<0.001, ****<0.0001 by analysis of variance with Dunnett's multiple comparisons test. n.s.: non-significant. N=30-73 cells observed in 3-5 independent experiments. Bars: mean ± s.e.m..
(E) Average barbed end polymerization rates for indicated WAVE1 variants. Errors bars represent SD.
(D) SPR analysis of the binding characteristics of camrelizumab with PD-1 expressed in 293T cells, insect cells or E. coli cell, which enabled different levels of glycosylations. The binding affinity is presented as KD. The data presented here is a representative of two independent experiments with similar results.
DBA/2J mice were injected s.c. with 1× 105 P388 murine leukemia cells, followed by injection of the anti-hTAPBPL mAb (25, 50, or 100µg) or isotype Ab (25, 50, or 100 µg) 3 times per week. At the end of the studies, tumors from 100 µg anti-hTAPBPL mAb- or isotype Ab-treated mice were harvested. Single-cell suspension of the tumors was analyzed for the percentage of (E, F) CD4+ T cells, CD8+ T cells, and (I and J) CD4+CD25+FoxP3+ Tregs by flow cytometry.
(C, D) Equal numbers of wt and Trem2 ko BMDM were added and cell numbers were analyzed after termination of experiments by quantifying the CD68 positive cells on top of the sections. (n = 4, +/-SEM; t-test; n.s., nonsignificant, P=0.5004). Scale bar, 200 µm.
MYBL2 protein levels are reduced upon ETC-159 treatment in HPAF-II xenografts. Tumor lysates from vehicle or ETC-159-treated (56 h) mice were resolved by SDS-PAGE followed by immunoblotting with the indicated antibodies. Each lane represents an individual tumor
(A) A summary of significantly different plasma inflammatory protein markers compared to time baseline in metabolic cofactor supplementation and control studies. Red and blue colors denote the increased and decreased plasma levels compared to baseline, respectively. * Denotes significance (one-way ANOVA; FDR <0 .05).
(D) Summary of KEGG pathway analysis of npTh17 and pTh17 cells. Venn diagram shows pathways that are deregulated in one or both Th17 subsets. P (adj.) < 0.05 for all pathways. Some unique and shared pathways are indicated.
(N) Quantification of the number of PPO positive crystal cells upon dopamine sensing perturbation (domeMESO-Gal4, UAS-GFP/+, n= 29, domeMESO-Gal4, UAS-GFP; Dop2RRNAi, n= 26, domeMESO-Gal4, UAS-GFP; DATRNAi, n= 25). Data information: The quantification in N represents mean with standard deviation with whiskers indicating maximum and minimum values, box indicates the lower and upper quartiles. The statistical analysis applied in N is One-way ANOVA with Tukey's multiple comparisons test 'n' represents the number of lymph gland lobes analyzed, *P<0.05, **P<0.01, ***P<0.001, ****P<0.0001.
Synergistic rescue of GFAP expression by let‐7 and miR‐125. Total concentration of mimics in wells with miRNA was 50 nM (n = 3). Quantification of GFAP‐positive cells in each well normalized to the mean of the experiment is shown on the right.
Attenuation of mitophagic accumulation in the hippocampal mossy fibers of AD mice transduced with AAV-mCherry-Snapin. Note a marked reduction of mitophagosomes (white arrows) in mutant hAPP Tg mouse brains with elevated Snapin expression
E Volcano plots of DEGs that were upregulated (red) or downregulated (blue) in myeloid cells. Examples of DEGs were labeled.
Jurkat cells were infected with lentivirus expressing control luciferase shRNA or shRNAs targeting SERINC3, followed or not by infection with NL4-3 EGFP-Nef+ HIV-1 (red boxes). (G) Multiplex bead-based flow cytometry assay for detection of EV surface markers. Antibody-coated capture beads were incubated with EV samples. Captured EVs were detected with a mixture of APC-labeled anti-CD9, anti-CD63, and anti-CD81. Quantification of the median APC fluorescence values for all bead populations after background and isotype antibody correction. Results were relativized to the values obtained with control sample for each experiment. Dotted line represents values obtained for EVs isolated from control cell CM.
(A) expression of FUS does not alter expression of VAPB, PTPIP51 or mitofusin-2 (MFN2) in transfected NSC34 cells. Immunoblots of NSC34 cells transfected with EGFP as a control (CTRL), or wild-type or mutant EGFP-FUS. Transfected cells were purified via EGFP using a cell sorter and the samples probed on immunoblots as indicated. On the FUS immunoblot, samples were probed with FUS antibody to show endogenous and transfected proteins; tubulin is shown as a loading control.
(E) Bar chart showing the number of large (diameter greater than one micrometre) non-acidic Btl-GFP-positive compartments per SC. Data from 39 SCs (three per gland) are shown.
The proportion of CD133+ cells was determined by FACS analysis after growing triple KD and control cells in FTM vs. OCM for two passages. The graph is representative of two biological replicates.
First 57 nucleotides of ISR are sufficient to drive AGO1 translational readthrough. AGO1-TGA-FLuc constructs with different lengths of ISR (all in-frame with AGO1 and FLuc) were in vitro transcribed and in vitro translated using rabbit reticulocyte lysate. FLuc activity reflects readthrough activity. **, P = 0.012; *, P = 0.017.
D. Graph depicting median and the value of the intensity of oligo(dT) fluorescence in individual nuclei divided by nuclear volume in the indicated cell types either mock transfected or transfected with poly(I:C) for 4 hours. At least 43 nuclei analyzed per condition.
Left: Bar graph showing the distribution of CD34 and GPR56 fractions at the end of the 5-day culture of purified CD34-GPR56+ cells from AML E2112376 with indicated compounds. Right: statistical analysis shown only for the CD34+GPR56+ fraction. See Dataset EV11 for full statistical analysis. PRI: PRI-724, n = 3. Unpaired t-test, bars and error bars represent mean and standard deviation of three individual treatments, *** p<0.0005, ** p<0.005, * p<0.05.
(D) Overexpression of PGC1α was achieved through adenovirus transduction in C3H/10T1/2 cells (WT) and confirmed by qRT-PCR (n=6). Noted TGFβ1 significantly decreased PGC1α expression. ***p<0.001, ****p<0.0001 by one-way ANOVA, mean ± SD.
(D) Protein structural analysis shows that all intramolecular suppressor mutations were located on the predicted PPR motifs. The predicted protein structure of Ccm1 is shown at left. Blue and green colors indicate the two α-helices in each predicted PPR motif and white color indicates additional α-helices in the N-terminus and the middle region. Red color indicates the positions of the suppressor mutations. Predicted PPR motifs occupy around 52% of the whole protein (453 of 871 residues). The box at right displays a magnified version of some PPR motifs where the substitutions are located.
C. Confocal images of fluorescently labeled λ DNA with dSaCas9 (n = 11) and wild-type SaCas9 (n = 16) bound to its DNA target. DNA-bound SaCas9 was visualized by labeling the 5' end of the crRNA with Cy3. The λ DNA molecule was either suspended between two microspheres held by two optical traps under 5 pN or stretched by laminar flow. The fluorescence intensity of Cy3 alongside the image is shown to indicate the on-target binding of SaCas9.
(D) pDCs were left untreated (un) or treated for 6 h with Rapamycin or with EBV without or with a 30 min pretreatment with Wortmannin (Wort). Autophagy was observed by confocal microscopy by monitoring LC3 punctate‐positive cells. Scale bar: 5 μm. Data shown are representative of three experiments performed.
, F) Shank2-/- dams attack their pups inducing injury in the head and body region (arrowheads), Mann-Whitney test, *P=0.013, Shank2+/+, n = 12, Shank2-/- n = 9. Data information: All data are presented as mean ± SEM.
Wild type (WT) and TRIM21 knockout (KO) mice were infected with 0.5 x 10^5 FFU LCMV clone 13 (6 mice per group), and either received anti-N mAb KL53 (+) or control (-) intraperitoneally on days 1 and 3pi. Two mice were uninfected (UI). Viral titres in the spleen, liver, lung and kidney of all mice were determined by FFA day 8pi. Each data point represents one mouse, with results from two repeat experiments combined.
(c) Immunoblot for LC3 in the same cells maintained in the presence of serum untreated (−) or treated with inhibitors of lysosomal proteases (PI) for the indicated times. GAPDH is shown as the loading control.
(C) Human recombinant His-ESM1 and GST-β-catenin protein were pull down with either Ni sepharose or Glutathione sepharose.
A Normalised cumulative nucleosome (150 ± 30 bp size class) position frequency profiles for 4013 S. pombe genes aligned at the transcription start site (TSS) plotted from low MNase (biorep1) and high MNase (biorep 2) datasets. P-values (calculated using a two-tailed unpaired t-test) for the difference in means between random n = 100 subsets of the frequency values at the points indicated by the dotted lines ("-4" nucleosome and "+4" nucleosome) are shown.
F Western blot analysis show Hh and proliferation target protein expression levels. Data show the mean ± SD of tumor (n = 6) for each treatment. *P 0.05 versus Ctr.
(A) A schematic diagram of the Pax5-Jak2 protein containing a C-terminal biotin acceptor sequence that can be biotinylated in vivo by the E. coli biotin ligase BirA upon expression from the Rosa26BirA allele
(a) [3H]thymidine incorporation at 72 h by wild-type (WT) and Irgm1-/- CD4+ T cells activated with soluble mAb to CD3 and irradiated syngenic wild-type splenocytes.
h, schematic representation of Cre-LoxP system to assess EV function in co-culture of Nrl.Cre+/- photoreceptors (PRs) with mTmGfloxed reporter retinal cells in non-proximity (transwell) versus physical proximity (contact);
E HeLa cells expressing Dox-inducible RIPK3 WT, D160N, K518R or 3xKR were incubated overnight with 1 µg/ml Dox and pre-treated with 20 µM zVAD.fmk, 5 µM BV6 for 1 h. After pre-treatment, 10 ng/ml TNFα were added for 1 and 2 h. Strep-RIPK3 was immunoprecipitated by using anti-Strep-beads. Co-immunoprecipitated phosphorylated MLKL and RIPK1, as well as protein expression of indicated proteins were analyzed by Western blotting. β-Actin served as a loading control.
DC(WT) and DC(NLRC3-KO) mice were immunized with MOG(35-55) peptide in CFA adjuvant and pertussis toxin to induce EAE. CFSE proliferation assay of naive 2D2 CD4+ T cells stimulated with MOG(35-55) plus DCs sorted from DC(WT) and DC(NLRC3-KO) mice 26 d after EAE induction.
G) Graph showing the relation between the M. florum cell diameter (d) and its cell mass (CM) according to cell mass Equations 4-7 (see Materials and Methods). For each equation, the mean cell mass (CMmean) is indicated by a colored line, and the range of probable values (CMmin - CMmax) is shown by a light-colored shading. The mean values of the average cell diameter measured by TEM and STED (see panel D) are indicated by black dashed lines. The portion of the graph where all the CMmean curves converge is enlarged and devoid of colored shadings for representation purposes. CMmean interception points encompassing all other interception points are encircled, and their corresponding x and y coordinates are indicated by fuchsia dashed lines (most probable cell diameter and most probable cell mass ranges).
Aci2 was grown with alanine and glutamate supplied at 25 different ratios from 1:16 to 16:1 with the total supply kept constant at 0.1%w/ Data Information: Data were collected at 600nm.
Steady state levels of endogenous AK2 in presence and absence of MIA40. 72 h before experiments, HeLa cells were transfected with control siRNA or siRNAs directed against MIA40 or ALR. Cell lysates were analysed by immunoblot against the indicated proteins. MIA40 depletion led to a strong decrease in AK2 and ALR levels but not of the control proteins. ALR depletion did not affect AK2 levels. Reported values are the mean of 3 independent experiments; error bars represent ±SD. Student's t-test was performed. * represents p<0.05,.
G-H, TAMs (CD11b+F480+) were isolated by FACS. Expression of selected immune stimulatory and immunosuppressive genes in TAMs was determined by RT-qPCR (n=3). Data are presented as mean fold change ± SEM compared to TAMs from mock-irradiated tumours (n=3). Statistical significance was determined by Mann-Witney.
(D). Statistical diagram of the quantal size in Fig. 5A and Appendix Figure S6A-D. The secretion amount of each group was standardized with respect to the control group. Data information: Green color represents the amino acids which are found to modulate foot probability based on structure analysis, and red color means amino acids which does not regulate foot probability. , * indicates PTP-MEG2 mutants overexpression group compared with the WT overexpression group. # indicates the overexpression group compared with the control group. **, P<0.01; *** P<0.001 and #, P<0.05; ##, P<0.01; ### P<0.001. N.S. means no significant difference. Data were from 6 independent experiments. All the data were analyzed using one-way ANOVA and showed as the mean ± s.e.m.
(C) PCA clustering of all RNA molecules in the SN control (green) and PD samples (blue).
Cartoon of a simplified Plasmodium life cycle indicating in red the stages important for our work. Note that transfection is performed in blood stage parasites. Schematic cartoon of a sporozoite with an indicated apical cross section. Subpellicular (cytoplasmic) microtubules (green) can be found below the three membrane layers (plasma membrane and inner membrane complex) of the pellicle (bottom).
C | Quantification of Fo.B cells (top, percentages) and CD38-/CD95+/GL-7+ GC cells (percentages and absolute numbers, bottom panels) in WT (black) and IgD-/- (green) animals after 4, 7, 10 and 14 days post immunization, mean ±SD (numbers of animals indicated in the top plot). Statistical significance was analyzed by a two-tailed unpaired t-test.
number of metastatic lesions per lung (C) in vehicle and glufosinate (20mg/kg) treated mice (pool of 2 independent experiments; 10 mice per condition in total).
D. Time-lapse stills depicting RH Cb-EmeraldFP parasites invading in absence of detectable F-actin at the junction (orange arrow). The nucleus (purple) is squeezed through the TJ (red arrowhead) during invasion. Actin accumulation at the posterior pole of the parasite is strongly detected in all cases (blue arrow). E. Analysis of nucleus deformation during live imaging shown in (D). The nucleus appears to not show constriction once its passing through the TJ when the F-actin ring is not present. F. The posterior end of the parasite also deforms during the invasion process.
(C) In 786-0 cells, FLAG-tagged GDH1 was co-transfected with HA-tagged ubiquitin for 48 hours, and then the cells were treated with or without aa starvation for 6 hours. Immunoprecipitation (IP) was performed using an antibody against FLAG, and the ubiquitination of FLAG-GDH1 was identified by LC-MS/MS.
(A) Superposition of the ATPγS-MjMR-DNA complex (green) and apo-MjMR (3AV0, magenta) structures. Alignment was done using their NBDs (1.3 Å rmsd in the positions of 311 Cα atoms). The coiled-coils of the DNA-bound Rad50 molecules are shifted (arrow) to more parallel orientation. The entire structures can be superimposed with a 1.9 Å rmsd in 692 Cα positions.
(D) SNU-368 shTFAM cells with R62D-actin-NLS or WT-actin-NLS were infected with firefly luciferase expressing lentivirus and transplanted into livers of nude mice. Representative bioluminescent imaging for each group (n =10)
F: 53BP1/CD34 co-immunostaining in kidneys from young and aged mice (left panels) and quantification (right panels) of 53BP1 foci per glomerular endothelial cell. Original magnification X630. Scale bar = 10 μm. Panels are representative images of 6 young and old mice, respectively. Data information: Data are means ± SEM. Statistical analysis: t-student test: young versus old mice.
TAG (nmol/ μg protein) in the 4 DO fat body expressing UAS transgenes with the r4-Gal4 driver. Bars show group mean +/- SEM (n = 6), points show values from individual MS runs. Unpaired T-Test. ** p < 0.01
F. Western blot analysis of RNF43 WT and R519X for cytoplasmic β-catenin levels.
F G2A and C7AC8A mutations cause cytoplasmic distribution of ISP1 during zygote to ookinete differentiation. Scale bar = 5 μm.
B, Genome-wide DNA methylation data showing the number and total size of DNA methylation valleys (DMVs) and partially methylated domains (PMDs).
B, C: Quantification of protein expression level for PAX6 (B, n=6, technical replicates per line for ESCs; n=7, technical replicates per clone for control; n=8, technical replicates per clone for WS5A; n=9, technical replicates per clone for CP2A) and NESTIN (C, n=6, technical replicates per line for ESCs; n=7, technical replicates per clone for control; n=8, technical replicates per clone for WS5A; n=9, technical replicates per clone for CP2A) for iPSC-derived NSCs using flow cytometry.
(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 Changes of HXT2 mRNA localization appear to be independent of the cytoskeleton. Cells were either treated for 15 min with 30 mg/ml latrunculin A or with 30 mg/ml benomyl. White arrowheads point to small-budded and yellow arrowheads to large budded cells. E Quantification of (D) of three in dependent experiments with at least 50 cells each. Values > 1 indicate a stronger signal in the mother, < 1 a stronger signal in the bud and around 1 equal distribution. Boxes represent the interquartile range from the 25th to the 75th percentile with the median. Whiskers represent the 10th and 90th percentile, respectively.